1. Amino Acids

Question 1

Which is the amino terminus of the following dipeptide: alanylvaline

Answer 1

Alanine is the amino terminus (meaning that the amino group -NH₃ is available for forming new peptide bonds)

Question 2

Naming convention of peptides (e.g. dipeptides)

Answer 2

We write the from NH₃⁺ (amino terminus) –> to the COO^- group (carboxy terminus)

Question 3

What is the impact of Proline in alpha helices?

Answer 3

Proline disrupts alpha-helices due to being large and bulky

Question 4

What is the impact of Proline in beta sheets?

Answer 4

Proline allows for kinking in the chain and is GOOD for forming beta-sheets

Question 5

What is another name for Aspartate? (synonymous for MCAT)

Answer 5

Aspartic Acid

Question 6

*Why can Tyrosine be found both inside and outside?

Answer 6

Due to the benzene ring and -OH (hydroxy) group

Question 7

What is the general structure of an α-amino acid?

Answer 7

• central (α) carbon
• carboxyl group
• α-Amino group
• R-group
• α-Hydrogen

Question 8

What type of amino acids are proteinogenic amino acids?

Answer 8

• All proteinogenic AAs are α-amino acids
• “α” describes the amino group’s position
• Some biologically active amino acids are not α

Question 9

Types of amino acids

Answer 9

Alpha α

Beta

Gamma

Question 10

Are enantiomers possible for α-amino acids?

Answer 10

Proteinogenic amino acids are L-isomers

L ≠ S in all cases, so we can’t base it just on that

All but cysteine and glycine are S enantiomers

Question 11

What is the fisher layout of L-amino acids?

Answer 11

W/ amino group on the left

Question 12

What are the amino acid exceptions to L=S?

Answer 12

• L-Cysteine (is an R configuration - clockwise)
• Glycine is ACHIRAL (w/o D or L designation)

Question 13

S configuration is (clockwise/counterclockwise)

Answer 13

S configuration is COUNTERCLOCKWISE; and most proteinogenic amino acids are S configuration

*Cysteine is the exception and is R configuration

Question 14

Basic amino acids

Answer 14

• Lysine - Lys, K
• Histidine - His, H
• Arginine - Arg, R

BASIC bitches Lyk Halloween & dress up like pirates, Arg!

Question 15

Acidic AAs

Answer 15

Aspartate = Aspartic acid

Glutamate = Glutamic acid

Question 16

Polar amino acids

Answer 16

• Asparagine
• Glutamine
• Serine
• Threonine
• Cysteine

Ganster CATS survive polar weather

Question 17

Non-polar amino acids

Answer 17

• Glycine
• Alanine
• Leucine
• Isoleucine
• Methionine
• Valine
• Proline

Vivid MAGILP - non-polar

Question 18

Aromatic AAs

Answer 18

• Phenylalanine
• Tryptophan
• Tyrosine

Question 19

What are peptides?

Answer 19

Linear chain of amino acids or residues (residues = amino acids)

Question 20

Oligopeptides vs. Polypeptides

Answer 20

Oligopeptides: 2-20 residues

Polypeptides: longer chains of residues

Question 21

What is a peptide bond?

Answer 21

a specialized amide bond between the COOH and NH2 groups on adjacent amino acid residues

Question 22

What allows for the resonance in the peptide bond?

Answer 22

Delocalizable electrons → allow for resonance

C-N has partial double bond character

Rotation around the C-N amide backbone is restricted

Question 23

What can break down peptide bonds?

Answer 23

Peptides can be broken into single amino acids for digestion by hydrolytic enzymes, or strong acids and heat

(reverse of condensation)

Question 24

What are titrations?

Answer 24

In essence, limiting reactant problems

• Mechanism: one reagent is limiting (analyte), the other is excess (titrant)
• We add what we have in excess of until we just barely consume all of the limiting reactant- the “endpoint” of the titration
• We use wither color indicator or an electrode to monitor when it reaches the endpoint

Question 25

What is **monoprotic acid-base titration**?

Answer 25

1. determines # of equivalents of titrant 2. pH is monitored to determine **equivalence point (EP)** 3. EP is found at steepest slope on titration curve 4. EP is where the Equivalents of Acid and Base are equal

Question 26

What is the **equivalence point**?

Answer 26

The point at which Equivalents of acid and equivalents of base are equal; found at steepest slope on titration curve

Question 27

\*Map out polyvalent/polyprotic acid-base titration; where does the Isoelectric point occur?

Answer 27

Question 28

Isoelectric point

Answer 28

pI is the pH at which a particular molecule carries no net electrical charge in the statistical mean pI (isoelectric point) occurs halfway between the 2 closest 1/2 EPs (aka pKas)

Question 29

How to calculate the isoelectric point?

Answer 29

pI (isoelectric point) is calculated by averaging the two closest pKa's

Question 30

Zwitterion

Answer 30

An amino acid at it's **isoelectric point** (meaning net neutral charge)

Question 31

How do you calculate Histidine's isoelectric point?

Answer 31

The pKas are 2, 6, 9 So you average pH 6 and 9 ⇒ pH=7.5

Question 32

Half equivalence points (other name, where on graph)

Answer 32

Equal concentrations of adjacent forms; **pKa's** Found at **plateaus** of the curve

Question 33

Equivalence points

Answer 33

When there is a dominant form; the **verticals** of the curve

Question 34

General pIs of acidic amino acids? Basic amino acids?

Answer 34

Acidic amino acids have pI's around pH ~3 Basic amino acids have pIs around pH ~10

Question 35

What factors cause denaturation of proteins?

Answer 35

* high temperatures * high salt concentrations * detergents * adding urea (high concentration)

Question 36

Which amino acid has a side chain that can become **ionized** in cells?

Answer 36

Histidine has ionizable side chain; its **imidazole ring** has a nitrogen atom that can be protonated

Question 37

What are reasons for conjugating proteins?

Answer 37

Conjugated proteins can have lipid or carbohydrate "tags" added to them * to direct their delivery to a particular organelle * to direct their delivery to the cell membrane * to add a cofactor needed for their activity

Question 38

If carbon backbones are close together (forming triple helix), what type of amino acid helps reduce steric hindrance to make this possible?

Answer 38

Glycine has smallest side chain; reduces steric hindrance

Question 39

Aliphatic vs. Aromatic

Answer 39

**Aromatic** : describe a cyclic (ring-shaped), planar (flat) molecule with a ring of resonance bonds that exhibits more stability than other geometric or connective arrangements with the same set of atoms **Aliphatic:** can be a ring structure, but NOT aromatic