1
Q
Isotopes
A
- Basis of why mass #s are rarely whole
- Many elements have different isotopes, which have varying #s of neutrons
- Isotopes w/more neutrons are often unstable (radioactive)
2
Q
Electronegativity
A
- Measure of how strongly electrons are attracted to nucleus
- Elements w/more protons are more electronegative so polar bonds are particularly strong in molecules such as OH and CO
3
Q
Hydrogen Bond
A
- Biggest consequence of polar covalent bonds
- Electrostatic attraction between partial positive + negative charges of 2 water molecules
4
Q
Cohesion
A
- Explains phenomenons such as water rising in trees
- Explains how water moderates temperature because hydrogen bond formation or disruption buffers heat energy
5
Q
Does water facilitate chemical reactions well?
A
- Yes, since it’s a very good solvent
- All polar molecules + ions dissolve easily in water (known as hydrophilic); non-polar molecules don’t dissolve in water + are hydrophobic
6
Q
Hydrophobic Interactions
A
- Describe non-polar molecules being forced together, as being together minimizes disruption of hydrogen bonding in surrounding water
7
Q
Van Der Waals Force
A
- Describes attraction of non-polar molecules to each other b/c of transient dipoles, caused by random localization of electrons in different areas of their orbitals
- Occurs between all molecules but is only relevant for non-polar molecules
8
Q
How strong are ionic bonds that are relevant in biological settings such as proteins?
A
- Not strong: they’re actually relatively weak
- However, ionic bonds in salt crystals are much stronger: strength is similar to or higher than that of covalent bond
9
Q
Which acids are most important in biology?
A
- Weak acids like the carboxyl group. They dissociate partially + reversibly
- Oxygen is more electronegative, so it grabs electron pairs and releases H+
10
Q
Titration Curve
A
- Measure the pH after adding increasing amounts of NaOH, equivalent to removing protons from the sol’n
- While pH is expected to rise quickly and dramatically, this isn’t the case. pH rises slowly b/c there is large reservoir of undissociated acetic acid which keeps releasing protons
- Adding acid at pH = 6 reverses this process and slowly lowers pH since added protons would reform undissociated acetic acid and are thereby removed
11
Q
Why is acetic acid called the conjugate base?
A
- B/c it can accept protons
- Weak acids act as buffers, since over a certain range the pH doesn’t change much even if you add a lot of base
- To make a buffer of sol’ns in both directions, must add equal amounts of weak acid and conjugate base to reach half-equivalence point of titration curve
12
Q
Why are buffers important in bio?
A
- B/c it’s important for the f(x) of many molecules that pH is constant, which is why our blood + intracellular fluid is buffered
13
Q
Can you read protonation state off of titration curve?
A
- Yes
- Ex/ at pH = 7, the COOH group discussed is largely COO-
14
Q
2 important chemical rxns in metabolism
A
- Condensation + hydrolysis
15
Q
Condensation
A
- Formation of a polymer linked by covalent bonds, releasing 1 water molecule w/each monomer added
- This is anabolic: requires E input
- Ex/ DNA replication, protein synthesis, starch formation
16
Q
Hydrolysis
A
- Breaking of covalent bonds w/help of water to transform a polymer into its constituent monomers
- This is catabolic: releases E
- Ex/ digestion of food molecules for E generation
17
Q
Does breaking a covalent bond require or release E? What about for forming a covalent bond?
A
- Breaking a single covalent bond requires E, forming releases
- Though we refer to ATP hydrolysis as releasing E, we mean the entire chemical rxn, involving at least 2 covalent bonds being broken + 2 covalent bonds being formed
18
Q
General Functions of Proteins
A
- Do all work in a cell: build structures like hair, replicate DNA, catalyze metabolic rxns, transport materials inside cells + across the membrane, etc
19
Q
What are proteins made of?
A
- Amino acids, which are ionized at neutral pH
20
Q
How are the 20 amino acids classified?
A
- According to the properties of their side chains: non-polar + hydrophobic amino acids, polar amino acids + charged amino acids
21
Q
Peptide Bond Formation
A
- Condensation rxn
- Occurs between carboxyl group of 1 amino acid + the amino group of the next amino acid, generating a peptide backbone consisting of NCCNCC… repetitions
- Amino acid always starts w/amino group (N-terminus) + ends w/carboxyl group (C-terminus)
22
Q
Primary Structure
A
- # of amino acids used + sequence in which they’re arranged
- Determines all properties of resulting protein
23
Q
What does the flexibility of the polypeptide backbone ( due to its consistence of single covalent bonds) give rise to?
A
- Rotation about the single bond (full rotation for the C-C bond, less so for N-C bond)
- This allows polypeptides to fold into proteins, occurring in 2 steps: 1) H bonds form w/in polypeptide backbone between O of carboxyl group + H of amino group. 2) This gives rise to 2 secondary structures that form quickly after polypeptide is made: alpha-helix + beta-pleated sheet. These H bonds don’t involve side chains at all
24
Q
Alpha-Helix
A
- H bonds form in direction of helix, generating stable rod-like structure
- Side chains point outwards, away from helix
25
Beta-Pleated Sheet
- H bonds form w/in plane of sheet, generating stable sheet
| - Side chains point away from plane, up or down
26
Are there obvious rules of when you'll find alpha helices and beta sheets within a protein?
- No
| - Protein structure determination is the only way to confirm presence/absence of secondary structures w/in a protein
27
Proline
- A unique amino acid: side chain is covalently bonded to both C and N atom of peptide backbone
- Generates a kink in peptide b/c ring prevents free rotation of N-C bond
- Backbone H can't form b/c backbone N lacks H, so formation of secondary structures (alpha helix, beta pleated sheet) is impossible
- Often last amino acid of alpha helix
28
General Function of Tertiary Structures and What Mediates It
- Finishes folding of polypeptide
| - Mediated by side chain interactions
29
Which interactions contribute to tertiary structure formation?
- Ionic, H and disulphide bonds, along w/hydrophobic interactions
- All of these are typically between amino acid side chains in interior of protein
30
What happens to the disulphide bonds and proteins of keratin when curling your hair?
- Disulfide bonds reduced/broken
- They're then reformed to keep hair in new shape
- In keratin protein, coiled coils form through hydrophobic interaction + you see disulfide bonds between alpha-helices to provide additional strength
31
What is the most important determinant of protein folding and tertiary structure?
- Hydrophobic interactions b/c stretches of hydrophobic amino acids automatically rearrange towards interior of a protein while hydrophilic amino acids rearrange to be on outside, interacting w/water
32
Coiled Coil
- Important for many structural proteins
- 2 alpha-helices wrapped around each other
- Hydrophobic amino acids at every 4th position generates band of hydrophobicity running along length of the alpha-helix + slowly rotating around it. This interaction ensures that 2 such alpha-helices come together at that band, resulting in coiled coil (like a rope consisting of intertwined strands)
- Occurs in proteins, giving strength to tendons, hair, feathers
- Can be a tertiary structure if both alpha-helices are from same polypeptide
- If 2 alpha-helices from dif polypeptides, this is quaternary structure
33
Do primary, secondary and tertiary structures require or release E?
- Primary (peptide bond formation) requires, secondary/tertiary folding releases (occurs spontaneously)
34
Quaternary Structure
- Indicates several polypeptides interacting to form bigger protein complex such as hemoglobin
- Many don't form quaternary structure: they're fully folded after tertiary structure formation
35
Importance of Amino Acid Sequence (Primary Structure) For Folding and Function
- A single amino acid mutation in hemoglobin protein changes the shape, resulting in sickle shape of RBCs since they contain only hemoglobin
- A typical protein sufficiently diluted in watery sol'n denatures at high temp (unfolds), but will renature (refold) when temp is lowered. This is evidence that primary structure is sufficient for protein folding: all info about protein folding + f(x) is encoded by primary structure
36
Protein Turnover
- Very important b/c proteins often get damaged: fever, pH change, other chemical damages
- Chaperones help proteins fold properly after synthesis or after stress-related unfolding
37
Nucleotide General Function and Structure
- Make RNA + DNA, signal + E storage as monomers
| - Made of 5-C sugar, nitrogenous base + phosphate group
38
What are the four nucleotides in RNA? What is the difference in DNA?
- Cytosine + uracil (pyrimidines) and guanine + adenine (purines)
- Thymine replaces uracil in DNA. DNA lacks hydroxyl group at C-2 (deoxyribose)
39
How do nucleotides polymerize?
- Via phosphodiester linkages (condensation rxn), w/3' hydroxyl group of polymer forming a covalent bond w/5' phosphate group of incoming nucleotide
- So, a long RNA/DNA molecule always starts w/5' phosphate group, ends w/3' hydroxyl - polymerization occurs in 5' to 3' direction
40
What does 5' and 3' refer to?
- The position of the C atom where the functional group is attached
41
What is DNA made up of?
- 2 antiparallel strands held together by H bonds between bases
- Purine bases only pair w/pyrimidine bases (G w/C, A w/T). G-C forms 3 H bonds, so more stable than A-T which only forms 2
- Double helix w/sugar-phosphate backbone on outside + bases on inside, arranged like ladder rungs
- Double-helix results from 2 strands being wound around each other. Has major + minor groove
- Overall DNA sequence of genome carries genetic info
- Base pairing + double helical structures make DNA more stable than RNA
42
Major Groove of DNA
- 2 sugar-phosphate backbones more widely spaced, allowing DNA-binding proteins to recognize bases in the interior
- Very important for transcription factors + restriction enzymes, which recognize a unique DNA sequence
43
RNA General Function and Structural Information
- Since it can execute info, came first in evolution
- Can work like enzyme: catalyzes certain rxns b/c it can fold into complicated 3D structures similar to proteins. Folding occurs b/c nucleotide bases w/in same macromolecule pair via H bonds (in contrast to DNA, where nucleotide bases of dif macromolecules pair)
- Stem-loop structure: important RNA structure - contributes to regulation of mRNA f(x)
44
What comprises all chemical reactions in a cell?
- Metabolism
45
Definition of Energy
- Potential capacity to do work
46
What drives energy conversions in a chemical reaction?
- The tendency of E to become evenly distributed or dispersed over time
- Overall disorder in universe increases as E is dispersed
- The fact that these types of rxns (like tea cooling down) only proceed in 1 direction is described by 2nd law of thermodynamics, based on probability
47
How can a cell release free energy or drive a chemical reaction?
1) W/chem rxn creating disorder in the cell (like digesting a polymer). Creates change in entropy in a closed system, delta S. This doesn't refer to overall change of entropy in entire universe
2) W/chem rxn releasing heat (enthalpy = delta H), generating disorder/dispersing E in surrounding environment. Entropy outside closed system increases
48
What is the equation for free energy?
- delta G = delta H - T delta S
49
What does it mean if delta G is negative?
- E is released/dispersed, rxn proceeds spontaneously b/c it's favourable
50
How many types of reactions can occur?
- 4: depending on whether delta H and T delta S are positive or negative
51
Negative Delta H and Positive T Delta S
- Heat is released, disorder increased
| - Always spontaneous (exergonic) since delta G is always negative
52
Negative Delta H and Negative T Delta S
- Heat is released, disorder decreased
- Ex/ in protein folding, heat is released since favourable ionic bonds + other side-chain interactions occur. But disorder decreases b/c we get nicely folded protein. Since S depends on temp, this process occurs only below a certain temp. Above certain temp, T delta S becomes bigger than delta H + overall delta G is positive, so no protein folding above act 50 degrees
53
Positive Delta H and Positive T Delta S
- Heat used, disorder increases
- Spontaneous above certain temp
- Ex/ dissolving NaCl in water. Heat sucked away from environment, which is why glass gets colder. Heat required to break strong crystal bonds; creation of disorder drives the rxn
54
Positive Delta H and Negative T Delta S
- Heat used, disorder decreases
- Never spontaneous (endergonic)
- Applies to most anabolic rxns
- So anabolic rxns only occur by coupling them to exergonic rxns to make overall delta G negative
55
Reversibility of Reactions
- In theory, all rxns reversible
- If left alone, will proceed to pt of chem equilibrium: no more net change takes place
- At equilibrium, relative [ ]s of A + B are such that fwd + reverse rxns occur at same rate and delta G = 0
56
Is delta G dynamic?
- Yes, it changes as rxn proceeds
- Explains why adding reactants to a rxn speeds up fwd rxn: it increases [ ]s of reactants, making delta G more negative. This is another ex that negative delta G is essential for a rxn to occur
57
How is energy stored and transferred in cells?
- By ATP
| - ATP hydrolysis is an exergonic rxn + can be used to drive endergonic rxns such as making a polymer
58
Why is ATP useful as energy currency?
- B/c its delta G is intermediate between what you gain in respiration + what you expend in anabolism
- Comparison: like how $20 bill is most useful b/c it's intermediate between what you earn + what you want to buy. However, we don't get any "change" in a chem rxn. Leftover of coupled rxn is negative delta G that must be dispersed to drive this rxn
59
What do exergonic rxns require to get started?
- Activation E to put molecules into a transition state favourable to the rxn
60
How can polymerization require E input, while ATP hydrolysis releases E?
- B/c in biology, we refer to entire chem rxn of polymerization or ATP hydrolysis
- Looking carefully at these rxns, both involve simultaneous breaking of covalent bonds + formation of new covalent bonds. Added enthalpies of broken + formed covalent bonds as well as delta S determine overall delta G, which is negative for ATP hydrolysis + positive for polymerization rxns
61
Catalysts
- Increase rate of spontaneous rxns (negative delta G)
- Don't change delta G values
- Not used up by catalysis
62
Enzymes
- The catalysts of biology
- Lower activation E
- Crucial in our bodies b/c at 37 degrees, most spontaneous rxns don't occur since activation E barrier can't be overcome
- When reactants (substrate) bind to active site of enzyme forming an enzyme-substrate complex, enzyme often undergoes small shape change, bringing substrate into transition state
63
Transition State
- Characterized by lower activation E, speeding up rxn
- As soon as products leave active site, enzyme reverts to original shape
- Induction of transition state occurs by binding substrates in correct orientation by exposing reactants to altered charge environments, promoting catalysis, or by inducing a strain on substrate that facilitates breaking of covalent bond
64
Why is a constant pH important for enzyme activity?
- W/dif pH, enzyme would be inactive since negative charge may no longer be there
- Many enzymes require cofactors to catalyze a rxn: these are small organic molecules or ions that aren't amino acids + are associated more or less tightly w/enzyme
65
What occurs when the enzyme is saturated?
- All active sites are occupied
- Further increase in [substrate] won't increase rate of product formation
- Max speed of rxn/turnover rate is reached, varies widely from enzyme to enzyme
66
How can enzymes be regulated?
1) Competitively w/regulator binding the active site
| 2) Allosterically w/regulator binding somewhere else on enzyme
67
Is competitive or allosteric inhibition more efficient?
- Allosteric b/c less inhibitor molecules are required
- This is b/c you need more competitor molecules than substrate molecules for effective competitive inhibition, but you only need more allosteric regulators than enzymes b/c nothing else binds at allosteric site
68
Functions of Sugar
- E storage, building block for nucleic acids, structural component
69
Disaccharide
- Table sugar: made of fructose + glucose
70
Typical Structure of Sugars
- A multiple of CH2O, like C3H6O3
| - 2 functional groups: 1 carbonyl group + several hydroxyl groups
71
How are glucose and galactose related to each other?
- They're optical isomers
| - So they have dif structure
72
What happens to straight-chain glucose in a sol'n?
- It forms another covalent bond to become ring form of glucose
- Since this converts C-1 from symmetric to asymmetric C atom (as C-1 in ring form has 4 dif groups attached to it vs 3 in straight chain form), you get 2 glucose isomers (alpha + beta glucose)
73
How are sugar polymers (polysaccharides) formed?
- By covalent bonds called glycosidic linkages between C-1 of 1 sugar w/any OH-group of 2nd sugar
- Alpha 1,4 linkage gives rise to maltose + eventually starch
- Beta 1,4 linkage gives rise to cellobiose + eventually cellulose
74
What causes the spiral shape of starch?
- The fact that bulky CH2OH groups are on same side, thus bending the polymer
75
Why is cellobiose a symmetrical and straight molecule?
- B/c the 2nd glucose in cellobiose is flipped compared to starch
76
What do all lipids have in common?
- They're insoluble in water
77
Structure of Fats and Oils
- Consist of 3 fatty acids + 1 glycerol connected by covalent bonds
- Fatty acids have 1 carboxyl group + long hydrocarbon chain. They're amphiphilic (hydrophilic carboxyl group + hydrophobic hydrocarbon chain)
78
Why do fats and not starch provide long-term storage?
- B/c fats provide more E/weight than starch but take longer to mobilize
79
What kind of interactions do phospholipids have with water?
- Amphiphilic
- Hydrophilic head group + 2 hydrophobic fatty acid tails are attached to glycerol
- Allows them to self-assemble into lipid bilayers w/hydrophobic fatty acid tails pointing inward, away from, water
80
What do lipid bilayers do to avoid exposed edges?
- Assemble into a globular compartment
| - Energetically most favourable since no more hydrophobic parts are exposed to water
81
Are lipid bilayers (cell membranes) fluid?
- Yes, very
| - Phospholipids are in constant lateral motion
82
What happens when a fatty acid contains double bonds?
- They are unsaturated
- They cause kinks in fatty acid tails, so they cannot be packed as closely together as straight + saturated fatty acids
- This is why butter is solid at room temp (only straight-chain fatty acids) + oils are fluid (many unsaturated fatty acids)
83
Function of Unsaturated Fatty Acids in Lipid Bilayers
- Increase fluidity + permeability of membrane
- Ex/ fish + plants adjust amount of double bonds in phospholipids to keep membrane fluidity stable over wide range of temps
84
Why are membranes very fluid?
- To allow proteins inserted into the membrane (integral membrane or transmembrane) to interact w/each other
85
How are membrane proteins usually integrated into the membrane?
- Via 1 or multiple alpha-helices
- This works if all amino acids composing alpha-helix are hydrophobic b/c their side chains point outward + interact w/lipids, while H bonds required to stabilize alpha-helix are all along length of alpha-helix cylinder
- This insertion produces asymmetry since integral membrane proteins can only move laterally, not vertically
- So side of protein pointing outward never changes: protein just moves around w/in plane of membrane like a phospholipid
86
Freeze Fracture
- Splits membranes into 2 lipid leaflets b/c freezing tightly binds phospholipids to surrounding water molecules by H bonds, while 2 lipid leaflets are held together only by van Der Waals forces (in frozen state)
87
Main Function of Membranes
- Serve as barrier, selectively transport molecules cell needs/wants to get rid of
- Scientists can analyze them by preparing beaker of water separated into 2 compartments. Divider contains small hole covered w/artificial membrane. Solutes added on 1 side, after certain time you can measure [solute] on other side. Tells you that membranes are selectively permeable
- Gases + small polar molecules pass freely across membrane, large charged molecules can barely cross + ions can't at all
88
What does membrane transport give rise to?
- Diffusion: the passive mixing of substances resulting in net transportation along [ ] gradient. Diffusion occurs as long as there's a [ ] gradient
89
Brownian Motion
- Random walk of individual molecules b/c of thermal motions + collisions
- Distance traveled is proportional to sqrt(time), so you don't get very far
90
What happens when small molecule is equally distributed on both sides of membrane?
- Still moves across membrane, but no more net movement so no more diffusion + delta G = 0
- Any [ ] gradient flattens over time until equilibrium is reached
91
Do high temperatures and small molecule size speed up diffusion?
- Yes
92
Osmosis
- Diffusion of water across selectively permeable membrane
93
Hypertonic Solution
- Net water flow out of cell to dilute more concentrated solution outside of cell
94
Hypotonic Solution
- New water flow into cells to dilute more concentrated fluid in cell as opposed to out of it
95
Isotonic Solution
- Same [solute] as inside cell, so no net water flow
96
Why do membranes need integral membrane proteins and what are the two types?
- To transport molecules (ions, polar molecules) across the membrane
- 2 ties are those that only facilitate diffusion (passive transport) + those that transport molecules against their [ ] gradient (active transport)
97
Passive Transport
- Involves either gated channel proteins or carrier proteins
- Gated channel proteins allow ions to flow along their electrochemical gradient when it's open. They're closed in default state - open upon changes in electricity or binding of regulators
- When sugar binds to either side of glucose carrier, shape change occurs, resulting in transport of sugar to other side. Sugars can be transported in both directions. Carrier proteins can be saturated since they must bind to their substrate, so at a certain point diffusion rate can't increase anymore
- Both display saturation kinetics: there's [ ] at which maximal transport is reached. Saturation occurs much earlier in carrier than in channel protein
98
Active Transport
- Requires E
- Primary active transport: relies on ATP hydrolysis to overcome + delta G of transporting against [ ] gradient
- Secondary active transport: uses E from [ ] gradient set up by primary active transport
99
Most Important Example of Primary Active Transport
- Sodium potassium pump to counteract hypotonic drinking water
- Moves 3 sodium ions out + 2 potassium ions in, controlling osmolarity + generating resting potential + setting up ion gradients
100
Sugar Sodium Co-transporter
- Example of secondary active transport
- Uses E from sodium inflow to transport sugar into cells w/high interior [sugar]
- Ex/ cells lining gut take up nutrients from food. To max sugar uptake, they use a sodium sugar co-transporter to take up every sugar molecule from gut lumen. On other side, sugar crosses membrane into extracellular fluid w/sugar carrier since sugar molecules are constantly removed/shipped to rest of the body
101
Why do energy conversion process occur so quickly?
- B/c our cells are tiny, so the diffusion processes are required only over very short distances
102
Prokaryotes
- Can live in any environment
- Can oxidize anything
- Have greatest metabolic diversity of all organisms
- Much smaller than eukaryotes
- DNA sits in nucleoid, not surrounded by a membrane
103
Eukaryote
- Has nucleus surrounded by nuclear envelope consisting of 2 membranes
- Compartmentalization is key to eukaryote's ability to have much larger cells
104
How are plant cells unique?
- They have a cell wall, chloroplasts + modified lysosome known as vacuole
- Due to cell wall, they don't need sodium potassium pump
105
What is compartmentalization mediated by and what does it give rise to?
- Largely mediated by endomembrane system
- Gives rise to organelles: nucleus, ER, Golgi, vesicles + lysosomes. Membrane leaflet facing cytosolic side always faces cytosolic side in ER, Golgi, vesicles + cell membrane
106
Nucleus
- Surrounded by nuclear envelope made of 2 membranes
- Contains DNA stored as chromosomes + nucleolus, where ribosomes are made from rRNA + proteins (ribosomal proteins made in cytoplasm + brought back to nucleolus)
- Assembled ribosome subunits + mRNA transported through nuclear pores to cytoplasm
- Nuclear proteins like transcription factors brought into nucleus through nuclear pores
107
Rough ER
- Close to nucleus, its membranes are contiguous w/nuclear envelope
- Membrane proteins made here
- Rough b/c ribosomes attached to outside of ER membrane. Become attached when they start translating a membrane protein
- 1st few amino acids encode signal sequence that targets ribosome to rough ER, ensuring that freshly made membrane protein is immediately inserted into ER membrane during translation
- Secreted proteins released into ER lumen
108
Smooth ER
- Membrane lipids made here
- Detox occurs in smooth ER + usually means oxidation, like adding hydroxyl groups that make a molecule more hydrophilic so it can be excreted
109
Golgi
- Stack of membranes generated by vesicles coming from ER + fusing on cis face w/Golgi, other vesicles bud off trans face
- Proteins + lipids further modified here + proteins are sorted to reach their final destination
110
Pulse-Chase Experiments
- Demonstrated travelling of proteins through end-membrane system
- Adds radioactively labeled amino acids for short time to culture medium (pulse), then washes cells + adds unlabeled medium for various amounts of times (chase) before looking at cell by e- microscopy
- After labeling, radioactively labeled proteins show up in rough ER, later in Golgi, secretory vesicles + extracellular fluid
111
Receptor-Mediated Endocytosis
- Molecules to be transported are recognized by receptors which initiate endocytosis (budding off a vesicle into interior of cell)
- Vesicle (now called endosome) may fuse w/other vesicles carrying special digestive enzymes + proton pumps until endosome becomes lysosome w/low pH where contents digested into its monomeric components + released to cytosol
112
Autophagy
- Self-eating: lysosomal membranes can surround entire organelles + chunks of cytoskeleton like muscle fibres to digest them in case of need (damage or starvation)
113
Comparison of Mitochondria and Chloroplasts
- Endosymbiotic organelles
- Mitochondria: power plants of cells: most ATP produced here. Citric acid cycle occurs in matrix. Respiratory enzymes are integral membrane proteins located in invaginations of inner membrane. Invaginations (cristae) max area for inserting membrane proteins
- Chloroplasts: convert light E to chem E in photosynthesis. Carbon fixation occurs in stroma yielding sugars, amino acids + all fatty acids. Light rxns of photosynthesis occur in stacks of membranes (thylakoids) which have separated from inner membrane
- Both have outer + inner membranes. Space enclosed by inner membrane (matrix in mitochondria + stroma in chloroplasts) is where DNA, RNA + ribosomes are found
114
What are mitochondria and chloroplasts descendants of?
- Bacteria that were at one point taken up by ancestral eukaryotic cell through phagocytosis
- Evidence: double membrane, have their own genome w/genes more similar to bacterial genes, own ribosomes similar to bacterial ribosomes, unique system for proteins + lipid import which suggests that they evolved separately from endomembrane system
115
Cytoskeleton
- Contains structural elements important for cell shape + movement - most important are actin filaments + microtubules
- Both animal + plant cells have cytoskeleton
116
Actin Filaments
- Polar w/+ and - end
- Polymerize + depolymerize from monomers through non-covalent protein-protein interactions. Monomer fires to single actin protein - 1 polypeptide
- Many actin-binding proteins regulate actin stability + polymerization
- Found below cell membrane (cortically) + responsible for cell shape + its changes
- W/myosin, mediate muscle contraction, cell shape changes, cytoplasmic streaming + cytokinesis. Works b/c myosin II forms bipolar complexes w/myosin heads at opposite ends. Heads walk toward + end of actin filaments. Bipolar myosin II complex bound to antiparallel actin filaments leads to contraction of these filaments
117
Microtubules
- Much bigger diameter, form cylinder of alpha beta tubular dimers
- Polar w/+ and - end
- Many microtubule-binding proteins present that regulate growth/shrinkage of microtubules
- Organize cells by moving organelles + providing tracks for intracellular transport
- Vesicles move along MTs to their destination - like vesicles moving along axonal MTs to synapse of nerve cells. Also move chromosomes during cell division
- Have 2 dif motor proteins: kinesin motor walking in 1 direction + dynein motor walking in opposite direction - necessary requirement for efficient intracellular transport
- Form cilia + flagella made of 9 doublet MTs + 2 central MTs
118
Cilia and Flagella
- Cilia: beat back + forth. Found on lung epithelium lining cells to remove debris from lung, in oviduct to move egg cell + single-celled eukaryotes
- Flagella: larger, beat more whip-like, found on sperm. Bending mechanism is same - many dynein motors try to move 1 MT doublet past another b/c all MT doublets linked to each other by elastic proteins. Sliding results in bending of cilia/flagella
119
Intermediate Filaments
- Intermediate in size between actin + microtubules and are diverse
- No polarity, don't polymerize/depolymerize, serve to provide additional mechanical strength to cells or nucleus
- Often form rope-like structures via coiled coils
120
Cell-Cell/ Cell-Matrix Adhesion
- When in multicellular animals, cells adhere to each other + to extracellular matrix (ECM)
- ECM fulfills structural roles in tendons + cartilage which consist of collagen, a coiled-coil protein
121
Integrin
- Transmembrane protein that binds to ECM and via adaptor proteins to actin cytoskeleton, attaching cells to their environment
- Adhesion sites on basal side of epithelial cells are focal adhesions. Attach muscles to bones via tendons + skin to underlying basal lamina (another type of ECM)
122
How did cell adhesion evolve?
- From cell recognition - especially phagocytosis (earliest effective mechanism of obtaining nutrients)
123
Epithelium
- Sheet of cells where all are stably attached to each other
- Has 2 sides: apical + basolateral
- Ex/ in intestinal epithelium lining gut: apical side points to gut lumen + basal side points toward body interior
124
Tight Junction
- Seals cells together, preventing passage of larger molecules from 1 side of epithelium to other
- Particularly obvious in epithelium lining our guts, where we must keep bad molecules out + good molecules in
- Sodium-sugar co-transporter found only on apical side + kept there by tight junction. So they also separate apical from basolateral membranes
125
Tight Junction Role in Glucose Co-transporter and Glucose Carrier
- Both made in rough ER, but sorted in Golgi to dif vesicles which may travel in part along microtubule tracks to their destination (apical + basolateral membrane)
- Tight junction ensures that sugar co-transporter is restricted to apical membrane + that potentially harmful molecules in food can't enter body
126
Gap Junctions
- Create channels that connect cells in some animal tissues
- Small molecules like Ca ions can diffuse freely from 1 cell to next. Important in heart, where contraction spreads from pacemaker cells across heart via diffusion of Ca ions through gap junctions
127
End-Product Inhibition
- Process in which metabolic pathways are nearly always regulated by final product to avoid overproduction
128
Cooperativity
- Occurs w/2 or more identical enzyme subunits forming enzyme complex
- 1st inhibitor molecule binding to allosteric site induces conformation change in subunit it binds + induces partial conformation change in neighbouring subunit. This change facilitates binding of 2nd inhibitor molecule
- Get sigmoid (S-shaped) inhibition curve w/increasing [inhibitor] leading to switch-like behaviour of multi-subunit enzymes
129
What is first step in metabolic pathway usually catalyzed by?
- A multi-subunit enzyme negatively regulated by cooperative allostery via end product of pathway
130
Catabolic Pathways
- Long + complex to release E slowly: only way for cell to capture some of E
- Burning glucose to CO2 + H2O releases all free E in 1 rxn w/out capturing any E for the cell. Better to split rxn into many steps that release only small amount of free E, just enough to keep rxns going + are coupled to E storage (ex/in form of ATP)
- Complete oxidation of glucose in cells releases 686 kcal/mol
- Half of that captured as ATP, other half released as heat to drive rxns
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How can we describe the burning of glucose as?
- A redox rxn. Can be efficient (releases much free E) w/O2 as e- acceptor or can be inefficient in absence of O2 (fermentation)
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Reduction and Oxidation
- Reduction: gain of e-'s or H atoms
- Oxidation: loss of e-'s or H atoms
- Red + ox always coupled to make redox rxns. So they're 2 half rxns/redox pairs
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How do electrons move in the oxidation of glucose?
- Further away from C atoms
| - # of C-H bonds decreases, # of C-O bonds increases
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How is oxidation energy stored?
- In intermediate NAD which gets reduced to NADH, which is later oxidized, releasing E
- NADH is temporary e- carrier (E carrier), crucial for redox rxns, just as ATP is crucial E carrier for non-redox rxns
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How do we know if NADH gets oxidize or NAD+ gets reduced?
- Any 2 half rxns can be coupled in redox rxn, all half rxns fully reversible
- Direction of e- flow depends on which 2 half rxns are coupled. Whether e-'s flow to NAD+ or away from NADH depends on other half rxn it's coupled with: coupled w/O2 as e- acceptor, e-'s flow away from NADH. Coupled w/oxidation of glucose intermediates, e-'s flow towards NAD+
- Can measure direction of e- flow by setting up 1 half rxn in a beaker and reference half rxn in 2nd beaker, connecting 2 with wire + measuring e- flow in V
- Resulting V is redox potential. When coupling 2 random half rxns, e-'s flow from more - to more + redox potential
- Redox rxns special in that delta G can be easily calced
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Is O2 a good e- acceptor?
- Yes! Best in biological rxns
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Glycolysis
- Starts w/some E-consuming rxns (adding P to trap glucose inside cell + rearranging glucose into 2 C3 compounds), followed by E-releasing ones: oxidation of C3 compound glyceraldehyde 3-P coupled w/reduction of NAD+, releasing much free E. In this case, it's coupled to formation of high E P bond + still enough free E left over to make rxn favourable
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Hydrolysis of High Energy Phosphate Bonds
- Used to generate P bond in ATP of slightly lower E
| - Called substrate-level phosphorylation b/c P is transferred from substrate directly to ADP
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What are the unfavourable steps in the beginning of glycolysis driven by?
- Highly favourable oxidation that follows sequential coupling
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Sequential Reactions
- Rxns where product is reactant for next rxn
- Delta G values are additive
- If overall value is -, rxn proceeds
- Obvious way for unfavourable rxn to proceed is direct coupling to favourable rxn like ATP hydrolysis
- Favourable rxn removes all product of unfavourable rxn, making it favourable (since delta G depends on [reactants and products]
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Where does glycolysis occur?
- In cytosol
| - End product of glycolysis is pyruvate - further oxidized in mitochondrial matrix to acetyl-coenzyme A
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Acetyl-CoA
- High E bond; E carrier like ATP
- Allows transfer of 2-C group to another molecule at start of citric acid cycle
- High E bond can be generated again by large amount of free E released by pyruvate/NAD+ redox rxn
- Key mechanism in metabolism b/c sugars, fats + many amino acids broken down to acetyl-CoA
- Building block for making fats + other metabolites
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Function of Citric Acid Cycle
- Finishes oxidation of glucose by converting 2-C compound to acetyl-CoA to 2 CO2
- C2 added in 1st rxn, 2 CO2 split off in following oxidations; rxns catalyzed by dehydrogenase + redox rxns. Result: reduced e- carriers (FADH2 and NADH), 1 GTP (this is only step that's not a redox rxn)
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FAD
- Used b/c oxidation of succinate doesn't release enough E to reduce NAD
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Electron Transport Chain
- Required to get rid of all NADH since a cell needs more ATP than NADH + cell needs NAD+ for citric acid cycle to continue
- Series of redox rxns coupled to transport of protons across inner mitochondrial membrane into inter membrane space
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Why doesn't NADH deliver its electrons directly to O2?
- B/c these rxns must be catalyzed + NADH can only bind to 1st enzyme complex of e- transport chain. This ensures gradual release of E that's used to transport H+ across membrane in each complex
- FADH2 gives up its e-s to ubiquinone through dif complex (complex II) b/c its oxidation releases less E
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Ubiquinone and Cytochrome C
- Hydrophobic e- carriers shuttling e-'s from 1 complex to next by diffusing laterally w/in membrane
- Ubiquinone reduced on 1 side of membrane by taking up a e- and a proton and is oxidized on other side of membrane by giving up an e- and a proton - transporting 1 proton across the membrane
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The Point of Redox Rxns
- Release necessary E for conformation change required for H+ transport across membrane
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How is oxygen held in place?
- By heme group in complex IV until all 4 e-'s accepted - important b/c intermediate stages are very reactive radicals w/free e-'s
- Ex/ cyanide is powerful poison b/c it irreversibly binds active site instead of )2, so ETC is shut down
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Electrochemical Proton Gradient
- Induces protons to move back across membrane
| - Voltage diff provides majority of proton-motive force
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What happens when protons flow through the protein channel ATP synthase?
- ATP produced w/about 3 protons sufficient to make 1 ATP: called oxidative phosphorylation + contributes majority of ATP produced in cells
- ATP formation also called chemiosmotic mechanism
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Do ATP synthase and electron transport chain function independently?
- Yuh! Can be proven by making vesicles containing only ATP synthase, then increasing [proton] outside vesicle. Causes protons to flow inward through ATP synthase + results in ATP production in interior of vesicle
- ETC not needed in vitro to make ATP: can be uncoupled from ATP synthesis
- ATP synthase is evolutionarily older + there are organisms w/ATP synthase but no ETC
- ATP synthase can f(x) in reverse, pumping out protons agains [ ] gradient via ATP hydrolysis
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Example of Uncoupled ETC and ATP Synthase
- Occurs in brown fat of newborns + hibernating animals where ETC is coupled to proton channel to produce heat instead of being coupled to ATP synthase to product ATP + heat
154
Regulation of the Cycles
- Glycolysis shut down by high [ATP], citric acid cycle by high [NADH], ETC by high proton gradient
155
What happens to the ETC in the absence of oxygen?
- It shuts down b/c no e- acceptor - ATP synthase stops
- Pyruvate oxidation + citric acid cycle can't operate anymore b/c they need much NAD+ which is provided by NADH + H+ oxidation in ETC
- Only fermentation can provide E: only ATP produced is from glycolysis
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Fermentation
- Occurs in muscles during strenuous exercise
- Step backward. Since O2 (e- acceptor) not there, pyruvate (product of glycolysis) is used as e- acceptor. This doesn't generate E, just replenishes NAD+ that was used in glycolysis
- Important in food production b/c acid + O2 absence prevents growth of bacteria, thus preserving food
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Why do diets that reduce fat or carbohydrate intake make little sense?
- Fats, carbs + protein are all metabolized to acetyl CoA + only there does the cell decide to make fat or use it up
- Brain consumes 20% of total E on average day + it can only be delivered as glucose
- Surplus food stored as fat b/c to has highest E content/weight, b/c fats have more C-H bonds than carbs or proteins so complete oxidation takes longer, giving you more NADH
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Why is reducing sugar consumption a good idea?
- B/c not historically big part of our diet
- Body's regulatory system gets messed by eating too much sugar
- Eating carbs like starch releases sugar slowly enough for body to deal with
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Why should we reduce snacking and eating at night?
- Carbs are always metabolized first, followed by fat + protein
- Regular snacking at night reduces/shuts down catabolism of stored fat
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Difference Between NAD and NADP
- Same properties + occur in plants + animals, but made by separate pathways + regulated independently
- NADP used only for anabolic pathways: excess of NADPH to drive biosynthetic reductions
- NAD used only for catabolic pathways: excess of NAD to accelerate oxidation of sugars + generation of NADH
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Why does photosynthesis take place in the same narrow range of wavelength as vision?
- B/c X-rays cause damage
- At visible light, e- transitions occur that can be transformed to chem E
- At IR/microwaves, only vibrational (heat) E
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Absorption Spectrum
- Chlorophylls absorb blue + red light, transmit green
- Carotenoids absorb blue + green light, transmit yellow, orange or red light
- O2 seeking bacteria congregate in wavelengths of light where alga is producing most O2
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What happens to an excited electron?
1) Decay by giving off light + heat
2) Decay by resonance E transfer
3) Decay by successive e- transfers
- Note: 2 + 3 only occur if molecules adjacent to each other
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Light Harvesting Complex
- Antenna (light harvesting complex) required b/c individual chlorophyll molecules are excited too rarely
- 100 chlorophylls + carotenoids in antenna, only 1 chlorophyll attached to e- accepted (called rxn centre)
- Antenna system embedded in thylakoid membrane
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How does excitation travel from one molecule to the next?
- Via resonance E transfer
- Chlorophyll in rxn centre acts like sink: excited state has lowest E
- All other pigments have excitation wavelengths shorter than chlorophyll (shorter than 680 nm)
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When does the transfer of light energy into chemical energy occur?
- When rxn centre chlorophyll gives up its excited e- to reduce pheophytin
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Noncyclic Electron Transport or Z Scheme
- 2 systems required b/c 1 quantum of light doesn't have enough E to transfer e- from H2O to NADP+ + make ATP
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What does the cyclic electron transport produce?
- Only ATP
| - Produced via proton-motive force
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Calvin Cycle
1) 3 CO2 added to 3 RuBP - fixation of CO2 occurs - produces the 6 3-phosphoglycerate
2) 6 ATP converted to 6 ADP + 6Pi and 6 NADPH converted to 6 NADP+ + 6H+ - reduction of 3-phosphoglycerate to 6 G3P occurs. 1 G3P leaves to form glucose + fructose
3) 5 G3P move along - regeneration of RuBP from G3P occurs. 3 ATP converted to 3 ADP + 3Pi. U end up w/ 3 RuBP + cycle continues
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Reaction With Carbon Dioxide During Photosynthesis
- RuBP + CO2 --> 2 3-phosphoglycerate, used in Calvin cycle
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Reaction With Oxygen During Photorespiration
- RuBP + O2 --> 1 3-phosphoglycerate (used in Calvin cycle) + 1 2-phosphoglycolate (when processed, CO2 is released + ATP is used)
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Do cells spend a lot of time and space dividing up their chromosomes?
- Yuh
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Karyotype
- Way of straining + organizing chromosomes that makes patterns in their structure more apparent
- Chromosomes for karyotype come from dividing cells b/c only during division can we see chromosomes
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What becomes apparent when we look at a karyotype?
1) # of chromosomes is always same for given species but varies greatly from 1 species to next
2) In eukaryotes, chromosomes often come in identical pairs - homologs. Humans have 22 homologs + 2 sex chromosomes - 23 pairs of chromosomes
3) At cell division, each chromosome has been duplicated once. Duplicates are chromatids. Held together by conglomeration of proteins - centromere. 1 pair of chromatids goes to each daughter cell
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Mitotic Chromosomes
- Chromosomes in karyotype
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DNA Condensation During Cell Division
- DNA raps around proteins - histones - that help keep long DNA strands tightly packed - not tangled
- Combo of DNA + proteins is chromatin
- By time of cell division, all chromosomes have been duplicated. Includes duplicate copies of both homologs. Identical duplicates, which appear as chromatids, remain stuck together by centromere at beginning of cell division
- Duplicate/sister chromatids constitute a single mitotic chromosome at beginning of cell division
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Mitochondria and Cell Division
- Have genetic material + essential to cell survival
- Like little bacteria that live in cytoplasm. Even a few can reproduce + repopulate cytoplasm w/as many mitochondria as cell needs. So cells are bound to inherit at least 1 mitochondria!
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How many of each chromosome do most organisms need?
- Exactly 1
- Only case where you can survive w/extra chromosome past infancy is Down syndrome - results from extra chromosome 21
- Extra copy of any other chromosome is lethal (sex chromosomes are exceptions)
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Steps A Eukaryotic Cell Undergoes to Ensure That Every Cell Division is Preceded by One Duplication of Chromosomes
1) DNA replication (S phase)
2) Mitosis (M phase) - process by which somatic cells make identical copies of themselves by creating daughter cells that inherit 1 copy of each chromosome OR meiosis - process by which germ cells make non-identical copies of themselves by creating daughter cells that inherit 1 copy of each homolog. So daughter cells end up w/half DNA of mother cell
3) Cytokinesis - dividing cytoplasm in 2 (optional)
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Gaps Between M and S, and S and M
- Cell is resting
- M and S: G1. S and M: G2 (cell preparing to divide at G2)
- Cell cycle represent among of time spent in each of these processes
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Cell Cycle
- Cytokinesis not included, but normally occurs after mitosis
- Time length in each stage can vary a lot, even among cells of some organism
- Interphase = all phases of cell cycle except M phase
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How does a cell prevent, for instance, M-phase (mitosis) from occurring before S phase (DNA replication) is done?
- Quality control system: check for completion of each step before continuing to next. Checkpoints at end of each phase of cell cycle - certain conditions must be fulfilled before next phase begins
- Ex/ cell won't proceed to G2 until all DNA has been replicated in S phase
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Hydroxyurea
- Prevents DNA replication
| - Cell gets big but never divides: checkpoint keeps cell in S phase + prevents it from proceeding to G2
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How can we inactivate the S to G2 checkpoint?
- By adding another drug - caffeine
- If you add both caffeine + hydroxyurea, cells proceeds through caffeine-inactivated S to G2 checkpoint + enters mitosis
- Since there aren't enough chromosomes for 2 daughter cells, they both die
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Cyclins and Cdks
- [different versions of these proteins] rise and fall w/cell cycle. Interfering w/their [ ]s affects ability of cell to proceed through cell cycle
- There are cyclins and cdks through every step of cell cycle
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Where do cells that have stopped cycling arrest in?
- G1
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G1 to S Checkpoint
- Critical; cell that passes it almost always goes to divide
- Looks for external chem signals from other cells, which are good for, for instance, activating cyclin E during pregnancy in mammals, resulting in proliferation of breast cells necessary for lactation
- Cell division tightly regulated by complex signals among cells to ensure that you have right # of right cells in right places
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Unregulated Proliferation of Cells - The Basis of Cancer
- If something wrong w/checkpoint controls that regulate cell division, cells divide continuously + at wrong time
- Ex/ defect in cells that causes continuous over-expression of cyclin E contributes to breast cancer - breast cells divide as if during pregnancy, even when there's no pregnancy
-
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How do cells divide up their chromosomes equally?
- Mitosis:
1) During S phase of interphase, nucleus replicates DNA + centrosomes
2) Chromatin coils + supercoils, becomes more compact, condensing into visible chromosomes which have identical, paired sister chromatids
3) Nuclear envelope breaks down - kinetochore microtubules appear + connect kinetochores to poles
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G2
- Replication of centrosome (+ centrioles sometimes)
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Mitosis Prophase
- Centrosomes move to poles
- Spindle forms
- Chromosome condensation - chromatids become evident
- Kinetochores form
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Mitosis Prometaphase
- Nuclear envelope breakdown
- Polar microtubules + kinetochore microtubules form
- Kinetochore microtubules probe cytoplasm + attach to kinetochores
- Chromosomes begin arriving at metaphase plate
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Mitosis Metaphase
- Sister chromatids bound to kinetochore microtubule on opposite spindles
- Due to tension resulting from kinetochore microtubules pulling on sister chromatids, chromosomes line up on metaphase plate
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Mitosis Anaphase
- Centromeres separate
- Kinetochore microtubules shorten
- Spindle elongates
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Mitosis Telophase
- Spindle breaks down
- Chromosomes decondense
- Nucleus reforms
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What is the trick for getting the chromosomes to separate evenly?
- Get them lined up on metaphase plate
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Ingredients for Metaphase Mitotic Spindle
- Keep chromatids paired until it's time to segregate
- Have unstable kinetochore microtubules that can probe cytoplasm + only become stable upon being captured by kinetochore
- Ensure 2 kinetochore microtubules from same spindle pole can't capture both chromatids of a chromosome
- Have checkpoint that senses when all chromatids have been captured + only then allow chromatids to separate
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Mitosis Cytokinesis
- In animals: actin + myosin form "purse string" that constricts + divides cell
- In plants: vesicles fuse to make cell membrane + plate, which eventually become new cell wall
- Optional b/c some cells don't bother. Ex/ muscle cells have many nuclei b/c they go through mitosis w/out cytokinesis
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Sex
- Produces progeny w/diverse characteristics, unlike mitosis
- Mixing genetic material of 2 organisms
- Mitotic reproduction of cells is asexual
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How do you ensure that your progeny gets the right number of chromosomes?
- Each organism creates a gamete cell that has half genetic material + they combine gametes to get organism w/complete genome
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Gametes
- Have 1 homolog of each chromosome
| - Names to multiples of n: 1n = haploid, 2n = diploid, 3n = triploid, 4n = tetraploid...
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Differences Between Somatic Cells and Gametes
- Somatic cells are diploid, gametes are haploid
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Meiosis I Prophase I
- DNA begins to contract
- Synapsis: pairing of homologous chromosomes
- Chiasmata form, crossing over
- Unlike mitosis, meiosis can take a while
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Meiosis I Prometaphase I
- Nuclear envelope breakdown
| - Spindle fiber forms
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Meiosis I Metaphase I
- Microtubules attach to kinetochores (1/homolog, not 1/chromatid)
- Chromosomes line up at metaphase plate held together by chiasma
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Meiosis I Anaphase I
- Separation of homologous chromosomes into separate cells
- Each cell now as 2 copies (2 chromatids) of each homologous chromosome - these chromatids not identical b/c of crossing over
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Is telophase in meiosis I optional?
- Yuhh
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Difference Between Meiosis II and Mitosis
- Meiosis II is same as mitosis except it has half # of homologs
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Metaphase II Meiosis II
- Chromosomes line up on plate + chromatids separate to end up in dif cells
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What is Down syndrome caused by?
- Prob in meiosis, not mitosis
- During Anaphase I of Meiosis, non-disjunction event occurs. Instead of both separating, both chromosome 21 homologs end up in single gamete, other gamete has no chromosome 21. When egg w/extra chromosome joins w/normal sperm to make embryo, embryo will have 3 copies of chromosome 21
- Frequency increases dramatically in older women since the eggs of older women have been waiting for longer + arrested in meiosis
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Two Ways to Think About Meiosis
1) Diploid organism divides its chromosomes in haploid gametes so that when haploid cells fuse you get back diploid organism
2) 2 haploid cells combine to form diploid so that chromosomes can be shuffled before undergoing meiosis to produce another haploid
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Why isn't it a problem if cells have too many or too few chromosomes?
- Not about abs # of homologs: it's the ratio
- Trisomies like Down syndrome cause probs b/c 1 chromosome has 3 homologs while rest have 2 - ratio is unbalanced
- Multiples of n are often ok, but meiosis doesn't work w/odd #ed ploidy. Since odd # of homologs so 1 homolog must go unpaired on metaphase plate of meiosis I, therefore progeny ends up w/multiple trisomies (almost never perfect triploidy). So tetraploid wouldn't have these probs b/c they're balanced + all homologs can pair w/partner at meiosis I
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Why are many crop varieties selected to have high ploidy?
- High ploidy means bigger fruit
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Continuous Variation
- Blending of traits
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How did Mendel stack the odds in his favour with his pea experiment?
1) He chose an organisms with which he could do controlled crosses, resulting in many progeny so that he could do stats
2) He started w/true breeding trait: as long as he bred a strain w/itself, all progeny had same traits for characters he was interested in
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What happened in the F1 and F2 generation of Mendel's experiment?
- F1: Recessive (wrinkled) trait disappeared: only dominant round trait was visible
- F2: wrinkled peas reappeared in 1/4 of progeny
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Mendel's Conclusions
1) Traits he studied don't mix: exist discretely - even in F1 generation where recessive trait was nonexistent
2) Only 1 entity is inherited by each gamete. Particular trait that gamete acquires is chosen at random. Then gametes randomly unite to form new organism. Each plant has 2 discrete units - genes - for each trait. Each parent contributes 1 of these genes to progeny. Genes come in 2 flavours - alleles - 1 resulting in dominant + 1 in recessive trait
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Homozygous
- When 2 parents have 2 of same allele (like SS and ss)
| - Mendel's parents generation had SS and ss
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Heterozygous
- One of each allele (Ss)
- Since 1 allele is dominant, F1 in Mendel's experiments (b/c he crossed ss with SS) show trait of dominant allele
- When hetero F1s crossed, progeny have 1/4 chance of being homo for recessive allele
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Law of Segregation
- Refers to segregation of alleles into each gamete
- Component of random chance
- Proportion of progeny w/given trait indicated by probability given possible combos of alleles progeny might inherit
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Phenotype vs Genotype
- Phenotype: traits an organism shows
| - Genotype: set of alleles it has
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Test Cross
- If you cross plant w/dominant phenotype but unknown genotype w/plant having recessive phenotype (known genotype), you get 2 dif results depending on genotype of plant w/dominant phenotype: if homo, all progeny have dominant phenotype. if hetero, half w/dominant + half w/recessive
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Chromosome Difference Males and Females
- Women have 2 X chromosomes, men have X and Y
| - Men are hetero, females are homo
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Is maleness or femaleness dominant?
- Maleness
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Sex-Linked Traits
- Traits that run in fam but predominantly affect males
- Ex/normal man + woman produce colour-blind children. Colourblindness = recessive since it turns up in children of unaffected parents. Both parents hetero or you wouldn't see it. If sex + colourblindness follow law of independent assortment, ratio is 1/8 male colourblind, 3/8 male normal + same for females. But we actually see 1/2 female normal, 1/4 male colour-blind and 1/4 male normal. B/c recessive colour-blindness allele always on Y chromosome
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Why is colour-blindness on the Y chromosome always recessive?
- Y is small, doesn't have gene for colourblindness, so Y can't have allele for gene that doesn't exist. Absence of gene is type of allele
- Colourblindness gene makes protein (opsin) that detects green light. Colourblindness trait results from gene on X chromosome that's nonfunctional + cannot make this protein properly - has been mutated
- Y has no gene, so always recessive for colour-blindness trait
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Hemizygous
- When gene is missing from 1 of the chromosomes
- Functional allele is wild type, defective allele is mutant
- If multiple alleles common on pop, gene is called polymorphic
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Two Possibilities of Ratios for Linked Genes and Why This Didn't Turn Out
- If dominant alleles in cis (alleles on same homologous chromosome), expect 1/2 BbVv and 1/2bbvv
- If in trans (alleles on dif homologous chromosomes), expect 1/2 Bbvv and 1/2bbVv
- Chromosomes ar mixture of cis + trans linked B and V due to crossing over. Chromatids exchange arms. If this breaking/rejoining occurs between B and V in BV chromatid that exchanges w/bv chromatid, 1 chromatid ends w/Bv + other w/bV. This linkage w/crossover is called recombination
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Sturtevant's Discovery of Crossover Application
- Can determine order genes arranged on chromosome
- Recomb occurs at random pts on chromosome. Farther apart 2 genes are = more likely recombination will occur between them. Recomb frequency is measure of distance between 2 genes on same chromosome
- Knowing distance allows you to determine order on chromosome. A gene is a locus - genes are defined by their location on chromosome. Bunch of genes linked together is linkage group, corresponding to set of genes on same chromosome
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Contributions to Continuous Variation
1) Dominance usually incomplete, called incompletely dominant/semi-dominant
2) Some genes have multiple alleles, encoding gene products w/degrees of partial f(x) whose effects are additive. Resulting variations of trait depend on which combo of alleles is present in single locus. These can form allelic series where alleles can be placed in order of severity of their corresponding phenotype
3) Environment can affect phenotype of gene. Like tans, showing dif of expressivity of phenotype - refers to degree which individuals of same genotype vary in degree of phenotype expression. High expressivity means consistently strong phenotype among individuals of same genotype. Low expressivity refers to phenotype that is weak in many. Penetrance - phenotype is all-or-nothing + ppl w/same genotype don't always show expected phenotype. Usually expressed as %. Expressivity + penetrance don't necessarily reflect environmental effects but usually component of it
4) Multiple genes may contribute to a trait - polygenic/multigenic
5) Epistasis: complex interactions between genes
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Frederick Griffith Experiment
- He injected smooth virulent and rough non-virulent bugs into mice. Also heat killed S bugs which didn't kill mice. But injected those w/R-bugs and R-bugs had been transformed into live S-bugs, so mice died
- Substance from S-bugs that transformed R-bugs called transforming principle which was genetic material
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Hershey-Chase Experiment
- Took virus that had DNA core surrounded by protein coat + radioactively labelled DNA w/32P and/or 35S. Allowed virus to infect bacteria + blended mixture. Protein coats heard off bacteria so whatever stayed behind w/bacteria must be genetic material of virus. Since infected bacteria now produced more virus containing 32P + no 35S, followed that 32P-containing DNA must be viral genetic material
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What does DNA structure suggest about how DNA could replicate itself and how DNA determines a phenotype?
1) Sequence of nucleotides doesn't affect overall structure so info can be encoded arbitrarily by sequence of base pairs
2) 2 strands bind by complementary base pairing so that 2 strands contain identical info. If you separate 2 strands + make new partner strand for each, you create 2 identical DNA helices - DNA is replicated
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What happens to DNA strands during replication?
- Semiconsesrvative replication - each old strand made + remained annealed to new strand. Meselson + Stahl labelled DNA by growing bacteria w/heavier isotope of N, making DNA heavy. Used centrifugation in caesium Cl to get weight. After 1 duplication in presence of normal N, duplicated DNA was half as heavy + after 2 duplications DNA was half as heavy + half DNA was normal (light) weight. Only semiconservative would produce this
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How does DNA duplication occur?
- Just need 4 nucleotides + enzyme + ragged end (stretch of DNA that's partly double stranded + partly single stranded)
- DNA polymerase grabs nucleotide complementary to next nucleotide in line on template strand. Takes nucleotide + breaks bond between alpha + beta P. Then attaches alpha P to 3' hydroxyl group of last nucleotide on strand that's being extended
- So DNA synthesis occurs 5' to 3'
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Why aren't there many ragged ends in a live cell after DNA gets damaged and what do cells do to solve this?
1) It has to unwind strands
2) It has to create ragged ends
- Helices expends E to unwind DNA + primate adds short stretch of complementary RNA, a primer, which acts as ragged end so DNA polymerase can work
- They initiate replication at origins of replication
- As helices unwinds DNA in each direction from origin of replication, bubble forms w/replication forks on either end where old stranded DNA is split to act as template for formation of 2 new strands
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What does a cell do to deal with the single-stranded DNA behind the primer in a replication bubble?
- The lagging strand keeps putting down primers every few hundred bases so that polymerase can make complementary strange for lagging strand
- End up w/lots of short DNA stretches beginning w/primer + running into next primer along DNA
- Stretches of DNA on lagging strand are Okazaki fragments
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DNA Polymerase I
- Chews up RNA primers + fills gaps using newly synthesized DNA as primer
- DNA ligase joins ends of newly synthesized strand + DNA replication complete
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What does the cell do to deal with the fact that polymerase makes mistakes?
1) Polymerase has proofreading mechanism that immediately removes bases that aren't complementary to template strand
2) Mechanism at work during recombination called mismatch repair
3) Mechanism at work during rest of time called excision repair - also works on thymine dimers formed by exposure to UV light
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Beadle and Tatum
- Reckoned that if genes code for proteins + you have metabolic pathway where each step is catalyzed by dif enzyme, then we can identify mutants that are arrested at each step in pathway. Mutants that lack enzymes necessary for pathway got stuck + couldn't produce compounds downstream in pathway. But mutants could be rescued by providing missing compounds in growth media
- They isolated mutants that required certain metabolic precursors in order to grow - called auxotrophs as opposed to protrophs
- They found mutants encoding enzymes at each step in pathway, leading to one-gene, one enzyme hypothesis
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How does information from DNA in nucleus get to cytoplasm?
- DNA acts as intermediary mRNA
| - Central Dogma: genetic info flows from DNA to RNA to protein
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Difference in RNA
- Has uracil instead of thymine
| - Has 2' hydroxyl that DNA doesn't have
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Transfer of Information to Complementary Strand of RNA
- Transcription; occurs when RNA polymerase sits on DNA at beginning of gene, unwinds DNA + starts creating strand of RNA complementary to DNA
- RNA polymerase extends RNA strand until it gets to gene's end
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Transcription
- Same as DNA polymerase making DNA except RNA polymerase doesn't need 3' hydroxyl to get started + it incorporates triphosphate ribonucleotides instead of deoxyribonucleotides
- Newly synthesized mRNA now has all info of DNA encoding that gene
- When RNA leaves nucleus + enters cytoplasm, it carries all info that protein synthesis machinery needs to make protein encoded by that gene
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Codon
- 3 DNA letters
- Corresponding amino acid identified for each one
- Some codons tell ribosome that protein is done - stop codon
- Often, several diff codons code for same amino acid... code is degenerate
- Knowing DNA sequence allows you to determine amino acid sequence but amino acid sequence doesn't determine DNA sequence
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Why can't you add mRNA to a ribosome so that a protein with the correct sequence comes out the other end?
- Ribosomes can't rely on natural affinity of codon to an amino acid like how polymerase relies on natural affinity of base pairs for each other
- No particular affinity between given amino acid + corresponding codon
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tRNA
- Acts as adapter between nucleic acid + protein
- Each tRNA has little loop of 3 nucleotides that stick out
- These residues - anticodon - bind according to base-pairing rules to codon in mRNA
- Other end is amino acid encoded by that codon
- At least 1 tRNA for every amino acid
- By ribosome causing tRNAs to sequentially bind to mRNA codons + then by catalyzing polymerization of amino acids on other end of tRNAs, creates string of amino acids whose sequence is determined by sequence of mRNA - translation
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What determines what amino acid gets attached to each tRNA since association of amino acid w/tRNA determines correspondence between amino acid + codon?
- A class of enzymes, 1 for each amino acid, catalyzes attachment of specific amino acid to a tRNA
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Aminoacyl tRNA Synthases
- Enzymes which determine code
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Arbitrariness of Genetic Code
- Codon used for each amino acid was decided by chance long ago + became fixed
- All organisms must have had a common ancestor billions of years ago the used same genetic code as we use today
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Transcription
- DNA transcribed into mRNA
- Resulting mRNA strand starts slightly before stretch of DNA that encodes protein + extends past coding region, then stops
- RNA polymerase must know where genes start + stop
- 2 strands of DNA that constitute a gene have dif sequences, so RNA polymerase must know which strand to transcribe to produce functional protein
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Sense Strand
- Not transcribed but which has same sequence as mRNA
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Template Strand
- Transcribed strand that has sequence complementary to mRNA
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Promoters
- RNA polymerase recognizes them at beginning of gene
- Itself is not transcribed
- DNA transmits info directly to protein - info that tells protein where to start transcribing + in what direction
- Also termination sequence in DNA telling RNA polymerase when to stop
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The Three-Frame Problem
- When synthetic RNA put in translation mix, get 3 dif proteins b/c there are 3 dif reading frames
- Inefficient b/c if mRNA were translated like this, only 1 of 3 reading frames would encode functional protein
- Translation mix is artificial - in actual cell, ribosome picks right reading frame + sticks to it
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How does the ribosome know the right reading frame?
- Right reading frame always starts w/AUG
- Called start codon
- Ribosomes have 2 subunits that are large complexes of rRNA + proteins. At start of translation, small subunit finds 1st AUG in mRNA + binds to it along w/methionine tRNA
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A Site and P Site
- Large ribosomal subunit has these 2 binding sites
- Small subunit, tRNA and mRNA recruit large subunit
- When large ribosomal subunit recruited to complex, it binds so met-tRNA is in P site
- tRNA corresponding to next codon in line binds to A site
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How is the carboxyl group of methionine transferred?
- W/help of enzymatic properties of ribosome, from 3' hydroxyl of met-tRNA to free amino group of amino acid bound to tRNA in A site, forming 1st peptide bond
- Ribosome releases met-tRNA + shifts distance of 1 codon in 3' direction
- tRNA that was in A site which now has NH-met-ser-3'hydroxyl moves to P site + tRNA corresponding to next codon assumes A site
- Process repeats until ribosome reaches stop codon
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Release Factor
- Binds to A site, causing last tRNA to release peptide chain + ribosomal complex to disassemble
- Peptide then folds into functional protein
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Why isn't there at least 1 tRNA for every codon?
- Some tRNAs can use more than 1 codon
- 5' residue of anticodon (corresponding to 3' residue of codon) has some wobble - doesn't always have to match up perfectly w/3' residue of codon
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Are the steps in the process of converting the information from DNA to protein always sequential?
- Nah
- Ex/ in prokaryotes, no nucleus + therefore translation can begin before transcription is complete
- Many ribosomes can bind to same transcript, starting at start codon, one after the other - polysome
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Sickle Cell Anemia and the Role of DNA in Heredity
- Pauling's thought: since hemoglobin is protein that carries O2, hemoglobin might be defective protein in sickle cell anemia
- Digested purified hemoglobin from normal + affected individuals, separated fragments by charge + size
- Only 1 fragment differed in affected ppl, so only 1/a few amino acids in this fragment of hemoglobin were changed
- Sickle cell is missense mutation that changes single amino acid in protein
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Categories of Mutations
1) Point mutations - small changes in single gene
| 2) Chromosomal mutations - changes that affect large portion of chromosome, often affecting many genes
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Point Mutations
- Silent mutations don't affect protein sequence b/c of degeneracy of code
- Missense mutations change 1 amino acid to another
- Nonsense mutations change amino acid to stop codon, truncating the protein
- Frame shift mutation results from insertion/deletion + changes reading frame from that pt onward. Deletions/insertions that are multiples of 3 nucleotides don't change frame, merely delete amino acids from/insert amino acids into peptide chain
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Chromosomal Mutations
- Deletions remove large piece of chromosome including many genes
- Duplications duplicate large chunks of chromosome
- Inversion: piece of DNA flips around, re-entering chromosome in reverse orientation
- Translocations: piece of DNA jumps from 1 chromosome to another chromosome
- Reciprocal translocations - 2 chromosomes trade pieces
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Mutagens
- Anything extraneous to organisms that cause changes
- Their effects depend on whether change occurs in somatic tissue or germ line tissue
- Somatic: change could kill cell, sicken it, make it cancerous. Mutation will be inherited by mitotic progeny, change not transmitted to progeny of organism b/c somatic cells don't make gametes
- Germ line: possibility that egg/sperm will end up w/mutated gene + transmit to progeny. Progeny will have mutant allele in all its cells, likely transmit gene to its progeny. So it will become part of repertoire of alleles present in that pop of organisms. Natural selection acts to produce new species
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Real Viruses
- Set of instructions for subverting host, thus making it do something not in host's best interest
- Instructions encoded by viral DNA tell cell to stop doing cell stuff + start making more virus
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Virions
- Consist of simply protein coat/capsid + nucleic acid
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Phage Strategies for Survival
- Virulent phage undergo lytic reproductive cycle
- Temperate phage undergo lysogenic cycle. Phage binds to bacteria, injects its DNA, causes bacteria to produce more phage proteins + more phage DNA + when cell is used up, cell lyses + newly assembled viruses are released
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Virus Approach in Lysogenic Reproductive Cycle
- "Wait-and-See"
- Inserts its DNA (prophage) into bacterial chromosome + waits while bacteria divide (replicating prophage along with their own DNA)
- When moment is right, prophage pops out of chromosome + resumes lytic reproductive cycle
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Virus Phenotypes
- Can change the way viruses are able to infect + lyse bacteria
- If high multiplicity of infection, more than 1 phage will enter same bacterium
- DNA of 2 phage may recombine, allowing one to map phage genes
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Retroviruses
- Bend rules of central dogma by making DNA copy from RNA genome
- DNA copy of retrovirus can be integrated into host chromosome + remain there before it starts producing viral particles again
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Bacteria Transfer of Genetic Information Through Bacterial Sex
- Bacteria have mutations that confer phenotypes you can identify - auxotrophic phenotypes
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Specialized Transduction
- When prophage excises itself from chromosome, it can be sloppy + pick up gene from bacterial chromosome
- Bacterial gene becomes part of virus genome + will be inserted into chromosome of another bacteria when infected by that phage
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Generalized Transduction
- Sometimes phage do poor job of chopping up bacterial DNA + instead of packaging phage DNA into visions they package chunks of bacterial chromosome
- When those visions infect another bacterium, chunk of bacterial DNA gets injected into bacteria + can be incorporated into chromosome
- Since adjacent genes more likely to be transferred together, generalized transduction can be used to map genes
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Transformation
- Bacteria might take up naked DNA floating around in their environment
- Genomic DNA can then be integrated by recombination
- Type of non-genomic DNA - plasmids - small DNA circles that also can be used to transform tracteria. Plasmids don't integrate but are able to be duplicated by DNA replication machinery
- They can carry + express few genes
- R-factors: plasmids that carry antibiotic resistance genes
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Conjugation
- Most sex-like way bacteria exchange DNA
- E. coli bacteria have 2 strains: F+ and F-plasmid. Dif: F+ have F-plasmid - male-like b/c they can conjugate w/F- bacteria + donate 1 strand of their plasmid to F- cell making it F+
- Useful for genetics b/c if F-plasmid gets integrated into chromosome, then 1) conjugation occurs much more frequently, 2) F DNA takes some of chromosomal DNA w/it during conjugation and 3) transferred DNA can be incorporated into chromosome of F-cell by recombination
- Integrated F strains are Hfr (high frequency of recombination)
- Upon conjugation, entire chromosome acts like big F-plasmid + 1 strand threads its way into F-cell
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How do bacteria regulate the high price of making proteins?
- They regulate transcription of genes: synthesize only those proteins they currently need
- B/c bacteria can metabolize range of C sources, they only turn on genes that code for metabolic proteins that are needed. Called inducible as opposed to constitutive (always on) enzymes
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E.Coli's Use of Lactose
- E.coli make 3 proteins (B-galactosidase, B-galactoside permease + B-galactoside transacetylase)
- Genes all in a row + transcribed from same promoter in 1 big RNA
- Transcribed only in response to lactose. W/out lactose, lac-repressor binds to specific DNA sequence called lac operator which is between promoter + point where transcription of induced genes begins
- When repressor binds to operator, it blocks transcription of those genes
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What happens when lactose enters the bacteria?
- It acts as an inducer, binds repressor, repressor changes conformation + releases from operator
- Inhibition of transcription is lifted + genes are transcribed
- Unit of regulated transcription is called operon
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Lac-Repressor Protein
- Constitutive - has advantages:
1) Repressor only needs to be expressed at very low level (using inefficient promoter)
2) Regulates several other inducible proteins. By expressing little repressor, bacterium can prevent unnecessary expression of B-galactoside permease, B-galactosidase + B-galactoside transacetylase
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Trp Operon
- End product of tryptophan synthesis, tryptophan, acts as co-repressor by binding to + activating DNA binding conformation of repressor protein
- Presence of tryptophan (as opposed to absence of lactose) blocks transcription
- Protein that binds near promoter can facilitate transcription, acting as enhancer
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Scale Bar
- Which side of the scale bar genes are on indicates which strand is coding
- Indicates thousands of base pairs
- Lots of space between genes
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Opsin Gene
- Represented by squares connected by zig-zag lines
- This region of DNA transcribed from top to bottom
- Exons: the part of protein sequence that codes
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How is the coding region interrupted by non-coding DNA?
- RNA that's transcribed from gene is processed to produce final mRNA that's translated
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Introns
- Non-coding sequences in eukaryotic genes
- Removed by splicing out of transcript. Flanking axons joined together
- Process involves small ribonucleoprotein particle (snRNPs) that act as enzymes to catalyze rxn
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snRNP
- Recognize specific sequences at boundaries of intron + exons
- 1 snRNP binds 1 sequence at exon-intron boundary, another binds dif sequence at intron exon boundary
- Others bind to form complex that snips out intron + joins ends of exon
- Methylated guanosine cap added to 5' end - helps translation + RNA stability
- 3' untranslated region snipped off + string of 100 adenosine nucleotides, poly A tail, added to 3' end also improves stability
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Telomeres
- Used to prevent gene from getting shorter + disappearing in linear DNA
- Telomeres: short repetitive DNA stretches at ends of chromosomes that don't code for any gene
- Hundreds of copies added to ends by telomerase to compensate for shortening during replication
- Provide buffer between ends of chromosome + DNA encoding for genes so no genes lost
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Centromeres
- Another source of non-coding DNA are repeats usually associated w/centromeric region of chromosome
- May be involved in binding kinetochore proteins
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Transposable Elements
- DNA elements that can hop around genome
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Retrotransposons
- Make copies of themselves by being transcribed + then using reverse transcriptase to make DNA copy of transcript that re-inserts into genome
- Some retrotransposons look like retroviruses + encode retroviral proteins but can never leave cell b/c they can't make functional coat proteins
- LINES don't look like retrovirus but encode reverse transcriptase + endonuclease that helps them insert into genome
- Alu elements don't encode any proteins but rely on reverse transcriptase produced by other elements to allow them to jump
- Mutated version of functional gene
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DNA Transposons
- Splice themselves out of genome + jump back in by encoding special enzyme - transposase
- Jumping genes appear to be DNA parasites
BIOL 112 Midterm
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