Protiens & Amino Acids

Question 1

What is the primary structure of the protein?

What type of bond is present here?

Answer 1

• linear amino acid sequence of the polypeptide chain

- only peptide (covalent) bonds

Question 2

What is the secondary structure of a protein?

What bond is present here?

Answer 2

• local spatial arrangement of polypeptide backbone e.g alpha helixes, beta pleated sheets
• hydrogen bonds

Question 3

What is the tertiary structure of a protein?

what type of bonds are found here?

Answer 3

• overall 3D configuration of the protein

- different types of non-covalent e.g hydrogen bonds

Question 4

What is the Quaternary structure of a protein?

what type of bonds are found here?

Answer 4

• more than one polypeptide chain associated

- different non-covalent bonds e.g hydrogen bonds

Question 5

How is a peptide bond formed?

Answer 5

• linking of 2 amino acids in a hydrolysis reaction

- expulsion of water

Question 6

What are some features of peptide bonds?

Answer 6

• planar (flat)
• rigid (cannot rotate)
• always have trans formation
• bonds either side of a peptide bond can rotate
• peptide bond C-N has partial double bond characteristics.

Question 7

Define the isoelectric point.

Answer 7

The pH at which the protein has a net charge of 0

Question 8

Features of a globular protein

Answer 8

• compact

- usually have several types of secondary structure

Question 9

Features of a fibrous protein

Answer 9

• extended formation

- single type of repeating secondary structure

Question 10

How do polypeptide chains fold?

Hint: hydrophilic & hydrophobic

Answer 10

• hydrophobic on inside

- polar, charged & hydrophilic on outside to interact w water

Question 11

Can protein folding be random?

Answer 11

No- would take too long
Each step is ordered w localised folding & stable conformations maintained
*misfolding can lead to disease

Question 12

How is the amino acid sequence created?

Answer 12

-the nucleotide sequence of a gene determines the amino acid sequence of a protein

Question 13

What is the general structure of an amino acid

Answer 13

-central carbon, NH2,COOH, R-group & H

Question 14

What is a zwitterion?

Answer 14

State of amino acid when NH2 protonated (NH3+) & COOH deprotonated (COO-)

Question 15

What are amino acids classified according to?

Answer 15

• their R groups

- these determine the protein folding & acid base behaviour

Question 16

Define the following:

aliphatic, aromatic, hydrophobic, hydrophilic, polar, non-polar, acidic, basic

Answer 16

Aliphatic= only C and H
Aromatic= phenyl ring

Question 17

What does the pKa value tell you about an amino acid?

Answer 17

It’s a measure of how strongly acidic an amino acid is

e.g pKa of 2.5 means the amino acid is strongly acidic

Question 18

If the pH is higher than the pKa, what does this tell you in regards to protonation/ deprotonation?

Answer 18

• This means the acid is fairly weak

- therefore not likely to protonate -so more commonly in its deprotonated form

Question 19

The protein serum albumin has an isoelectric point of 5. Would it move towards a positive or negative electrode?
(at physiological pH)

Answer 19

• physiological pH is 7
• at pH 5, net charge is 0
• going up in pH to 7 means it’s more basic (more OH-)
• more negative charged therefore would move to positive electrode

Question 20

The protein serum albumin has an isoelectric point of 5. Would this protein move to the positive or negative electrode at a pH of 5?

Answer 20

• wouldn’t move
• pH = isoelectric point
• no net charge so protein cannot move

Question 21

The isoelectric point of histones is very high, around 10.8
What charge will histones have under physiological conditions?
Why do you think they have this charge?

Answer 21

-physiological conditions= pH7
-going down in pH from 10.8 to 7 means it’s getting more acidic
-more H+ ions so histamine will have a positive charge
They have this charge as they can bind to DNA which is negatively charged

Question 22

Give some features of enzymes

Answer 22

• catalysts
• increase rate of reaction
• DO NOT alter eqm of chemical reaction
• decrease activation energy
• can form ESC by binding to active site

Question 23

Describe the active site of an enzyme

Answer 23

• occupies a small part of the enzyme
• formed by amino acids from different parts of the primary sequence
• it is a cleft or crevice (excludes water)
• has a complimentary shape to the substrate
• substrates can bind to enzymes via weak bonds

Question 24

What does the rate of reaction depend on?

Answer 24

The substrate concentration

Question 25

Define Km

Answer 25

The substrate conc required to achieve half of Vmax

-provides an idea of the strength of binding of the substrate to the enzyme

Question 26

What does a low Km value suggest?

Answer 26

-low Km means the enzyme has a HIGH affinity for the substrate

Question 27

What is the relationship between rate of reaction & enzyme concentration?
What is the effect of enzyme concentration on the Km value?

Answer 27

• rate of reaction is DIRECTLY PROPORTIONAL to the enzyme concentration
• e.g if enzyme concentration is doubled, rate doubles
• if enzyme concentration halves, rate is halved
  2. Enzyme concentration doesn’t change Km

Question 28

What is a competitive inhibitor?

What effect does it have on Km & Vmax?

Answer 28

• binds at active site, reduces proportion of enzyme molecules bound to the substrate (blocks active site)
• adding enough substrate will ALWAYS overcome the effect of the inhibitor, so no effect on Vmax
• Km increases as the substrate has a lower affinity for the enzyme

Question 29

What is a non-competitive inhibitor?

What effect does this have on Km & Vmax?

Answer 29

• binds to enzyme at allosteric site, decreases concentration of functional enzyme
• enzyme no longer functional so increasing substrate conc has no effect, Vmax decreases
• Km unaffected as enzyme concentration has no effect on Km

Question 30

Define the term Vmax.

Answer 30

The maximum rate of reaction achieved when all the enzymes are fully saturated with substrate