Chapter 2 Protein Composition and Structure Flashcards
1
Q
Why are alpha amino acids chiral?
A
There are 4 different groups bonded to the alpha carbon.
- amino group, carboxylic acid group, hydrogen, R group
2
Q
What are the 2 forms of alpha amino acids?
A
L and D isomer
- chiral alpha amino acids exist in 2 forms as mirror images
3
Q
Which isomer of amino acids make up proteins?
A
L isomer
4
Q
At a neutral physiological pH, what is the ionization state of amino acids?
A
Free amino acids in neutral pH predominantly exist as dipolar ions (zwitterions)
- (+) amino group NH3+, (-) carboxyl group COO-
5
Q
What does the ionization state of amino acids depend on?
A
pH
- at low pH (acidic), both carboxyl (COOH) and amino group are protonated (NH3+)
- at high pH (Basic), both groups are deprotonated (NH2 and COO-)
6
Q
4 groups of amino acids
A
hydrophobic, polar, positively charged (basic), and negatively charged (acidic)
7
Q
Characteristics of hydrophobic amino acids
Examples
A
contain nonpolar side chains (diff sizes and shapes) that
- can’t interact w/ polar substances (water)
- pack together to form compact structures
- glycine: achiral, simplest amino acid
- tryptophan: bulkiest hydrophobic amino acid (indole group as side chain)
8
Q
Characteristics of polar amino acids
Examples
A
- contain a hydroxyl group (-OH) = more hydrophilic and reactive than hydrophobic aa but are still attached to hydrophobic side chain
- cysteine: contains a sulfhydryl group (thiol, -SH) that can come together and form disulfide bonds
- histidine: often found in enzyme active sites (imidazole ring can bind + release protons during enzyme rxns)
9
Q
What allows histidine to be able to bind and release protons?
A
It has a pKa near 6 (close to physiological pH) so it can accept/donate protons at those pH values
- when pH = 7, imidazole ring is uncharged but it can be (+) charged or uncharged based on its environment
10
Q
Characteristics of positively charged amino acids
Examples
A
- (+) charged at physiological pH (side chains)
- complete (+) charges make the aa highly hydrophilic
- arginine: contains guanidinium group (strong positively charged group that can be methylated)
11
Q
Characteristics of negatively charged amino acids
Examples
A
- (-) charge at physiological pH (side chains are neg)
- aspartic acid and glutamic acid = often called aspartate and glutamate (side chains usually lack proton that’s present in acid form)
12
Q
Which amino acids have readily ionizable side chains?
A
seven amino acids
- histidine, cysteine, tyrosine, lysine, arginine, aspartic and glutamic acid
- terminal alpha-carboxyl group and terminal alpha-amino group
these aa are able to donate/accept protons + form ionic bonds
13
Q
Possible reasons why the 20 amino acids are conserved within all species
A
- provide chemical versatility
- have been available from prebiotic reactions (before origin of life)
- other aa are too reactive
14
Q
What does a peptide (amide) bond formation involve?
A
- linking of a-carboxyl group of 1 amino acid to the a-amino group of another
- loss of water molecule
15
Q
Primary structure of proteins
A
amino acid sequence makes up primary structure
polypeptide chains
- amino acids linked together by peptide bonds
16
Q
Residue
A
Each amino acid unit in a polypeptide
17
Q
How do polypeptide chains have directionality?
A
- a-amino group is at the beginning
- a-carboxyl group is at the end
- N terminal is the beginning
- C terminal is the end
18
Q
What does the polypeptide consist of?
A
- backbone/main chain: repeating part
- variable part: consists of the amino acid side chains
19
Q
What kind of bonds can the polypeptide backbone form?
A
hydrogen bonds
- carbonyl (C=O): good hydrogen bond acceptors
- NH groups: good hydrogen bond donors
20
Q
Proteins vs oligopeptide
A
- proteins: 50 to 2000 amino acid residues
- oligopeptides: polypeptide chains of small #s of amino acids
21
Q
What is the mean molecular mass for an amino acid?
A
110 g/mol
Can also be referred to in daltons
- 100 g/mol = 100 daltons
22
Q
Disulfide bonds in proteins
A
- cross-link a linear polypeptide chain
- formed from oxidation of 2 cysteine residues
23
Q
Cystine
A
two linked cysteines (thru disulfide bonds between S-H of each cysteine)
-SH with -SH –> S–S (disulfide bond)
24
Q
Who determined the amino acid sequence of insulin?
What was the significance of this?
A
Frederick Sanger in 1953
It was a landmark in biochemistry that showed for the first time that a protein
- has a precisely defined aa sequence
- consists only of L aa that are linked by peptide bonds
25
Why is it important to know amino acid sequences?
- structure eludes function
- determines 3D structure of proteins
- alterations in sequences can lead to abnormal protein function + disease
- reveals evolutionary history
26
Features of peptide bonds
- planar (6 atoms lie in a plane)
- has partial double bond character due to resonance (shorter = 1.32 Anstroms)
| 6 atoms = Ca, C, O, N, H, Ca
27
How/why are polypeptide chains conformationally restricted?
peptide bonds have partial double bond character = rotation of bond is prohibited + conformation constrained
28
Which configuration of the peptide bond is favored?
Trans configuration
| 2 a-carbons are on opposite sides of peptide bond = less steric
29
Which amino acid is commonly found in the trans and cis form?
Proline with its adjacent amino acid
- steric differences btwn cis and trans form are minimal
| bc N is bonded to 2 tetrahedral carbons
30
What are torsion (dihedral) angles?
rotation about the N-Cα bond and the Cα-carbonyl bond
## Footnote
- determines the path of polyhedral chain
- not all torsion angles are allowed due to steric collisions
31
Phi φ
angle of rotation about the bond between the N and α-Carbon
32
Psi Ψ
angle of rotation about the bond between the carbonyl carbon and α-Carbon
32
What is a Ramachandran plot?
a 2D plot that illustrates the allowed Ψ and φ angles
| not all angles are allowed due to steric collisions
32
Secondary structures of proteins
## Footnote
Examples
3D structures formed by hydrogen bonds between peptide N-H and C=O groups of aa near each other in linear seq
## Footnote
α helices, β pleated sheets, turns
33
α helix structure
tightly coiled backbone with R groups extending outward in helical array
34
What stabilizes an α helix?
hydrogen bonds between the C=O group of one amino acid with the NH group of another amino acid **4 residues ahead**
## Footnote
all of the backbone CO and NH groups are hydrogen bonded except the aa at the ends of the helix
35
How many amino acids per turn are in an α helix?
3.6 amino acid residues per turn
36
How are amino acid residues spaced out in α helices?
separated by a rise (or translation) of 1.5 Anstroms and a 100 degree rotation
| = 3.6 aa residues per turn
37
Pitch of an α helix
The length of one complete turn along the helix axis, 5.4 Anstroms
## Footnote
equal to the rise (1.5 Anstroms) and # of residues per turn (3.6) = 5.4 Anstroms
38
What does a Ramachandran plot for α helices reveal?
| direction of rotation about the axis of α helices found in proteins
Essentially all α helices found in proteins are **right-handed** (clockwise)
- more energetically favored (less steric clash btwn side chains and backbone)
## Footnote
- left and right handed helices are allowed, but right-handed is more common
39
How do some amino acids disrupt α helices?
## Footnote
Examples
- branching at β-carbon destabilizes helix due to steric clashes
- side chains that contain hydrogen-bond donors (-OH) or acceptors in close proximity to the main chain compete
- proline lacks NH group and its ring structure prevents it from fitting into an α helix
## Footnote
- branching: valine, threonine, isoleucine
- hydrogen bond donors/acceptors in side chain: serine, aspartate, asparagine
40
How are β sheets stabilized?
Hydrogen bonds between 2+ β stands
41
β sheets
## Footnote
Types
- formed by adjacent β strands
- β strand is almost fully extended (unlike α helixes which are tightly coiled)
## Footnote
parallel, antiparallel, mixed (based on direction of adjacent β strands)
42
Antiparallel β sheets
NH and CO group of each amino acid bonded to NH and CO group on adjacent chain/sheet
| fully paired - one aa with one aa
43
How are amino acid residues spaced out in β sheets?
Distance = 3.5 Anstroms
- side chains of adjacent aa point in opposite directions
| alpha helices = 1.5 Anstroms
44
Parallel β sheets
- NH group of each aa is hydrogen bonded to the CO group of an aa on the adjacent strand
- CO group is hydrogen bonded to NH group of aa two residues farther along the chain
| one aa paired/bonded with two aa on adjacent strand
45
How can polypeptide chains change direction?
- **reverse turns** (β or hairpin turns): the CO group of residue i is hydrogen bonded to the NH group of residue i+3
- **loops**: rigid and well defined
## Footnote
turns + loops are on surface of protein and participate in interactions
46
Tertiary structure of a protein
the overall course of the polypeptide chain
47
Characteristics of globular proteins
- highly compacted structure
- a lack of symmetry
- soluble in water
## Footnote
globular proteins have imp functions such as regulatory, signaling, and enzymatic activities
ex. myoglobin
48
What is unique about membrane-embedded proteins?
- exterior/surface of the protein has many hydrophobic amino acids
- interior has many polar and charged amino acids surrounding a water-filled channel
| ex. porin protein
## Footnote
generally, hydrophobic aa cluster up on the interior of a protein whereas polar + charged aa are on the exterior
49
Protein motifs (aka supersecondary structures)
## Footnote
Example
certain combinations of secondary structures
| motifs generally exhibit similar functions
## Footnote
helix-turn-helix motif (common in DNA binding proteins)
50
Protein domains
some polypeptide chains fold into compact regions that may be connected by a flexible segment of polypeptide chain
| compact regions = independently folding regions
51
Fibrous proteins
## Footnote
Examples
Form long, extended structures that have repeated sequences
- provide structural support for cells/tissues
## Footnote
collagen, α-keratin
52
Structure of α-keratin
2 right-handed α helices that intertwine to form a left-handed super helix (α-helical coiled coil)
| - member of a superfamily known as coiled-coil proteins
53
What stabilizes the 2 helices of α-keratin?
ionic and van der Waals interactions
53
coiled-coil proteins
## Footnote
Example
characterized by a central region of 300 amino acids that contain imperfect repeats of a sequence of 7 amino acids called a heptad repeat
| heptad repeats from each helix can interact with each other
## Footnote
α-keratin
54
Structure of collagen
- 3 helical polypeptide chains --> form a **superhelix cable**
- glycine at every 3rd residue
- recurrent seq of glycine-proline-hydroxyproline
55
Properties of collagen helix
- triple helix
- no hydrogen bonds within a strand
- each strand adopts an extended conformation
- helix is stabilized by steric repulsion of the pyrrolidine rings of proline and hydroxyproline
56
Which amino acid can fit in the interior of collagen? Why?
Glycine bc it's the smallest aa
- inside of superhelical cable is crowded
| which is why glycine is at every 3rd residue
57
How does osteogenesis imperfecta occur?
| osteogenesis imperfecta = brittle bone disease
When other amino acids replace the internal glycine of collagen (leads to improper folding of collagen)
| defects in collagen structure = pathological conditions
58
Quaternary structures
The spatial arrangement of subunits and the nature of their interactions
| subunits = each polypeptide chain in a protein
59
Types of quaternary structures
- homodimers: 2 identical polypeptide chains
- dozens of different polypeptide chains (ex. hemoglobin = α2β2 heterotetramer)
60
Characteristics of viral coat proteins
complex quaternary structures
- ex: rhinovirus coat has 60 copies of each of 4 subunits
| rhinovirus = has few unique subunits
61
Ribonuclease
A single polypeptide chain consisting of 124 amino acid residues cross linked by 4 disulfide bonds
62
What did Christian Anfinsen discover?
- When ribonuclease is placed in a solution with urea and β-mercaptoethanol, a denatured protein formed
- When the denatured protein was put in a solution w/o urea and β-mercaptoethanol (dialysis), it slowly regained enzymatic activity and properties of the reformed protein were identical to the native protein
## Footnote
ribonuclease = degrades RNA --> denatured protein was randomly coiled w no enzymatic activity
63
What did urea and β-mercaptoethanol do to ribonucleases?
- urea: disrupted all noncovalent bonds of ribonuclease
- β-mercaptoethanol: reduced disulfide bonds by bonding with cystine instead
| ribonuclease has 4 disulfide bonds
64
What did Christian Anfinsen's experiment demonstrate?
Demonstrated that the information needed to fold a polypeptide chain into a functional protein (w/ 3D structure) is inherent in it's primary structure/ amino acid sequence
## Footnote
denatured ribonuclease was able to regain it's structure and activity through dialysis --> all info needed to fold into a 3D structure is in it's primary structure
65
How can a denatured protein regain enzyme activity?
if the disulfide bonds were oxidized under suitable conditions
- urea must be removed fully
- a trace of β-mercaptoethanol must be present
## Footnote
these conditions allows for the slow formation + breakage of disulfide bonds until the lowest energy, most stable active form is regenerated
66
Which amino acids are commonly found as alpha helices?
alanine, glutamate, leucine
67
Which amino acids are commonly found in Beta strands?
valine, isoleucine
68
Which amino acids are commonly found in turns?
Glycine, asparagine, and proline
69
Why is the prediction of secondary structures from amino acid sequences difficult?
While some amino acids may favor certain secondary structures more, these preferences aren't usually strong
## Footnote
the exact same sequence VDLLKN can be found in 1 proteins alpha helix and anothers Beta sheet
70
71
How does protein folding and unfolding work?
It is an "all or none" process which results from cooperative transition
## Footnote
conditions that disrupt protein structure are likely to denature the whole protein
72
What is the state of a protein at the denaturation midpoint?
Half the molecules are fully folded and half are fully unfolded.
73
How does the process of protein folding occur?
Through cumulative selection
- partly correct folding intermediates are retained since they are more stable than unfolded regions
| ex. typing monkey analogy = random typing but correct letters are kept
74
Nucleation-condensation model
simulation of the folding of a protein is based on this model
- suggests that certain pathways are preferred (ones with more favorable structures)
75
How does the folding funnel depict the thermodynamics of protein folding?
- protein has maximum entrophy and minimal structure at top of funnel
- folded protein is at the bottom of the funnel
## Footnote
- bottom of the funnel = least entrophy and lowest energy
- percentage of protein in native conformation increases as it goes down funnel
76
77
What are the two approaches used to predict 3D structures from amino acid sequences?
- ab initio (from the beginning)
- knowledge based methods
78
The ab initio approach
Predictions that attempt to predict the protein foliding without prior knowledge about similar sequences in known protein structures
79
Knowledge based methods approach
- use knowledge on the 3D structures of many proteins
- unknown amino acid structure is examined for compatibility of known amino acid structures --> the known structures are used as models
80
What happens to proteins in neurological diseases?
| Alzheimers, Parkinson, Huntington disease
Proteins aggregate and form amyloid fibrils/plaques
- proteins that are normally soluble are converted into insoluble fibrils rich in β sheets
## Footnote
insoluble fibrils are prone to aggregate --> aggregates recruit more proteins and convert them into the incorrect form
81
# Importance of postranslational modifications in proteins
What occurs when collagen lacks vitamin C?
Prevention of hydroxylation of collagen --> abnormal collagen fibers which can't maintain normal tissue strength
| known as scurvy
## Footnote
addition of hydroxyl groups stabilize collagen
82
Distance of typical C-C covalent bonds
1.54 Anstroms
- 1 A = 0.1 nm or 10^-10 m
83
Hydrogen bond donor vs acceptor
- donor: includes the atom (which H is covalently bonded to) and H
- acceptor: lone pair of electrons that is on the atom less tightly linked to the H
