Chapter 1: Amino Acids, Peptides, and Proteins Flashcards Preview

MCAT Biochemistry > Chapter 1: Amino Acids, Peptides, and Proteins > Flashcards

Flashcards in Chapter 1: Amino Acids, Peptides, and Proteins Deck (81):
1

Asparagine.

What is different about its side group when pH changes?

structure?

single letter?

three letter?

polar amino acid.

Chiral L-amino acid.

Because asparagine has an amide side group, its amide nitrogren does not gain or lose protons when pH changes. (Does not become charged).

 

single letter code: N

asparagi N e

three letter: asn

 

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2

What is the isoelectric point of:

Acidic amino acid?

Neutral amino acid?

Basic amino acid?

 

Acidic amino acid pI: below 6

Neutral amino acid pI: 6

Basic amino acid pI: above 6

3

Histidine 

structure?

exception?

single letter?

three letter?

Negative amino acids. Chiral L-amino acids.

Basic Amino Acids.

Has 2 nitrogens in its amino group.

Has an imidazole ring side chain which is ionizable.

  • It has a nitrogen that can be protonated

 

Single letter code: H

three letter: his

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4

Can bases cleave peptide bonds?

yes bases can cleave peptide bonds, causing proteins to become inactive

5

Name the Aromatic side chain amino acids

Titty Penis Titty

Remember: Put a penis between 2 titties and you get a nice Aroma (aromatic)

__________________________________________

Tryptophan, Phenylalanine, Tyrosine 

6

Tyrosine 

structure?

single letter?

three letter?

aromatic amino acid.

also polar

Chiral L-amino acid.

Same as phenylalanine, but with an -OH attached.

 

single letter: Y

t Y rosine

three letter: tyr

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7

what amino acids are hydrophobic? hydrophilic?

which are neither?

 

Where are they found in a protein: exterior or interior?

 

  • Hydrophobic amino acids: have long alkyl side chains 
    • Alanine, Valine, Leucine, Isoleucine, Phenylalanine
    • Found in the interior of proteins, away from water on the protein surface
  • Hydrophilic amino acids: have charged side chains or amides (CONH2) in side chain
    • Charged: Aspartate, Glutamate, Lysine, Arginine, Histidine
    • Amide: Asparagine and Glutamine
    • Found on the outer part of proteins, near the water

 

8

α-amino acids

amino acids that have a carbonyl group and an amino group both attached to the α-carbon

 

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9

Phenylalanine

structure?

single letter?

three letter?

aromatic amino acid.

also nonpolar

Chiral L-amino acid.

 

single letter: F

F enylalanine

three letter: phe

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10

What is the only amino acid with an Achiral carbon?

glycine 

11

What amino acids are the only ones to have chiral carbons in there side chains?

Isoluecine (nonpolar, nonaromatic) and

Threonine (polar)

12

Proline

structure?

single letter?

three letter?

nonpolar, non aromatic amino acid.

Chiral L-amino acid.

 

 

single letter: P

three letter: pro

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13

Can nonpolar hydrophobic groups form Hydrogen bonds and/or Disulfide bonds?

nonpolar hydrophobic groups cannot form either bond because they are found within proteins

14

At human blood, is the carboxylic acid group and the amino group protonated or deprotonated?

At 7.4 pH:

Carboxylic acid group is deprotonated. (7.4 > 2)

Amino group is protonated (7.4 < 9-10)

__________________________________________

The amino acid is therefore a neutral zwitterion at 7.4 pH

15

All chiral eukaryotic amino acids are:

L-amino acids or D-amino acids?

What is the exception?

All chiral eukaryotic amino acids are L-amino acids.

__________________________________________

Glycine is a D-amino acid since it is achiral

16

What is the configuration of all amino acids (R or S?):

What is the exception?

All amino acids have an S-configuration.

__________________________________________

Cysteine has an R-configuration.

Remember: The Sistine (Cysteine) chapel in Rome (R)

17

What is the pKa of a carboxylic acid group?

What is the pKa of an amino group?

What happens when the pH is greater than pKa or lower than pKa?

pKa of carboxylic acid = 2

If pH is lower than 2: Carb acid gains proton.

If pH is higher than 2: Carb acid loses proton.

__________________________________________

pKa of amino group = 9-10

If pH is lower than 9-10: Amino group gains proton.

If pH is higher than 9-10: Amino group loses proton.

18

How do amide groups in side chains affect amino acids during pH change?

What 2 amino acids have amide side chains?

amide groups on amino acids do not gain or lose protons as pH changes.

The amide group does not become charged.

__________________________________________

Asparagine and Glutamine are polar amino acids with amide groups.

 

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19

Tryptophan 

structure?

single letter?

three letter?

largest aromatic amino acid.

also nonpolar

Has a double ring. 

Chiral L-amino acid.

 

single letter: W

tWyptophan

three letter: trp

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20

α-carbon

the carbon attached to the carbonyl carbon 

 

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21

Isoleucine.

What exception is it?

structure?

single letter?

three letter?

nonpolar, nonaromatic amino acid.

Chiral L-amino acid.

Exception: has a Chiral Carbon in its side chain.

 

single letter: i 

three letter: ile

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22

Leucine

structure?

single letter?

?three letter

nonpolar, nonaromatic amino acid.

Chiral L-amino acid.

 

 

Single letter: L

three letter: leu

 

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23

Protein Secondary Structure

What stabilizes secondary structure?

what else affects it?

What are the 2 common secondary structures?

the local structure of amino acids linked by hydrogen bonds.

Stabilized by hydrogen bonding.

The double bond character of the amides peptide bonds causes them to be rigid; which affects the secondary structure

Does not affect the connections between amino acids (primary structure)

α-helix = rod/coil shaped

β-pleated sheets = rippled

 

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24

Name the Polar side chain Amino Acids

 

Slide Through All Girl Coochies

__________________________________________

Serine, Threonine, Asparagine, Glutamine, Cysteine

__________________________________________

Remember: you "Slide" on polar ice caps

They are Hydrophillic because they are polar

25

Define peptide bond

Draw it too

Do they have Double bond character?

an amide bond that connects carboxyl groups to amino groups of amino acids.

They have double bond character

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26

What is the charge of a NEUTRAL amino acid in:

In very Acidic conditions?

In very Basic conditions?

SOLVE BY DRAWING THE AMINO ACID AND ASSIGNING CHARGES

 

(Neutral Amino acid charge)

Acidic conditions (protonated): +1

Basic conditions (deprotonated): -1

27

Define Denaturation.

Is the peptide chain broken?

What causes Denaturation?

When a protein becomes inactive because it loses its secondary structure and tertiary structure 

Becomes unfolded.

Does not break the peptide chain.

__________________________________________

High heats, pH changes, Urea, and other solvents

they can disrupt hydrogen bonds, electrostatic bonds, disulfide bonds, hydrophobic forces, etc.

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28

What happens to a functional group when:

__________________________________________

pH is lower than the pKa 

__________________________________________

pH is higher than the pKa

When pH is lower than the pKa, it is likely in acidic conditions. The functional group gains a proton.

__________________________________________

When pH is higher than the pKa, it is likely in basic conditions. The functional group loses a proton.

29

Name the nonpolar, nonaromatic amino acids?

Are they Hydrophobic or Hydrophillic?

Where are they found in/on proteins?

Good Ass Vagina Licking Is My Passion:

________________________________________

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline 

________________________________________

They are hydrophobic since they are nonpolar

(hate water/polar ice caps)

________________________________________

Found inside proteins because they are hydrophobic

30

Cysteine:

What is its exception?

structure?

single letter?

three letter?

polar amino acid.

Chiral L-amino acid.

Only amino acid with (R) configuration.

Remember: Cysteine Chapel is in Rome (R).

Contains a Thiol (SH)

 

single letter: C

three letter: cys

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31

How does Proline affect Protein Secondary Structure?

Where is proline found in protein secondary structures?

Proline has a rigid cylic structure which interrupts the secondary structure in a peptide chain.

__________________________________________

Because of this, proline is found only at the beginning of α-helix and in the folds of Β-pleated sheets

32

what 2 amino acids have chiral carbons in their side chains?

Isoleucine (nonpolar, nonaromatic)

and Threocine (polar)

33

Aspartate 

structure?

Single letter code:

three letter:

negative amino acid.

Chiral L-amino acid.

Deprotonated version of aspartic acid.

 

Single letter: D 

aspar D ate

three letter: asp

 

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34

Do peptide bonds allow the protein to rotate? Why or why not?

Peptide bonds have double bond (π) character, so they prevent the protein from rotateing freely at that point.

35

Protein Tertiary Structure

What factors contribute to tertiary structure? (6)

 

the 3D shape of a single polypeptide chain, formed by curls and folds of the peptide chains

__________________________________________

Stabilized by:

  1. Disulfide bonds between two cystines
  2. Hydrogen bonds
  3. Electrostatic (ionic) interactions between acidic and basic side chains (salt-bridges)
  4. Van der Waals forces
  5. Hydrophobic side chains are repelled away from water toward the center of the protein
    • This increases entropy, which is favorable
  6. Proline causes a kink in the structure

 

 

36

When protonated, what charge does a carboxylic acid group have on an amino acid?

What about when its deprotonated?

Protonated Carb acid group: 0 (neutral) charge

(-COOH)

__________________________________________Deprotonated Carb-acid group: (-) charge

(-COO-)

 

37

What is the charge of a BASIC amino acid in:

In very Acidic conditions?

In very Basic conditions?

SOLVE BY DRAWING THE AMINO ACID AND ASSIGNING CHARGES

(Basic Amino acid charge)

Acidic conditions (protonated): +2

Basic conditions (deprotonated): -1

38

How many steps is the titration of neutral amino acids?

How many steps is the titration of charged amino acids?

neutral amino acids: 2 steps (because 2 protons are lost)

charged amino acids: 3 steps (because 3 protons are lost)

39

Lysine 

 

structure?

Single letter?

positive amino acid. Chiral L-amino acid.

Has 1 Nitrogen in its amino side chain.

Basic amino acid.

 

single letter: K

lysine (licK)

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40

what is the pH of human blood?

7.4

41

When protonated, what charge does an amino group have on an amino acid?

What about when its deprotonated?

Protonated Amino group: (+) charge

(-NH3+)

__________________________________________

Deprotonated Amino group: 0 (neutral) charge 

(-NH2)

42

Peptide Bond Formation 

What happens? (What is nucleophile/electrophile?)

What type of reaction is it?

What byproduct is released?

What is formed?

Peptide bond formation is a Dehydration Reaction

Water is removed and an amide is formed 

_________________________________________

Amino group: Nucleophile

Carboxyl group: Electrophile

________________________________________

Amino group does a nucleophillic attack on carboxyl group, then they bond and release water

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43

Protein primary structure

What stabilizes primary structure?

What is the front terminus and the back terminus?

the linear sequence of amino acids in a polypeptide chain.

Peptide bonds stabilish primary structure.

From N-Terminus (front) to C-Terminus (back)

44

All amino acids are chiral except what amino acid?

Are they optically active or inactive

All amino acids are chiral, except Glyceine.

__________________________________________

Chiral = optically active

__________________________________________

Glyceine is achiral and optically inactive

45

What 4 groups are found on an amino acid

carboxylic acid group (-COOH) + amino group (-NH3+) + R-group (side chain) + H group

46

Serine

structure?

single letter?

three letter?

polar amino acid.

Chiral L-amino acid.

Have -OH on side group.

 

single letter: S

three letter: ser

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47

What is the only amino acid with (R) configuration?

Cysteine

Remember: Cysteine chapel is in Rome (R)

48

Name the Positive amino acids.

Are the Basic or Acidic and why?

Lick All Holes

Lysine, Arginine, Histidine 

__________________________________________

All have amino side chains

All have positive charged nitrogen atoms 

_________________________________________

They are basic because they have amino side chains

49

amino acids

Are amino acids amphoteric? What does amphoteric mean?

molecules that contain two functional groups:

Carboxyllic acid group (-COOH)

and

Amino group (-NH3+)

__________________________________________

Amino acids are amphoteric.

They can accept or donate protons

50

Arginine

structure?

single letter?

three letter?

 

Negative amino acid. Chiral L-amino acid.

Has 3 nitrogens on its side chain.

(+) charge is spread (delocalized) over all 3 N's.

Basic Amino Acid

 

single letter: R

R ginine

three letter: arg

 

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51

Glycine 

structure?

single letter?

three letter?

nonpolar, nonaromatic amino acid.

Only achiral and D-amino acid.

Has an H side chain.

 

single letter: G

three letter: gly

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52

Hydrophobic vs Hydrophillic amino acid residues:

Where are each positioned? (inside/outside proteins?)

Why are they there?

Hydrophobic residues are found inside proteins because they are far away from water.

__________________________________________

Hydrophillic residues are found outside proteins because they love water.

Also, because they increase entropy (disorder) and make protein folding spontaneous (-ΔG)

53

How do you calculate the Isoelectric Point of a

Neutral Amino acid?

The average of the Carboxylic acid group and Amino group pKa's

 

pI = (pKa carb acid + pKa amino) / 2

 

pKa carboxylic acid: 2.5

pKa amino group: 10

54

Alanine

structure?

Single letter code? 

3 letter code?

nonpolar, nonaromatic amino acid.

chiral L-amino acid

-CH3 (methyl) side chain

 

Single letter: A

three letter: ala

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55

Define Conjugated Proteins?

Define Prosthetic groups?

Proteins that have other molecules attached to them which gives them a certain fuction. 

Prosthetic groups are the molecules attached to the proteins and give them function.

 

56

When does an amino acid become a neutral zwitterion?

When the pH reaches the amino acid's isoelectric point (pI).

__________________________________________

The isoelectric point is the pH when the molecule is neutrally charged

57

Define amphoteric compounds.

Are amino acids amphoteric?

Amphoteric compounds = compounds that can gain or lose protons.

__________________________________________

Amino acids are amphoteric.

58

Name the Negative side chain Amino Acids

Are they basic or acidic and why?

Ass Grab:

Aspartate and Glutamate

________________________________________

They have carboxylic acid side groups, so they are acidic

________________________________________ 

Aspartate is the same as Asparganine, but it has a carboxylic acid group instead of amide group.

Glutamate is the same as Glutamine, but it has a carboxylic acid group instead of amide group.

 

 

 

59

Methionine

structure?

single letter?

three letter?

nonpolar, non aromatic amino acid.

Chiral L-amino acid.

 

single letter: M

three letter: met

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60

Define Zwitterions

Molecules that have positive and negative charged groups on it.

 

 

zwitter means hybrid in german

hybrid ions

61

Does the primary structure of proteins contain all of the information needed for folding at the higher protein structural levels?

yes,

the primary structure encodes for all of the folding information for the other structures

62

Protein Quaternary Structures.

Do all proteins have quaternary structures?

What are the 4 roles of quaternary structures?

the arrangment of multiple folded polypeptide chains into one protein. 

Only proteins with multiple polypeptide chins have quaternary structures.

__________________________________________

Roles: 

1) Increase stability of the protein.

2) Reduce the amount of DNA required to code the protein

3) Bring catalytic sites close together

4) Structural changes in one polypeptide chain affects the activity of other chains.

63

Isoelectric point (pI)

the pH when a molecule is neutrally charged.

64

What is the charge of an ACIDIC amino acid in:

In very Acidic conditions?

In very Basic conditions?

SOLVE BY DRAWING THE AMINO ACID AND ASSIGNING CHARGES

 

(Acidic Amino acid charge)

Acidic conditions (protonated): +1

Basic conditions (deprotonated): -2

65

Glutamate

structure?

single letter?

three letter?

Negative amino acid. Chiral L-amino acid.

Deprotonated version of Glutamic acid. 

 

 

single letter: E

glutamat E

three letter: glu

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66

During titration, what does a functional group do when the pH is near the pKa?

The functional group acts as a buffer and its pH changes very slightly until the functional group is deprotonated.

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67

What happens to Amino Acid protons in acidic conditions?

In acidic conditions, amino acids gain protons (protonate) and become (+) charged

__________________________________________

Low pH = proton gain

68

What happens to Amino acids at different pH's:

Low pH?

Neutral pH?

High pH?

Low pH: Fully protonated amino acid

Neutral pH: Neutral Zwitterion

High pH: Full deprotonated amino acid

69

What happens to Amino Acid protons in basic Underconditions?

Under basic conditions, amino acids lose their protons.

Become (-) charged

__________________________________________

High pH = proton loss

70

How do you calculate the Isoelectric Point of a 

Basic Amino acid?

The average of the amino side chain group and Amino group pKa's

 

pI = (pKa amino side chain + pKa amino) / 2

 

pKa amino group: 10

 

71

How do you calculate the Isoelectric Point of a 

Acidic Amino acid?

The average of the Carb Acid side chain group and Carb Acid group pKa's

 

pI = (pKa carb acid side chain + pKa carb acid) / 2

 

pKa carboxylic acid: 2.5

72

What happens to ionizable groups in acidic conditions?

what about basic conditions?

 

ionizable groups, such as amino acids:

  • gain protons in acidic conditions (low pH)
    • because the acid around them is giving them protons
  • lose protons in basic conditions (high pH)
    • because the base around them is taking their protons

 

73

Threonine

What exception is it?

structure?

single letter?

three letter?

polar amino acid.

Chiral L-amino acid.

Exception: Has a Chiral carbon in side chain.

 

 

single letter: T

three letter: thr

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74

pKa

pKa = -log Ka

__________________________________________

Tells us how strong an acid is.

Lower pKa = strong acid  

High pKA = Weak acid

75

Are they hydrophobic or hydrophillic?:

Amino acids with long alkyl chains

and

Charged Amino acids

Amino acids with long alkyl chains are hydrophobic.

__________________________________________

Charged amino acids are hydrophillic

because they can be polar (hydrophillic)

76

define polypeptide

polypeptide = a molecule composed of 20+ amino acids

77

Glutamine.

What is different about its side group when pH changes?

 

single letter?

three letter?

polar amino acid.

Chiral L-amino acid.

Because Glutamine has an amide side group, its amide nitrogren does not gain or lose protons when pH changes. (Does not become charged).

 

single letter: Q

Q lutamine

three letter: gln

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78

Valine

structure?

single letter?

three letter?

nonpolar, nonaromatic amino acid.

Chiral L-amino acid

 

single letter: V

three letter: val

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79

Peptide Bond hydrolysis

What are the 2 enymes that break peptide bonds?

When a peptide bond is broken by adding an H to the amino group and an -OH to the carboxyl group.

Is a hydrolysis reaction (uses water).

__________________________________________

Trypsin and Chemotrypsin are enzymes that break peptide bonds via hydrolysis. 

 

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80

Which aromatic amino acids are also polar/nonpolar?

Tyrosine (Y) is aromatic and polar

 

Tryptophan (W) and Phenylalanine (F) are aromatic and non polar

81

Protein folding/unfolding: Entropy and Solvation Layer

What is more favorable?

Why is this important?

When proteins are folded in an aqueous solution (water)

  • Protein has less surface area; more order; decreased entropy (disorder)
  • Water (solvation layer) has increased entropy
  • Thus, proteins are folded so that the solvation layer of water around the protein has increased entropy
    • More favorable
  • Importance:
    • Increased entropy of the solvation layer (water) drives protein folding

When proteins are unfolded in an aqueous solution (water)

  • Protein has more surface area; more disorder; more entropy
  • Water (solvation layer) has less entropy
  • This is unfavorable to water.