Protein

Question 1

Which two proteins carry oxygen in the body?

Answer 1

Haemoglobin and Myoglobin

Question 2

Why do we need oxygen transportation molecules?

Answer 2

We are too big to just let diffusion take care of it.

Oxygen is relatively insoluble in water- so we need to bind it to a molecule to carry it.

Question 3

List functions of Proteins.

Answer 3

• Catalysts
• Transporters
• Structural support (eg collagen)
• Locomotive
• Immunity
• Ion Channels
• Receptors
• Ligands (cell signalling)

Question 4

What is a protein?

Answer 4

Macromolecule made up of amino acid subunits joined using peptide bonds. Thee amino acid sequence is determined by the base sequence of the gene that codes for that protein.

Question 5

What affects folding and thus function of proteins?

Answer 5

The 3D structure of the protein is highly related to the function. The structure is a result of the chemical and physical properties of the amino acids in the peptide chain.
For example which parts of the molecule carry charge? Hydrophilic or phobic? Acidic or basic? Aromatic?

Question 6

Name the four basic sutures of amino acids:

Answer 6

• amino group(-NH2)
• carboxyll group (-COOH)
• Hydrogen Atom
• distinctive R group (side chain)

Question 7

What happens when you put an amino acid in water?

Answer 7

It ionises NH3+ and COO-

Question 8

What group do you use to classify amino acids?

Answer 8

Side chain only, when peptide bonds from there is only a NH3+ at the N terminus and a COO- at the C terminus.
The other amino and carboxyll groups on intermediate amino acid residues are involve in peptide bond formation.

Question 9

What makes a side chain aliphatic?

Answer 9

Only contains hydrogen and carbon

Question 10

What is made in the process of peptide bond formation?

Answer 10

Water and combined amino acid residues.

Question 11

What happens to the amino acid if the pK is higher than the pH of the environment its in?

Answer 11

The amino acid will be more prominent in its protonated form and so will be positively charged.

Question 12

What does the pK tell you?

Answer 12

How likely something is to ionise - the lower the pK the more acidic.

Question 13

What is a protein primary structure?

Answer 13

The linear amino acid sequence of a poly peptide chain.

Question 14

What is a secondary structure for a protein?

Answer 14

Local special arrangement of the polypeptide backbone- eg helices

Question 15

What’s a proteins tertiary structure?

Answer 15

The over all three dimensional structure.

Question 16

What is the quaternary structure of a protein?

Answer 16

Association between different polypetides.

Question 17

What are the bond angles of peptide bonds?

Answer 17

Planar

Question 18

Why are petite bonds rigid?

Answer 18

peptide bond resonance is a result of a partial double bond characteristic (C-N) making it unable to rotate and planar.

Question 19

What conformation do peptide bonds have/

Answer 19

Trans form (Alpha carbons on opposite sides of the horizontal chain - in cise form they would repel and cause a steric clash)

Question 20

In the peptide chain are their bonds that can rotate?

Answer 20

Yes bonds either side of the peptide bond

Question 21

What is the isoelectric point?

Answer 21

The pH at which there is no verbal net charge.

Question 22

Peptides and oligopeptides are proteins with a short amino acid length, what’s the cut off before its long enough to be called a polypetides or protein?

Answer 22

100amino acids

Question 23

What are conjugated proteins?

Answer 23

Proteins that have chemical components other than amino acid residues covalently bonded to them.

Question 24

What. Determines the peptide back bone folding to a shape?

Answer 24

The conformation angles

Question 25

What bonds stabilise alpha helices?

Answer 25

N-H and C=0 form H bonds with each other with a gap of 4 amino acids between them

Question 26

Which amino acids have strong impacts into the likelihood of alpha helix formation?

Answer 26

Ala and Leu are strong helix formers
Proline (the only IMINOACID)breaks helix formation because it cannot rotate the N-C(alpha)
Glycine also breaks alpha helices because the R group is so small it supports other conformations.

Question 27

So beta strands run parallel or antiparallel in beta sheets?

Answer 27

Anti-parallel, parallel or mixed- either is possible and gives different properties

Question 28

Name a alphahelical protein

Answer 28

Ferritin

Question 29

Name a beta sheet protein.

Answer 29

fatty acid binding proteins

Question 30

What features does the tertiary structure (the interactions between far away amino acids) give a protein?

Answer 30

Whether the protein is fibrous (collagen) or globular (carbonic anhydrases)

Question 31

Define Motif

Answer 31

Folding pattern containing one or more elements of secondary structures

Question 32

Define domains

Answer 32

Part of polypeptide chains that fold into distinct shapes and often have a specific functional role.

Question 33

How do proteins fold relative to their like or dislike of water?

Answer 33

Hydrophobic areas are buried on the inside of the molecule with a hydrophilic outer layer in general.
The reverse is true of membrane proteins- they are inside out.

Question 34

List examples of tertiary proteins shapes

Answer 34

Haemoglobin has 2 alpha and 2 beta subunits

Ribosomes have 55 protein subunits and 3 RNA molecules

Question 35

What structure can disulphide bonds contribute to?

Answer 35

Covalent disulphide bonds with in one polypetide chain is a tertiary structural feature.

If more that one protein is involved in the bonding its quaternary

Question 36

How is folding of proteins organised?

Answer 36

Localised folding with more stable conformations preserved.