proteins

Question 1

what are some differences between fibrous proteins and globular proteins?

Answer 1

1. fibrous proteins have an elongated, rope-like structure while globular proteins have a compact and spheroidal structure
2. fibrous proteins have a repetitive a.a. sequence while globular proteins have specific, non-repetitive a.a. sequence
3. fibrous proteins generally perform structural functions while globular proteins generally perform metabolic functions

Question 2

describe the structure of an amino acid

Answer 2

1 basic amine group (-NH2)
1 acidic carboxyl group (-COOH)
1 hydrogen atom
1 R group

Question 3

how are zwitterions formed?

Answer 3

the carboxyl group loses on H+ ion which associates with the amine group to form —COO- and —NH3+ respectively. the resulting amino acid contains one positive charge and one negative charge, forming an electrically neutral, dipolar ion

Question 4

why can amino acids act as buffer?

Answer 4

amino acids are amphoteric as they possess both acidic and basic properties

Question 5

are amino acids with non-polar R groups hydrophobic?

Answer 5

yes

such amino acids tend to be located in the interior to be shielded from the aqueous medium

Question 6

are amino acids with polar R groups hydrophobic?

Answer 6

no, they are hydrophilic

Question 7

are amino acids with charged R groups hydrophobic?

Answer 7

no, they are hydrophilic

acidic a.a. have a net negative charge while basic a.a. have a net positive charge

Question 8

how are peptide bonds formed?

Answer 8

through a condensation reaction, a peptide bond is formed between the amine group of one a.a. and the carboxyl group of another

Question 9

how does the ability of polypeptides to buffer solutions compare to that of amino acids?

Answer 9

amino acids have a better ability to buffer solutions compared to polypeptides

Question 10

what are the 4 levels of protein structure?

Answer 10

primary structure
secondary structure
tertiary structure
quaternary structure

Question 11

what is defined as the primary structure of a protein?

Answer 11

the unique number and linear sequence of amino acids that constitute the polypeptide chain

Question 12

what are the two types of secondary structure of a protein?

Answer 12

alpha helix and beta pleated sheet

Question 13

where do hydrogen bonds form?

Answer 13

hydrogen bonds are formed between the NH group of one amino acid and the C=O group of another

hydrogen bonds are individually weak but collectively stabilise the struture

Question 14

what is the shape of an alpha helix?

Answer 14

the alpha helix takes the form of an extended spiral spring

Question 15

where are the R groups in an alpha helix located?

Answer 15

the R groups project outside the helix, perpendicular to the main axis

this is to prevent steric interference with the polypeptide chain and with each other

Question 16

what is the shape of a beta pleated sheet?

Answer 16

the beta pleated sheet takes on an extended zigzag, sheet-like conformation

Question 17

what is the difference between hydrogen bonds occurring in alpha helix and those occurring in beta-pleated sheet?

Answer 17

in the beta pleated sheet, hydrogen bonding can occur between C=O and N-H groups within the same polypeptide chains OR between C=O and N-H groups of neighbouring chains
while in alpha helix, hydrogen bonding occurs between the O atom of the C=O group of an a.a. residue and the H atom of an a.a. residue situated 4 a.a. residues ahead

Question 18

what is defined as the secondary structure of protein?

Answer 18

the regular coiling and folding of regions of the polypeptide chain giving rise to repeated patterns

Question 19

what is defined as the tertiary structure of protein?

Answer 19

the further bending, twisting and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation of a protein

Question 20

what bonds are involved in the tertiary structure of protein?

Answer 20

1. ionic bonds
2. hydrogen bonds
3. hydrophobic interactions
4. disulfide bonds

Question 21

what is defined is the quaternary structure of protein?

Answer 21

the overall protein structure that results from the association of two or more polypeptide chains to form a functional protein

Question 22

what is a multimeric protein?

Answer 22

proteins with more than one or more polypeptide/subunits

Question 23

what is the structure of haemoglobin?

Answer 23

haemoglobin is a multimeric protein consisting of 4 polypeptide chains, namely 2 alpha and 2 beta chains. it is a tetramer made up of 2 identical dimers.

Question 24

why is haemoglobin soluble in aqueous mediums?

Answer 24

each polypeptide chain is folded such that hydrophobic a.a. residues are generally buried in the interior of the molecule and those at the surface are generally hydrophilic.

Question 25

describe subunit cooperativity in haemoglobin

Answer 25

when an iron (ii) ion in the first haemoglobin subunit binds 1 molecule of oxygen, the F helix is pulled closer to the haem group
this creates a strain on the other haemoglobin subunits
so the remaining subunits change their 3D conformation slightly, allowing their respective haem groups to bind oxygen more readily, increasing the remaining subunits’ affinity for oxygen

Question 26

what is the amino acid sequence of a collagen polypeptide?

Answer 26

a collagen polypeptide is made up of a repeating tripeptide sequence of glycine-x-y
x is often proline
y is often hydroxyproline or hydroxylysine

proline residues prevent collagen from forming an alpha helix

Question 27

what kind of protein is collagen?

Answer 27

fibrous protein

Question 28

name the levels of protein structure involved in collagen

Answer 28

primary structure
secondary structure
quaternary structure
NO tertiary structure

Question 29

how is the quaternary structure of collagen formed?

Answer 29

three parallel alpha chains wind around each other with a gentle, right-handed rope-like twist to form tropocollagen

Question 30

what bonds are responsible for holding together tropocollagen?

Answer 30

hydrogen bonds between the N-H group of gly residue in one alpha chain and the C=O group of another residue in a neighbouring chain
hydroxyl groups of hydroxyproline and hydroxylysine participate in inter chain hydrogen bonding
covalent cross links are present, giving the collagen fibre high tensile strength

Question 31

describe how a collagen fibre is formed

Answer 31

tropocollagen molecules are linked to each other by covalent cross linked between the C terminus of one molecule and the N terminus of another, giving rise to collagen fibril
the aggregation of collagen fibrils form collagen fibre

Question 32

what is defined as denaturation?

Answer 32

the loss of the specific 3D conformation of a protein molecule

Question 33

what are the 5 denaturants of proteins?

Answer 33

heat
changes in pH
organic solvents
urea
detergents

Question 34

how does the iron ion held in a porphyrin ring relate to the structure of haemoglobin?

Answer 34

the iron ion binds one of the oxygen atoms in a molecule of oxygen. the iron ion can combine reversibly with oxygen and enhances the release of oxygen in metabolically active tissues

Question 35

where do hydrophobic interactions, ionic bonds and disulfide bonds occur in proteins?

Answer 35

hydrophobic interactions occur between hydrophobic R groups of amino acid residues
ionic bonds occur between oppositely charged R groups of amino acid residues
disulfide bonds occur between sulfhydryl groups of any 2 cysteine residues