Proteins

Question 1

What is the structure of an amino acid?

Answer 1

Central carbon atom, covalently bound to

• Amino group
• Carboxyl group
• Hydrogen atom
• R group (side chain)

Question 2

How do amino acids ionise?

Answer 2

Amino group gains hydrogen ion
NH2 + H+ —–> NH3+

Carboxyl group gives up hydrogen ion
COOH —–> COO- + H+

Question 3

Which group in the amino acid is acidic?

Answer 3

The carboxyl group

Question 4

Which group in the amino acid is basic?

Answer 4

The amino group

Question 5

How are amino acids classified? Why?

Answer 5

Based on the properties of the R groups

Because in polypeptide chains, only the hydrogen atom and the R group of the amino acids remains

Question 6

What is an amino acid residue?

Answer 6

What remains of an amino acid after it has been jointed to another amino acid

• R group
• hydrogen atom

Question 7

What are the types of properties of the R group?

Answer 7

Chemical properties

Physical properties

Question 8

What are the possible chemical properties of the R group?

Answer 8

Polar/non-polar

Hydrophobic/hydrophilic

Acidic/basic/neutral

Question 9

What are the possible physical properties of the R group?

Answer 9

Aliphatic/aromatic

Question 10

What does the pKa value of amino acids measure?

Answer 10

How acidic the amino acids are

Question 11

What does a low pKa value mean?

Answer 11

The amino acid is more acidic

Question 12

What does a high pKa value mean?

Answer 12

The amino acid is less acidic

more basic

Question 13

What happens to the amino acid if pH > pKa? Why?

Answer 13

Higher pH means fewer hydrogen ions present
amino acid gives up hydrogen ions
becomes deprotonated

Question 14

What happens to the amino acid if pH < pKa? Why?

Answer 14

Lower pH means more hydrogen ions present
amino acid takes up hydrogen ions
becomes protonated

Question 15

What is physiological pH?

Answer 15

7.4

Question 16

What is the primary structure of a protein?

Answer 16

Amino acids joined together in a linear chain

Question 17

What reaction occurs when two amino acids are joined together?

Answer 17

amino acid1 + amino acid 2 —–> polypeptide + water

Question 18

What bond joins two amino acids together?

Answer 18

Peptide bond

Question 19

What is the amino terminus of a polypeptide?

Answer 19

The amino group NH2 end of the polypeptide chain

Question 20

What is the carboxyl terminus of a polypeptide?

Answer 20

The carboxyl group COOH end of the polypeptide chain

Question 21

What are the properties of peptide bonds?

Answer 21

Planar

Rigid

Trans conformation

Question 22

What is meant by peptide bonds being planar?

Answer 22

The central carbon atom
N-H
C=O

are all in the same plane

Question 23

What is meant by peptide bonds being rigid?

Answer 23

No rotation about the peptide bond

Question 24

What atoms are involved in a peptide bond?

Answer 24

C-N

C from C=O
N from N-H

Question 25

What is meant by the peptide bond having a trans conformation?

Answer 25

Heavier groups are on opposite sides of the peptide bond | the heavier groups are the central carbon atom, R group, H atom altogether

Question 26

What is the importance of the amino acid sequence in the primary structure?

Answer 26

Determines the way the polypeptide chain folds the structure of the protein and hence its function

Question 27

What are peptides/oligopeptides?

Answer 27

Chains of a few amino acids joined together

Question 28

What are polypeptides/proteins?

Answer 28

Chains of many amino acids joined together

Question 29

What type of bond is a peptide bond?

Answer 29

Covalent bond

Question 30

What is the secondary structure?

Answer 30

The spatial arrangement of the polypeptide backbone

Question 31

What are the types of secondary structures?

Answer 31

Alpha helix Beta strand

Question 32

What do layers of beta strands form?

Answer 32

Beta pleated sheet

Question 33

What holds the alpha helix and the beta pleated sheets together?

Answer 33

Hydrogen bonds between C=O and N-H

Question 34

What are the types of beta sheets? What do they each mean?

Answer 34

Parallel - run in same direction Anti parallel - run in opposite directions

Question 35

How does the polypeptide chain fold up into an alpha helix or beta pleated sheet if peptide bonds are rigid?

Answer 35

Bonds next to peptide bonds are free to rotate

Question 36

What is the tertiary structure?

Answer 36

Secondary structure folds up to form a 3D conformation

Question 37

What are the types of tertiary structures? What do they each mean?

Answer 37

Globular - spherical shape Fibrous - long strand-like shape

Question 38

What is the general function of fibrous proteins?

Answer 38

Structural support Maintain shape

Question 39

How many types of secondary structures are there in fibrous proteins?

Answer 39

Single repeating secondary structure

Question 40

How many types of secondary structures are there in globular proteins?

Answer 40

Several different types

Question 41

What is a classic example of a fibrous protein?

Answer 41

Collagen

Question 42

What is a protein domain?

Answer 42

Part of polypeptide chain that folds into a distinct shape | has a specific function

Question 43

How do water-soluble proteins generally fold up?

Answer 43

Non-polar hydrophobic side chains are buried within Polar/charged hydrophilic side chains are on surface

Question 44

How do integral membrane proteins generally fold up? Why?

Answer 44

Non-polar hydrophobic chains are on the surface interact with hydrophobic tails Polar/charged hydrophilic chains form a channel within interact with water in and out of cell

Question 45

What is the quarternary structure?

Answer 45

Different polypeptide chains coming together to form a multi-subunit protein

Question 46

What is an example of a protein with a quarternary structure?

Answer 46

Hb

Question 47

What is an example of a protein with a tertiary structure?

Answer 47

Myoglobin

Question 48

What does pI stand for?

Answer 48

Isoelectric point

Question 49

What is the pI of proteins?

Answer 49

pH at which protein has no overall charge

Question 50

Do acidic proteins have a low or high pI value? Why?

Answer 50

Low | low pH means more hydrogen ions, neutralises negative charge of acidic amino acid

Question 51

Do basic proteins have a low or high pI value? Why?

Answer 51

High | high pH means fewer hydrogen ions, because already have positively charged amino acids

Question 52

What happens to the protein if pH > pI? Why?

Answer 52

High pH means fewer hydrogen ions amino acid gives up hydrogen ions becomes deprotonated

Question 53

What happens to the protein if pH < pI? Why?

Answer 53

Low pH means more hydrogen ions amino acid takes up hydrogen ions becomes protonated

Question 54

What are conjugated proteins?

Answer 54

Proteins covalently linked to additional chemical components that are not amino acids

Question 55

What are some examples of roles of proteins? Give examples for some roles

Answer 55

Structural support e.g. collagen Enzymes e.g. hexokinase Transporters e.g. Hb Carriers, channels etc. Receptors, ligands etc.