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MCAT > Biology: Biochemistry TRP Chapter 4: Amino Acids > Flashcards

Biology: Biochemistry TRP Chapter 4: Amino Acids Flashcards

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MCAT flashcards
1
Q

Draw and name the 3, 1 and full letter word for each category of amino acids

Basic
Acidic
Nonpolar
Polar

A

Acidic: Aspartic acid (Asp, D) - Glutamic acid (Glu, E)

Basic: Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

Nonpolar:

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2
Q

At the physiological Ph, the acidic amino acids are ___________ at the physiological PH

A

depronated (anionic)

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3
Q

What causes the acidic amino acids to be acidic, and what functional group is present for the R-group?

A

The 2 carboxylic acids of glutamate and aspartic acid make the amino acid acidic, and the functional group for the R is carboxylic acid

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4
Q

The depronated form of glutamate and aspartic acid is called _____ @ physiological PH

A

aspartate and glutamate

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5
Q

How is histidine different from the other two amino acids in the basic group?

A

Because lys and Arg contain basic R groups and therefore only can be catatonic (protonated) at the physiological PH. But Histidine acts as an acid and a base because the side chain has a pka close to 7.4 (physiological ph), therefore it can either be protonated or deprotonated

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6
Q

Aliphatic meaning

A

alkyl

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7
Q

Hydrophobic side chains can either be ________ or _____ (functional groups)

A

aliphatic or aromatic

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8
Q

The stronger the hydrophobic group, the ________ the hydrophobic force repelling it from H20

A

stronger

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9
Q

Define: Polar amino acids

A

R groups polar enough to form H bonds w/ H20 but not act as acid or base

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10
Q

What can be attached to the COOH groups of these 3 polar amino acids (serine, theonine, and tyrosine) that regulates protein activity? Describe the mechanism of this process

A

Hydrophilic phosphate groups are attached to serine, threonine, and tyrosine by kinase - resulting in a change in structure due to the hydrophilic phosphate group. This modification is an important means of regulating protein activity

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11
Q

Describe the 2 Sulfur containing amino acids: What are they called, are they polar/nonpolar, are what functional groups do they contain?

A

Cysteine: contains thiol (sulfhydryl) polar
Methionine: contains thioester , nonpolar

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12
Q

What is a thiol? what is a thioeseter?

A 
thiol = alcohol with an S instead of O
thioester = ether with an S instead of O
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13
Q

In what way is proline unique?

A

Bound to nonpolar side chain - creating secondary a-amino group ring structure - important for protein folding

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14
Q

What makes an amino acid amphoteric? Describe what this means

A

Because it contains carboxylic and amino group - means it can act as acid or base

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15
Q

The pka of carboxylic acid is ___, and of ammonium it is _______

A

2, 9

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16
Q

List the 2 rules about Henderson-Hasselbalch equation that are necessary for MCAT

A

PH solution < Pka acidic group = acidic group protonated

PH solution > pka acidic group = acidic group deprotonated

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17
Q

Define: Zwitterion

A

neutral amino acids PH

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18
Q

Isoelectric point

A

PH at which molecule unchanged (zwitterionic)

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19
Q

Define: Peptide bonds and state function

A

2 covalent bonds amino acids - link amino acids together in polypeptide chains and disulfide bridges

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20
Q

Polypeptide

A

Linking amino acids together with peptide bonds

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21
Q

List the pattern structure of the backbone of amino acid

A

N-C-C-N-C-C

22
Q

Define: Residue

A

part of polypeptide chain ; individual amino acid is termed this when part chain

23
Q

Amino terminus (N-terminus)

A

1st end made during polypeptide synthesis

24
Q

Carboxy terminus (C-Terminus)

A

Last end during polypeptide synthesis

25
Q

Define: Proteolysis/proteolytic cleavage

A

Hydrolysis of a protein by another protein

26
Q

Define: Proteolytic enzyme/protease

A

Protein that does cutting/proteolysis

27
Q

Cysteine contains what functional group in side chain?

A

thiol

28
Q

Disulfide bond: define

A

Sulfur-sulfur bond formed when 2 thiols react

29
Q

Cysteine vs cystine

A

cy

30
Q

List some things that can cause denaturation

A

urea, extreme PH, extreme temperatures, changes in salt concentration (tonicity)

31
Q

Define: Primary proteins structure

A

Simplest protein structure - same as the sequence of the peptide bond

32
Q

Define: Secondary protein structure

A

Hydrogen bonds between backbone groups - initial folding of polypeptide chain in shapes stabilized by H-bonds

33
Q

What amino acid never has an a-helix and why?

A

Proline - due to structural issues

34
Q

Does urea affect primary or secondary structure?

A

Only the primary - it breaks H-bonds and unfolds the a and B helices

35
Q

The mechanism of reducing agents involves:

A

the breaking of disulfide bonds

36
Q

Define: Quarternary structure

A

Interactions between polypeptide subunits

37
Q

Define: subunit

A

single polypeptide chain part of a larger complex containing many subunits (multisubunit complex)

38
Q

The arrangement of subunits in a multi-subunit complex is also called:

A

Quaternary structure

39
Q

The interactions between subunits are instrumental in what type of function? Give ex.

A

Protein function. Cooperative binding of oxygen by each of the 4 subunits of hemoglobin.

40
Q

Kinetic vs. Thermodynamic

A

Thermodynamics is not about things moving and changing but instead about how stable they are in one state versus another, while kinetics is about how quickly or slowly species react

41
Q

Biological catalyts

A

enzymes

42
Q

Describe how enzymes change rate of rxn and what is NOT affect during this change

A

Alter rate of rxn by lowering the AE but they do not affect the deltaG - kinetic not thermodynamic function

According to induced fit model, binding of substrate induces a conformational change in the enzyme by stabilizing the transition state

43
Q

Thermodynamically unfavorable rxns take place by:

A

rxn coupling

44
Q

A common rxn that the cell uses to drive ATP in the cell when rxn coupling is needed is:

A

ATP hydrolysis

45
Q

What are the two ways ATP hydrolysis drives unfavorable rxns?

A
  1. Conformational change in protein

2. Transfer of a phosphate group from ATP to a substrate

46
Q

active site is the site for

A

catalysis

47
Q

cofactors

A

metal ions/small molecules required for activity in enzymes (vitamins, etc)

48
Q

List methods of enzyme/protein regulation. Give examples if necessary

A
  1. Covalent modification: Attaching groups to regulate activity, lifespan, cellular location, etc
    ex. Phosphorylating (by protein kinase) serine, threonine, or tyrosine residues - phosphorylation of these sites on an enzyme can activate or inactivate the enzyme
  2. Proteolytic Cleavage: Many enzymes and proteins activated by cleavage by a protease
  3. Association: Some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit
    ex. some proteins have continuous rapid catalysis if regulatory subunit is removed, others need association w/ another peptide to function
  4. Allosteric Regulation: regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site (allosteric site)
49
Q

Negative feedback/feedback inhibition

A

An end product shutting off enzyme early in the pathway / product is a negative inhibitor

50
Q

Feedforward stimulation

A

Stimulation of enzyme by substrate or by molecule used in synthesis / substrate positive inhibitor

51
Q

Reaction rate (V)

A

Amount of product formed per unit time (mol/s)

MCAT (6 decks)

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