Midterm Flashcards

Question

Valance shell anatomy

Answer 1

Valance shell anatomy – basis for the rules of covalent bond formation a. Ex. CO2 (O=C=O) - Carbon is bound to two oxygen atoms each with a double covalent bond - Each Oxygen shares 2 e- with carbon per bond (4 e- total required to fill shell) - Ex. Hydrogen only makes one single bond to reach chemical satisfaction

Answer 2

organic molecules consisting of only carbon and hydrogen Components of fossil fuels – all hydrocarbons o Example: petroleum o The name originates from partially decomposed organic matter found in the fuel Living cells don’t have full hydrocarbon structures – have a ‘dressed’ up structure to get a different behaviors; exist as components of more complex molecules o Ex. Phospholipids o Ex. Cholesterol – storage fat within bilayer Hydrophobic – non-polar covalent bonds between carbon and hydrogen make hydrocarbons insoluble o Non-polar – equally shared May participate in reactions that release large amounts of energy – contain lots of energy o Fossil fuel combustion o Energy storage in animals o 1g of fat stores 2x the energy as 1g of carb/sugar – we store energy primarily as fat

Answer 3

Isomers – compounds with the same molecular formula but different structures Different structures create differences in properties o Properties – melting points, boiling points, binding properties 3 types of isomers: 1. Structural isomers a. Differ in the covalent arrangement of atoms – same number of carbons b. Straight vs branched - May differ in double bond presence/position – create isomers, even if they are both linear - differing amounts of hyd for double vs single bond c. Number of possible isomers increases with the number of carbon atoms - C5H12 vs C8H18 2. Cis/trans isomers a. Formerly referred to as geometric isomers b. X substitute must be identical on each side to be considered a cis/trans isomer c. Carbon-carbon double bonds are rigid structures i. Double bonds o Shorter o Rotation is not possible ii. Single bonds o capable of rotation o longer d. Spatial arrangements affect stability and bonding abilities – molecules interact very specifically; need structural details in order to function • Connectivity of atoms does not change between cis and trans isomers – spatial arrangement/placement of atoms differ e. 2 spatial arrangements possible when carbons involved in a double bond with one another have two different atoms attached i. Cis isomer: - Both X substituents are on the same side of the double bond - X are heavier than carbon - Having both larger atoms on the same side may cause interference with each other - Not necessarily less stable ii. Trans isomer: - The X substituents are on opposite sides of the double bond - **Small differences in spatial orientation may significantly affect the activity of the molecule - Example: human vision – reaction occurs to covert cis to trans to cis 3. Enantiomers (we won’t discuss these in this course) - Not superimposable - can’t have them on top of each other and have the functional groups line up - They are mirror images

Answer 4

Functional groups – determine behaviour a. Hydrocarbons – provide framework for more complex carbon containing organic molecules o Non-polar – can’t participate in hydrogen bonding b. Functional groups – replace hydrogen on hydrocarbons; allow molecule to form hyd bonds o Contribute to chemical reactivity directly or indirectly due to shape o Number of groups and arrangement are important (ex. effects of estrogen vs testosterone) o Some impart polarity

Answer 5

``` Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group ```

Answer 6

a. Name – alcohols i. names usually end in “ol” (ex. ethanol) b. Functional: i. Polar due to electroneg oxygen ii. Can form hyd bonds with water – helps dissolve organic compounds with -OH (ex. sugar)

Answer 7

Carbon double bonded to oxygen 2 types – depends on other 2 bonds on C 1. Ketones – 2 carbons (within a carbon skeleton) a. Ends in “one” (ex. acetone) b. Methyl group within carbonyl (ex. acetone) – still a carbonyl, not methyl group 2. Aldehydes – 1 carbon and 1 hyd (the end of a carbon skeleton) a. Ends in “al” (ex. propanal) b. Cannot extend further on hyd side May be structural isomers (same molecular formula with different placement) – different properties Form 2 major sugar groups i. Ketoses ii. Aldoses

Answer 8

Carbon is double bonded to O, bond to C, bond to OH (not hydroxyl; part of carboxyl) a. Names – carboxylic acid or organic acid (ex. acetic acid) b. Acid – can donate H+ because bond between O and C is very polar c. Carboxylate ion – ionized form (-1 charge); found in cells this way i. Deprotonated carboxyl group

Answer 9

a. Name – amines b. Base – can bond to H+/proton i. Found in cells in ionized form (+1 charge) ii. NH2 or NH3+ c. Ex. glycine

Answer 10

S bonded to hyd a. Name – thiols b. Functions i. 2 sulfhydryl groups can react – form cov bond; crosslinking helps stabilize protein structure - Ex. crosslinking cytosine in hair protein maintains curls/straightness of hair (perming is reforming crosslinking bonds) ii. Important in creating complex proteins

Answer 11

Double bond to one O, single bond to 3 more (exception to octet rule) a. Name – organic phosphates (PO4) b. Functions i. Contibutes neg charge to molecule (ex. dna and rna have net neg charge) - -2 when at the end of a molecules - -1 when located internally within chain of phosphates ii. Molecues can react with water – release energy

Answer 12

C with 3 hyd bonds a. Name – methlated compounds b. Function i. Nonpolar & nonreactive - Will affect molecular weight and weak interactions - Changes size and therefore chemical characteristics ii. Addition to dna or molecules bound to dna – affects expression of genes iii. Arrangement in male and female sex hormones affect shape and function

Answer 13

ATP – energy currency of the cell (can be immediately spent) • Organic molecule is adenosine – composed of adenine and ribose sugar Attached to three phosphate groups via high energy covalent bonds • Inorganic phosphate (Pi) – P group that has been cleaved off ATP by enzymes to release energy o Inorganic – no longer attached to carbon containing molecule o Adenosine diphosphate (ADP) is left – has one more high energy bond

Answer 14

• Monomers – individual units of the molecule; similar or identical building blocks covalently linked to one another • Macromolecules – polymers built from monomers o Poly=many and meros=parts o Very diverse molecules (ex. proteins) Less difference exists between polymers from individuals that are related to one another – ie. there is more similarity in macromolecular structure between parents and children

Answer 15

Enzymes – protein polymers that increase the rate of reactions; would otherwise occur to slowly to sustain life o Catalyze synthesis and breakdown Synthesis – dehydration reaction (water is formed; one monomer contributes hydrogen and the other monomer contributes a hydroxyl group) a. Not always strictly the case - Ex. amino acid example – one AA donates O-, one donated 2 H+ b. This reaction is repeated until the entire polymer is synthesized ``` All polymers are assembled with the same sequence of events (ex. chain of amino acids) Degradation – hydrolysis (adding water) a. Broken off – monomer - The rest is still a polymer b. This is how we digest food ```

Answer 16

Carbs Lipids Proteins Nucleic acids

Answer 17

Carbohydrates – include sugars and sugar polymers; CnH2On Monosaccharides – monomer - Mono=one sacchar=sugar - Most common monosaccharide is glucose (C6H12O6) – has unique connectivity Monosaccharides consist of a carbonyl group and many hydroxyl groups – location of carbonyl group determines whether it’s a: 1. Aldose (aldehyde) – end of carbon chain a. Ex. galactose and glucose 2. Ketose (ketone) – middle of carbon chain a. Ex. fructose Sugar names generally end in ‘ose’ – size of the carbon skeleton may be used 1. Hexose: 6 carbon framework 2. Triose: 3 carbon framework 3. Pentose: 5 carbon framework Linear vs cyclical 1. Glucose – often depicted as a linear molecule; carbon 1 is not engaged 2. Larger sugars – long enough to form cyclical structure (ex. pentose and hexose sugars) a. Cyclical structures – most stable and most commonly found in solutions Alpha vs beta sugars 1. Alpha – OH group points down 2. Beta – OH group points up

Answer 18

Sugars are used: 1. As a fuel source in the cell - Canadian money – sugar - Can be quickly broken down and produce ATP - most energy is stored as lipids - take longer to break down 2. To assemble other complex molecules a. Can be converted to other molecules (ex. amino acids) – requires many different enzymes 3. If not immediately used (in 1 or 2) – will be stored as disaccharides or polysaccharides - Formed by dehydration reaction - Only store sugar as polysaccharide in muscle and liver – the rest/most of energy is stored as lipids Polysaccharides – macromolecules a. Covalently linked via glycosidic bonds – covalent bonds; called glycosidic when covalently bonding 2 sugar monomers together - Can have a few (oligosaccharide) to 100,000 monomers covalently linked b. Uses - Storage molecules - Structural molecules Storage molecules – can be broken down when the cell needs energy; storage types differ depending on cell storing them 1. Starch – plant storage form of glucose; stored as granules in plastids within cell - All glucose monomers are alpha – linked 1-4 - Hydrolysis – releases glucose from the starch when energy is needed a. Animal cells also have the enzymes needed to hydrolyze starch – we can break alpha 1-4 bonds to digest them b. Types of starch 1. Amylose – unbranched starch 2. Amylopectin – branched starch - Includes 1-6 linkages (linking more fingers makes stronger) - When its branched – it can continue to create alpha 1-4 bonds Glycogen – animal storage for glucose 1. More branched than amylopectin – with higher frequency (linking whole hand) 2. Stored in human liver and muscle cells a. Doesn’t persist for very long in the cell unless it is replenished 3. Hydrolyzed at an increased rate when the cell needs energy a. Epinephrine released by adrenal gland – causes increased rate of hydrolyzation of glycogen in liver for cells Structural 1. Cell wall material – a protective framework exterior to Fungal and Plant cells and bacteria; have a sugar layer (cell wall) - Allows it to with stand osmotic pressure - Humans/animals – do not have a cell wall - Bond position determines architecture and polysaccharide function – whether or not it is digestible (ex. cellulose – not digestible) 2. Cellulose – component of plant cell wall; all glucose monomers are beta a. Animals do not have the enzyme to cut beta linkages - Passes through as insoluble fiber - Cleans out the intestinal tract – speeds up ‘conveyer belt’ to remove from body; self cleaning - Cows have prokaryotes living within them that digest cellulose - Cows themselves cannot digest cellulose 3. Chitin: polysaccharide component of fungal cell wall - Similar to cellulose - Includes a nitrogen containing side group

Answer 19

Properties 1. The only group not formed from repeating monomers a. Form a diverse group – fats (triglyceride), phospholipids and steroids 2. Do not mix with water i. The only nonpolar group - Non-polar hydrocarbons - Exception – some consist of a few polar covalent bonds involving oxygen Fats – molecules assembled via dehydration reactions 1. Glycerol sugar – forms the neck of the structure - Has hydroxyl groups – serve as location for dehydration reactions with fatty acids (also have OH group) - Fatty acids tails – attached to glycerol via ester linkages Number of FA: a. Monoglyceride – 1 FA b. Diglyceride – 2 FA c. Triglyceride/triacylglycerol – 3 FA i. Primary fat/energy storage - May be the same fatty acids or different fatty acids - Varying lengths FA Composed of (see above diagram) - Carboxylic acid - Non-polar tail – hydrocarbon chain Types - May be saturated or unsaturated 1. Saturated fats – no double bonds - Solid at room temp – allows for tight packing - Makes them straight – increased van der Waals interactions between them - Saturated with hydrogen 2. Unsaturated fats – contain one or more double bonds - Liquid at room temperature - Naturally occurring varieties are in the cis conformation – creates a kink in the chain Functions 1. Primary energy storage form - 1g fat stores twice as much energy as 1g of sugar - We would weigh way more if we had to store everything as sugar - Fats allow lowest weight with highest energy 2. Protects organs and provides insulation - Thermal insulation – we are endotherms

Answer 20

Omega-3 fatty acids – cannot be synthesized in the body and must be supplied by diet - Counting 3 carbons from noncarboxyl end -> that’s where the double bond will be/start - Omega 6 -> double bond will start 6 up from bottom (non carboxyl end) Phospholipids: a. Major component of cell membranes - Spontaneously assemble into the membrane structure – bilayer formed by nonpolar tails are nonpolar inward and polar head groups face ECF and ICF b. Polar head group and 2 FA - Can be both saturated or both unsaturated - one straight, 1 bent – most common in animal cells c. It will circularize to close off nonpolar section completely - Structure – 2 fatty acids are attached to a glycerol molecule (sugar; used in fat molecules to provide a bridge) d. Phosphate group (PO4-) – attached to third hydroxyl of glycerol - Neg charge e. Head group – attached to phosphate - Determines unique identity of phospholipid - Polar – hydrophilic Ex. choline - Fatty acids – hydrophobic & nonpolar Steroids: - Four fused carbon rings – forms a carbon skeleton; hydrocarbons (nonpolar) - Examples: Vertebrate sex hormones and cholesterol – estrogen and testosterone

Answer 21

Proteins are the work horse of the cell Functions – enzymes, transporters, structural (fibrous & cytoskeleton proteins) - More than 50% of the cell’s dry weight Proteins function as: 1. Defense molecules - Ex. antibodies (ex. created by covid vaccines) 2. Enzymes – catalyze reactions 3. Storage – keep molecules within the cell 4. Transport – channels and carriers 5. Cell communication – cell to cell communication - Produce proteins that can be excreted (hormones) - Local and long distance 6. Structure - Internally – cytoskeleton proteins - Outside – ex. collagen (fibrous protein) 7. Movement – within the cell using cytoskeleton - Within muscle fibers – allow lengthening the shortening to contract Thousands of proteins - Varied 3D structure – fold in very specific way; structure is characteristic of their function - How an enzyme will engage with its substrate - Can then design inhibitors and antagonists – manipulate in order to enhance human life (drug development) - DNA provides info to make proteins - Unique function

Answer 22

Amino acids – monomers; repeated units of proteins 1. Consist of a. Centrally located carbon atom: the alpha carbon b. Ionized carboxylic acid terminus (COO-) c. Amino terminus (NH3+) d. R group – 4 groups of AA based on R groups - Non-polar – hydrophobic (“boring”) Ex. alanine – R group is CH3 (methyl group) - Polar – hydrophilic Ex. serine – R = CH2OH - Acidic – donate protons in solution becoming anionic; hydrophilic (because they carry a charge) Carboxyl group is also an acid Ex. Aspartic acid – R = CH2COOH - Basic – accept protons in solution becoming cationic; hydrophilic (because they carry a charge) Ex. lysine – R = (CH2)NH3+ Polypeptides – long string of amino acids bonded together via peptide bonds (cov bonds between AA formed by dehydration reactions ) 1. Some proteins a. Are just one polypeptide b. Most are more than one polypeptide – fold into specific final shapes & assembled to fit specific function a. - Has polar components (between N and H) – makes hydrophilic 2. Polypeptides are constructed from a unique combination of amino acids - There are 20 different amino acids - The DNA sequence of the gene dictates the amino acid sequence of the protein 3. All polypeptides will consist of an amino terminus and a carboxy terminus (carboxyl group) a. The number of side chains (R groups) out number the two termini – add elements of ionization and polarity - Chemical nature of the R groups determine the ‘personality’ of the protein as a whole – functions of R groups contribute to overall behaviour of protein Denaturation – protein structure may be affected by salt concentration, temperature and pH; results in loss of function - Ex. frying an egg – denaturation of albumin (?) protein - Ex. milk expiration

Answer 23

1. Primary Structure – amino acid sequence of the protein 2. Secondary Structure – folding sequence of peptide chain of primary structure; due to local interactions a. Hydrogen bonds – between different locations of the polypeptide sequence; create secondary structure - Backbone hydrogen bonding – not between R groups b. Two types: alpha helices and beta-pleated sheets - Alpha – loops - Beta – folded sheets - Can have multiple alpha and beta sheets within the same secondary structure – will not always; depends on the specific AA 3. Tertiary Structure – chemical interactions between R groups of individual amino acids that form polypeptide; 3D folding pattern due to a. Chemical interactions – covalent bonds, ionic bonds, disulfide bond, hydrogen bond - Becomes more complex as r group bonds form between beta and alpha sheets – not all proteins have multiple beta/alpha complexes b. Ex. Disulfide bonds form between S of cysteine amino acids in the polypeptide chain 4. Quaternary Structure- two or more polypeptides (in their tertiary structure) come together to form a functional molecule a. Uses hyd bonds, covalent bonds, ionic bonds b. Form either - Globular – 7 main functions - Fibrous – primarily structural

Answer 24

Structure of Nucleic acids Nucleotide – monomers; Each nucleotide has three components: a. Pentose sugar (five carbon sugar) – “prime” when numbering carbons on sugar (5’ and 3’ end) - Deoxyribose (DNA) – no oxygen - Ribose (RNA) – alpha hydroxyl group on carbon prime 2 b. Phosphate group – gives negative charge c. Nitrogenous base – contain nitrogen as part of chemical structure i. Purine – double ringed structures (Ag makes good rings; is pure) - Adenine - Guanine ii. Pyrimidine – single ringed structures - Cytosine - Thymine (DNA only) - Uracil (RNA only) Nucleic acid – polymers; nucleotides joined by covalent bonds via dehydration reactions - Sugar phosphate backbone – phosphate group off of 5’ carbon of one nucleotide bonds to the 3’ carbon on sugar of the next nucleotide - Covalent bonds WITHIN chains (hyd bonds between chains of DNA) - Nitrogenous base face interior – allow dna to form double stranded molecules with hyd bonds between bases Nucleic acids range in size – very specific; depend on function of DNA a. 100s to 1000s nucleotides - 1000s – lots of combinations of functional units; makes the number of potential nucleotide combinations infinite - 4 types of nucleotides in many different combinations (ex. words in language) b. The various combinations account for much of the genetic variation seen in the world - Between family – more genetic cohesiveness - Lots of variation

Answer 25

Genes – encode the primary amino acid sequence of a protein (information manual within the cell) - Made of deoxyribonucleic acid (DNA) - DNA was discovered in 1953 by Watson and Crick Types of nucleic acid: DNA – always double stranded and is found as a double helix 1. Two polynucleotides are wrapped around one another a. Nitrogenous bases always protrude from the sugar phosphate backbone into the center of the double helix - Cytosine & guanine, thymine & adenine - Base pairing – hold adjacent bonds together via hydrogen bonds A :: T (2 hyd bonds) C ::: G (3 hyd bonds) - Complementary strands – amount of one = amount of other - Most DNA molecules have thousands or even millions of base pairs 2. Adjacent strands are held together by hydrogen bonds a. 2 hydrogen bonds between T and A b. 3 between G and C 3. Carries the information needed to make proteins a. DNA -> transcription -> mRNA -> translation -> protein - Ex. DNA -> transcription -> Insulin mRNA is created -> translation -> makes insulin protein (functional unit) 4. Is able to self replicate – allows new cells to form; important in development RNA is always single stranded 1. Has ribose sugar 2. Uracil instead to thymine

Answer 26

Microscopes were invented in 1590 – know scientist and contribution & general timeline a. 1665: Robert Hooke was the first to see and describe living cells (they were dead tho) - Dead cells taken from Oak tree bark – eukaryotic cells b. 1674: Antony van Leeuwenhoek was the first to observe living cells - Bacteria that he named animalcules – prokaryotic cells - Smaller – used a better microscopes Microscopes – critical for cytology (the study of cells) & histology (the study of tissues) o The study of cell structures Artifacts – seen in the microscope image but are not present in the actual sample; problem with all types of microscopy o Due to errors – bubble or vacuole structure o Be mindful of when looking at samples

Answer 27

1. Light microscopy a. Compound light microscope – any microscope that uses visible light to observe specimens (ex. a light bulb) a. Able to observe due to excitation (provides energy that comes up through sample) - Light is beneath specimen b. Uses two lenses to observe specimens i. Objective Lens – lens is located closest to the specimen - 3 lenses to choose from - 10x-100x - Magnifies & inverts the specimen ii. Ocular Lens – lens is located within the eye piece of the microscope - Magnifies the specimen 10x - Good for – larger structures - Animal cells – euks - Nucleus & mitochondria 2. Electron microscopy: 2 types a. Scanning Electron Microscopy (SEM): i. Can only view the surface of an object – cannot visualize internal cell detail ii. The specimen must be coated with a thin film/stain of heavy metal - Metals are very electron dense – the electron beam will have something to interact with - Ex) gold iii. Allows a wide range of magnifications to be achieved - (15x-100,000x) – can be in the range light micro provides with better resolution b. Transmission Electron Microscopy (TEM): i. Can examine internal cell structure ii. Electron beams do not penetrate thick cell wall – requires thin sectioning (cell must be cut in order to be viewed) iii. Process - Inject the cell with resin so that it solidifies the sample – can see where everything is - Create thin sections of cell to examine the inside using microtone (diamond knife) - Coat the slices with metal to engage with electrons – stains improve contrast and allow to see different positions of objects better - Must be stained before they can be viewed Ex. Uranium is a type of stain - Stains improve the contrast between different cell structures iii. More for research labs – determine specific structures

Answer 28

``` Magnification a. Calculating Magnification: - For a compound microscope: total magnification= objective lens magnification X ocular lens magnification Example: o ocular lens= 10x o objective lens = 100x o total magnification= 10 x 100 = 1000 ``` Resolution – the ability to distinguish fine detail and structure/the ability to distinguish 2 points a certain distance apart (he closer 2 objects are, the harder it may be to tell there’s 2 different objects) a. Resolving power is a numerical value - 6nm resolving power = can distinguish two points as clean and seperate if they are at least 6nm apart b. Light must pass between objects in order for two objects to be seen as distinct from one another – must be a short enough wavelength (otherwise they will be seen as one object) - Wavelength – shorter wavelengths will care more energy and have better resolution - Longer – less energy with poorer resolution c. The General Principle of Resolution: the shorter the wavelength of light the better the resolution will be

Answer 29

Electron microscopes – use beams of electrons instead of light a. Resolution o Electrons also travel in waves – are much shorter than light waves & therefore achieve a better resolution b. Magnification o Achieve a much greater magnification than light (as high as 500,000x) - If you keep the magnification constant (both light and electron at 1000x) – resolution will be better on electron microscope The added ability of these microscopes allow us to view internal cell structures and viruses o Were able to see pathology in tobacco – small infectious particles were the first virus identified Heavier and more expensive

Answer 30

• The smallest object visible with the human eye is 0.10mm A compound microscope can be used to view an object as small as 0.20μm o 1000x smaller than eye An electron microscope can be used to view objects as small as 0.20nm o 1000x smaller than light microscope o Using the same magnification an electron microscope will also provide an image with a better resolution than a light microscope

Answer 31

separates intracellular materials so that they may be studied in depth Plasma membrane has organelles within – cytoplasmic soup; indicative of cells function o Emulsify membrane with detergents to isolate organelles and material Apply intermediate steps with subsequent increases in g forces (increasing RPM) in centrifuge o Lower speeds – will sediment large cellular material at the bottom of the tube into pellet o Higher speeds – will sediment smaller cellular material into pellets Process a. Disruption of membrane – cytoplasmic material will fall out b. Put it into a centrifuge and apply centrifugal force - Creates a pellet – biggest intracellular material - Within the supernatant – smaller material c. Take supernatant into another centrifuge - Apply increased centrifugal force for longer - New pellet material (Intermediate material) d. Take supernatants – even smaller materials - Increased centrifugal force for longer - New pellet material e. Take supernatant – the ribosomes will now be in here - Increased centrifugal force for longer (ex. 150,000g for 3 hrs) - Can examine ribosomes

Answer 32

Prokaryotes (Pro=before karyon=nucleus) a. Subtypes - Bacteria - Archaea b. Do not have a nucleus/membrane bound nuclear structure – DNA is not bound by a membrane - Single piece of circular DNA (circular chromosome) – both differ from euks - Located in the nucleoid – contains genetic material of prok - Freely located (not within membrane) – you will almost 100% find it here c. Do not have organelles d. Can have additional external structures that promote attachment - Ex. sticky sugar layers/capsule e. Analogous to bachelor suite – no specialized compartments - Cellular processes still occur - Easier to maintain f. These are single celled with rare exceptions – disruptions to cell effect entire organism Eukaryotes (Eu=true karyon=nucleus) a. Subtypes - Protists – no longer a cohesive group - Fungi - Plant - Animals b. DNA is located inside of a nucleus – bound by a double membrane - Multiple, linear chromosomes – 46 in human cells - Dogs have 78 – also linear - Additional DNA is located in other areas of the cell (ex. mitochondria) c. Have membrane bound organelles – structures within membrane that provide a function (ex. mitochondria allows metabolism) - Perform various cellular functions d. Analogous to a 3 bedroom apartment – each room has a function - More expensive to maintain and reproduce - Same cellular processes are occurring e. Mainly multicellular organisms

Answer 33

Plasma Membrane – provides the boundaries of every cell a. A selective barrier – has the capacity to control what is entering and exiting - Allows vital nutrients and O2 to enter (O2 is a precursor for metabolism) - Allows wastes such as CO2 to exit Cytosol – viscous fluid that fills the boundaries of the cell (viscous due to dissolved materials)l; internal cellular components are suspended within o Cytoplasm – fluid, organelles, dissolved nutrients o Cytosol – liquid only Chromosomes – composed of DNA (always dna if the cell is living; viruses can be RNA) o Genetic material – forms the ‘recipe’ for protein synthesis (ex. insulin) Ribosomes – serve to synthesize proteins according to information that originates within the DNA sequence a. They are different sizes in prokaryotes and eukaryotes -> excellent target for antibiotics -> selective toxicity - Some drugs have very poor selective toxicity b. Info from dna -> protein is the product - dna to mRNA (intermediate) – transcription - mRNA to protein – translation

Answer 34

Different sizes do exist – there are limitations o Cells can only be so small before they lost the ability to perform key tasks Euks vs proks – there are exceptions to both (can have small euks and large proks) 1. Eukaryotes – much larger than prokaryotes a. Eukaryotes are 10-100μm in diameter • Upper limit is 100x larger than lower limit of proks 2. Proks – smaller a. Typical prokaryotic cell: 1-5μm diameter b. Smallest cell: 0.10-1.0μm in diameter – living cell (viruses are smaller but nonliving; typically in nm range) Mycoplasma species – prok: o Small disease causing bacterium o Does not have a cell wall that most proks do have – allows it to be smaller The surface area to volume ratio of the cell – very important a. Small cells – have much higher surface area to volume ratio than one large cell of the same size - proks are smaller; euks are larger - Important for cells that function in absorption/material exchange b. Smaller – promotes better and quicker nutrient exchange • Greater SA to volume ratio c. Larger – low SA to volume ratio creates increased difficulty in transferring and distributing nutrients • An increase in cell size will not correspond to an increase in membrane surface area d. Bigger organisms have a greater number of cells – cells are not larger

Answer 35

Euks only Nucleus – can be more than one; contains most of the DNA inside of the eukaryotic cell (some in the mitochondria and chloroplasts as well) a. ~5μm in diameter b. Enclosed by a nuclear envelope: - Double membrane – 2 bilayer structures - Contains pores – at intervals that provide port locations; allows entry and exits for large polar molecules - Regulate the entry/exit of protein and mRNA - Protein – would to cytoplasm to nucleus - mRNA – would go nucleus to cytoplasm c. Shape is supported by nuclear lamina – protein framework attached to the inside face of the nuclear membrane - There may also be a nuclear matrix Inside Chromosomes – units of organized nuclear DNA; composed of genes (recipe book) a. Chromosomes – long segments of DNA complexed together with protein (histones) i. Histones – coil DNA; organizes DNA to create more compact structure • Bacterial cells – 4x longer than cell; must be coiled to fit inside cell ii. Chromatin – DNA and protein together; uncoiled • When the cell is not dividing • Chromosomes are uncoiled and active iii. During cell division – the chromosomes are condensed and easily visible as individual units (‘condensed and shrink wrapped’ recipe book) b. The number of chromosomes in the nucleus of a cell is dependent on the species and the class of cell – does not indicate complexity of species i. Humans • 46 chromosomes in somatic cells – diploid o One from mom, one from dad o liver, muscle, epithelial cells (anything that is not a sex cell); will have one from mom and dad in each cell • 23 chromosomes in sex cells – haploid o Will have only one from either mom or dad o Sperm brings half, egg brings half – creates diploid cell ii. Dogs • 78 chromosomes in somatic cells: diploid • 39 chromosomes in sex cells: haploid The Nucleolus – prominent in the nucleus when the cell is not dividing; disappears during division a. Protein from cytoplasm is complexed together with ribosomal RNA (rRNA) made from the DNA template - Forms large and small ribosomal subunits – exported to the cytoplasm and assembled into ribosomes b. Cells may have more than one nucleolus to produce more ribosomes and produce more proteins - Common in muscle – requires lots of proteins c. mRNA – made in the nucleus from the DNA template; exported through the nuclear pores to the cytoplasm; used by the ribosome to synthesize protein

Answer 36

Structure - made of rRNA and protein (2 types of biomaterial) - 2 subunits – large and small Ribosomal quantity is dependent on cells needs o Large quantity of protein synthesis = many ribosomes o Nucleoli will also be more prominent 2 cellular locations: a. Free in the cytoplasm: - Make proteins destined to stay in the cell (ex. enzymes) b. Bound ribosomes – attached to RER and the nuclear membrane i. Rough endoplasmic reticulum – continuous with nucleus - Has ribosomes on surface Make protein destined to: • Be inserted into membranes • Be packaged into organelles • Be secreted from the cell – a cell that secretes large quantities of protein will have more bound ribosomes

Answer 37

Types o Some are physically connected o Some are vesicular – sacs composed of membrane ``` Membrane bound organelles – largely function to synthesize, store, and export molecules Includes: o Nuclear membrane – connected to the ER o Endoplasmic reticulum o Golgi apparatus o Lysosomes o Vacuoles o Plasma membrane ```

Answer 38

2 types o Smooth ER – does not have any bound ribosomes o Rough ER – has ribosomes attached giving it a rough appearance; continuous with nucleus SER functions in: 1. Lipid production – oils, phospholipids and steroids; fat synthesis a. Ex. ovarian cells and testicular cells synthesize sex hormones – steroids - These cells have lots of SER – increased supply and demand 2. Detoxification of drugs and toxins a. Consuming a greater amount of drugs causes increase in amount of smooth ER and associated detox enzymes -> increased drug tolerance • Sensitivity will decrease for any substance that can be detoxified o Nonspecific – increase in tolerance for one drug will cause increase for many o Higher doses of the drug are necessary to achieve the same effect • If smooth ER is not used – tolerance will go back down 3. Stores calcium ions a. Releasing calcium – serves to activate the cell • Ex. muscle cell – causes contraction; have more smooth ER RER functions to: 1. Produce more membrane phospholipids which are then inserted into the membrane – membrane will become larger/have different characteristics 2. Bound ribosomes – produce proteins not to stay in cytoplasm a. Inserted into the membrane of the rough ER • Has its own proteins b. Transported to other organelles – within the same cell • Ex. lysosomes – digestive c. Secreted by the cell • Ex. insulin – a protein produced by bound ribosomes and secreted from the cells in the pancreas into the blood

Answer 39

1. Polypeptide is synthesized by a bound ribosome reading mRNA -> it is inserted into the cavity of the rough ER via a protein pore a. Inside the ER – protein folds into its final 3D shape - Not fully done -> will have more resemblance to final shape 2. Often glycosylated – short sugar chains linked to the polypeptide; produce a glycoprotein 3. Packaged into transport vesicle once ready for export – portion of ER blobs off with proteins inside 4. The transport vesicle now buds from the ER membrane and the protein travels to the golgi apparatus where it will be further processed

Answer 40

Receives transport vesicles from ER; modifies and stores proteins Consists of flattened sacs stacked atop one another – cisternae; are not interconnected 2 faces 1. Cis face – receiving end; protein enters 2. Trans face – shipping side; proteins released • Gives rise to vesicles which bud off Proteins move through pancakes/cisternae a. Modified as it travels through golgi • Different cisternae have unique enzyme packages – products are refined in stages b. Modifications • glycosylated – carbohydrate groups on glycoproteins may be modified/substituted in the golgi • phosphate groups may also be added to proteins – serve as identification tags later on in protein transport • Membrane proteins may also be modified The number of golgi stacks correlates with the quantity of protein that the particular cell secretes - Lots of protein – more cisternae Products of the golgi – may have external molecules on vesicle structure for docking to target (‘stamp’); proteins are: 1. Secreted from the cell - Secreted from trans face – eventually fuse with plasma membrane for export via exocytosis 2. Added to the - plasma membrane – become part of bilayer - organelle membranes (ex. lysosome membranes) Protein products are not proteins that just function in the cytoplasm of the cell

Answer 41

Analogous to the stomach of the body; membrane bound sacs containing digestive enzymes Digestive enzymes a. Lysosomal enzymes and lysosomal membranes – made by the rough ER and modified by the golgi apparatus i. Digestive enzymes must be kept within a membrane – they are acidic and would damage the other cell components • Enzymes are reusable ii. If you open the lysosomes – cell commits suicide if the cell is old and worn; cells materials can then be recycled b. Unique 3D shape of proteins protects from self destruction Can fuse with: a. Vacuoles containing food that has been engulfed by the cell i. Lysosomal enzymes break down the food; release the nutrients back into the cell • metabolized to generate energy – end product is usually carbon dioxide gas ii. Vacuoles containing engulfed bacteria -> Kills the organism & digests contents - Leukocytes/white blood cells – some are phagocytes (phagocytosis) iii. Damaged organelles -> called autophagy (eating yourself; not committing suicide of entire cell) - Breaks down to release their components for cell use - Allows the cell to continually renew itself Tae-Sachs Disease – rare disorder; results when a lipid digesting enzyme is missing from lysosomes o Lysosomes become engorged with fat -> accumulates in the brain, impairing brain function (unable to break down wastes & neurons can’t function) o A child with Tae-Sachs disease will die within a few years

Answer 42

Multi-functional membrane bound sacs; content inside a. Derived from the ER and the golgi – creates vacuole within the cell o Can store food, transport solutes and remove excess water from the cell Central vacuole of a plant cell functions to: 1. Store - Sap – sugar and water mixture - Water – can enlarge and engorge - Nutrients, chemicals, waste products Ex. excess ions - Poisons – protect from predation 2. Breakdown ingested material with its enclosed enzymes 3. In flowering plants – contain pigments which attract pollinators - Pigments are expensive to make

Answer 43

only in plants and algae (euks) Function – carry out photosynthesis a. Photosynthesis – the conversion of light energy from the sun into chemical energy of sugar molecules (co2 + light energy -> sugar) i. Used by euks that can photosynthesize – plants and algae ii. Reverse cellular respiration • CO2 + light energy -> glucose + o2 Structure – many membranes which partition the organelle into compartments a. Inner & outer membrane – not folded - Contain thin intermembranous space b. Stroma – fluid within inner membrane - Contains enzymes, DNA, ribosomes (70s) c. Thylakoids – network of interconnected sacs within stroma Thylakoid space – within thylakoids; hollow space • A lot of photosynthetic activity • Contain chlorophyll pigments – light is absorbed as it enters d. Granum – thylakoids stacked on top of each other - Grana – plural - Function to absorb suns energy - Also originated from bacteria o Multiple membrane o 70s ribosomes o Its own DNA

Answer 44

evolved by an endosymbiosis Endosymbiosis – endo (inside) symbiosis (+/+ mutually beneficial) a. Both were originally proks that began living inside of larger cells b. Endosymbiont – small cell living within host cell - Ex. cyanobacteria – photosynthetic bacteria; originated chloroplasts Similarities to proks a. Single circular DNA b. 70s ribosomes – smaller than euks c. Reproduce by binary fission – splitting in half; method proks use to reproduce - Not as complex as mitosis d. Enclosed by a double membrane - Inner membrane – very similar to the plasma membrane of prokaryotes; same types of proteins

Answer 45

membrane enclosed organelle Function a. Enzymes inside oxidize/reduce (modification of chemical structure) cell components forming H2O2 i. Destructive – H2O2 is toxic • Bad modifications – the original chemical structure was the correct one and needed • Redox reactions ruin proteins ii. An enzyme is present to convert H2O2 to water – depleted so it’s not toxic to us b. Used in fatty acid breakdown and detoxification - Breaks down fats inside cell - Detoxifies cells Structure a. Bound by a single membrane - Enzymes and contents of peroxisome are toxic and therefore sequestered (closed off from rest of cell)

Answer 46

in proks & euks; a network of protein fibers that extend throughout the cell cytoplasm and: (analogous to skeletal system); strength and support Functions a. Provide structural support b. Assist in the movement of organelles - Ribosomes can move along like “train tracks” c. Anchor organelles within the cell (“twist ties” them into position) d. Assist in movement of the cell - Requires interaction with motor proteins e. Maintain cell shape f. Can be rapidly assembled/taken down - Constantly being remodeled – not being worn Composition – three different proteins Microfilaments 1. Structure a. Composed of actin – globular proteins o Solid rods – no gap in the middle o Globular proteins (actin balls) – polymerized b. Arranged in a twisted double chain – helical structure; makes it very strong o Made it withstand force 2. Functions a. 3 dimensional network – supports shape of cell o Actin density creates more viscous cytoplasm near the surface of the plasma membrane (not as dense in center of cell) b. Important in muscle contraction – thin filaments Intermediate Filaments 1. Structure a. Long and thin b. Differ depending on the type of cell c. Composed of various fibrous proteins o Have a ropelike structure – polymerized proteins 2. Functions a. Reinforce cell shape and to anchor organelles in place – morphology b. Usually permanent cell fixtures – strong due to the way fibers rope around each other o Made to withstand force Microtubules 1. Structure a. Straight, hollow tubes – not solid throughout! b. Composed of tubulin protein o Each unit is a dimer composed of two slightly different tubulin proteins o Length of the microtubule is increased by adding dimer units to the end of the structure 2. Function a. Centrioles – composed of microtubules which grow out of the centrosome o Important in cell division b. Shape and support the cell c. Organelles can also be moved along microtubules – train tracks d. Make up euks cilia and flagella o Extend from the surface of some cells o Important for cellular motility

Answer 47

Unique to plants a. Animals do not have b. Other organisms that do have will have different kinds Composition/structure 1. Varied composition a. Cellulose is most common – sugar arrangement • We cannot digest this • Dietary fibre – passes through us quickly; cleans our intestines out b. Greater thickness than the plasma membrane 2. Structures connecting cells a. Plasmodesmata – channels connecting adjacent cells; allows movement of materials into other cells b. Middle lamella – thin sticky layer; glues adjacent cell walls together 3. Secondary cell wall – not all plants have a. Thickened for protection and support – plant will be well equipped to grow very tall and large Functions o Protects against osmotic rupture o Maintains cell shape

Answer 48

Composition – similar to cytoskeleton but external a. Composed of glycoproteins – RER and golgi add sugars to proteins within the cell b. Mainly collagen in animals – most abundant protein in the body c. Proteoglycans – sugar/protein complexes; forms a mesh structure d. Fibronectin – receptors on cell membrane; anchor transmembrane proteins to extracellular matrix proteins - Binds to cell surface receptors - Ex) integrins Plant vs animal cells 1. Plant cells – joined together by plasmodesmata channels a. Membrane bound channels filled with cytoplasm 2. Animal cells – connected by tight junctions, desmosomes and gap junctions a. Tight junctions – prevent materials from moving into body; tightly packed cells • Epithelial tissue b. Desmosomes – loose attachments between cells; creates one continuous sheet; more flexibility • Heart muscle and cardiac muscle c. Gap junctions – allow movement between cytoplasm’s • Important in cardiac muscles – allows sheet of muscle to contract together; signal is spread through at the same time

Answer 49

• Selectively permeable – allows nutrient uptake and waste removal o Channels and carriers – allows hydrophilic molecules to pass through the membrane with ease • Membranes with different functions will have very different structure and chemical composition

Answer 50

Semi fluidity – key characteristic; vital for function Fluid mosaic model – mosaic refers to proteins floating within 1. Proteins within membrane – can be anchored or can float a. Proteins have many functions i. RBC – anuclear; not highly complex (lose a lot of their function) o There are more than 50 different proteins in the plasma membrane of a red blood cell alone ii. More complex cells (nuclear) – have many more b. Lots of variability between and within cells i. Different cell types – have different proteins ii. In a single cell – plasma membrane and the organelle membranes contain different proteins o Contraction o Detoxification and metabolism Membrane is held together via hydrophobic interactions – Van Der Waals forces (non polar can’t bond) a. Fatty acids – are amphipathic (polar and nonpolar regions); double bonds prevent them from packing closely together (creates kink) - Bent tails of phospholipids allow proteins to move throughout the cell membrane (not static) - Keeps the membrane fluid – able to move around Fluidity of phospholipids a. Lateral diffusion – can move around within their own leaflet b. Can also move to different leaflet i. Difficult due to polar head group through the nonpolar material - Movement is catalyzed by flipases and flopases enzymes ii. Can be done to expose receptor to kill cell

Answer 51

Internal temp must be maintained – organisms evolved to have phospholipid composition that keeps the membrane semipermeable at environmental temperatures Fluidity is maintained with decreasing temperature a. Colder – causes phospholipids to solidify • FA form Van Der Waals – interactions increase with decreasing temp b. Heat – causes increased movement; less bonds • Fevers – assist in slowing growth of the bacteria so immune system can handle it • Phospholipid composition dictates freezing temperature Saturated vs unsaturated fatty acids a. Saturated – more van der waals; more difficult to disrupt with heat; solid at room temp b. Unsaturated – less van der waals; easier to disrupt with heat • One double bond is sufficient to decrease melting point – subsequent double bonds will effect melting point less Long chain vs short chain fatty acids a. Shorter tails – less van der waals; easier to disrupt with heat b. Longer – more van der waals; harder to disrupt with heat Can change degree of saturation a. Tail length will be constant because membrane diameter is constant – diameter is required for function • Diameter is 8-10nm (ECF to ICF side of membrane) Cholesterol in animal plasma membranes – provides heat and cold stability a. Behaves as a buffer – can only manage to a certain degree; extreme temp changes will still cause melting and freezing b. Dual functions - High temperatures – cholesterol prevents melting by hindering phospholipid movement - Low temperatures – cholesterol interferes with close packing of fatty acid tails; interferes with freezing

Answer 52

Integral – penetrate membrane interior 1. Most are trans-membrane proteins – spread from ECF side to ICF side a. Hydrophobic regions – interact the FA • R group of AA will be hydrophobic – Van der waals interactions between R groups and phospholipids FA tails (cannot bond) b. Hydrophilic regions – AA R groups • Areas with other proteins (interfaces) • Facing ICF or ECF 2. Some penetrate only part of the membrane interior (not transmembrane) a. Lipid anchored proteins Peripheral membrane proteins: 1. Can be on ECF or ICF face a. Not embedded in the membrane b. Often attached with ionic interactions (not as strong as covalent) 2. Loosely bound to the surface of the cell a. Often attached to exposed integral proteins • On ICF – can have attachments to integral proteins and cytoskeleton proteins • On ECF – can have attachments to extracellular matrix b. Have anchoring attachments to structures on both sides of membrane • Attachment on ICF – to the cytoskeleton • Attachment on ECF – to the extracellular matrix

Answer 53

1. Strengthen membrane framework a. Ex. Integrins – transmembrane proteins; bound to the cytoskeleton on ICF and to the extracellular matrix on ECF i. Act as a bridge across the membrane 2. Cell to cell recognition a. Ex. Glycoproteins – carbohydrates bound to ECF surface of the membrane; used for recognition 3. Form tight membrane junctions between different cells a. Ex. epithelial cells – each has a ‘clip’ that will attach to the other and pull them close together so materials & keeps bacteria out of the body 4. Enzymes a. Carrying out sequential steps in a pathway – product of one enzyme becomes the reactant for another i. Membrane provides framework b. Proteins bind to enzyme – enzymes catalyze reaction i. Ex. tyrosine kinase enzyme 5. Receptors – binding initiates signal transduction a. Bind to chemical messengers/ligands that have been secreted from other cells – signal transduction to ICF i. Ligand specific (ex. hormones) ii. Triggers a series of events – turn on or turn off processes occurring within the cell 6. Transporters – provide selective permeability a. Non-polar molecules are able to directly pass through the membrane – without the proteins b. Polar molecules and ions are not able to move through the hydrophobic interior i. Require transport proteins to enter and exit the cell

Answer 54

Structure 1. Carbohydrates are short branched chains a. Less than 15 sugar units ->called oligosaccharides • Oligosachh – short chains of sugar b. Branched – have units coming off main chain 2. Covalently bonded to: a. Protein – glycoprotein b. Lipids – glycolipids 3. Variability between a. Species to species • Between people and animals b. Individuals of the same species • Between different people c. Cell to cell • RBC will have blood group antigens but liver cells do not Function o Cellular recognition – found only on ECF (with few exceptions) o Allow immune cells to recognize and reject foreign cells such as bacteria and transplanted tissues

Answer 55

Continuous bidirectional movement a. Nutrients enter and wastes exit - Ex. oxygen moves into the cell and carbon dioxide exits the cell b. Maintains ion concentrations c. Maintains the selective permeability of the cell Diffusion rate effected by 1. Size - Bigger – harder - Smaller – easier 2. Shape 3. Chemical nature a. Non-polar compounds – able to cross the plasma membrane easily from areas of [high] to areas of [low] • Ex. O2, CO2 and hydrocarbon molecules (nonpolar) • No assistance required o Passive transport – high to low o More efficient – protein synthesis requires energy b. Polar and charged molecules – cannot pass directly through the membrane • Diffusion occurs very slowly – transporters assist in movement; would otherwise occur too slowly to sustain life o Transporters – movement occurs in microseconds

Answer 56

Integral proteins 1. Channel proteins – form a hydrophilic channel through the membrane a. Transmembrane integral proteins i. Lipophilic components facing FA tails ii. Hydrophilic components facing channels b. Creates pore – substrate specific i. Ex. Na+, K+, Cl- channels ii. Ex. aquaporins – allow the movement of 3 billion water molecules per second c. Diffusion rate will be effected by concentration gradient (higher = faster) 2. Carrier Proteins – binds to molecules & undergoes conformational changes a. Highly degree of substrate specificity i. Physically interacting with what they’re moving b. Ex. Glucose transporters i. Increase glucose rate of transport by 50,000x ii. Beta cells of the islets of Langerhans of the pancreas – release insulin - Insulin binds to receptor – causes the insertion of GLUT transporters within the membrane - Facilitate movement of glucose from high to low concentration (with GLUT) a. Movement is not always passive (ex. apical membrane of GI tract has SGLT)

Answer 57

movement from [high] to [low] Diffusion – the ability of particles to spread out through any region of space; movement is from regions of high concentration to regions of lower concentration (ex. perfume) a. Movement of particles will continue until chemical equilibrium is established – concentrations are equal on either side of the membrane b. Occurs due to kinetic energy/thermal energy within molecules – occurs spontaneously - Higher temp – more kinetic energy; faster movement - Lower temp – less kinetic energy Non-polar material – move naturally across membranes from [high] to [low] Ex. Co2 and o2 - O2 moves from the lungs into the blood – moves from blood to cell - Co2 is the opposite Polar molecules and ions – diffuse passively across the membrane through transport proteins

Answer 58

Osmosis – movement of water across a semi-permeable membrane; always passive a. Able to diffuse across membrane – will move towards higher concentration of non-permeable solutes; increases water volume - Will establish osmotic equilibrium (equal concentration) b. Always from low solute concentration to high regardless of identity of solute Tonicity – ability of solution to cause cell to gain or lose water; non permeable solutes a. Hypotonic – water moving in will cause cell to swell and burst - Kills the cell b. Hypertonic – water moving out will cause the cell to shrivel and become dehydrated - Cell will be ‘asleep’ – requires water and will obtain metabolic activity once water content is restored

Answer 59

plant and animals cells must regulate water gain/loss in order to survive Organisms that lack a cell wall – may live in an isotonic environment to compensate o Human cells and most animal cells o There is no net movement – there is still movement Organisms living in hypotonic environments – have mechanisms to prevent cell lysis a. Altered membrane permeability to water will slow movement of water into the cell b. Contractile vacuoles: have pumps to force water out of the cell - Even though water comes in – will be pumped out (in hypotonic solution)

Answer 60

Cell membrane – semi fluid Tonicity: Isotonic – animal cell is immersed in solution that has equal solute concentration to the cell - No net water movement - 0.9% is isotonic Hypotonic – animal cell is immersed in solution that has lower solute a. concentration than the cell -> hypotonic solution relative to the cell - Osmolysis – result of net water movement into cell; causes swelling - Lethal once it bursts Hypertonic – animal cell is immersed in solution that has a higher solute concentration than the cell a. Shrivels & dehydrates – net movement of water out of the cell • Asleep – becomes metabolically inactive until water volume is re-established – not lethal o Single celled bacteria can dehydrate and become inactive until later o Animals and plants can’t do this as well b. Clinically – can use hypertonic solutions to decrease swelling in the brain c. Honey – can be left at room temp because any bacteria that moves into honey will shrivel because it’s such high sugar solute concentration in environment

Answer 61

plants, bacteria, fungi, some protists Cell wall – rigid o Plants, bacteria, fungi and some protists all have a cell wall – animal cells do not o Allows structural maintenance when the organism is placed in a hypotonic environment Plant cell: Hypotonic – turgid & firm a. Turgor pressure – the wall exerts a counter force on the cell; cell membrane is pushed up against the wall • Especially important in small plants – allows mechanical support; don’t have a lot of skeletal support Isotonic – flaccid/limp; membrane is not against wall Hypertonic – plasmolysis; can lead to wilting and death a Plasmolysis – cell membrane pulls away from cell wall; leads to wilting and death • Cell wall does not offer assistance • Become metabolically inactive – can kill them

Answer 62

facilitate the movement of polar molecules and ions across membranes Always specific to molecules they bind o More pathways facilitate more movement – more transport proteins present will result in greater rate in a membrane for a particular solute, the greater the rate of diffusion will be across the membrane. More pathways = more movement All cells have different proteins – can change depending on immediate needs

Answer 63

allows polar molecules to diffuse down their concentration gradient Passive process -> does not require energy; driven by the concentration gradient a. Substantially increase the speed that polar molecules are able to cross the membrane - Would otherwise diffuse very slowly b. The transport protein is usually very specific to certain materials 2 modes 1. Channel proteins – provide a corridor for the movement of hydrophilic/ionic materials a. Can be gated – only open in response to certain stimuli: usually electrical, chemical, mechanical • Ex. K+ voltage gated channels in neurons 2. Carrier Proteins – not free diffusion because the protein binds and carriers across; even through movement occurs high to low (still passive) a. Ex. glucose transporter • Interior of the transporter changes shape to allow – conformational changes o Binding of the molecule is triggers the change in shape Many sugars, amino acids and water (aquaporins) all use facilitated diffusion to cross the membrane o Water is small but polar – requires protein channels to diffuse across the plasma membrane at a reasonable rate; would otherwise occur too slowly to sustain life Aquaporins – specific for water transport • Important in the kidney – renal system o Increased water permeability – brings water back into body when you’re dehydrated  Influenced by hormones

Answer 64

involves the expenditure of energy to move a solute against its concentration gradient Energy sources o Primary – ATP (money currency of cell) o Secondary – energy source stored within another concentration gradient Are all carriers – allows the maintenance of concentration gradients across the plasma membrane Ex. Na+/K+ ATPase – movement of 3Na+ out of the cell and 2K+ into the cell coupled to the use of 1 ATP molecule - Electrogenic pump – creates charge separation; moving more pos charge causes inside to become neg with respect to outside - Occurs in animal cells – most of energy consumed goes towards this pump 4 stages 1. Solute that is to be transported binds to a specific site on the transport protein found on the cytoplasmic side of the plasma membrane 2. ATP molecule containing three phosphate groups, transfers one of the phosphates to the transport protein 3. Phosphorylation causes conformational change so that the solute can be released on the other side of the membrane 4. Dephosphorylation returns to its original shape - Makes the transport protein available to transport a new molecule Co-transport – gradients initially established by ATP can be used to do work when moving down gradient; energy stored within; one moving down concentration will other is moving up Secondary active transport – couple the movement of one material down its concentration gradient (energy releasing) to the movement of another material up its concentration gradient (energy requiring) Ex. sucrose transporter • Moves sucrose into the cell against the concentration gradient – higher concentration within cell o Sucrose moves low to high • H+ moves into the cell down its concentration gradient – higher concentration outside cell o H+ moves high to low – was initially established by proton pump Types a. Symporter – both are moving in the same direction relative to each other b. Antiporter – moves solutes are moving in opposite directions relative to each other

Answer 65

voltage differences exist across the membrane of the cell Membrane separates opposing charges 1. Electrochemical gradient – 2 forces drive movement of ions a. Concentration difference – chemical force b. Charge different – electrical force - Inside of cell is approx. -70mV more neg than the. Outside - Attracts positive charge in – if you create channels to allow permeability - The negative cytoplasm will function to pull cations into the cell Maintained by electrogenic Pumps – pumps that create charge separation a. Ex. proton pumps – common to prokaryotic and eukaryotic cells - Move protons from low to high concentration using ATP - Creates an electrical charge separation and a steeper concentration gradient - Gradient can be used to perform work and synthesize ATP - Energy is stored as a voltage difference Ex. Na+/K+ ATPase moves 3Na+ out for every 2K+ in using energy stored in an ATP molecule

Answer 66

large molecules require (ex. protein) Occurs via vesicular transport – diffusion and osmosis are not sufficient for large molecules Exocytosis – exports materials from the cell (ex. sugar and proteins) Steps: 1. Transport vesicle buds off golgi – filled with molecules to be exported 2. Bilayer of vesicle fuses with the bilayer of plasma membrane – becomes part of membrane o Makes the membrane slightly larger – plasma membrane is dynamic; will not stay continuous in size 3. Inner components of vesicles are released into ECF - Ex. insulin is released from pancreatic cells via exocytosis - Insulin causes uptake of glucose by cells to lower blood glucose concentration - Ex. Neurotransmitters are also released via exocytosis Endocytosis – imports materials to inside - Budding inward from plasma membrane – takes material and internalizes in ICF in membrane bound vesicle - Food vacuole – large compartment bound by membrane Three types of endocytosis 1. Phagocytosis – large materials a. Cellular eating - Cell engulfs particle – wrapping it with pseudopods - Pseudopods – reach out around the external molecule to enclose b. Particle is then packaged in a vacuole - Vacuole fuses with a lysosome – digestive enzymes breakdown the contents of the vacuole - Food particle is broken down – can be used by cell c. Specificity – less specific than receptor mediated; more specific than pinocytosis - ex. immune cell will bind to bacteria (not specific in the sense that it’s not e. coli, just bacteria) 2. Pinocytosis – small materials a. Cellular drinking - Droplets of fluid are taken up into tiny vesicles – much smaller than vacuole • Invagination of cell still occurs b. Very non-specific – any solutes that are dissolved in the extra-cellular fluid are also taken up - Sampling of ECF fluid 3. Receptor-mediated endocytosis – large particles a. Receptor proteins in membrane – highly specific to their ligand b. Endocytosis occurs with receptors bound to ligands – membrane pinches inward; forms coated pit - Some other molecules by be caught in as well

Answer 67

Metabolism – manages all material, metabolites, and energy resources of the cell; cell is constantly being broken down and refreshed Enzymes – all metabolic processes require for efficiency • Highly specific – allows cell to control Types 1. Catabolic – break molecules/polymers into smaller fragments; increase entropy a. Bonds are broken – always releases energy as ATP • Energy can be harvested b. Hydrolyze polymers – broken down; hydrolyzation requires enzymes • Occurs stepwise – can occur multiple times • Ex. polysaccharide – can break off monosaccharide o Monosaccharide – catabolized into 6co2 and release more energy 2. Anabolic – build molecules and polymers from smaller starter materials; decrease entropy a. Bonds are formed – always requires energy • Ex. co2 photosynthesizes to glucose (anabolic reaction)

Answer 68

Bioenergetics – the study of how energy flows as it occurs Energy – can be used to do work (rearrange matter) Chemical energy – energy stored within the bonds of molecules; can be released during chemical reactions a. Ex. photosynthesis – co2 forms bonds to create glucose • Sunlight – energy input • When hydrolyzed – energy is released Laws of thermodynamics 1. Energy can be transferred and transformed but it may not be created or destroyed - Ex. can convert light energy to chemical energy 2. Energy conversions are not 100% efficient and some energy is lost as heat each time a. Heat – increases the entropy of the system - Inefficient conversions – used to maintain our body temp within set point - Too much heat – will cause sweating b. Entropy – disorder of the system - Disorder always results in the release of energy - Glucose is ordered – co2 is a gas (disordered) Processes a. Non-spontaneous processes – require an input of energy in order to proceed - Order is being created b. Spontaneous processes – does not require energy; occur without adding energy to the system - Entropy of the universe is always increasing – spontaneous

Answer 69

always a change; easier to measure dG= dH – TdS 1. dG = the free energy available to do work a. Positive – costs you energy o Necessary b. Negative – energy is being given off (overall in the big picture of reaction) o Preferred 2. T = temperature in Kelvins (+273.15) 3. dS = change in entropy (amount of order/disorder) a. Large pos value = lots of disorder o Will make the G value negative (larger value subtracted from temp) 4. dH = change in enthalpy a. Negative dG – the process is spontaneous and releases energy - Exergonic reaction – energy releasing • Extra energy is used to build fats – store as energy o Breakdown fat and release energy when required b. Positive dG – the process is non-spontaneous and requires energy - Endergonic reaction – energy requiring

Answer 70

Activation energy – all chemical reactions have a particular activation energy that must be overcome in order for the reaction to proceed Barrier to forward movement of reaction – needed to destabilize bonds of the reactants so they break easier a. Also required when forming bonds – provides energy for order formation - Allow molecules to be close enough together to form bonds Transition state – highest energy state; must be reached to break bonds and release energy Enzymes – protein molecules (mostly); act to increase the rate of a chemical reaction (fast enough to sustain life) a. They are not consumed during a chemical reaction – are not altered during reaction; can use again right away - Will be eventually broken down when old b. High specificity – to a particular chemical reaction for specific substrates - Allow cell more control – according to needs of cell - Unlike increasing heat – nonspecific c. Lower the activation energy of the reaction – doesn’t need to climb to as high of an energy level (“chair lift”); expels less energy Heat – increasing thermal energy causes an increase in the rate of a reaction • Non-specific – all reactions would see an increase in rate - Heat absorption – provides thermal energy to break bonds (reform into products); allows it to reach transition state

Answer 71

unique conformation of tertiary structure is highly specific Usually end in ‘ase’ and are named after their substrate • Ex: maltase – catalyzes the breakdown of the disaccharide maltose (cov linked with glycolytic bond) - Breaks down in small intestine Act on specific reactants – substrates Steps: 1. Enzyme has empty active site – substrate will enter into active site (the “doing site”) a. Active site – groove on the surface of the enzyme; caters to specific shape of substrate (allows for specificity) • Induced fit hypothesis – enzyme will change shape to that of the substrate; will mold shape when substrate enters and binds - Lock and key – less likely b. Remainder of enzyme supports the activation site 2. Substrate enters into the active site – attaching to enzyme with weak bonds (hyd bonds, van der Waals, ionic bonds – all favourable) a. Induced fit hypothesis – applies pressure/strain to substrate bonds; easier to sever • Places amino acids of the active site in proper position to catalyze the reaction b. Binding energy is created by changing shape – causes activation energy to decrease; creates opportunity to form favourable bonds • Favourable bonds – ionic, van der Waals, hyd bonds; all cause energy to be released o Energy is then used to put rxn on sale 3. The strained substrate bond reacts with water – converts reactants into products a. Hydrolyses reaction – water provides chemical satisfaction; provides atoms for each separate product 4. The enzyme releases the newly formed products and is released unchanged from the reaction ready to catalyze a new reaction - Single enzyme – may act on thousands or even millions of substrate molecules per one second - A reaction occurs up to a 10 million times faster in the presence of one enzyme

Answer 72

Shape of an enzyme is critical to its function – environment may cause change of shape and function • Shape changes – cannot be metabolically active Factors – pH and temp 1. Temperature – optimal temp maximizes contact between the enzymes active site and substrate molecules (37°C for human enzymes) a. Hot denaturation – causes weak bonds to break (will not break cov bonds) • Unfolds and loses shape • More irreversible than cold – render nonfunctional b. Cold denaturation – causes more bonds to form due to decreased thermal energy & motility; alters shape • More reversible that hot – can recover from additional bonds forming • Goes into state of dormancy • Affects fluidity of membrane as well 2. pH – most human enzymes function best near neutral pH a. At pH values higher and lower than 7, enzyme function is impaired • Increasing acidity is increasing h+ o COO- and NH3+ will become COOH and NH3+ b. Pronation will prohibit ionic bond from forming – enzyme will unfold and loose its shape c. Antimicrobial defense through acidity in stomach

Answer 73

most enzymes require in order to function; non-protein molecules (sidekicks) Cofactors can be either organic or inorganic – alters protein folding a. Inorganic cofactors – usually ions of zinc, copper or iron - Charged and able to interact with enzyme - Ex. putting mg2+ between 2 coo- allows attraction – 2 pos charge satisfies 2 neg charges b. Organic cofactors – called coenzymes - Essential vitamins – dietary components that often function as coenzymes - Ex. biotin – allows cov bonds between carbons

Answer 74

chemical that interferes with activity in order to turn it off Varying affinities a. Tight covalent bonds – high affinity; irreversible b. Non cov bonds – weakly associated lower affinity; reversible - Hyd bonds, ionic, van der waals Competitive and allosteric – both can be reversible and irreversible 1. Competitive – site in active site; satisfies shape and physically occupies a. Competitive inhibitors – block substrate from binding • Can be overcome by increasing customary substrate – will displace competitor 2. Allosteric – bind to enzyme away from active site a. Allosteric inhibitors – causes a change in shape of active site so substrate can no longer bind • Cannot be overcome by increasing customary ligand

Answer 75

vital metabolic regulator If more product is produced than required, the product can inhibit an enzyme early in the pathway Ex. A -> B -> C -> D a. D product will inhibit ab enzyme = binds to location on enzyme ab and shuts it down (thus inhibiting pathway) • Often behaves as noncompetitive inhibitor accumulation of metabolic products inhibit enzyme activity early in the pathway a. **behavior is observed with allosteric inhibitors – often non competative but can be either or b. Ex. threonine substrate (AA) – binds to enzyme - Intermediate A -> B -> C -> D enzymes - Product binds to allosteric site of initial enzyme – causes noncompetitive inhibition c. Ex: The amino acid isoleucine can slow its own production by behaving this way

Answer 76

Chemical work - Endergonic reactions -> Anabolism a. Positive dG - dG = dH - TdS - Creating order - Unfavorable reaction due to high dS Transport Work – movement of materials against the concentration gradient a. Secondary active transport – does not require ATP • Ex. Can use proton movement (high to low) or other gradients b. Primary active transport – uses ATP Mechanical Work - Muscle contraction - Flagellar rotation – bacterial movement

Answer 77

Energy coupling – pairs endergonic (mortgage) reactions with exergonic reactions (paycheck) a. ATP hydrolysis is exergonic and can be used to do work (endergonic) -> Releases 30.5kJ/mol of energy -> -G - Measured under standard conditions – under 25°C and under certain concentrations; only meant for comparison purposes - Cell conditions are not standard and much more energy is available from the hydrolysis as a result Enzymes work to couple exergonic reactions with reactions that require energy

Answer 78

Negative phosphate groups – repulsion of like charge creates high energy bonds; causes energy release when the bonds are cleaved (used to perform work) a. Artificial systems – hydrolysis of ATP will be used to heat the surroundings b. In the cell – energy released from ATP hydrolysis is used to perform work - Small amounts of energy will be lost as heat – not completely efficient; can be used to warm the body • Ex. shivering Enzymes couple exergonic reactions with endergonic – creates net exergonic reactions a. Often occurs by the transfer of a phosphate group to an intermediate – raises the energy of the intermediate ATP is produced using energy that arises from catabolic reactions in the cell ADP + Pi -> ATP a. Endergonic – energy requiring Catabolic reactions produce ATP – create disorder; energy is used to make ATP a. -dG reactions release energy – harnessed to make ATP - 10 million molecules of ATP are consumed (broken) and regenerated (made) per second ATP -> ADP + Pi a. Exergonic – energy releasing • Anabolic reactions require ATP – create order

Answer 79

Reaction at equilibrium – no longer be used to perform work; balanced and has no incentive to move forward or reversed (standstill) a. Ex. water that is flowing downhill – spontaneous & energy powers water mill - Once water is balanced on both sides – will not be able to power mill b. dG=0 -> Dead cell - As soon as we achieve an “equilibrium” in cell – disequilibrium is created - Constant inward and outward movement of materials keeps the cell from ever reaching equilibrium Catabolism – a series of reactions A -> B -> C -> D etc - Enzyme for each step - Creates downward flow in neg G situation – prevents equilibrium Product pull forces secondary reactions a. Le chateliers principle – keeps forward movement because products are being used • Consumption of products prevents accumulation • Accumulation – will create feedback inhibition ``` Cellular catabolism: a. Begins with: Glucose + O2 -> high energy • Glucose – food to be catabolized • O2 – gives help to process reaction b. Finishes with CO2 + H2O -> low energy • Co2 is a waste product • Harvested the rest of the energy ```

Answer 80

Stop production of enzyme – stop transcription of the gene a. Slow process • Prevents transcription and translation – cuts off process early on Regulate the activity of the enzyme post-production – turns the final protein molecule on or off; protein is still there a. Faster process b. Phosphorylation is commonly used – can activate or inactivate • When neg phosphate group is attached o Another neg charge will repel o Pos charge will attract • Changes shape

Answer 81

the function at one site of an enzyme is affected by the binding of a regulatory molecule at a different site (allo is other; steric is shape) Regulatory molecule o Activators – stabilize the active conformation o Inhibitors – stabilize the inactive conformation Multiple subunits – assemble into functional unit o Each subunit has its own active site – each may be active or inactive o Each active site may be active or inactive (active binds to substrate) Cooperativity – substrate binding will to active site of multiunit enzyme and change shape of all enzymes (stabilizes) a. Characteristic of all allosteric binding; amplifies the response of the enzyme to the substrate - Can increase the catalytic activity of the enzyme - Can also be an inhibitor Ex. Hemoglobin is an allosteric protein that does not work as an enzyme – same behaviour as an allosteric enzyme but does not catalyze reactions a. Exhibits cooperative behavior • Regulatory activators – pH, temp, o2 concentration b. Works to transport O2 from the lungs -> tissues -> inside of the red blood cells • O2 is nonpolar – needs a transporter to bind and move throughout the plasma o We only carry 1.5% of o2 in blood – polar and non polar doesn’t allow o 98.5% is attached to hemoglobin c. Cooperative binding of o2 • In the lung – binding of O2 to one hemoglobin subunit triggers a conformational change in protein; increases the affinity for O2 at all other binding sites o Low temp, neutral pH, and low co2 • In the tissues – O2 is low & is released from one site; the affinity for O2 at all other sites is decreased o Higher temp, low pH, and high co2 d. Mature RBC – clean out organelles (including nucleus) creates more space for hemoglobin Ex. covid – causes build up of co2 – causes increased acidity a. pH denatures proteins ATP can act as allosteric inhibitor a. Catabolism produces energy - If there is already a lot of energy/ATP present – will inhibit catabolic reactions b. ATP is a high energy signal – cell has lots of energy if there’s lots of ATP - ATP binds to allosteric enzymes and turns off catabolism – inhibitory c. AMP and Pi indicate low energy within cell - Bind to allosteric enzymes and turn on catabolism – activator d. Replenishes ATP supply o Stimulates phosphofructokinase – phosphorylating enzyme o Phosphorylates fructose phosphate – makes biphosphate

Answer 82

Euks – has membrane bound organelles o Different compartments facilitate different reactions depending on what enzymes are present Cellular compartmentalization creates order in metabolic pathways a. Enzyme teams may form complexes - Products become reactants for subsequent reactions - Products can be substrates for multiple reactions

Answer 83

Sources of energy – organic molecules serve as sources of fuel for the cell Many types of energy 1. The sun – the origin of all chemical energy a. Photosynthesis: co2 + h2o -> (energy from sun) -> o2 + glucose • + dG (endergonic & nonspontaneous) - Disordered co2 gas -> ordered glucose • Reverse of cellular respiration 2. Glucose – can be directly catabolized to release energy a. Polysaccharides, proteins, amino acids and lipids must be enzymatically processed before they can be catabolized Energy is converted between various forms o Some energy is always lost as heat – there will be less available in end outcome that if there hadn’t been intermediate steps o Chemicals are recycled Oxidation of organic molecules a. High energy molecules -> broken into lower and lower energy molecules (stepwise) - - dG (exergonic & spontaneous) b. Require enzymes because of high activation energy (enzymes decrease)

Answer 84

Aerobic Cellular Respiration – requires oxygen a. Chemical formula (opposite of photosynthesis) - C6H12O6 + 6O2 -> 6CO2 + 6H2O + ATP + heat b. Extremely efficient - 32% -> results in a lot of loss but still gets lots of energy; drives cells - One mole of glucose release 2870kJ of energy (G = -2870) c. Processes - Glycolysis - Intermediate/pyruvate processing - Krebs/citric acid/TCA cycle - Electron transport chain Anaerobic respiration – o2 is substituted for something else Fermentation – alternate pathway; occurs as a mode of energy production in the absence of oxygen a. Antient – thought to be the first ever metabolic pathway - Used by some prokaryotes as their primary means of energy production b. Partial oxidation of organic carbon sources - Unlike other processes – complete oxidation - Its inefficient compared to aerobic Consists of glycolysis followed by either – most classical (but there are many types) i. Alcohol Fermentation – produces ethanol as an end product - We drink – fermented drinks are the result of metabolic wastes ii. Lactic Acid Fermentation – produces lactic acid/lactate as an end product - Lactic acid – acidic organic molecule

Answer 85

Redox Reactions – energy stored in organic molecules is released via electron transfers from one reactant to another Redox – always occurs together/coupled a. Oxidation – loss of electrons - OIL – oxidation is loss - Reducing agent – electron donor (is oxidized) b. Reduction – gain of electrons - RIG – reduction is gain - Oxidizing agent – electron acceptor (is reduced) Not all redox reactions involve the complete transfer of electrons from one molecule to another Ex. Oxidation of methane (CH4) to CO2 a. CH4 = reduced carbon • C-H covalent bonds are non-polar – electrons are shared equally o Carbon has equal share of electrons b. Co2 = oxidized carbon • C-O covalent bonds are polar – unequal sharing; electrons are held more closely to oxygen (electroneg) o Carbon has less share of electrons Oxygen is a potent oxidizing agent – more bonds to oxygen = oxidized a. High positive reduction potential – very electronegative b. Use oxygen to produce energy • Energy is required to strip an electron from a molecule • Transferring an electron to oxygen will release energy o Oxygen usually want it more – explosive transfer o This energy may be used to perform work in the cell – coupling Electrons always travel together with a proton (H+) – as hydrogen atom a. If you remove a hydrogen from glucose – removing an electron C5h12o6 + 5o2 -> 6co2 + 6 h2o + energy Co2 – no hydrogen therefore no electrons o bonds to oxygen – oxidized h2o – reduced form of oxygen o low energy stepwise breakdown

Answer 86

Heavily reduced organic molecules – have large potential energies/lots of electrons a. Lipids especially; also carbs, proteins, etc b. Energy is released during catabolism – oxidation of these molecules - Transfer of these electrons during catabolic reactions forms a lower energy source of electrons Organic molecules don’t spontaneously decompose because of the high activation energy barrier a. Enzymes are needed to reduce this barrier and allow the reaction to occur b. Catabolism of an organic molecule in a single step would release too much energy too quickly -> energy would not be harvested - Stepwise reactions – each has its own enzyme; allows slow and efficient energy harvesting

Answer 87

Electrons always travel together with a proton (H+) – as hydrogen atom If you remove a hydrogen from glucose – removing an electron ``` C5h12o6 + 5o2 -> 6co2 + 6 h2o + energy a. Co2 – no hydrogen therefore no electrons o bonds to oxygen – oxidized b. h2o – reduced form of oxygen o low energy ``` stepwise breakdown

Answer 88

Electron carrier that temporarily holds electrons that are removed from organic molecules during catabolism Dehydrogenase enzymes – strip electrons from glucose Glucose + NAD+ -> 6CO2 + NADH a. Glucose is oxidized b. NADH is reduced NAD+ can be reduced (carry e-) a. First e- is used to neutralize the pos charge = NAD • H+ is also produced b. Second is transferred completely = NADH Recyclable – transfers the electrons to O2 oxidizing NADH to NAD+ NADH produced during glucose oxidation can be used to perform cellular work o NADH + H+ + o2 = NAD+ + H2o Redox reactions • NADH is being oxidized • Oxygen to water is the reduction (collected the electrons as H) Energy is released and harvested in the electron transport chain – does not go directly NADH to oxygen (goes through a chain) a. Protein and associated molecules capable of aerobic respiration are in o Inner mitochondrial membrane of eukaryotes o Plasma membrane of bacteria b. Electrons move from the high energy end of the chain -> the low energy end of the chain o Each of the electron transfers is exergonic – prevent inefficient releases all at once; a series of redox reactions o Each electron carrier is more electronegative than the former - draws electrons along the chain  If they were not – would be endergonic  O2 is the most electronegative – final electron acceptor Glucose -> (NAD+) -> NADH-> (O2) -> H2O o Uses 10 NADH 2 types of electron carriers 1. NAD+ -> reduced to NADH+ + H+ - Can carry 2 e- 2. FADH2 -> reduced to FAD - Can carry 2 e-

Answer 89

1. Substrate Level Phosphorylation – Pi from a substrate molecule is removed and attached to ADP forming ATP a. Used in - Glycolysis - TCA cycle b. Produces very small quantities – tips, not cheque - We do not produce a lot of energy this way 2. Oxidative Phosphorylation – phosphate group originates as Pi in cytoplasm a. Transfer of electrons to O2 – exergonic due to electronegativity of o2; provides energy for ADP -> ATP - Produces the majority of ATP b. Occurs in the electron transport chain – subsequent steps; each wants the electrons more than the last i. Electrons originate on NADH + H+ and FADH2 - Transferred to O2 – most electronegative & at end of chain: 2 e- combines with 2H+ and ½O2 = H2O (forms water) - ~90% of energy release during cell respiration ~32 ATP are available in the glucose structure a. Substrate level – 4/32 ATP b. Oxidative phosphorylation – 28/32 ATP

Answer 90

does not require oxygen to occur Glycolysis occurs in the cytosol of both prokaryotes and eukaryotes Steps 1. 6-carbon glucose – oxidized into 2 3-carbon pyruvate • 10 reactions – each requires its own enzyme • Requires 2 ATP & puts out 4 ATP 2. ATP o Energy requiring phase – 2 ATP o Energy payoff phase – 4 ATP Net production o 2 ATP – substrate level phosphorylation o 2 NADH – reduced NAD+ o **25% of the available energy in glucose is released during glycolysis o No CO2 is released – not created as waste in this step; all carbons are present in 2 pyruvate

Answer 91

must have oxygen available 2 pyruvate molecules produced during glycolysis must be groomed for entry into the citric acid cycle In euks: Pyruvate moves from cytoplasm -> mitochondrial matrix a. Mitochondrial matrix – within the second membrane (innermost area) In prokaryotes the intermediate step takes place in the cytoplasm Pyruvate -> Acetyl a. Pyruvate dehydrogenase complex – multi-subunit enzyme - Remove COO- from pyruvate as CO2 b. Acetyl coA production - CH3COO- is produced from the remaining 2 carbon structure - Coenzyme A is added to the CH3COO- via a sulfur bond -> forms acetyl coA - Starting material for the TCA cycle - Of higher potential energy relative to pyruvate Products per pyruvate • 1 NADH • 1 Acetyl coA

Answer 92

oxygen must be present Occurs in o Euks – mitochondrial matrix (within inner membrane) o Proks – cytoplasm Cycle – oxidizes Acetyl coA completely o 8 steps – each has its own enzyme a. Acetyl coA enters cycle – combines with oxaloacetate (4 carbon) • Forms 6 carbon citrate b. 7 additional steps – oxidizes citrate back to oxaloacetate • 2 carbons lost – CO2 waste Products a. 2 CO2 from the remaining 2 carbon of glucose b. Per acetyl coA (1 cycle) i. 1 GTP – substrate level phosphorylation • Same as ATP in terms of energy – guanine instead of adenine ii. 3 NADH are formed iii. 1 FADH2 is formed

Answer 93

All FADH2 and NADH produced will be starting material for the electron transport chain o 2 NADH H+ from glycolysis o 2 NADH H+ from pyruvate processing total o 6 NADH H+ from krebs total o 2 FADH2 from krebs total 6 CO2 – all carbon from glucose has been completely oxidized ATP o 2 ATP from glycolysis o 2 GTP from krebs total

Answer 94

NADH and FADH2 hold most of the energy that originated in glucose – will be oxidized and recycled in ETC Within mitochondrial matrix - There are 1000s of copies of this chain in the membrane - Cristae folds increase the surface area making the high copy number possible Each ETC has 4 complexes and an ATP synthase enzyme: I/II/III/IV a. Consist mainly of protein – multi-subunit structures • Can have non protein components attached to change its substrate desire – make successive carriers more electronegative (higher electron affinity) b. Each complex has tightly bound prosthetic groups – needed for function As electrons move down the chain there is a decrease in free energy - Carriers alternate between oxidized and reduced forms Carriers in ETC: 1. Complex I: NADH is first oxidized to NAD+ & transfers 2 e- to complex I a. FMN – flavoprotein; first carrier that accepts electrons b. FMN transfers e- to Fe-S c. Fe-S transfers e- to ubiquinone i. Ubiquinone – a non-protein molecule; hydrophobic & mobile through the membrane interior o also called coenzyme Q o carries electrons to complex II 2. Other electron carriers in the chain are cytochromes a. Many different varieties • Iron is included in the structure b. Undergoes oxidation and reduction – electrons are continually transferred 3. Complex II a. FADH2 enters the chain – transfers 2 e- to ubiquinone • Less ATP (1.5) produced per FADH2 – only 6 H+ moved instead of 10 H+ 4. Complex IV a. Final carrier is cytochrome a3 • Transfers electrons to oxygen – final electron acceptor • Oxygen combines with 2 H+ from the mitochondrial matrix – forms water 2e- + 2H+ + ½O2 = H2O b. FADH2 enters the chain at complex II • Contributes 2 electrons like NADH but enters the chain later o Worth less ATP as a result

Answer 95

Chemiosmosis – energy coupling Proton motive force – as electrons are passed between carriers in ETC, the release of energy is used to push H+ up gradient at complex I, III, IV - Protons flow from intermembranous space (high [H+]) into mitochondrial matrix (low [H+]) down gradient through ATP synthase ADP + Pi -> ATP - H+ enters binding sites inside rotor portion – causes ATP synthase to spin - Energy released from gradient is used to form high energy covalent bonds in ATP ATP synthase – fifth protein complex at the end of the ETC a. Multi-subunit structure – four components; each subunit consists of many polypeptides b. ATP produced via chemiosmosis i. 10 NADH per glucose - 10 H+ per NADH - 25 ATP ii. 2 FADH2 per glucose - 6 H+ per FADH2 - 3 ATP

Answer 96

Max efficiency = 32 ATP o 4 ATP from substrate level phosphorylation – glycolysis & Krebs cycle o 28 ATP from oxidative phosphorylation – ETC Energy from the proton gradient is used to drive cellular transport (under normal circumstances) o Pyruvate from cytoplasm -> mitochondria o ATP from mitochondria -> cytosol after production Percent efficiency a. 32 ATP x 30.5 kJ/mol = 976 kJ/mol of energy for use - There is 2870 kJ/mol available in glucose b. 34% of energy is harvested - The rest is lost as heat – maintains body temp

Answer 97

Oxidation of organic fuel in order to produce energy in the absence of oxygen Organisms that use: 1. Obligate anaerobes – incapable of tolerating O2 (killed in the presence of oxygen) a. Oxygen gas is very poisonous – we need enzymes to deal with toxic oxygen radials - Obligate anaerobes lack the enzymes b. May use only fermentation or anaerobic respiration for energy production - Anaerobic respiration – ETC must be present; uses different molecules 2. Facultative anaerobes – capable of using respiration or fermentation a. If O2 is present – aerobic respiration will be used - Much greater ATP production – in respiration b. If O2 is not present – anaerobic metabolism will be used

Answer 98

a. Uses the ETC with alternative final electron acceptors i. Still generates a proton motive force – all steps of ETC are present - 10 NADH - 2 FADH2 - 4 ATP equiv via substrate level phosphorylation b. Less energy is available – still better than fermentation i. O2 is the most electronegative – other transfers won’t release as much energy - Higher electronegativity = more energy released when accepting e- - Less energy = less protons moving across complexes I, III, IV ii. Ex. SO42- is an electron acceptor (replaces O2) -> H2S is the reduced product (replaces H2O) Some prokaryotes living in anaerobic environments will do this

Answer 99

NOT anaerobic respiration No ETC Glycolysis -> produces 2 pyruvate -> pyruvate is converted to end product i. Does not require O2 ii. Consumes NADH H+ -> NAD+ - NAD+ is used in glycolysis iii. 2 ATP produced from glycolysis – low energy production 2 types 1. Alcohol Fermentation a. Bacteria and yeast do this – humans do not have enzymes for it - Bubbles are seen in the reaction mixture from CO2 b. Occurs in the cytoplasm of proks and euks i. Begins with Glycolysis – 2 ATP and 2 NADH are produced - Glucose -> 2 pyruvate ii. Pyruvate -> converted to acetaldehyde (2C) and CO2 - Acetaldehyde – poisonous; too much in your body will make you feel sick iii. Acetaldehyde -> converted into ethanol (alcohol) - Responsible for yeast – ethanol burns in the oven (you don’t get drunk when you eat bread) iv. NADH is also oxidized back to NAD+ - NAD+ can return to glycolysis 2. Lactic Acid Fermentation a. Fungi and bacteria – production of cheese and yogurt b. Human skeletal muscle – switches to lactic acid fermentation when O2 is limited - Lactic acid is sent to the liver to prevent acidity damaging muscles – converted to pyruvate & enters into the intermediate step for normal catabolic processing - Also occurs in vagina – acid protects against STIs c. Process i. Begins with glycolysis – 2 ATP and 2 NADH are produced - Glucose -> 2 pyruvate ii. Pyruvate -> converted into lactic acid (3C) - Lactic acid will immediately deprotonate – drops the pH of surrounding - Lactate – the deprotonated form iii. NADH is also oxidized back to NAD+ - NAD+ returns to glycolysis

Answer 100

Free glucose is not common o Glycogen – can be catabolized to release free glucose Disaccharides, proteins and lipids – more commonly consumed as energy for ATP o These structures must be processed – may enter into glycolysis or the TCA cycle as intermediates Proteins – may be cleaved into free amino acids o Amino acids can be used for anabolic reactions – protein synthesis o Amino acids may also be used for ATP production via catabolism – when in excess a. Process i. Must first undergo deamination – removes the amino group from the carbon skeleton (pathway does not recognize nitrogen) ii. Amino group – used to produce urea and other waste products such as ammonia - Urinated away Fats – can be cleaved into fatty acids and glycerol a. Glycerol – converted into a three carbon glycolysis intermediate - Then goes through the rest of the pathway b. Fatty acids – are consumed in beta oxidation process i. Beta oxidation – converts the fatty acid -> many acetyl coA molecules • Goes directly into TCA -> combines with oxaloacetate ii. Worth large amounts of NADH/FADH2/GTP in the TCA cycle c. Fats store large quantities of energy – 1 gram of fat stores twice as much energy as one gram of sugar

Answer 101

Anabolic (require energy); create order • Not all food is completely catabolized for energy Catabolites (various stages of breakdown) from food – serve as carbon skeletons to build larger organic molecules in the cell 1. Glycolysis and TCA cycle intermediates can be used for building reactions a. Glycolysis – 10 steps produce 10 reactants that can be used b. TCA – 8 steps produce 8 reactants 2. Glucose can be synthesized from pyruvate – work backwards by adding energy and building sugars 3. Fatty acids can be synthesized from acetyl coA All anabolic reactions consume ATP – ATP can later be released when the molecule is catabolized

Midterm Flashcards

(125 cards)