Biochem #1 Flashcards
1
Q
amino acids are found in _____
A
proteins
2
Q
____ amino acids are the only ones found in humans
A
L-amino acids
3
Q
All amino acids are chiral except for _____
A
glycine
4
Q
All chiral amino acids used in eukaryotes are _____, so the amino group is drawn on the left in a Fischer projection (S absolute configuration). What is the exception?
A
L-amino acids
EXCEPTION: cysteine: L-amino acid but has R absolute configuration due to CH2SH group having priority
5
Q
name the hydrophobic amino acids
A
alanine, isoleucine, leucine, valine and phenylalanine (interior of proteins)
6
Q
name the hydrophilic amino acids
A
histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine
7
Q
what does E6V mean?
A
6th amino acid E has been changed to V
8
Q
Define amphoteric and give an example (in the context of biochemistry, specifically protein biochemistry)
A
Amino acids are amphoteric: they can either accept a proton or donate a proton
9
Q
what does Pka mean in terms of protonation?
A
The Pka of a group is the pH at which, on average, half of the molecules of that species are deprotonated. [HA=A-]
pH < pKa majority protonated
pH > pKa majority deprotonated
Ex: Glycine at pH 1 will have a positive charge
10
Q
when pH
A
protonated
11
Q
when pH=pKa
A
half protonated and half deprotonated
12
Q
when pH>pKa
A
deprotonated
13
Q
in a titration curve, the number of plateus is____
A
the number of H’s that are being dealt with/the number of PkA values associated with the molecule.
14
Q
zwitterion
A
(dipolar ions): a molecule that has both a positive charge and a negative charge
o Amino acid glycine @pH = 7
15
Q
At very acidic pH values, amino acids tend to ____
A
be positively charges
16
Q
At very alkaline pH values, amino acids tend to ______
A
be negatively charged
17
Q
isoelectric point
A
every molecule is electrically neutral. The pH at which the molecule is electrically neutral.
o Amino acids with acidic side chains have relatively low isoelectric points, while those with basic side chains have relatively high ones.
o pH
18
Q
the titration curve is nearly vertical when the molecule is ____
A
neutral
19
Q
the titration curve is nearly vertical when the molecule is ____
A
neutral
20
Q
dipeptide
A
consist of two amino acid residues
21
Q
tripeptide
A
consist of three amino acid residues
22
Q
oligopeptide
A
used for small peptides up to 20 residues
23
Q
polypeptide
A
> 20 residues
24
Q
peptide bonds are formed ____
A
from the amino group on one amino acid attacking the carboxyl carbonyl carbon on another amino acid
25
what are the products of a peptide bond forming?
peptide bond between two amino acids and water leaves as it is a condensation reaction.
26
draw the resonance around a peptide bond
The resulting C-N bond has double bond character due to resonance in the amide bond. This makes rotation around the C-N bond restricted (rest of the bonds are sigma bonds).
27
draw the resonance around a peptide bond
The resulting C-N bond has double bond character due to resonance in the amide bond. This makes rotation around the C-N bond restricted (rest of the bonds are sigma bonds).
28
describe primary structure of amino acid
linear arrangement of amino acids coded in an organism’s DNA. Sequence of AA listed from N to C.
o Stabilized by the formation of covalent peptide binds between adjacent AA
o Codes everything needed for folding.
o Sequencing: lab technique that can be used to find the primary structure of a protein (from DNA and also the protein itself)
29
describe secondary structure of amino acid
the local structure of neighboring amino acids
o The result of H-bonding between nearby amino acids. 2 main types:
o α-helices: a rodlike structure in which the peptide chain coils clockwise around the central axis.
Stabilized by H-bonds between carbonyl O and amide H atom 4 residues down the chain.
Side chains point away from the helix core.
Important for keratin: a fibrous structural protein found in human skin, hair, and fingernails.
o β-pleated sheets: can be parallel or antiparallel, the peptide chains lie alongside of another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one side chain and amide hydrogen atoms in an adjacent chain.
Pleated or rippled shape to accommodate as many bonds as possible.
The R groups point above and below the plane.
o Proline
Make a kink in peptide chain
Rarely found in α-helices except in helices that cross the cell membrane.
Also not found in β-pleated sheets
Used for turns.
30
alpha-helices
a rodlike structure in which the peptide chain coils clockwise around the central axis.
Stabilized by H-bonds between carbonyl O and amide H atom 4 residues down the chain.
Side chains point away from the helix core.
Important for keratin: a fibrous structural protein found in human skin, hair, and fingernails.
31
beta pleated sheets
can be parallel or antiparallel, the peptide chains lie alongside of another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one side chain and amide hydrogen atoms in an adjacent chain.
Pleated or rippled shape to accommodate as many bonds as possible.
The R groups point above and below the plane.
32
where do the R groups point in alpha helices and beta pleated sheets
alpha: point away from the helix core
beta: point above and below the plane.
33
what does proline do in secondary amino acid structure?
Make a kink in peptide chain
Rarely found in α-helices except in helices that cross the cell membrane.
Also not found in β-pleated sheets
Used for turns.
34
fibrous proteins
structures that resemble sheets or long strands (collagen)
35
globular proteins
tend to be spherical (myoglobin)
36
tertiary structure of amino acids
3D shape, primarily the result of moving hydrophobic amino acid side chains into the interior of the protein
o Determined by hydrophobic and hydrophilic interactions between side chains
o Hydrophilic side chains are oftentimes on the outside of the protein.
Due to entropy:
• Solvation layer: after a solute dissolves in solvent, when solvent molecules go around the solute.
• Water molecules must rearrange to specific arrangements to maximize hydrogen bonding which is negative change in entropy (more order) and is non-spontaneous (ΔG>0).
• Putting hydrophilic molecules there allows the water to spread out, increasing entropy.
o Other interactions:
Hydrogen bonding as well
Salt bridges: acid-base interactions between AA with charged side groups
Disulfide bonds: the bonds that form when two cysteine molecules become oxidized to form cystine.
• Create loops in the protein chain
• Loss of 2 protons and two electrons
37
why is glycine useful in polypeptide formation?
it is very small and reduces steric hindrance.
38
what bonding is present in tertiary amino acid structure?
H-bonding, salt bridges, cystine formation.
39
do all proteins have quaternary structure?
no
40
quaternary structure
Ex: hemoglobin with 4 subunits
not all proteins have quaternary structure. Only exists for proteins that have more than one polypeptide chain. For these, the quaternary structure is made up of smaller subunits to make the functional form of the protein.
o Ex: hemoglobin and immunoglobin G both contain 4 subunits.
o Why they are good:
More stable
Reduce amount of DNA needed to produce protein complex
Bring catalytic sites close together
Cooperativity (allosteric effects): one subunit can undergo conformational or structural changes, which either enhance or reduce the activity of other subunits.
41
conjugated proteins
: derive part of their function from covalently attached molecules called prosthetic groups (can be organic molecules such as vitamins or metal ions such as iron)
o Lipoproteins, glycoproteins, and nucleoproteins have lipid, carbohydrate, and nucleic acid prosthetic groups.
o Heme: prosthetic group on hemoglobin’s subunits as well as myoglobin which contains an iron atom in its core and binds to and carries O (hemoglobin is nonfunctional without it)
can direct proteins to a specific place or help them with their activity
42
glycoprotein
protein with sugar attached (conjugated)
43
lipoprotein
protein with lipid attached (conjugated)
44
nucleoproteins
protein with nucleic acid attached (conjugated)
45
denaturation
a protein loses its three-dimensional structure.
o Can be reversible or not
o Main causes are heat and solutes.
Heat: increases kinetic energy of the protein causing the hydrophobic or hydrophilic bonds to break (energy overcomes the strength of the interaction)
• Ex: egg whites
Urea (solute): directly interfere with the forces that hold the protein together, break disulfide bridges.
Detergents such as SDS can also disrupt noncovalent bonds and promote denaturation.
46
what happens to denatured proteins?
lose their 3D structure
47
what causes proteins to denature?
heat, pH, chemicals
48
sickle cell disease is caused by mutations in ______
hemoglobin
49
In alpha amino acids, the carboxyl and amino group are bound to the _____
alpha carbon
50
the _____ determine the properties of amino acids and therefore their functions
side chains
51
there are ____ proteinogenic amino acids which go in proteins but there are also other ones that are not involved in protein synthesis but play important roles in the body nonetheless
20
52
what makes an amino acid optically active?
the alpha carbon is chiral
53
which amino acids have sulfur
methionine and cysteine
54
which amino acids can H bond
serine and threonine
55
do the amide nitrogens on asparagine and glutamine gain or lose protons?
no
56
when the pH of a solution is approximately equal to the pKa of the solute, the solution acts as a ____
buffer
57
what is the pI of an acidic amino acid?
lower (it is 3.2 for glutamic acid)
58
Amino acids with acidic side chains have pI values _____; amino acids with basic side chains have pI values ____
well below 6
| well above 6
59
a peptide is drawn from the ____ terminus to the ____ terminus
N terminus to the C terminus
60
trypsin vs. chymotrypsin
trypsin: cleaves at the carboxyl end of KR
chymotrypsin: cleaves at the carboxyl end of FYW
61
peptide bond formation is an example of a ____ or ____ reaction
condensation or dehydration reaction
During condensation reaction, two molecules combine to form a single molecule with the loss of a small molecule; in dehydration reaction, this lost molecule is water.
62
is an amino acid on its own considered an oligopeptide?
no
63
Sequencing technique
lab technique that can be used to find the primary structure of a protein (from DNA and also the protein itself)
64
what is the key to forming secondary structures?
alpha helices and beta pleated sheets formed via intramolecular hydrogen bonds
65
alpha helices are stabilized by H-bonds between carbonyl O and amide H atom ____ residues down the chain.
4
66
where do the side chains point of amino acids in an alpha helix?
away from the helix core
67
the _____ is an important component in the structure of _____, a fibrous structural protein found in human skin, hair, and fingernails
alpha helix
| keratin
68
where do the side chains point of amino acids in a beta-pleated sheet?
above and below the plane
69
proline has a ____ structure
rigid
70
what creates the difference between fibrous and globular protein?
tertiary and quaternary structure
71
what is the primary determinant of tertiary structure?
moving hydrophobic and hydrophilic R groups around
72
disulfide bonds
part of tertiary structure: the bonds that form when two cysteine molecules become oxidized to form a cystine bond.
73
disulfide bonds create ____ in the protein chain
loops
74
the forming of disulfide bonds is an ____ reaction
oxidation
75
what are the intermediates of tertiary protein folding?
molten globules
76
why do hydrophilic residues like to be on the outside?
they can form more H bonds with water molecules and this allows water to take on more positions, increasing entropy, and making this structure more stable.
77
do all proteins have quaternary structure?
no
78
what are some benefits of quaternary structure?
- more stable (further reduces the surface area of the protein complex)
- reduces the amount of DNA needed to encode the protein complex
- bring catalytic sites close together (intermediates from one reaction can be shuttled to another quickly)
- induce cooperativity
79
conjugated proteins derive part of their function from covalently attached molecules called ____ groups
prosthetic
80
what are the possible types of conjugated proteins and their names based on the prosthetic group?
can have metal ions or vitamins (the heme group containing an iron atom at its core is an example of a prosthetic group)
lipid: lipoproteins
carbohydrate: glycoproteins
nucleic acid: nucleoproteins
81
what are the types of stabilizing bonds in tertiary structure?
hydrogen bonds, van der waals, covalent bonds, ionic bonds
82
explain denaturation via heat
when the temperature of a protein increases, its average kinetic energy increases which can be enough to break the hydrophobic interactions that hold a protein together.
83
explain denaturation by solutes
solutes such as urea denature proteins by directly interfering with the forces that hold the protein together. They can disrupt things such as disulfide bonds and the hydrogen bonds that hold secondary structure together
84
how is quaternary structure held in place?
interactions between subunits
85
denaturation does not usually involve ____
the breaking of the peptide chain
86
what is a hypotonic solution?
lower solute solution
87
which amino acids have a chiral carbon in their side chain?
threonine and isoleucine
88
based can ____ peptide bond hydrolysis
catalyze
89
is threonine ionizable?
no
90
in collagen there is a lot of ____ because it has a triple helix and the carbon backbones are ____
glycine
| very close together
