proteins

Question 1

proteins contain the elements

Answer 1

carbon, hydrogen, oxygen and nitrogen, and in some cases sulphur and phosphorus

Question 2

every amino acid molecule has

Answer 2

an α-carbon atom bonded covalently to four groups:
- amino group (–NH2)
- carboxyl group (–COOH)
- a hydrogen atom
- an R group (differs in each amino acid and accounts for the unique physical and chemical properties of the amino acids)

Question 3

empirical formula of an amino acid

Answer 3

NH₂.R.CH.COOH

Question 4

what determines if an amino acid is hydrophobic?

Answer 4

they have non-polar R groups (i.e. many C-C and C-H bonds in the R group, with even charge distribution)

Question 5

what determines if an amino acid is hydrophilic?

Answer 5

it has polar or charged R groups

Question 6

acidic amino acids are

Answer 6

amino acids with negatively charged R groups

Question 7

what causes negatively charged R groups in amino acids

Answer 7

the presence of a carboxyl group in the R groups

Question 8

basic amino acids have

Answer 8

positively charged R groups

Question 9

what causes positively charged R groups in amino acids

Answer 9

the presence of amino groups in their R groups

Question 10

neutral amino acids have

Answer 10

uncharged R groups at neutral pH

Question 11

neutral amino acids can be both ___ depending on the functional groups in their R groups

Answer 11

non-polar and hydrophobic
or
polar and hydrophilic

Question 12

a polypeptide is

Answer 12

a polymer of many amino acids linked by peptide bonds

Question 13

what are at the two ends of polypeptides?

Answer 13

at one end, free -NH₂ (called the N-terminus)
at the other end, -COOH (called the C-terminus)

Question 14

describe the formation of a dipeptide

Answer 14

• 2 amino acids can react with each other via a condensation reaction.
• The amino group (-NH₂) of one amino acid molecule reacts with the carboxyl group (-COOH) of an adjacent amino acid, with the elimination of 1 water molecule.
• The covalent carbon-nitrogen bond that is formed is called the peptide bond.

Question 15

the free amino group at one end and a free carboxyl group at the other end of a dipeptide enables

Answer 15

further condensation reactions between the dipeptide and other amino acids

Question 16

what determines a polypeptide’s characteristic three-dimensional conformation?

Answer 16

a specific amino acid sequence

Question 17

what determines how a protein works

Answer 17

its specific three-dimensional conformation

Question 18

how is the specific 3D-conformation of a polypeptide’s chain maintained

Answer 18

by the types of bonding / interactions present in itself

Question 19

what are the four levels of protein structure

Answer 19

primary structure, secondary structure, tertiary structure, quaternary structure.

Question 20

the primary structure is defined as

Answer 20

the simple linear sequence of amino acid residues which are attached together by peptide bonds, making up the polypeptide chain.

Question 21

the secondary structure refers to

Answer 21

the way the polypeptide chain bends or folds due to the presence of hydrogen bonds which occur at regular intervals between the H atom of N-H and O atom of C=O of the peptide bonds

Question 22

the hydrogen bonds in polypeptides results in

Answer 22

a regular repeating organization / pattern of coiling or folding within a segment of a polypeptide chain, which contributes to the overall conformation of the protein.

Question 23

polypeptide chains typically ___ to form a ___
or
___ into ___

Answer 23

1) coil to form a helix (α-helix)
2) fold into sheets (β-pleated sheets)

Question 24

the alpha helical structure is stabilised by

Answer 24

intramolecular hydrogen bonds which occur between the H atom of N-H of one amino acid and O atom of C=O of another amino acid that is 4 amino acid residues ahead of it

Question 25

the α-helix makes a complete turn for every

Answer 25

3.6 amino acids

Question 26

average length of α-helix

Answer 26

10 amino acids

Question 27

intramolecular hydrogen bonds in alpha helix are linear, so maximally stable. thus, the helices are

Answer 27

stable, spring-like and capable of extending and contracting

Question 28

β-pleated sheets are formed when

Answer 28

a single polypeptide chain folds back and forth, or when two regions of the same chain lie parallel to each other, held by H-bonds

Question 29

chains are arranged in which two directions?

Answer 29

parallel or anti-parallel (back and forth)

Question 30

the beta pleated sheet structure is stabilised by

Answer 30

the large numbers of hydrogen bonds between the H atom of N-H group and O atom of C=O group on adjacent segments

Question 31

where can hydrogen bonding occur in polypeptides?

Answer 31

among two or more segments of same chain (intrachain sheet for secondary protein structure) or among two or more segments of different chains (interchain sheets for quaternary protein)

Question 32

why is the beta pleated sheet structure very stable and rigid?

Answer 32

because all the N-H groups and C=O groups of the peptide bonds are involved in hydrogen bonding

Question 33

tertiary structure refers to

Answer 33

the irregular manner in which the helical and non-helical regions of a polypeptide are folded to form a precise, compact globular structure

Question 34

what bonds may occur in the tertiary structure?

Answer 34

Ionic bonds, hydrophobic interactions, hydrogen bonds and disulfide bonds

Question 35

ionic bonds are formed between ___ in proteins

Answer 35

amino acids with acidic and basic R groups

Question 36

what do hydrophobic interactions look like in proteins?

Answer 36

Hydrophobic R groups of amino acids tend to cluster together by hydrophobic interactions. (This arrangement makes the structure very stable.)

Question 37

hydrogen bonds are formed between ___ in proteins

Answer 37

- amino acids with polar R groups - between N-H and C=O groups of amino acids in secondary structure

Question 38

where are disulfide bonds formed in proteins

Answer 38

The sulfhydryl group (-SH) of the amino acid cysteine and another sulfhydryl group (-SH) of a second cysteine

Question 39

why are proteins soluble in water

Answer 39

Amino acids with polar R groups tend to be on the surface of the protein molecule in contact with water. Each water molecule is able to form hydrogen bonds with another water molecule and with the polar amino acid residues.

Question 40

tertiary structure gives rise to

Answer 40

precise clefts and grooves in the protein (important in the function of enzymes!)

Question 41

quaternary structure refers to

Answer 41

the interaction between more than one polypeptide chains to form an intact functional protein.

Question 42

what holds the separate polypeptide chains together?

Answer 42

Hydrophobic interactions, hydrogen, ionic and disulfide bonds between the R groups of amino acids hold the separate chains together. For example, haemoglobin has 4 polypeptide chains linked by various bonds.

Question 43

haemoglobin is... / structure of haemoglobin

Answer 43

a tetramer consisting of 4 polypeptide chains, 2α chains and 2β chains, held together by hydrogen bonds, hydrophobic bonds and charge interactions between R groups. The α and β subunits (chains) are very similar to each other in structure, but not identical.

Question 44

what are allosteric proteins

Answer 44

proteins which involve a change in shape and activity that results from a molecule binding at a specific site

Question 45

describe how haemoglobin changes shape as an allosteric protein

Answer 45

Each molecule of haemoglobin molecule has four subunits which can each bind one oxygen molecule. When the first molecule of oxygen binds to haem in one of the subunits, the protein undergoes a change in conformation which brings about a change in the properties of the three remaining subunits so that they are able to bind oxygen more strongly. This is known as cooperative binding. The protein thus becomes a better oxygen carrier.

Question 46

structure of collagen

Answer 46

The basic structural unit of collagen is tropocollagen (note: monomer is still amino acid). It consists of three polypeptide chains that are wound around each other (like the strand of a rope) into triple helix. The triple helix is stabilised by extensive hydrogen bonds between N-H group of glycine on one chain and C=O group of other amino acids on the other chains. Each polypeptide chain is about 1000 amino acids long and consists of a repeating sequence of typically Gly-X-Y, where X and Y can be any amino acid. Glycine (R group = H atom) is found at every third amino acid within each polypeptide chain. Being small in size, glycine allows the three strands to lie close together to form a tight coil. Other amino acids would be too large. Each completed triple helix of collagen (tropocollagen) lies parallel in a regularly staggered arrangement with other triple helices to form microfibrils followed by fibrils, joined and stabilized by extensive covalent cross-links and hydrogen bonds between neighbouring triple helices, resulting in stability and high tensile strength. Covalent cross-links are formed between lysine and/or hydroxylysine residues in the tropocollagen molecules lying next to each other Hydrogen bonds are formed between proline and other amino acid residues in the tropocollagen molecules – less important than covalent cross-link

Question 47

why is collagen insoluble in water

Answer 47

due to extensive hydrogen bonding, which prevents free hydroxyl (-OH) groups from interacting with water.

Question 48

solubility of fibrous and globular proteins in water

Answer 48

fibrous: insoluble globular: soluble

Question 49

why are fibrous proteins insoluble in water

Answer 49

due to the large number of hydrophobic R groups of amino acids residues on the exterior of the molecules.

Question 50

why are globular proteins soluble in water

Answer 50

due to the hydrophilic R groups of amino acid residues jutting outwards from their molecules.

Question 51

what do globular proteins form when dissolved in water

Answer 51

colloidal suspensions

Question 52

amino acid sequence in fibrous proteins

Answer 52

Repetitive regular sequences of amino acids. For example, every third residue in collagen is glycine and the sequence glycine-X-Y recurs frequently. Actual sequences may vary slightly between two examples of the same protein.

Question 53

amino acid sequence in globular proteins

Answer 53

Irregular amino acid sequences. Sequence highly specific and never varies between two examples of the same protein

Question 54

overall shape of fibrous proteins

Answer 54

Long polypeptide chains form parallel strands, cross-linked at intervals forming long fibres or sheet.

Question 55

overall shape of globular proteins

Answer 55

Polypeptide chains tightly folded into a compact globular or spherical shape

Question 56

most important level of structure in fibrous proteins

Answer 56

secondary structure (little or no tertiary structure)

Question 57

most important level of structure in globular proteins

Answer 57

tertiary structure. quaternary structure may not be present.

Question 58

function of fibrous proteins

Answer 58

Since secondary structures are tough, fibrous proteins impart strength and rigidity. Hence, are involved in support, structural and mechanical functions.

Question 59

function of globular proteins

Answer 59

Since tertiary structures give rise to specific clefts and grooves, globular proteins perform metabolic functions

Question 60

stability of fibrous and globular proteins respectively

Answer 60

fibrous: stable structure globular: relatively unstable structure

Question 61

examples of fibrous proteins

Answer 61

collagen, elastin

Question 62

examples of globular proteins

Answer 62

enzymes, insulin (hormone), haemoglobin, antibodies (globulins)

Question 63

how does near or below freezing point temperature affect proteins?

Answer 63

At near or below freezing point, proteins are inactivated (not denatured) as they have very little kinetic energy for effective collisions.

Question 64

what is the effect of increasing temperature on proteins?

Answer 64

When temperature increases, the kinetic energy of proteins increases, which may lead to increased activity (e.g. greater ability to transport oxygen in the case of haemoglobin or faster rate of reaction for enzymes etc.)

Question 65

at optimum temperature, the level of protein activity is

Answer 65

at its maximum

Question 66

what happens to a protein('s activity) beyond optimum temperature

Answer 66

the level of activity decreases sharply. This is because any further increase in temperature leads to the breakage of bonds (e.g. hydrogen bonds and hydrophobic interactions) that hold the protein in its 3-D conformation. The protein is said to be denatured and is no longer effective in carrying out its function. This is because the 3D conformation of the protein has changed.

Question 67

what is renaturation of a protein

Answer 67

where a protein folds back into its original conformation

Question 68

is renaturation of the protein possible?

Answer 68

it can occur, provided that the conformation of the protein is not drastically altered.

Question 69

in what two ways does changes in pH affect proteins?

Answer 69

1. neutralising charges of amino acids at binding site 2. changing conformation of the protein

Question 70

describe how changes in pH neutralises charges of amino acids at binding site

Answer 70

A protein is made up of many amino acids with charged R groups (e.g. glutamic acid) in its structure and binding site. If pH increases / decreases, the excess OH- / H+ ions combine with the positive / negative charges of amino acids at the binding site, neutralising them. The uncharged amino acid R groups at the binding site can no longer form ionic bonds, so the protein loses its ability to bind to specific molecules.

Question 71

describe how changes in pH changes conformation of the protein

Answer 71

As acidity increases or decreases, the number of H+ ions increases or decreases. This will disrupt the ionic bonds within the protein that were previously responsible for maintaining the overall structure of the protein. As a result, the conformation of the protein is altered. Protein becomes denatured; particularly at extremes of optimum pH values, thus function is lost. Unlike the effects of heat on proteins, the effects of pH are normally reversible, at least within limits. Restoring the pH to the optimum level usually restores the rate of reaction.