Biochem Lecture 2

Question 1

Go through your AA cards

Question 2

Draw the basic structure of an AA at pH 7

Answer 2

Question 3

At physiological pH, AA’s are a _______ ion.

Answer 3

zwitter ion

Question 4

Alpha carbon on AA’s is a chiral center so what does that mean for optical isomers?

Answer 4

It means there will be two optical isomers, aka two enatiomers

Question 5

Only L/D AA’s are found in eukaryotic proteins.

The common AA’s are called “________” AA’s

Answer 5

Only L amino acids are found in eukaryotic proteins

Common AA’s are called proteiogenic

Question 6

How many common AA’s are there?

How many of these can humans synthesize vs how many must be consumed?

What are the essential AA’s (list them)

Answer 6

There are 21 common AA’s

12 of them can be synthesized

The ones that have to be consumed are called “essential AA’s”; leucine, isoleucine, lysine, valine, histidine, methionine, phenylalanine, tyrptophan, threonine

Question 7

In general hydrophobic AA’s are found in the _____ of a protein.

Hydrophillic are found in _____ of a protein

Answer 7

Hydrophobic found on interior

Hydrophillic found on exterior

Question 8

What are the beta branched AA’s?

Answer 8

Valine, Leucine, Isoleucine

Question 9

Which are the aromatic AA’s?

Answer 9

Phenylalanine, Tyrosine, Tryptophan

Question 10

Which AA incorporates the alpha amino group into its side chain?

Answer 10

Proline

Question 11

What are the dicarboxylic acids?

Answer 11

Aspartate, glutamate (these are capable of ionizing)

Question 12

What are the hydroxy AA’s?

Answer 12

Serine, Threonine

Question 13

Carboxaminde AA’s

Answer 13

Asparagine, Glutamine

Question 14

Which are the Diamino AA’s

Answer 14

Histidine, Lysine, Arginine

Question 15

Arginine has a ______ group

Histidine has a _____ group

Answer 15

Arginine has a guanidinium group

Histidine has an imidazolium

Question 16

Which of the AA’s have polar side chains?

Answer 16

Serine, Threonine, Asparagine, Glutamine

Question 17

Cystine is a _____ AA.

It results from the oxidation/reduction of 2 cysteines?

Answer 17

Cystine is a derived AA
It results from oxidation of two cysteines

Creates a disulfide bridge

Question 18

What kind of reaction forms a peptide bond?

Answer 18

A dehydration reaction

Question 19

Peptide bonds have double bond character… what is the concequence of that on rotation?

Answer 19

At physiological pH, there is a peptide bond plane/common plane

Question 20

What type of structure does pro-insulin have that when it gets turned into insulin it becomes one molecule and not two?

Answer 20

Disulfide bridges from cystine

Question 21

Which AA’s are basic.

Which AA’s are acidic

Answer 21

Basic: Lysine, Arg

Acidic: Aspartate, Glutamate

Question 22

If pH > pI, then the protein will be ____

If pH < pI then the protein will be ____

What is pI?

Answer 22

pH > pI means negative protein

pH < pI means positive protein

pI is the isoeletric point, pH at which the molecule carries no net charge

Question 23

Explain where the phi and psi angles are on a peptide

Answer 23

Question 24

Explain how to find the net charge of an AA at physiological pH (pH=7)

Answer 24

the COOH and the NH3 group cancel each other out so you only have to figure out which AA’s are charged and count them up

+1 : Lysine, Arginine, Histidine

-1 : Aspartate, Glutamate

Question 25

Explain how titration works. Draw the peptides at different pH’s and what their charges are going to look like.

Answer 25

Question 26

How does 2D electrophoresis work?

Answer 26

You first seperate things based on their apparent molecular weight.

Then, you seperate them based on charge (pI).