2ci: Amino Acid + Protein structure

Question 1

What are proteins

Answer 1

Polymers of amino acid monomers.

Question 2

In what way do R groups vary

Answer 2

In size, shape, charge, hydrogen bonding capacity and chemical reactivity.

Question 3

How are amino acids classified

Answer 3

According to their R groups: basic (+ charge), acidic (- charged), polar (hydrophilic), non-polar (hydrophobic)

Question 4

acidic R groups…

Answer 4

• negatively charged
• hydrophilic
• key component = carboxylic acid group COOH

Question 5

Basic R groups…

Answer 5

• end with a positively charged group
• hydrophilic
• key component of their R group is amine group NH

Question 6

Polar R groups…

Answer 6

• slightly charged
• hydrophilic
• key component: carbonyl, hydroxyl, sulfer, amine

Question 7

Hydrophobic R groups…

Answer 7

• hydrophobic
• do not have charges
• non- polar
• mainly consists of hydrocarbons

Question 8

The wide range of functions carried out by proteins results from…

Answer 8

The diversity of R groups

Question 9

What is the primary structure

Answer 9

The sequence in which the amino acids are synthesised into the polypeptide (no folding)

Question 10

What is the N-terminus and the C-terminus

Answer 10

Due to the make up of amino acids, there is an amino group at one end (N-terminus) and a C-terminus on the other end (C-terminus)

H2N- R - R - R - COOH

Question 11

What is the secondary structure

Answer 11

Hydrogen bonding along the backbone of the protein strand results in the regions of the secondary structure.

Three types of secondary structure:
- alpha helix
- beta sheet
- turns

Question 12

What are alpha helixes

Answer 12

Formed by twisting the polypeptide chain into a spiral/ helix and then stabilised with hydrogen bonding.

R groups stick out

Question 13

What are beta sheets

Answer 13

Has parts of the chain running alongside each other, forming a sheet.

R groups sit above and below the sheet

Can be anti-parallel (chains run in opposite directions) or parallel (chains run in same direction)

Question 14

What are turns

Answer 14

Turns reverse the direction of a polypeptide chain.

Question 15

What is the tertiary structure

Answer 15

The polypeptide folds into a tertiary structure.

confirmation is stabilised by interactions between and R groups:
- hydrophobic interactions
- ionic bonds
- LDF
- hydrogen bonds
- disulfide bridges (covalent bonds between R groups containing sulfer)

Question 16

What do hydrophobic interactions do

Answer 16

hydrophobic amino acids tend to cluster together on the interior of a protein, away from the surface (and away from the water)

Question 17

What is the quaternary structure

Answer 17

Exists in proteins with two or more connected polypeptide subunits (which are linked by bonds between the R groups of the polypeptide chains.)

describes the spatial arrangement of the subunits.

Question 18

What is a prosthetic group

Answer 18

A non- protein unit tightly bound to a protein and necessary for its function.

Eg haemoglobin- the ability of haemoglobin to bind to oxygen is dependant upon the non-protein haem group.

Question 19

effect of increasing temperature (on a protein)

Answer 19

Disrupts the interactions that hold the protein in shape.

The protein begins to unfold and eventually becomes denatured.

Question 20

Effect of changing pH

Answer 20

-charges on acidic and basic R groups are affected by pH.
- as the pH increases or decreases from the optimum, the normal ionic interactions between the charged groups are lost. it gradually changed the conformation of the protein until it becomes denatured.