1
Q
Carbon and Organic Molecules
A
- organic molecules contain carbon(significant amount, not CO or CO2)
- atomic number is 6
- first shell has 2 electrons second cell has 4
- carbon is versatile
2
Q
Carbon is…
A
- versatile, meaning it can form 4 bonds with other substances
- 4 electrons in the outer shell
- needs 4 electrons to fill the out shell (to make an octet)
- makes up to 4 bonds, can be polar or nonpolar
- polar molecules dissolve more readily in water, water is polar
- Big idea Carbon is the backbone of all of these molecules because of its versatility, it can form single bonds, doubles or triple bonds.
3
Q
The Carbon atom
A
-C-C and C-H bonds are nonpolar
-Oxygen- high electronegativity, so C-O bonds are polar
-polarity has to do with differences in electronegativity, if one atom is a bigger electron charge hogger then they get a charge
- they are equal sharing of electrons
oxygen is a big electron hog, so it has a high electronegativity
4
Q
Carbon bonds; stability
A
- bonds are stable within a large temperature range
- organisms can exist within a large temperature range
- molecules in our body don’t fall apart because it is cold or hot, they remain integrated
5
Q
Hydrocarbons
A
- molecules predominately made of H-C bonds
- they are hydrophobic and poorly soluble in water
- the design of the organic molecule is C’s using all 4 of its bonds, to bond with H
- lines represent covalent bonds
- carbons are saturated with H’s around them
6
Q
functional groups
A
- define the function of the organic molecule
- with certain characteristic properties
- groups of atoms that come up over and over again in different biological functions
- R means that there is other stuff over here
- big idea is that we take our basic organic hydrocarbon and we modify them by adding different groups, these different groups have different chemical properties and they behave differently
7
Q
bees wax vs. sugar cube
A
- both are made of very long hydrocarbon chains, but what makes their properties so different is which functional group they have
- the sugar is hydrophilic because it dissolves easily in water
- honey is a lipid that doesn’t interact with water
8
Q
isomers
A
- identical molecular formulas, different structures
- molecular formula tells us that atoms that make up a moelcule but doesn’t say exactly how those atoms are put together
- isomers are where the molecular formulas are the same but the structure is different
- example: 2 cats, both made of the same parts, but they are put together differently
- we know the atoms we just don’t know the arrangements
9
Q
molecular formula
A
tells us the atoms that make up a molecule but doesn’t say exactly how those atoms were put together
10
Q
structural isomers
A
- same atoms, different bonding relationship
- difference is just the arrangement
- example: propanone and propanal, differ by the placement of the methyl group
11
Q
stereoisomer
A
- same atoms, same bonding relationship, but different spatial arrangement
- same atoms, similar bonding but just different in 3D space
- cis-trans
- enantiomers
12
Q
cis-trans isomers
A
- positioning around DB
- cis is on the same side
- trans is on opposite sides
13
Q
enantiomers
A
-mirror images
14
Q
Stereoisomer (cis, trans) : retinal example
A
- Retinal- made from vitamin A, carrots help produce this
- you have a situation in order to become active form, light comes in and hits molecules in the back of the eye and changes it from trans to cis
- same atoms, same bonding arrangement just changes from cis to trans and now sets up a reaction for you to process what you are seeing
15
Q
Stereoisomer(enantiomers): Thalidomide example
A
- thalidomide- sedative commonly used in 1957
- mirror images
- comes in 2 forms, R and S thalidomide
- common drug given to pregnant women, solution contained both isomers of thalidomide
- R version is the one that helps sleep, S version is very similar but caused a bunch of birth defects
- babies born to mothers who took this had almost no limbs
- malformations in the embryonic period were caused by the S thalidomide
- teratogenicity- harmful to embryo or fetus
16
Q
macromolecules
A
- large, complex organic molecules
- thousands or millions of atoms
- looks at a stretch of DNA, not just a bunch of different atoms but together a bunch of regular sized molecules put together
- double helix forms the DNA in our body and made up of backbone of sugars, phosphates and nucleotide bases
- monomers are subunits of polymers
17
Q
When the monomer is a monosaccharide (glucose, fructose)….
A
the polymer is a polysaccharide (starch, glycogen, cellulose)
18
Q
When the monomer is an amino acid (arginine, leucine)…
A
the polymer is.. a polypeptide or protein (A and B chains of insulin are polypeptides and insulin is a protein)
19
Q
when the monomer is a nucleotide (sugar, phosphate, base in combination)
A
the polymer is a nucleic acid (DNA and RNA)
20
Q
macromolecule formation: condensation and dehydration
A
-polymers are made via condensation
- monomers “condense” into a polymer
-link monomers to form polymers
-dehydration reactions- type of condensation reaction
- 2 monomers and condense into a single long molecule
it releases water as the byproduct in the reaction
-instead of two monosaccrides we now have 2 disacchride
21
Q
monosaccharides
A
- these are the simplest sugars
- different structures-linear or ring
- can join together by dehydration and form a larger carbohydrate
- one sugar, taste sweet
- structure: 6 C’s in a row with H and OH except C 3 is OH and H
- D-glucose
- usually 5 or 6 carbons
22
Q
starch
A
- complex carbohydrate in nature
- what plants use to sore energy
- each circle is a glucose moelcule linked together, as you add another glucose moelcule, each is a dehydration reaction
- started with a monomer glucose and we get a big complex polymer, starch
23
Q
disaccharides
A
- monosaccharide joined by a condensation or dehydration reaction (byproduct is water)
- form glycosidic bonds- bond formed between two monosaccharides
- broken apart by hydrolysis
- examples: sucrose(sugar cubes- 2 mono combined) , lactose(2 disaccharides, galactose and glucose together)
- lactose in tolerant, you lack enzyme to properly break lactose down into 2 monosaccharides
24
Q
polysaccharide
A
- many sugars are made
- large polymers
- example: energy storage: starch, glycogen
- plants store extra chemical energy in form of starch in bodies, plants use glucose
- we use them in structural in animal bodies where we have an exoskeleton, outer shell is exoskeleton that is made of chitin
- structural: cellulose, chitin
- bunch of simple sugars together
25
macromolecule formation: Hydrolysis
- cleavage of polymers by water
- H+ attaches to the polymer, OH- attaches to the monomer
- it is the reverse reaction
- water comes in and breaks it
26
triglyceride
- main way we store fat
- we store it in fat cells
- sometimes we lose weight, a lot of hydrolysis goes into play, you have to break down and burn them for energy
- eat you, make triglycerides and stores it
- when u lose weight, hydrolysis takes the triglycerides out of storage and breaks them apart
27
Carbohydrate
- contain C, H and O
-Cn(H2O)n
most carbon atoms are linked to a H or OH
-sugars, simple and complex sugars
-breads, pastas and crackers
-D- glucose is C6H12O6
-number of different isomers of glucose- same atoms put together in slightly different way
-6 C's down the middle, H and OH on opposite sides
except for C3, it is OH and H
28
Monosaccharide: pentose
5 carbon sugar
- carbohydrates are made of 5 carbons
- fructose**
29
Monosaccharide: Hexose
- 6 carbon sugar
| - glucose
30
glycosidic bond
it is a bond formed between two monosaccharides to make a disaccharide
31
Polysaccharides and Energy storage: starch and glycogen
- starch (plants) glycogen (animals and fungi)
- different in branching pattern
- starch and glycogen and both polymers of glucose
- amylopectin and amylose are both part of starch
- glycogen is highly branched, amylopectin moderately branched and amylose is not branched
- all made from same stuff just constructed differently
32
Starch: Structure
- helical structure(spiral shape)
- amylose- simplest
- amylopectin- more complex
- not water soluble
- moderately branched, not very compact
- properties- C, H and O - very stable
- form storage of energy and glucose for plants
33
Glycogen
-similar to amylopectin, but more branching
-water soluble
-branched, very compact
-liver and muscle cells
-this is our starch
glucose is the main thing burning energy in our body
34
Why do plants use starch whereas humans use glycogen?
- whether plant or animal you have this, to access as quick of energy as you can
- starch and glycogen are long glucose put together
- plants use less highly branched
- can pack more energy in a compact space like glycogen- good for animals that need quick access
35
Cellulose
- bond orientation prevents branching; forms fibers
- not water soluble
- structural polysaccharide
- humans have no cellulose
- no branching so it forms stringy fiber
- we don't digest this
- food high in fiber is good for you because it slows down digestion of other things, stay full longer
36
Chitin
- exoskeletons, feeding mouthparts
- cell wall of fungi
- main component of anything with an exoskeleton like lobster, crab and insect
- animals and fungi are closely related and plants are distantly related
- plant cell walls are made of cellulose*
- fungi cell walls made of chitin*
37
lipids
- mostly C and H atoms
- nonpolar, very insoluble, don't interact well with water
- fats, phospholipids, steroids, waxes
- phospholipids make up the plasma membrane
- example: leafs are covered in a thin layer wax called cuticle and this is because they are to protect against water loose to the environment
- C-H bonds are nonpolar
- lipids are dietary fats
38
Fats
- a mixture of triglycerides
- glycerol + 3 fatty acids
- joined by dehydration/condensation reaction
- broken by hydrolysis - lost an H for each OH and releases water and have intact triglycerides
- dietary fat
- structure: has 3 carbons, attached to glycerol are 4 HC fatty acid tails
39
Saturated vs, Unsaturated fatty acid
- glycerides are categorized into either group
- unsaturated is healthier fat, saturated fat is the one you want to limit in your diet
- saturated fat tends to be a solid at RT
- unsaturated fat tend to be a liquid at room temperature
- difference has to be with the structure of the fatty acid tail, we have a glycerol head and the 3 fatty acid tails, describes whether or not those fatty acid tails are saturated with H or not
- if you have as much H as you can fit on that fatty acid tail it is saturated, and if you don't have as much then you have C=C bonds- unsaturated
40
Saturated fatty aids
all the C's are attached to as many things as it can attach you , you can not add anymore H bonds
41
Monounsaturated
- one C=C, not saturated with as many H's as possible because you could make that into a single bond and add another H
- where ever a DB is, it adds a kink to it, which changes its overall shape
42
polyunsaturated
having more than over C=C
| -unsaturated means that it is liquid at room temperature
43
trans fat
- unsaturated fats with at least 1 trans double bond rather than the more common cis double bond
- made artificially during processing
- increase heart disease risk by raising blood cholesterol levels
- unsaturated fat that acts like a saturated fat
- has a DB in there but instead of being a cis DB it is a trans DB (where H is, cis-same side and trans-opposite sides)
- trans fat is flat like a saturated fat
- same linear shape
- trans fat adds good flavor
- studies say they are worse then normal fats
- has to do with it not being encountered in nature often
- they stick around in the bloodstream, elevate cholesterol levels in the blood, we don't have the appropriate enzyme to break down the trans fat
44
Fatty acids and Energy
- fats are important for storage
- 1g of fat stores twice as much energy as 1g of glycogen or starch
- we store some energy as glycogen, small amount
- once you fill up the glycogen storage tanks you have extra calories that are stored as triglycerides and then stored as fats
- efficient way to pack energy in small space
- if you have a gram of fat in one hand and a gram of carbs in the other hand, then they weigh the same but there are twice as many calories in the gram of fat then there is in the gram of carbs
- same amount of stuff just the weight of it was different, energy stored up in fat
45
fatty acids: structural
- can also be structural
- cushioning and insulation
- body fat, eye socket pads
- example: eye is not right up to the bone, we have padding
- stomach fat protects all our organs
- cushioning protects from internal bleeding
46
phospholipids
- glycerol, 2 fatty acids and a phosphate group
- amphipathic
- membranes
- not entirely nonpolar or hydrophobic the are both
- every cell has a cell membrane and is made up of phospholipids
- head region is polar, tail is nonpolar
47
Phospholipid Bilary
- bunch of phsophlipids put together has a hydrophilic head and the tail is opposite
- bilayer- 2 layers, head region is exposed to outside of the cell, inside is like a sandwich and in the middle is a bunch of hydrophobic tails
- every cell in the body is surrounded by phospholipids
48
steroids
- 4 connected carbon rings
- usually insoluble in water
- example: cholesterol
- small structural differences matter
- testosterone vs. estrogen
- 4 rings of C stuck together
- nonpolar but depending whats going on right side could be semi soluble
- example: cholesterol- we need some because it is the basis for how we make a lot of other steroids in our bodies, testosterone and estrogen- which are both synthesized from a cholesterol
49
Testosterone/ estrogen
- derived/ synthesized from cholesterol
- testosterone and estrogen- they both have 4 carbon rings
- difference between he's in the size and color
- structure-difference seems minimal, but small changes to a molecule could be a big difference and really matter
50
Proteins
- C,H,O,N, trace amounts of other stuff
- building blocks=amino acids (20)
- variable side chain
- one of our macromolecules that are nitrogen rich
- monomers, which are the building blocks, which are amino acids, overall the 20 have the same general structures but difference in one carbon
- all of our amino acids have a central carbon attached to amino group and a carboxyl group, H
- what makes one amino acid different than another is the variable group- R
- polymers are called proteins
- bunch of AA together you get a polypeptide chain
51
Proteins do A LOT
1. gene expression- they determine which will turn off an on. which are used to taking information from DNA and help with translation
2. movement- motor protein- transports material on a cell
3. defense- cells defending themselves against foreign invaders
4. metabolism- metabolic reactions, almost all take place, whether breaking down or building up, have some type of protein enzyme facilitating that reaction
5. cell signaling- phospholipid bilayer, different signaling proteins and structural support, keeping it rigid
6. provide structure
52
Nonpolar side chains
- some amino acids are nonpolar some are polar, this means they have different chemical properties
- nonpolar amino acids come from non fatty acid foods
53
Polar side chains (uncharged) and Polar (charged)
- a lot of O and N
- is there a positive or negative
- some acidic and some basic
- some are polar and nonpolar, some are acidic or basic and some are charged and not charged
54
Glycine + Alanine
- take two aminoa cids and link them up to form a polypeptide chain
- glycine and alanine- strucure is the same only difference is the variable groups
- both amino group on left carboxyl group on right
- you take two separate amino acids and link together is carboxyl group and amino group of other combined
- this link forms a peptide bond
- with carbohydrates we have glycosidic bonds
- with amino acids we have peptide bonds
- we lost H2O
- starting with monomers and building polymers we get dehydration reaction or condensation, water coming out
55
Polypeptide chain
- you keep doing this over and over, you create one peptife bond then another peptide bond
- one side always has an amino group and as you add new amino acids you remove carboxyl group
- N terminus and C terminus with Amino group and side with the carboxyl group
- start and end and order which these AA were put together
- just making a bunch of amino acids stuck together by a polypeptide chain does not actually give us a functional protein yet
- in order to get a FP you have to go through a serious of folding
- order of AA is called primary structure
56
C and N terminus
- when two or more amino acids are linked together, one end of the resulting molecule has a free amino group, N
- the other end of the polypeptide, carboxyl end is the C, has a free carboxyl
57
Protein Structure" Primary structure
- is a linear order of amino acids- we added glycine then adenine and serine in the order from 1st amino to last
- determined by genes
- what dictates the primary structure is actually what;s being translated information in DNA
- DNA is the direction for making polypeptide chain, DNA is an information holding molecule
- depending on the order of the sequence of the nucleotides in the DNA this translated to a specific AA in a protein
58
Protein Structure: Secondary
- chemical and physical interactions cause folding
- hydrogen bonding
- a helices and B pleated sheets - key determinants of a proetins characteristics
- the way we get it to hold its shape is through H bonding
- depending on order of AA sequence, these AA start to work to interact with one another
- neg attracted to positive you get H bonding
- B pleated sheets- spirals or zig zag shapes
- random coiled regions-don't form alpha or beta regions, not organized way
- overall ow it all holds up and shapes determines what protein will do
59
random coiled regions
- don't form alpha or beta regions
| - this is very important to function
60
Protein Structure: Tertiary
- folding gives complex 3-D shape
- sometimes final level of structure
- overall structure of the entire protein
- folded up in a specific way and shape
61
Protein Structure: Quartenary
- Two or more polypeptides (protein subunts)
- proteins amde up of multiple polypeptide chains tha tthen come and interact with each other
- each individual one is called a protein subunit and come together to form overall larger structure
- hemoglobin: protein that binds oxygen to bloodstream
- made up of 4 subunits, 2 alpha subunits and 2 beta subunits, 4 different polypeptide chains that come together and fold in a certain way that you get hemoglobin
62
Subunits
- protein subunits, each individual one is a subunit and then come together to form overall larger structure
- hemoglobin is made of 4 subunits; 2 alpha and 2 beta. 4 different polypeptide chains that come together and fold in a certain way that you get hemoglobin
63
Proteins: structure vs. function
- shape is critical to protein
- shape held togethre by chemical bonds
- the end product, the 3D shape when you are done building is exactly how it folds up is crucial
- genetic mutation only may affect one amino acid out of a thousand, and this could ruin the entire polypeptide chain and how the protein is held up
- in order for a protein to do what they are supposed to do in the cell, not only are we supposed to have the amino sequence but you have to have the right 3D shape
- held together by a serious of chemical bonds, we have a peptide bonds holding one amino acid to another, various H bonds holding together alpha helices and beta pleated sheets
- in order for an enzyme to do any chemical reaction in the body it has to be in the right shape
64
What influences protein stability?
1. Hydrogen Bonds
2. Ionic Bonds
3. Hydrophobic effect
4. van der Waals forces
5. Disulfide bridge
65
1. hydrogen bond; influences stability
- bonds form between atoms in the polypeptide backbone and between atoms in different side chains
- alpha helix is maintained with serious of H bonds, dashed lines, plays a role in overall 3D structure
66
2. Ionic bonds; protein stability
- bonds form between oppositely charged side chains
| - positive charge and negative charge form this, one steals an electron from the other
67
3. Hydrophobic effect; protein stability
- nonpolar amino acids in the center of the protein avoid contact with water
- yellow middle, bunch of nonpolar AA in a row
- tend to not react great with water so all of them cluster together
- middle curve is formed because of all these hydrophobic side chains and nonpolar AA trying to protect nonpolar regions from outer portion that has water
68
5. Disulfide bridge; protein stability
- a covalent bond forms between 2 cysteine side chains
- 2 SS both a cysteine
- AA that has sulfur in it and 2 that are near each other and disulfide bridges form when u have two cystene close enough to interact
69
4. van der Waals; protein stability
- attractive forces occur between atoms that are optimal distances apart
- if too far apart no attractive force and if they have an attractive force and get to close together then the start to repel each other so there is- no optimal distance where they maintain folding by staying optimal distance apart
70
Protein folding- Alzheimers Disease
-insoluble plaques form in neural tissue
-protein misfolding
-hydrophobic portions exposed, not in inner portion
-people get protein plaques that build that build up with neurons of brain
plaques block transmission of neural signals from one cell to another
-as they build up they have a harder and harder time functioning
-start forgetting things that aren't important then you forget important things and they can't function at all
- plaques are a result of a misfolded protein so this protein gets degraded- when misfolding takes place, AA is the same and the hydrophobic portions instead of being closed in and protected are now exposed to the outside, soluble polar moelcule becomes less soluble and nonpolar, does not get broken down and builds up in the brain overtime
-changes the structure that it is no longer degraded and it builds up in the brain
71
Protein Denaturation
- denaturation is the process of unfolding a protein
- basically takes it back to an unfolded strand
- some cases you can fold it back up the right way
- causes of this- extreme heat, too hot or too cold, set point the H bonds weaken and lose overall 3D structure, pH changes-too acidic or too alkaline, they do not denature in boiling water
example: frying egg- goes from transparent to a solid egg- denaturation proteins an egg unfolding and that is thru adding heat
72
Nucleic Acids
- store, express and transmit genetic information
| - made of 3 parts- pentose sugar, phosphate and nucleotide base (double ring of C and N atoms)
73
Nucleotides: DNA
- deoxyribonucleic acid
- stores genetic information
- codes in sequence of monomer building blocks
- put NA together to form DNA or RNA
- genes are made of, in the nucleus of the cell and provides information to make a protein
structure: DNA lacks and O where RNA has the OH
- A, T,C and G
74
Nucleic Acid: RNA
- Ribonucleic acid
- involved in translation of DNA to form polypeptide chain
- protein built and assembled outside of the nucleus
- it takes the genetic information from DNA, transcribes it and brings it into the nucleus
- A, G, C and U
75
Structure of Nucleotides: purines
- 5 nitrogenous bases
- 2 purines- adenine and guanine
- DNA has A, T, C and G
- A and G have a double ring
- Antonia and Ghalib are pure
76
Nucleotides: pyrimidines
- 5 nitrogenous bases
- 3 pyrimidines- cytosine, thymine and uracil
- CUT the Py
- reason for T and U difference- where ever there is a T RNA replaces it with a you because if u look at the moelcule it has an extra methyl group and thymine requires more material to make compared to U. DNA is the information holding molecule, it is important to maintain a correct sequence. RNA just needs to take information from DNA, transcribe it and put it in the cytosol of the cell so it is easier to make.
- U has less energy and few components and not as stable
77
Nucleotides: Sugar-phospahte backbone
- joined by a phosphester bonds
- (Ester bonds: C-O-C)
- bunch of nucleotides stuck together, each has its own 3 parts
- the bond from sugar of one to the phosphate of another is called a phosphoester bond, lines one nucleotide to another
78
DNA's nucleotide structure
- A with T
- G with C
- hydrogen bonds hold the double helix together, its strong but not too strong
- DNA is two string of a nucleotide stuck together
- DB of DNA has a spiral shape
- to copy DNA they need to split apart- thats how we get a gene to transcribe from DNA to RNA
79
DNA vs. RNA
DNA
- deoxyribonucleic acid
- deoxyribose
- Thymine
- A, G, C
- 2 strands- double helix
- 1 form
RNA
- ribonucleic acid
- ribose
- Uracil
- A, G and C
- mostly single strand
- several forms
80
singing
- DNA is part of what makes you , you
| - features you have come from DNA
81
R-Group
-the rest of the molecule (figure with an R)
82
Sucrose and Maltose formation
- you start with glucose and fructose (monosaccharides)
- these two are then joined together by a glycosidic bond which forms a disaccharide
- then u get sucrose and maltose plus water when broken down
BIO 111
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