Lecture 3: Proteins

Question 1

What is the 6 roles of proteins in cells

Sic set
Of tits ya got there

Answer 1

Enzymatic catalysis: enzyme are proteins except for ribosomes
Transport: small molecules bound to proteins for transport eg 02 with haemoglobin
Structural role: eg collagen in connective tissue
Immune/defence: immune-protein antibodies, defence-snake venom
Chemical messengers: hormones eg insulin instructs cells to absorb glucose from the blood
Storage: energy source, chemicals can be stored in proteins

Question 2

Classification of proteins: on the basis of shape- 2 types

Answer 2

1. Fibrous proteins: are elongated, insoluble, has an animal origin and plays a structural role
   There are 3 main types:
   Collagens-connective tissue
   Elastins- elastic tissue eg arteries and tendons
   Kerotins- eg horn, nails, wool, hair
2. Globular proteins
   Which are oval shape, and soluble. They play a functional role in hormones, immune proteins and transport proteins

Question 3

Classification of proteins: on the bases of structure

Answer 3

A) simple proteins: consist of a string of amino acids joined by peptide bonds
B) conjugate proteins: have one non amino acid group in the string

Question 4

What is the general formula for amino acids

Answer 4

NH2-CH-COOH and an R group attached to the carbon in the middle
Nh2 is the amino group which acts as a base
COOH is the carboxyl group which acts as an acid
The R group is the variable
This is a charged molecule

Question 5

Effect of pH on amino acids
What happens if acidity increases (ie more H+ ions)?
What happens if its in a neutral solution?
What happens if its more alkaline (ie less H+ ions)?

Answer 5

1. The molecule will have a net positive charge
2. At neutral pH:
   If R group is uncharged (nett 0 charge)
   If R group contains acid group (net negative charge)
   If R group contains base group (nett positive charge)
3. The molecule will have a nett negative charge

Question 6

Classification of amino acids: they are classified according to their R group
What are the 2 classification types

Answer 6

1. Acidic aa (negative charge at neutral pH of 7) eg glutamic acid
2. Basic aa (positive charge at neutral pH of 7) eg lysine, arginine, histidine
   The rest have no nett charge at neutral pH
3. Neutral aa (0 nett charge at pH of 7)
   There are 5 groups under neutral depending on the R group
   A) R= aliphatic eg glycine, alanine, valine, proline, leucine
   B) hydroxyl containing eg serine, threonine
   C) sulphur containing
   D) aromatic containing
   E) amide containing

Question 7

How to amino acids join?

Answer 7

Refer to slide 17

Next few slides look important but are pictures

Question 8

Proteins start with an amino group and end with a carboxyl group
The type, number and sequence of these amino acids determines the chemical and biological properties of a protein
Proteins aren’t random polymers
The type, number and sequence of amino acids is determined from DNA

Answer 8

T

Question 9

Look at slide of disulphide bridges

Answer 9

Slide 22

Question 10

Rule
pH < pI: nett pos charge
pH > pI: net neg charge

Answer 10

Aer

Question 11

Lecture 4: proteins 2

You can separate proteins from one another on the basis of 3 things. What are they?

Answer 11

1. On the basis of charge (difference in charge)
   a) electrophoresis
   b) ion exchange chromatography- at a particular pH, proteins have different affinities for pos and neg charged ion-exchange resins and pass brought columns of such resins at different rates
2. On the basis of differences in size
   a) gel filtration- a set up where smaller proteins are able to pass through the pores into the interior etc etc
3. On the basis of differences in solubility
   a) pl precipitation: proteins are least soluble at their isoelectric points. If a mixture of proteins is adjusted to a pH equilevant to he pl of the ones in the mixture, that proteins may precipitate while the others remain in the solution
   b) (NH4)2 SO4 precipitation
   The above competes for a proteins hydration shell and decreases its solubility. Different proteins are precipitated from solution by different concentrations of the above

Question 12

Proteins have 4 levels of structural organisation. What are they, and explain each one

Answer 12

1. Primary structure: the numb type and sequence of amino acids in the chain. It provides essential info Ie aa content. You add a reagent which binds to the first aa in the line and causes it to break off. Just repeat this step to separate all aa.
2. Secondary structure: a long polypeptide chain of a protein has a highly organised secondary structure. There are 3 types of secondary structure
   A) a-helix: (within a polypeptide)- H bonding between the peptide bonds. Different proteins contain different amounts of a helix depending on aa composition. A helix is stretchable eg wool
   B) beta sheet (between polypeptides)- chains aren’t coiled but extended and hydrogen bonding occurs between individual chains. They are strong but not as flexible

Pg 16 of book
3. Tertiary structure:
Complex folding of the protein produces a specific 3D arrangement . This extensive folding has a number of bonds including, disulfide bond, polypeptide backbone, hydrogen bond, ionic bond, van der walls and hydrophobic interactions
4. Quaternary structure: structure held together by non-covalent bonds

Question 13

What is denaturing mean? What causes it to happen?

Answer 13

When a secondary or tertiary structure of a protein is disrupted (ie the helix unwinds and the complex folding is lost.
Denaturing is caused by factors which disrupt the bonding (hydrogen, electrostatic, hydrophobic) responsible for holding the protein in its correct secondary and tertiary shape:
A) changes in pH (disrupt the electrostatic bonds)
B) detergents (disrupt hydrophobic bonds)
C) organic solvents (ethanol) (disrupt hydrogen bonds)
D) heat (increases kinetic energy, increases vibration, disrupts all non-covalent bonding)