Proteins

Question 1

what is a gene

Answer 1

sequence of nucleotide bases in DNA molecules that codes for the production of a specific sequence of amino acids to make up a specific polypeptide (protein)

Question 2

what is transcription

Answer 2

DNA is transcribed and an mRNA (messenger RNA) molecule is produced

Question 3

what is translation

Answer 3

mRNA is translated and an amino acid sequence is produced

Question 4

what is the role mRNA

Answer 4

carry the information encoded in the DNA from the nucleus to the site of translation on ribosomes

Question 5

explain transcription

Answer 5

Part of a DNA molecule unwinds and the hydrogen bonds between the complementary base pairs break

exposes the gene to be transcribed

A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA which is catalysed by RNA

Free activated RNA nucleotides pair up, via hydrogen bonds, with their complementary bases on the exposed strand of the ‘unzipped’ DNA molecule

The sugar-phosphate groups of these RNA nucleotides are then bonded together in a reaction catalysed by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule

When the gene has been transcribed and the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule reforms

The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope

Question 6

what is the strand called which the RNA nucleotides pair with

Answer 6

antisense or template strand, and it is used to produce the mRNA molecule.

The other strand is known as the sense or coding strand

Question 7

how does RNA polymerase move along template strand

Answer 7

in the 3’ to 5’ direction

Question 8

what happens after the mRNA leaves nucleus

Answer 8

the mRNA molecule attaches to a ribosome in the cytoplasm

Question 9

what is tRNA

Answer 9

tRNA is a single stranded molecule of RNA that folds into a clover-like structre

triplet of unpaired bases at one end, known as the anticodon, and a region at the other end where a specific amino acid can attach

Question 10

what do tRNA molecules do

Answer 10

bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome

The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet on the mRNA molecule called the codon

Question 11

what is there at the beginning of each mRNA

Answer 11

Near the beginning of the mRNA is a triplet of bases called the start codon (AUG)
This is a signal to start off translation

Question 12

what bond is formed between two amino acids and what is produced by the end

Answer 12

A peptide bond is then formed, via a condensation reaction

continues until a ‘stop’ codon on the mRNA molecule is reached

The amino acid chain then forms the final polypeptide

Question 13

what direction does the ribosome move along the mRNA in translation

Answer 13

5’ - 3’

Question 14

describe the genetic code

Answer 14

non overlapping
degenerate: multiple codons can code for same amino acid limiting effect of mutation
universal

Question 15

what are proteins

Answer 15

polymers made of monomers called amino acids

Question 16

what is the structure of an amino acid

Answer 16

amino group H-N-H
R group: H - C - R
carboxylic acid O=C-OH

Question 17

what happens when a peptide bond is formed

Answer 17

A hydroxyl (-OH) is lost from the carboxylic group of one amino acid
A hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid. This is a condensation reaction so water is released

Question 18

what happens during a hydrolysis reaction

Answer 18

he addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids

Question 19

what are the first three levels of structure in proteins related to

Answer 19

Three are related to a single polypeptide chain
The fourth level relates to a protein that has two or more polypeptide chains

Question 20

what is the primary structure

Answer 20

The sequence of amino acids bonded by covalent peptide bonds

Question 21

what is the secondary structure

Answer 21

relates to hydrogen bonds forming between the amino group and the carboxyl group

weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

Question 22

when does α-helix shape occur

Answer 22

when the hydrogen bonds form between every fourth peptide bond

Question 22

when does the β-pleated sheet form

Answer 22

when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

Question 23

what is tertiary structure

Answer 23

change of the secondary structure leads to additional bonds forming between the R groups

Question 24

what are examples of addition tertiary bonds

Answer 24

Hydrogen (these are between R groups) Disulphide (only occurs between cysteine amino acids) Ionic (occurs between charged R groups) Weak hydrophobic interactions (between non-polar R groups) is common in 3D globular proteins

Question 25

what is quaternary

Answer 25

Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule eg. haemoglobin

Question 26

what structures contain hydrogen bonds

Answer 26

secondary and tertiary

Question 27

what are the structure of globular proteins

Answer 27

Compact Roughly spherical (circular) in shape Globular proteins form a spherical shape when folding into their tertiary structure

Question 28

why do globular proteins form spherical shape when folding into tertiary structure

Answer 28

Their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings Their polar hydrophilic R groups orientate themselves on the outside of the protein

Question 29

what is the function of globular proteins

Answer 29

The orientation of their R groups enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups easily transported around organisms and be involved in metabolic reactions

Question 30

give an example of a globular protein and explain its function and structure

Answer 30

Haemoglobin It has a quaternary structure as there are four polypeptide chains The four globin subunits are held together by disulphide bonds haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red binding oxygen in the lungs and transporting the oxygen to tissue to be used in aerobic metabolic pathways

Question 31

what is the structure of fibrous proteins

Answer 31

long strands of polypeptide chains that have cross-linkages due to hydrogen bonds

Question 32

do fibrous proteins have tertiary structure

Answer 32

little or no tertiary structure

Question 33

function of fibrous proteins

Answer 33

large number of hydrophobic R groups, fibrous proteins are insoluble in water Fibrous proteins are strong suitable for structural roles

Question 34

examples of 2 fibrous proteins

Answer 34

Collagen is a connective tissue found in skin, tendons and ligaments Elastin is found in connective tissue, tendons, skin and bone

Question 35

describe collagen

Answer 35

Collagen is an insoluble fibrous protein formed from three polypeptide chains closely held together by hydrogen bonds to form a triple helix In the primary structure of collagen almost every third amino acid is glycine Along with hydrogen bonds forming between the three chains there are also covalent bonds present

Question 36

how are collagen positions

Answer 36

The collagen molecules are positioned in the fibrils so that there are staggered ends When many fibrils are arranged together they form collagen fibres

Question 37

function of collagen | staggered ends????

Answer 37

structural protein forming connective tissues The presence of the many hydrogen bonds within the triple helix structure of collagen results in great tensile strength The staggered ends of the collagen molecules within the fibrils provide strength

Question 38

compare collagen and haemoglobin

Answer 38

triple helix / 4 polypeptide chains long and thin / spherical round structural / functional receptive amino acid variation / variable insoluble / soluble

Question 39

what does biological catalyst mean

Answer 39

they function in living systems ‘Catalysts’ because they speed up the rate of chemical reactions without being used up or undergoing permanent change They speed up reactions by reducing the activation energy of reactions

Question 40

are enzymes globular or fibrous with what type of structure

Answer 40

globular proteins with complex tertiary structures made up of two or more polypeptides and therefore have a quaternary structure

Question 41

are enzymes globular of fibrous and what does this mean

Answer 41

globular proteins This means their 3D shape is determined by the complex tertiary structure of the protein that makes up the enzyme and is therefore highly specific

Question 42

enzymes have a unique....

Answer 42

active site where specific substrates bind forming an enzyme-substrate complex

Question 43

for a reaction to occur what conditions?

Answer 43

Substrates collide with the enzymes active site and this must happen at the correct orientation and speed

Question 44

how does the 3d shape of active site change

Answer 44

Proteins are formed from chains of amino acids held together by peptide bonds The order of amino acids determines the shape of an enzyme If the order is altered, the resulting three-dimensional shape changes as determined by complex tertiary structure of protein that makes enzyme

Question 45

what does higher enzyme concentration lead to

Answer 45

The higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation

Question 46

what is a limiting factor

Answer 46

If the amount of substrate is limited, at a certain point any further increase in enzyme concentration will not increase

Question 47

method for investigating the effect of enzyme concentration on the rate of reaction

Answer 47

Add a set volume of hydrogen peroxide solution to a boiling tube Add a set volume of buffer solution to the same boiling tube Invert a full measuring cylinder into a trough of water Place the end of the delivery tube into the open end of the measuring cylinder and attach the other end to a bung Add a set volume of one concentration of catalase to the boiling tube and quickly place the bung into the boiling tube Record the volume of oxygen collected in the measuring cylinder by the water displaced every 10 seconds for 60 seconds Repeat the whole experiment for the different concentrations of catalase

Question 48

results of investigating enzyme concentration on the rate of reaction

Answer 48

As the concentration of catalase increases the volume of oxygen produced would increase This is because there would be more available active sites for hydrogen peroxide to use The volume of oxygen would plateau out after the initial rate of reaction due to the substrate decreasing, having been converted into the product (oxygen)

Question 49

how does primary structure of leptin allow it to be water soluble

Answer 49

{primary structure / sequence of the amino acids} determines the folding (of the polypeptide) forming a globular structure hydrophobic (R) groups located in the centre of the protein / hydrophilic (R) groups located on the outside of the protein water forms hydrogen bonds with { protein / hydrophilic groups}

Question 50

How does removing and substituting have different affects on protein structure

Answer 50

deletion could affect every codon (on the mRNA) / substitution will only affect one codon (1) deletion more likely to affect the position of { stop codon / start codon } (1) deletion results in a different sequence of amino acids / substitution may not affect the sequence of amino acids (1) substitution may code for the same amino acid (1) (same amino acid) due to the degenerate nature of the genetic code (1)

Question 51

how doe substitution affect the function of haemoglobin

Answer 51

(because) {one tripletis affected / a different triplet code is produced } (1) * (the mutation) could change one of the amino acids (1) * this would (change the bonds formed betweer the R groups / cause a change in the tertiary structure! (1) * the haemoglobin would no longer be able to bind to oxvaen (1)

Question 52

importance of primary structure for function of enzyme

Answer 52

(primary structure) determines interaction between {amino acids / R groups} (1) (primary structure) determines { folding / tertiary structure } (1) (therefore) affecting the shape of the active site (1) * (active site is) complementary to ATP (1)

Question 53

how can a base mutation lead to altered primary structure of an enzyme

Answer 53

changes in base will alter the triplet code which changes the codon and hence different amino acid sequence in primary structure

Question 54

how can an enzyme break down polysaccharide

Answer 54

hydrolysis of glucosidic bonds

Question 55

compare structure of globular and fibrous

Answer 55

both are chains of amino acids joined by peptide bonds (1) both contain named bonds (holding molecule in its three dimensional shape) (1) globular proteins have hydrophilic groups on the outside whereas fibrous proteins have hydrophobic groups on the outside (1) globular have tertiary or quaternary structures whereas fibrous have little or no tertiary structure (1) globular are folded into compact shapes whereas fibrous have long chains (1)

Question 56

how amino acids would be incorporated into a surfactant protein

Answer 56

mRNA of surfactant protein is attached to ribosome pairing of anticodons on tRNA and mRNA and a tRNA is specific to one amino acid. Amino acids join by peptide bonds and a tertiary structure is formed

Question 57

what is an allele

Answer 57

is it an alternative version of a gene found at the same locus on a chromosome

Question 58

Vinegar contains ethanoic acid. why would vinegar result in anthocyanin pigments leaving onion cell

Answer 58

increased permeability of (cell surface) membrane the low pH would {change the shape of / denature} proteins (in cell surface membrane) (as vinegar) affects bonds (in protein)

Question 59

explain how the primary structure of an enzyme determines its three dimensional structure and its properties

Answer 59

(primary structure) {position / sequence / order /eq} of the {amino acids / R groups} / eq; idea that this determines the {positioning / type} of the {bonds / folding / eq} ; determining the {shape / properties} of the active site / eq; idea of interaction of active sites and substrates e.g. enzyme substrate complex forms idea of {polar / hydrophilic} on the outside of enzymes / {non polar / hydrophobic} on the inside / eg;

Question 60

Describe the structure of an enzyme.

Answer 60

ref to an enzyme as a protein ; 2. ref to {3D / tertiary / globular} structure ; 3. ref. to named bonds (holding structure in place) ; 4. between the R groups ; 5. ref to active site ; 6. idea of specificity of active site