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Biochemistry > Polypeptides and Proteins > Flashcards

Polypeptides and Proteins Flashcards

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
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2
Q

Oligopeptides

A
  • contain only a few amino acid residues
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3
Q

Polypeptides

A
  • contain greater than 15-20 amino acid residues
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4
Q

Proteins

A
  • consist of polypeptides of greater than 50 residues
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5
Q

Monomeric proteins

A
  • one polypeptide
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6
Q

Multimeric proteins

A
  • more than one polypeptide
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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
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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

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9
Q

During ribosomal protein synthesis which side are amino acids added to on a growing peptide?

A
  • the C-terminal end
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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
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11
Q

Peptide structure and form favored

A
  • nearly planar

- trans form favored

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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)
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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
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14
Q

Peptide Structure Components

A
  • have an amino(N-) terminus and a carboxy (C-) terminus
  • a main chain including both terminus
  • side chains
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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
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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
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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
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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

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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
  1. As the pH increases the overall charge on the peptide will become more negative
  2. 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
  1. 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
  1. 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
Q

Cyanogen bromide (CNBr)

A
  • cleaves proteins specifically at methionyl residues

- cleaves amide bonds on the C-terminal side of the methionine residues

26
Q

Groups that may block N or C termini proteins

A
  1. N-formyl group (COH)
  2. N-acetyl group (COCH3)
  3. C-terminal amide (NH2)
27
Q

N-terminal and C-terminal naming

A
  • write the N terminal on the LEFT

- write the C terminal on the RIGHT

28
Q

Some proteins contain two or more polypeptide chains held together by

A
  • noncovalent interactions

- or covalent disulfide bonds

29
Q

Disulfides that form in polypeptides are called

A
  • disulfide bridges

- important bonds between cysteine residues

30
Q

Why is disulfides needed in thiols?

A
  • 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
Q

Cystinuria

A
  • a genetic disorder that produces unusually high levels of cystine that are excreted in urine
  • cystine forms kidney stones
  • treated with penicillamine
32
Q

Glutathionine

A
  • 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
Q

Oxytocin Peptide

A
  • hormone, stimulates uterine contractions during child birth
34
Q

Vasopressin Peptide

A
  • Anti diuretic hormone (ADH)

- stimulates water retention and elevates blood pressure

35
Q

Enkaphalins peptides

A
  • or endorphins

- opioid peptides, relieve pain, produce pleasant sensations

36
Q

Insulin Peptide

A
  • dimeric hormone peptide, lowers blood glucose levels
37
Q

Defining characteristics of proteins

A
  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
Q

Proteome

A
  • the complete profile of proteins expressed in a given biological system (cell, tissue, organism) at a given time and/or under specific conditions
39
Q

Proteomics

A
  • 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
Q

Applications of proteomics

A
  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
Q

Hypothesis of evolutionary relations of cytochrome C

A
  • organisms with few amino acid differences are closely related
  • peptide similarities can be used to construct phylogenetic trees
42
Q

BLAST

A
  • basic local alignment search tool
  • used to compare human myoglobin with human hemoglobin a chain
  • searches for maximum sequence identitity
43
Q

Conservative vs Nonconservative mututations

A
  • conservative mutations conserve the chemical property (charge) and size of the amino acid
  • non conservative mutations involve larger differences in polarity and size
44
Q

Mutations that involve a change in the erythrocyte shape

A
  • S mutation
  • consequence is sickling
  • Glu to Val
45
Q

Mutation that involves a change in the O2 affinity

A
  1. MI Iwate (decreases O2)
    - His to Tyr
  2. Suresnes (increases O2)
    - Arg to His
  3. Hiroshima (increases O2)
    - His to Asp
46
Q

Sickle cell disease

A
  • abnormal erythrocytes block circulation in capillaries and lyse due to their fragility causing anemia
  • S mutation involving the change in erythrocyte

Biochemistry (15 decks)

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