Protein Building Blocks: Amino Acids, Peptides, and Polypeptides

Question 1

How many genes in the genome? Transcriptome? Proteome?

Answer 1

20,000-25,000 genes; 100,000 transcripts; over 1,000,000 proteins

Question 2

What three things lead to more transcripts than genes in the genome?

Answer 2

Alternative splicing, Alternative promoters (different transcription start sites), mRNA editing

Question 3

What lead to more proteins in the proteome than in the transcriptome?

Answer 3

Post-translational modifications (addition of a sugar, etc.)

Question 4

What isomer are proteins made of?

Answer 4

L-amino acids

Question 5

Vasopressin

Answer 5

A nonapeptide that consists of a 1-6 disulfide bond resulting in a cysteine. Also, the C-terminus -OH is replaced with an NH2 resulting in a glycinamide.

Question 6

Insulin

Answer 6

Consists of 2 polypeptide chains (A and B) which are connected by two disulfide bridges. The A chain also has an intra-chain disulphide bond. Proinsulin is cleaved to form insulin.

Question 7

How many amino acids in a peptide? Protein?

Answer 7

less than 50; greater than 50

Question 8

Average size of a protein?

Answer 8

400 amino acids, largest is 30,000 (titin)

Question 9

Henderson-Hasselbalch Equation

Answer 9

pH = pKa + log([A-]/[HA])

Question 10

pH > pKa

Answer 10

proton off

Question 11

pH < pKa

Answer 11

proton on

Question 12

Titration Curve

Answer 12

Question 13

Define the pI

Answer 13

It is the isoelectric point or the pH in which the zwitterion exists. Found by averaging the pKa values surrounding it.

Question 14

Estimating the pH of a protein

Answer 14

determine the charge on all of the amino acids in the protein. If it is more negative, it will be more acidic. If it is more positive it will be more basic (higher pH). Keep in mind, if the protein goes below the pI, it will become more protonated and thus more positively charged. If it goes above its pI it will become more deprotonated and thus more negatively charged.

Question 15

What are the properties of 2-D Electrophoresis?

Answer 15

First, the proteins are applied to an isoelectric focusing gel which separates the proteins (horizontally for example) based on their pI values. Because many proteins will have the same pI value, they are then applied to an SDS-PAGE gel which will separate the proteins (vertically now) strictly by size.