Proteins And Amino Acids

Question 1

What are sequences of amino acids encoded by?

Answer 1

A gene

Question 2

How are amino acids classified?

Answer 2

According to chemical properties of the R groups

Question 3

What determines the acid-base behaviour?

Answer 3

R groups

Question 4

What are the components of an amino acid?

Answer 4

Amino group
Carboxyl group
H atom
R group

Question 5

What is a zwitterion? Why is it most common? One property

Answer 5

Net charge of 0 - equal number of positively and negatively charged ions
Most stable
Acts as an acid and a base

Question 6

Two ends of a polypeptide chain

Answer 6

Amino terminal (NH3+)
Carboxyl terminal (COO-)

Question 7

What is the acid base behaviour determined by?

Answer 7

The R group

Question 8

What is an amino acid residue?

Answer 8

Amino acid after it has formed a peptide bond with another amino acid

Question 9

Chemical properties of R groups

Answer 9

Hydrophobic/philic
Polarity
Acid or Base

Question 10

What are the two categories of R groups

Answer 10

Aliphatic - only C and H
Aromatic - phenyl ring

Question 11

What is a peptide bond?

Answer 11

Linking two amino acids
Removing a water molecule

Question 12

What is an amino terminus and Carboxyl terminus?

Answer 12

+NH3
COO-

Question 13

What is the shape of a peptide bond and what does it mean?

Answer 13

Planar
On the same plane

Question 14

What is the central C called?

Answer 14

C alpha

Question 15

What is a key characteristic of a peptide bond?
What property does this give it?

Answer 15

Partial double bond characteristic between the C and N

Very rigid

Question 16

Does a peptide have a cis or trans configuration?
Describe it

Answer 16

Nearly always trans

Cs on opposite sides of C-N bond

Question 17

What are Psi and Phi bonds?
What can they do?
What does this allow?

Answer 17

C alpha - C
C alpha - N

Rotate around the peptide bond

A 3D shape

Question 18

Define the isoelectric point

Answer 18

The pH at which there is no overall net charge

Question 19

What stabilises the alpha helix?

Answer 19

H bonds between the N-H and C=O

Question 20

What is the direction of the alpha helix

Answer 20

Right handed

Question 21

What are beta sheets composed of?
What is there parallelilty?
What are the bonds?

Answer 21

Adjacent B strands - can be parallel or anti parallel
Stabilised by H bonds between the H on NH and O on C=O

Question 22

Two comparisons between globular and fibrous proteins

Answer 22

G - compact F - extended
G - several types of secondary structures F - single type of repeating secondary structure

Question 23

How do polypeptide chains fold in relation to hydrophobic and hydrophilic regions?
Why>

Answer 23

Hydrophobic side chains inside

Charged, hydrophilic regions can interact with aqueous solutions

Question 24

Describe quaternary structures

Answer 24

Non covalent bonds between complementary hydrophobic and hydrophilic sub units - doesn’t have to be proteins

Question 25

What do proteins want to achieve when folding?

Answer 25

Finding the most stable conformation

Question 26

Why are some amino acid side chains charged at physiological pH?

Answer 26

They contain a carboxylic acid or an amine group

Question 27

What does the pKa value of an amino acid side chain tell you about that chemical group?

Answer 27

How likely the side chain will become deprotonated
When pH=pKa there are equal numbers of protonated and unprotonated groups

Question 28

What is the relationship between pH and pKa?

Answer 28

pH > pKa = acidic, proton donor
pH < pKa = basic, proton acceptor