Lecture 1

Question 1

α-carbon is chiral in all aa except

Answer 1

glycine

Question 2

what is chirality

Answer 2

non-superimposible mirror images

Question 3

all aa found in natural proteins are what type of aa?

Answer 3

L-amino acids

Question 4

what does the R group side chain do?

Answer 4

gives the aa different properties

Question 5

what is a zwitterion?

Answer 5

A zwitterion is a compound which contains a positive and negative charge, but with no overall electrical charge

Question 6

what are aa residues?

Answer 6

single aa within a protein

Question 7

what are the essential aa? which ones are they?

Answer 7

These are aa acquired throughout the diet; not created by the body.
histidine, isoleucine, leucine, methionine, phenylalanine, threonine, tryptophan, valine, lysine

Question 8

what are the conditionally non-essential aa? which ones are they?

Answer 8

these are aa required at some stage of growth or by some people who can’t synthesize them b/c of genetics or medical condition.
arginine, asparagine, glutamine, glycine, proline, serine, tyrosine

Question 9

what are the non-essential aa? which ones are they?

Answer 9

these are aa our bodies can synthesize.

alanine, asparatate, cysteine, glutamate

Question 10

which aa’s are the non polar, aliphatic?

Answer 10

glycine (G), alanine (A), proline (P), Leucine (L), Isoleucine (I), Valine (V), Methionine (M).

Question 11

Y are the non polar, aliphatic aa important? Where are they usually located?

Answer 11

They are important for hydrophobic protein interactions. They tend to be inside protein structures.

Question 12

what is special about proline?

Answer 12

• its a very rigid molecule
• it’s more like an imino acid than aa
• α-amino group is actually a secondary amine
• can disrupt the folding structures like α-helix or β- pleated sheets
• commonly found in sharp turns connecting β strands
• proline reduces flexibility b/c of it’s 2° amino group structure

Question 13

which aa’s are polar, uncharged?

Answer 13

serine (S), threonine (T), Cysteine (C), Asparagine (N), Glutamine (Q)

Question 14

what is polarity due to?

Answer 14

• OH groups
• S atom
• amide groups

Question 15

Why are the polar, uncharged aa important? Where are they usually located?

Answer 15

these groups can form H bonds with H2O, therefore they are hydrophilic. They are usually found on the surface of protein structures.

Question 16

What special functions do the polar uncharged aa have?

Answer 16

1. OH of S/T are sites for covalent modifications (ex. phosphorylation)
2. Cys forms covalent disulfide bonds important for protein folding
3. Asn & Gln are important N donors/carriers; can also participate in H bonding

Question 17

What stabilizes the secondary structure of a protein?

Answer 17

hydrogen bonds

Question 18

What aa are aromatic?

Answer 18

phenylalanine (F), tyrosine (Y), tryptophan (W)

Question 19

Why are aromatic aa important?

Answer 19

• relatively non-polar so can participate in hydrophobic interactions
• absorb light at 280nm; useful for protein quantitation

Question 20

What aa are positively charged (basic)?

Answer 20

histidine (H), arginine (R), lysine (K)

Question 21

what causes an aa to be positively charged? what causes an aa to be negatively charged?

Answer 21

• positively charged b/c of the amino group (NH3+) side chains
• negatively charged b/c of the carboxyl group (COO-) side chains

Question 22

What aa are negatively charged (acidic)?

Answer 22

aspartate (D), glutamate (E)

Question 23

salt bridges stabilize what structure?

Answer 23

tertiary structure

Question 24

what is transamination?

Answer 24

Transamination (or aminotransfer) is a chemical reaction between two molecules. One is an amino acid, which contains an amine (NH2) group. The other is a keto acid, which contains a keto (=O) group.

Question 25

what are the aa that participate in transamination?

Answer 25

pyruvate –> alanine
oxaloacetate –> aspartate
α-ketoglutarate –> glutamate

Question 26

What’s special about glycine?

Answer 26

• glycine has no optical activity
• smallest aa
• rotates easily
• fits in small places
• flexible
• allows structural flexibility b/c its small

Question 27

what are standard aa?

Answer 27

aa used directly in the process of protein synthesis

Question 28

what are non-standard aa?

Answer 28

aa modified after the protein is completed or used in other cellular processes (such as urea cycle)

Question 29

what is special about methionine?

Answer 29

• 1 of 2 aa that contain S atom

- methionine is important in methyl group transfers

Question 30

hydrogen bonds

Answer 30

• stabilize 2° structure (α-helix or β- pleated sheets)

- 1 H bond is not that strong but multiple H bonds can make a difference

Question 31

H bond donor

Answer 31

H bond donor is usually a H attached to an electronegative atom (O, N or F)

Question 32

H bond acceptor

Answer 32

H bond acceptor is usually a electronegative atom (O, N, or F)

Question 33

which 3 aromatic aa are special and y?

Answer 33

phenylalanine, tyrosine, & tryptophan are special because they can participate in Π-Π interactions

Question 34

why are cation-Π interactions important?

Answer 34

because they cause the activation of receptors

Question 35

what’s another name for salt bridge and how do they form?

Answer 35

salt bridges = ionic bonds
they form via 2 interactions:
- electrostatic - between the charges
- H-bonds