Specials - Protein Structure and Function

Question 1

What is the central Dogma

Answer 1

DNA (genes) >RNA > Amino Acids > Polypeptide (proteins)

Question 2

How many proteins in a bacteria cell?

Answer 2

~2 million

Question 3

How many proteins in a human cell

Answer 3

~1-3 billion

Question 4

What is a protein/polypeptide?

Answer 4

A chain/polymer of amino acids linked by peptide bonds (Polypeptide)

Question 5

What is a peptide?

Answer 5

Short polypeptides (approx. less than 50 aa)

Question 6

What is a dipeptides, tripeptides, or tetrapeptides?

Answer 6

Very short peptides (2,3,4 amino acids in length)

Question 7

What is a residue?

Answer 7

Individual amino acids in a polypeptide/protein

Question 8

What are proteins made of?

Answer 8

amino acids

Question 9

What is the term given to the the central carbon of an amino acid

Answer 9

Alpha carbon

Question 10

What are the parts of an amino acid

Answer 10

They have an amino, carboxyl group, central alpha carbon and a side chain
They can also have an ionised form

Question 11

How is a peptide bond formed?

Answer 11

condensation/dehydration reaction

Amino group targets carbonyl group foR the second amino acid, it releases water and they join together

Question 12

What are the main properties of a peptide bond

Answer 12

Rigid (cannot rotate), O-C-N-H of the Peptide bonds are co-planar

Question 13

Where can rotation occur in amino acids?

Answer 13

Rotation can occur at the single bonds between the α-carbon and is neighbouring atoms

Question 14

What is the more stable R-group orientation in an amino acid? I.e cis or trans

Answer 14

Trans (side chains alternate)

Question 15

What is the least stable R-group orientation in an amino acid?

Answer 15

Cis (due to repulsion of side chains)

Question 16

What direction are proteins drawn?

Answer 16

from N (amino) terminus to the C (carboxyl) terminus

Question 17

What determines the behaviour of a amino acid in a protein?

Answer 17

Its side chain (hydrophobic, polar, hydrophilic, nonpolar, positive and negative charged)

Question 18

What is the shape of a protein important for?

Answer 18

Its function

Question 19

Where does the shape of an active site in a protein/enzyme come from?

Answer 19

This shape is driven by the chemical properties and sequences of the amino acids in the protein

Question 20

What proteins have an active site?

Answer 20

Enzymes to allow substrates to bind

Question 21

How do enzymes interact with substrates?

Answer 21

A substrate binds to an active site can cause conformational changes which provide a function or strengthen the interaction

Question 22

What are the two types of models for proteins?

Answer 22

Induced fit (has conformational change) and “lock and key” model

Question 23

What is the induced fit model?

Answer 23

The model of the enzyme that shows the substrate binding to the active site and the active site altering slightly

Question 24

What is the lock and key model?

Answer 24

The model of the enzyme that shows the substrate fitting perfectly into the active site

Question 25

What is the primary structure of a protein

Answer 25

The unique sequence of amino acids of a protein

Question 26

How can we know what the primary structure of a protein is?

Answer 26

Looking at the DNA sequence of genes

Question 27

What is a secondary structure?

Answer 27

Localised folding of the polypeptide driven by hydrogen bonding interactions within the polypeptide backbone

Question 28

What is NOT involved in secondary structures

Answer 28

R groups

Question 29

What are the two types of secondary structures?

Answer 29

β sheet (aka β pleated sheet) and the α helix

Question 30

Can we predict the secondary structure of a protein from its DNA sequence?

Answer 30

Yes (due to favoured residues)

Question 31

How can β sheets be arranged?

Answer 31

They can be parallel (both strands going from N Terminus to C) or going in opposite directions

Question 32

What causes β sheets to be formed

Answer 32

H bonding between a backbone Amine (N-H) group on one strand, and a backbone Carbonyl (C=O) group on another strand

Question 33

What direction are α helices

Answer 33

right handed

Question 34

Number of amino acids in one turn of the helix

Answer 34

3.6