Polypeptides and Proteins Flashcards
(46 cards)
1
Q
Linear polymers of amino acids are covalently joined together by?
A
- formation of an amide, or peptide bonds between their a-carboxyl and a-amino groups
- the products formed by this linkage are called peptides
2
Q
Oligopeptides
A
- contain only a few amino acid residues
3
Q
Polypeptides
A
- contain greater than 15-20 amino acid residues
4
Q
Proteins
A
- consist of polypeptides of greater than 50 residues
5
Q
Monomeric proteins
A
- one polypeptide
6
Q
Multimeric proteins
A
- more than one polypeptide
7
Q
Amide bond/Peptide bond Formation
A
- are formed between the a-carboxyl group of one amino acid and the a-amino group of the next amino acids via the elimination of a water molecule
8
Q
What does the condensation of two amino acids form
A
- a peptide bond and releases water
- this reaction is not thermodynamically favorable and is coupled to ATP hydrolysis during protein biosynthesis
9
Q
During ribosomal protein synthesis which side are amino acids added to on a growing peptide?
A
- the C-terminal end
10
Q
Amino acid residue
A
- what remains after an amino acid is added to the chain and a molecule of water is eliminated to create a new peptide bond
11
Q
Peptide structure and form favored
A
- nearly planar
- trans form favored
12
Q
The free energy change for peptide bond formation at room temperature in aqueous solution
A
- about 10 kJ/mol
- favored reaction under these conditions is the hydrolysis of the peptide bond with equilibrium lying well to the right (adding H2O)
13
Q
What does it mean that polypeptides are metastable?
A
- their decay is very slow unless in the presence of highly acidic conditions(6M HCl at high temp) or a catalyst(proteases).
- Therefore, they hydrolyze rapidly only under extreme conditions or when catalysts are present
14
Q
Peptide Structure Components
A
- have an amino(N-) terminus and a carboxy (C-) terminus
- a main chain including both terminus
- side chains
15
Q
Peptide bond configuration
A
- delocalization of electrons creates a planar and stable peptide bond (rigid and flat)
- its a “covalent” bond
- resonated to become a double bond
- is in the trans configuration
- no rotation in the double bond form
16
Q
C-N bond properties
A
- C-N bonds between two amino acids are shorter tha other C-N bonds
- resonance hybrids so have partial double bond characteristics
17
Q
Can the backbone of a polypeptide rotate freely
A
- because of the rigidity 1/3 of the bonds in a polypeptide backbone can not rotate freely
- limits the number of conformational possibilities
18
Q
Where is rotation permitted in a peptide bond?
A
- between the adjacent atoms
- C-C and C-N bonds involving the a-carbon
19
Q
Why is the trans form favored in peptide bonds
A
- because the R groups on the adjacent alpha carbons can sterically interfere in the cis configuration
20
Q
When is the cis form an exception
A
- the bond in the sequence X-Pro, where X is any other amino acid
- the cis configuration is sometimes allowed, but trans is still favored
21
Q
What happens to the overall charge on a peptide when the pH increases or decreases?
A
- As the pH increases the overall charge on the peptide will become more negative
- As the pH decreases the overall charge on the peptide will become more positive
22
Q
Histidine (His) pH changes correlated with charge
when pH<6 and pH>6
A
- pH < 6 has a +1 charge
2. pH > 6 has no charge
23
Q
pKa of a side chain is affected by its environment how?
A
- in proximity of a negative charge the pKa is raised
2. in the proximity of a positive charge the pKa is lowered
24
Q
Proteases
A
- enzymes that cleave specific peptide bonds
25
Cyanogen bromide (CNBr)
- cleaves proteins specifically at methionyl residues
| - cleaves amide bonds on the C-terminal side of the methionine residues
26
Groups that may block N or C termini proteins
1. N-formyl group (COH)
2. N-acetyl group (COCH3)
3. C-terminal amide (NH2)
27
N-terminal and C-terminal naming
- write the N terminal on the LEFT
| - write the C terminal on the RIGHT
28
Some proteins contain two or more polypeptide chains held together by
- noncovalent interactions
| - or covalent disulfide bonds
29
Disulfides that form in polypeptides are called
- disulfide bridges
| - important bonds between cysteine residues
30
Why is disulfides needed in thiols?
- thiols are extremely reactive (easily give up H+ and e-)
- disulfide bridges within polypeptides stabilize the protein structure
- Exogoneus thiols such as DTT and BME must be added to maintain endogenous diols
31
Cystinuria
- a genetic disorder that produces unusually high levels of cystine that are excreted in urine
- cystine forms kidney stones
- treated with penicillamine
32
Glutathionine
- a tripeptide made of cysteine, glutamate and glycine found abundantly in animal bodies
- GSH is a powerful antioxidant and detoxifier, involved in redox rxns
- Glutathione peroxidase
33
Oxytocin Peptide
- hormone, stimulates uterine contractions during child birth
34
Vasopressin Peptide
- Anti diuretic hormone (ADH)
| - stimulates water retention and elevates blood pressure
35
Enkaphalins peptides
- or endorphins
| - opioid peptides, relieve pain, produce pleasant sensations
36
Insulin Peptide
- dimeric hormone peptide, lowers blood glucose levels
37
Defining characteristics of proteins
1. Function(biological role)
- enzyme, structural
2. amino acid composition
- molecular weight, net charge, isoelectric point (pI)
3. ***amino acid sequence (primary structure)
4. three dimensional shape- secondary and tertiary structures
5. number of subunits
6. non protein cofactors- metal ions, prosthetic group
38
Proteome
- the complete profile of proteins expressed in a given biological system (cell, tissue, organism) at a given time and/or under specific conditions
39
Proteomics
- the study of the entire protein systems (proteomes) including characterization of the component proteins, how they interact with each other, what kinds of metabolic networks or signaling networks they form
40
Applications of proteomics
1. Understanding the basis of protein-mediated diseases
- which proteins prohibit and inhibit disease
2. Drug Discovery
- proteins that cause disease can sometimes be inactivated by ligand binding. New "drugs" are designed to bind to such proteins
3. Understanding evolution
- quantification of evolutionary relationships
4. Understanding aspects of cell biology
- protein interactions, interaction domains, signaling cascades
41
Hypothesis of evolutionary relations of cytochrome C
- organisms with few amino acid differences are closely related
- peptide similarities can be used to construct phylogenetic trees
42
BLAST
- basic local alignment search tool
- used to compare human myoglobin with human hemoglobin a chain
- searches for maximum sequence identitity
43
Conservative vs Nonconservative mututations
- conservative mutations conserve the chemical property (charge) and size of the amino acid
- non conservative mutations involve larger differences in polarity and size
44
Mutations that involve a change in the erythrocyte shape
- S mutation
- consequence is sickling
- Glu to Val
45
Mutation that involves a change in the O2 affinity
1. MI Iwate (decreases O2)
- His to Tyr
2. Suresnes (increases O2)
- Arg to His
3. Hiroshima (increases O2)
- His to Asp
46
Sickle cell disease
- abnormal erythrocytes block circulation in capillaries and lyse due to their fragility causing anemia
- S mutation involving the change in erythrocyte
