BMP: AA. peptide, protein structure

Question 1

1. In water what do AA contain? what does this mean?
2. What are AA able to function as? Why?

Answer 1

1. A weakly acidic a-carboxyul group and weakly basic a-amino group therefore are ampophoteric (acid and base)
2. Buffers - they donate, accept protons depending on pH of solution

Question 2

1. What is the equation for an weak acid?
2. What does a large Ka mean?

Answer 2

1. HA <—> A- + H+
2. Ka = [A-][H+] / [HA]
3. Stonger acid as more weak acid dissociated

Question 3

What is henderson-hasselbach equation?

Answer 3

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

pKa = -logKa, ph = -log[H+}

Question 4

How many dissociation constants does an AA have? why?

Answer 4

2 - one for the a-carboxyl group and one for the a-amino gorup. An acidic/ basic AA will have an additional dissociation constant.

Question 5

When is a buffer at maximal capacity?

Answer 5

A bufffer has maximal capacity at its pKa when the concentations of acidoc and basic forms are equal

Question 6

What is the charge of a protein determined by?

Answer 6

The positive basic charge and negative acidic charge from AAs. The actual protein charge varies with solution of pH

Question 7

What happens during the titration of an AA with a stronh base e.g. NaOH?

Answer 7

As AA titrated with increasing amounts of NaOH it loses at least 2 protons.

The first from the a-carboxyl group which has a lower pKa then the next from the a-amino gorup which has a higher pKa

Question 8

What are the pKa value rnages for the a-carboxyl and a-amino groups?

Answer 8

a-carboxyl - 1.8 - 2.9

a-amino - 8.8 - 10.8

Question 9

Describe what happens during the titrartion in relation to a graph

Answer 9

Question 10

At neutral pH what form does glycine exist in?

Answer 10

dipolar form - both groups ionised with net charge of 0

Question 11

What is the isoleclectric point?

Answer 11

The pH at which the net chargeon a molecule is 0 and will not migrte in an electric field

Question 12

What happens if the pH of the surroundings is greater and less than PI

Answer 12

• pH surrroundings less than PI - net chrarge is +ve so migrates to cathode
• pH greater than PI - net charge -ve so migrates to anode

Question 13

What is the primary protein structure and why is this useful?

Answer 13

linear sequence of AA

mutations in primary sequence often leads to genetic diseases. Analysis of the normal and mutated sequence can be used to diagnosis or sstudy diseases

Question 14

What are examples of secondary structures

Answer 14

• a- helix
• b- sheet
• b- bend

The polypeptide backbone does not assume a random 3D structure, but instead generally forms regular arrangements of amino acids that are located near to each other in the linear (primary) sequence.

Question 15

How are AA joined together?

Answer 15

covalently bonded by peptide bonds between the a- carboxyl group of one AA and a-amino group of another

Question 16

How are peptide bonds broken

Answer 16

prolonged exposure to SA/B at elevated temp required to hydrolyse the bond non-enzymatically

not broken by hadnling or conditios which denature proteins e.g. elevated temp of high conc of urea

Question 17

Naming polypeptides

Answer 17

Order of amino acids in a peptide (sequence)

• The free amino end of the peptide chain (N-terminal) is written to the left, and the free carboxy end (C-terminal) is written to the right.
• All amino acid sequences are read from the N- to the C-terminal

•

Example: A tripeptide composed of:

an N-terminal Valine, a Glycine and a C-terminal Leucine =

Val-Gly-Leu or VGL

Naming of the polypeptide

• Linkage of many amino acids through peptide bonds results in an unbranched chain called a polypeptide.
• Each component amino acid in a polypeptide is called a ‘moiety’ or ‘residue’.
• When the polypeptide is named, all amino acid residues whose names end in –ine, -an, -ic, or –ate have these suffixes changed to –yl with the exception of the C-terminal amino acid.

•

Example: A tripeptide composed of:

an N-terminal Valine, a Glycine and a C-terminal Leucine =

valylglycylvaline

Question 18

Decribe and give examples of biologically active peptides

Answer 18

Example 1: Vasopressin (ADH) is a nanopeptide (9 residues) secreted by the posterior pituitary gland and causes the kidney to retain water.

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly

Example 2: Bradykinin is another nanopeptide that causes blood vessels to dilate, causing a fall in blood pressure. Produced from polypeptide originating from the liver.

Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg