Amino Acids And Proteins Flashcards
(110 cards)
1
Q
What are the strongest bonds?
A
Covalent bonds
E.g. Peptide bonds, disulfide bonds
2
Q
What are covalent bonds?
A
When two atoms share electrons
3
Q
What are ionic bonds?
A
Interactions of ions with one a full positive and the other a full negative
E.g. Salt
4
Q
What is a hydrogen bond?
A
A dipole-dipole interaction between a partially positive hydrogen atom and partially negative oxygen (FONS and H)
5
Q
What are van dear walks interactions?
A
Dipole dipole interactions
These are the weakest electrostatic bonds
6
Q
What are hydrophobes?
A
Nonpolar, hydrophobic molecules
E.g. The inside of the plasma membrane
7
Q
Why do hydrophobes tend to cluster together?
A
Nonpolar molecules tend to break the hydrogen bonds of water increasing enthalpy. To counteract this they cluster together in order to achieve to lowest possible enthalpy.
Enthalphy = energy state
8
Q
What do the core of proteins usually contain? (Usually globular proteins)
A
They have a hydrophobic center
9
Q
What is the hydropathy index?
A
Measure of hydrophobicity of amino acids
10
Q
What is a glycophorin?
A
An erythrocyte membrane spanning protein
-used as an example for hydropathy plots
11
Q
What are the four components of an amino acid?
A
Amino acid
Carbonyl group
Side chain (-R group)
Hydrogen
-all bound to central carbon
12
Q
What determines the chemical properties of the protein? E.g. Whether is is nonpolar, charged, polar uncharged
A
The R group
13
Q
What are the abbreviations for Alanine, Arginine, Asparagine, Aspartic acid?
A
Ala, A
Arg, R
Asn, N
Asp, D
14
Q
What are the abbreviations for Cysteine, glutamine, glutamic acid, glycine?
A
Cys, C
Gln, Q
Glu, E
Gly, G
15
Q
What are the abbreviations for Histidine, Isoleuine, leucine, lysine?
A
His, H
Ile, I
Leu, L
Lys, K
16
Q
What are the abbreviations for Methionine, phenylalanine, proline and serine?
A
Met, M
Phe, F
Pro, P
Ser, S
17
Q
What are the abbreviations of Threonine, Tryptophan, Tyrosine, Valine?
A
Thr, T
Trp, W
Tyr, Y
Val, V
18
Q
Which are the essential amino acids?
A
Phe, Val, Trp
Thr, Ile, Met,
His, Arg, Leu, Lys
“PVT TIM HALL”
19
Q
Which are the branched chain amino acids?
A
Leucine, isoleucine and valine
“LIV”
20
Q
Which amino acids are aliphtic (non-aromatic)?
A
Pro Ala Val Ile Leu "My friend PAVIL is not charismatic (aromatic)"
21
Q
Which amino acids are only mildly hydrophobic?
A
Gly
Ala
Pro
“The reason why there’s a GAP inside proteins”
22
Q
What is special about glycine?
A
Only mildly hydrophobic but confers flexility in proteins
23
Q
What is different about Cys?
A
It has a polar side chain -SH but acts more hydrophobic than glycine or alanine
It is considered a hydrophobic amino acid
24
Q
Which amino acids are aromatic?
A
Tyrosine
-hydrophobic
Tryptophan
Phenylalanine
-Phen/Phan indicate an aromatic
25
How can proteins be differentiated from nucleic acids using UV light?
Proteins absorbs at 280 nm
Nucleic acids absorb at 260
26
List the order of absorbance for the aromatic compounds.
Most Trp, Tyr, Phe least
27
Which amino acids are un charge at physiological pH?
```
Cysteine
Asparagine
Threonine
Serine
Glutamine
```
"My CATS a G"
28
Which amino acids are basic ?
Lysine
Arginine
Histidine
29
Which amino acids are negatively charged? (These are acidic)
Aspartate
Glutamate
30
What are the kinds of secondary protein structures?
Alpha helix
Pleated sheet
Beta turn
31
What kind of reactions forms a peptide bond?
Condensation (dehydration)
32
What is a peptide bond?
A covalent, amide bond between the alpha-carbonyl group of one amino acid and the alpha-amino group of another
("NCC-NCC-NCC" each NCC is an amino acid)
33
What are the characteristics of a pepdtide bone?
Rigid (no rotation)
Planar. (Flat)
Has dipole (slightly positive on one side and slightly negative on the other side)
34
What part of the peptide bond holds a dipole?
Carbonyl oxygen holds a negative dipole
Amide nitrogen holds a positive dipole
35
What is a primary structure of a protein?
The linear sequence of amino acids in the polypeptide chain
36
In which order is a protein written in?
From the N-terminus to the C-terminus
"NCC-NCC-NCC"
37
What is a secondary structure?
Where regions of amino acids fol into a limited number of distinct structures
38
What kind of bonds form secondary structures?
Hydrogen bonds between carbonyl and amide groups in the peptide bond
-the R groups are usually not involved
39
What is an alpha helix?
A rigid, right handed helix forming a rod-like structure. (3.6 amino acids per turn)
40
What forms an alpha helix?
H bonding between peptide bonds (4 residues apart)
41
Which amino acid destabilizes alpha helixes?
Proline because it is bulky and has a charged R group
42
What amino acid is to involved in alpha helixes because it allows too much flexibility?
Glycine
43
What is a beta sheet?
When 2 or more peptide chains are arranged parallel or anti parallel to each other
Form a "pleated sheet"
44
What forms a beta sheet?
Hydrogen bonds between adjacent peptide chain
45
What is seen in the R group of beta sheets?
The R group alternate above and below the plane of the sheet
46
What is a beta turn or reverse turn?
A 180 degree turn in a peptide chain
47
What do beta turns help form?
Compact globular shapes
48
How is the 180 degree turn created in a beta turn?
With 4 amino acids usually including proline and glycine
1 hydrogen bond between peptide bonds 2 residues apart
49
What is a tertiary structure?
An overall 3D arrangement of the entire peptide chain
-a spatial organization of secondary structures
50
What does the tertiary structure determine in a protein?
The function of the protein
-structural alterations (by mutations) abolish or alter the function
51
In the tertiary what can happen to the primary structure?
Residues far apart in the primary structure may be brought close together and may act as a functional unit
52
What is quaternary structure?
The spatial arrangement of polypeptide chains (several)
53
What does quaternary structure determine?
The function of the protein
54
What are some examples of quaternary structure?
Hemoglobin: 2 alpha and 2 Beta subunits
Immunoglobulin G: 2 heavy and 2 light chains
Creatine Kinase: a dimer (kinase= add a phosphate?)
Lactate dehydrogenase: a tetramer (involved in the breakdown of sugar)
55
How are tertiary and Quaternary structures stabilized?
By noncovalent bond interactions involving the atoms of the peptide bon and the side chains (R groups)
Ionic, H-bonds, van dear Walls, hydrophobic
May be further stabilized by covalent bonds (disulfide bonds)
56
What amino acids can stabilize Tertiary/Quaternary structure of proteins by forming disulfide bonds?
Cysteine
57
What are domains in proteins?
Discrete areas in a protein that may have different functions
-stable arrangements of several elements of secondary and tertiary structure
58
How do domains differs in small and large proteins?
Small proteins- one domain, one or few functions
Large proteins- multiple domains, multiple functions
59
Copying and shuffling of domains during evolution has led to formation of what in proteins?
Protein families
These proteins share common domains
60
What are super secondary structures?
Relatively large patterns of 3D structures from repeated secondary structures
61
What are super secondary structures often associated with?
Often associated with specific activity such as ATP binding
62
What is the Actin Fold?
A cleft between domains for binding and hydrolysis of ATP
Also seen in many ATP-binding and utilizing proteins
63
What is a told that use to compare amino acid sequence?
BLAST!!!!!
-Basic Local Alignment Search Tool
64
What can blast be used for?
To compare homologous proteins or DNA
65
What similarity do you need to highly similar protein structures?
~25%
Even though they may be so different they can have similar functionality
66
What are orthologs?
Genes in different species that have the same general function
Evolved from a common ancestor
E.g. Human alpha-globin and mouse alpha-globin
67
What are paralogs?
Imperfect copies of genes within a species (members of gene families)
Generally different but likely related functions
68
What is column chromatography?
A separation of a crude protein sample in a buffer (mobile phase) through a stationary porous matrix
69
How does column chromatography separate crude samples?
Based on some property of the protein
E.g. Charge, size, binding properties, hydrophobicity
-"properties of the stationary phase and it's interaction with the proteins form the basis of separation"
70
How is purification of a protein accomplished?
By sequential column chromatographies with different stationary phases
71
What is size exclusion chromatography?
| Aka gel filtration
Separation on the basis of the size
72
How does size exclusion chromatography work?
Solid phase is a porous bead
Smaller molecules enter the bead and migrate slowly
Large molecules are less likely to enter the beads and migrate more quickly
The largest get out the quickest
73
What is ion-exchange chromatography?
Separation on the basis of charge
At a given pH
74
How does ion-exchange chromatography work?
Beads are resins carrying a charge
Proteins with opposite charge bind the resin and migrate slowly
Proteins with same charge don't bind and migrate more quickly
The greater the charge, the greater the effect on migration
75
What kind of exchangers are seen in ion exchange chromatography?
Cation exchanger: negative charge
Anion exchanger: positive charge
76
What is affinity chromatography?
Separation on the basis of binding properties
Proteins have different binding properties
77
How does affinity chromatography work?
Ligand conjugated to beads
-only proteins that bind the ligand are retained on the column
The protein may be elated from the column by competition with free ligand
78
What is gel electrophoresis?
Separation of molecules in an electric field through a porous gel (sieving medium)
79
What are some gels used in gel electrophoresis?
Polyacrylamide for protein (amides are used in peptide bonds)
Agarose for DNA/RNA
80
How does Gel Electrophoresis work?
Migration toward electrode of opposite charge
81
What are the factores that affect gel electrophoresis ?
Size, conformation and charge affect the rate of migration though the gel
82
What is SDS-PAGE?
Separation on the basis of size
83
What does SDS-PAGE require??
Proteins to be unfolded without disulfide bonds
84
What is SDS?
Sodium dodecyl sulfate (SDS) is a strong ionic detergent that denatures the proteins and coats protein with a negative charge
85
What breaks disulfide bonds in SDS-PAGE
Mercaptoethnol- a reducing agent break disulfide bonds
86
What travels faster in SDS-PAGE?
Smaller proteins migrate more quickly
-This is opposite of exclusion chromatography
87
How is the protein detected in SDS-PAGE? (Stain)
Coomassie Blue
Silver Staining
88
How can SDS PAGE be used to estimate the size of a protein?
Molecular weight of unknown protein is compared to the standard proteins of known size
89
How many ionizable groups do all Free amino have as a minimum?
2
90
What amino acids have at least 3 ionizable groups?
Acidic and Basic Amino acids have 3
91
What is the Isoelectric charge?
The pH at which an amino acid has no charge
92
How is the isoelectric point (pi) of a protein determined?
By the total net charge including all charged R groups and the alpha-carboxyl and alpha-amino groups
93
What is isoelectric focusing of proteins?
Separation of proteins on the basis of their isoelectric proteins
94
What are ampholytes
A mixture of polyanionic and polycationic molecules with varying pI (isoelectric point)
95
How do isoelectric focusing work?
Ampholytes in a gel establish a pH gradient in an electric field
Proteins will migrate until they reach their pI
96
What charge does a protein carry at it's pI (isoelectric point)?
At pI, no net charge so they stop migrating
97
What is 2D gel electrophoresis?
A better separation technique for complex mixtures of proteins
Proteins are separated in 2 perpendicular direction using a different basis of separation i each
E.G. Isoelectric focusing and SDS-PAGE
98
What is proteomics?
The large-scale study of proteins complement of cells
99
How can the identity of individual proteins be determined in a 2D gel electrophoresis
Through mass spectrometry
100
What is a ligand?
The small molecule being bound by the protein
101
What is a receptor protein?
The protein that binds the ligand
E.g. cAMP being bound by a cAMP-binding protein
102
What are the receptor-ligand interaction mediated by?
Many weak noncovalent bonds
-covalent bonds are extremely rare
103
How do you determine if ligand receptor binding is of high affinity
The number of bonds between the two molecules
The higher number of bonds, the higher the affinity and a higher likelihood of being bound most of the time
104
Low affinity binding equilibrium shift will be toward what state?
The unbound state
105
High affinity binding will have an equilibrium shift toward which state?
The bound state (most of the time)
106
What is the association rate equation?
Association rate = Kon[A][B]
=association rate constant * concentration of A * concentration of B
107
What is the equation for equilibrium constant?
K= Kon/Koff =[AB]/[A][B]
108
What can you use to determine the affinity beside number of bonds?
Dissociation constant (Kd) (units are M)
Association constant (Ka) (units are M-1)
109
How can you tell if the binding is stronger using the Ka or Kb?
The higher the association constant Ka the stronger the bond
The lower the dissociation constant Kd the stronger the bond
110
Remember: Kd is equivalent to the concentration of ligand (A) at which receptor (B) is 50% bound
*placeholder
When Kd is smaller than concentration then it will favor the complex
When Kd is larger than the concentration then the free molecules will be favored
