Chapter 3- Proteins and Nucleic Acids

Question 1

protein functions

Answer 1

Is made of carbon, hydrogen, oxygen and nitrogen
Functions : cell growth; cell repair; replacement of materials; structural role (ex: cytoplasm, muscle, collagen and elastin in skin, collagen in bone and keratin in hair); protein. carrier molecules in cell membranes; antibodies; enzymes; hormones

Question 2

Basic building block of a protein

Answer 2

Amino acids are the monomers which form a protein

Sequence of amino acids determine the type of protein formed and hence its function.

Question 3

Structure of an amino acid

Answer 3

At one end of the molecule, there is an amino group (NH2) and at the other end there is a carboxyl group or an organic acid group, (COOH). The carbon has a double bond with the oxygen as well as a single bond to the OH. These two groups are attached centrally with a carbon atom that carried a hydrogen atom at one side and an R group on the other.

Question 4

What is a R group

Answer 4

A side chain that acts as a functional group as it helps to determine the internal bonds and so the shape of the polypeptide and hence its final function.
It is called a residual group.
The R group is different in each of the 20 amino acids that make up proteins. Once the amino acids are joined to one another by peptide bonds, they are often referred to as amino acid residues.

Question 5

Examples of amino acids

Answer 5

Glycine- there is only one hydrogen atom as its residual group
Alanine- CH3 is its residual group
Leucine- its residual group consists of CH at the centre with the groups: CH3, H3C, CH2 surrounding this.

Question 6

Examples of Polar amino acids

Answer 6

Aspartic acid- its residual group is CH2 and COOH
Arginine- its residual group is (CH2)3, HN, CNH, NH3
Serine- its residual group is CH2OH.

Question 7

Polar or charged R groups

Answer 7

All polar or charged R groups are hydrophilic groups

Non-polar amino acids are hydrophobic (ex: valine )

Question 8

Peptide bonds

Answer 8

Proteins are polymers
Two Amino acids are joined by condensation reaction, with one molecule of water lost.
This results in a peptide bond being formed. This new molecule is called dipeptide.
This bond can be broken by a hydrolysis reaction using one molecule of water.

Question 9

Polypeptides

Answer 9

Long chains of amino acids joined by peptide bonds are called polypeptides.
A chain of amino acids joined by peptide bonds is peptide.

The condensation reaction between amino acids in a polypeptide is catalysed by the enzyme peptidyl transferase present in the ribosomes.
The different R-groups of the amino acids making up a protein interact with each other forming different types of bonds.

Peptides differ in number, type and order of amino acids.

Question 10

Levels of protein structure

Answer 10

The shape of a protein is vital in determining the properties of that protein and its function in the living organism.

All proteins are organised at different levels- primary, secondary, tertiary and quaternary
Only some proteins have quaternary structure.

Question 11

Primary structure

Answer 11

This is the sequence, type and number of amino acids in the amino acid chain, as well as the position of the disulphide bonds if present.
The sequence, type and number of amino acids determine it’s function and also differentiates every protein from each other.
The sequence of amino acids influences how the protein folds and hence its shape and final function.

If one amino acid is changed then the function can be disrupted or even stopped completely

Question 12

Secondary structure

Answer 12

The amino acid chain takes a particular shape by folding or coiling as a result of bonds that form between certain amino acids in the chain.
The order of amino acids determine where the hydrogen bonds form and so what shape occurs.

Two forms of secondary folding: the alpha helix and beta pleated sheet.

Question 13

Alpha helix

Answer 13

The alpha helix is held permanently in place by hydrogen bonds between amino acids in one part of the chain and those a little further along the chain.

Question 14

The beta pleated sheet

Answer 14

The beta pleated sheet folds in a concertina-like way, with hydrogen bonds connecting to an adjacent pleated sheet.

Hydrogen bonds are weak bonds, but the number of them present in such protein molecule help them maintain the stability of the molecule overall.

Question 15

Tertiary structure

Answer 15

A 3D shape of the protein molecule
Occurs after the secondary structure has become further coiled or twisted into a more complex shape
The final shape depends on how the structure twists or coils.
These complex shapes are held together by different types of bond that form because of the position of certain amino acids in the chain
The sequence of the amino acids in the chain determines the exact shape of the molecule.

Question 16

What are the two types of tertiary structures?

Answer 16

Globular and fibrous

Question 17

What is a globular protein

Answer 17

When the protein folds and coils to form a 3D shape
This makes globular proteins important molecules in metabolic processes.
Ex: enzymes
The globular shape of an enzyme gives it its active site.
Globular proteins are usually soluble, long with enzymes, form protein-based hormones, plasma proteins, antibodies and the components of the cytoskeleton.

Question 18

What is a fibrous protein?

Answer 18

Has a long fibrous structure
Important in structural roles such as keratin in hair and nails, collagen in skin, bone and cartilage.
Ex: Fibrin, a blood-clotting protein is a fibrous protein

Question 19

Bonds and interactions that stabilise the tertiary structures

Answer 19

Hydrogen bonds: individual bonds are weak but multiple help stabilise the structure
Ionic bonds 
Hydrophobic interactions 
Both of these occur between the R groups
Covalent bonds such as disulphide bonds

Question 20

Quaternary Structure

Answer 20

When more than one polypeptide chains are made. Two or more subnits
In this case, two or more chains are held together and function as a whole.
This protein will not function unless all subunits are together.
In some cases the polypeptide chains are identical, but in other cases they are not.
Enzymes often consist of two identical subunits.
In some an inorganic molecule or ion is also required for the protein to function.

Question 21

What is a prosthetic group

Answer 21

A non-protein part of a protein molecule that is permanently attached to the molecule and is vital for the normal functioning of the molecule.

Question 22

What is a conjugated protein

Answer 22

A globular protein with a prosthetic group such as haem in haemoglobin.

Question 23

Haemoglobin

Answer 23

Is a conjugated (globular) protein molecule with a quaternary structure and a haem (prosthetic) group containing an inorganic ion- the metal iron, which gives the typical red colour.
Human haemoglobin contains four polypeptide chains- two alpha chains and two beta chains- each linked with a haem group.
The four chains are held together by a number of different bonds to make a stable globular molecule with a specific shape designed to carry out the molecule’s function of oxygen transport.

Question 24

Examples of other globular protein molecules

Answer 24

Enzymes (amylase, catalase)
Antibodies
Protein-based hormones such as insulin

Question 25

How do the enzymes carry out their function of catalysing chemical reactions?

Answer 25

They rely on their 3D shape

Question 26

What is insulin

Answer 26

Is a hormone produced by the beta cells of the Islets of Langerhans in the pancreas. Made of two chains 21 amino acids in chain A 30 amino acids in chain B These chains are held together by three disulphide bridges. It is important hormone in controlling glucose levels in blood.

Question 27

What is Collagen?

Answer 27

Fibrous protein with a quaternary structure Has three polypeptide chains twisted around each other like a rope Each chain is made of three repeating amino acids. This structure is supported by hydrogen bonds and covalent bonds between the chains. Multiple chains form a collagen fibril by forming cross link between each other. Then multiple collagen fibrils for a collagen fibre.

Question 28

Properties of collagen

Answer 28

Provides support and strength in many structures of the body such as the heart and arteries, tendons and bone, and cartilage and skin.

Question 29

Other examples of fibrous proteins

Answer 29

Keratin and elastin Elastin has the ability to stretch and return to its original shape. It is found in connective tissue, tendons and bone.

Question 30

Comparison between haemoglobin and collagen (helical structure)

Answer 30

Haemoglobin is folded into a right-handed alpha-helical structure Collagen is wound into a left-hand helical structure

Question 31

Solubility of haemoglobin and collagen in water

Answer 31

Haemoglobin is soluble in water | Collagen is insoluble in water

Question 32

Types of amino acid in haemoglobin and collagen

Answer 32

In a haemoglobin molecule, most of the 20 different amino acids are present The collagen molecules are formed by just a few different types of amino acid. One of the three amino acids that form most of the collagen molecules is called glycine.

Question 33

Role of haemoglobin and collagen

Answer 33

Haemoglobin is responsible for transporting oxygen Collagen provides strength in many areas of the body such as artery walls, tendons, cartilage and bone, and also provides the elasticity of the skin

Question 34

Biuret test for proteins

Answer 34

Add sodium hydroxide to the protein suspension. Shake this mixture. A small amount of copper sulphate was then added drop by drop, shaking between each addition. The colour should change to purple.

Question 35

Calcium ions

Answer 35

Part of bone and enamel structure as calcium phosphate A cofactor in blood clotting An ion involved in nerve transmission across the synapse and in muscle contraction

Question 36

Sodium ions

Answer 36

An electrolyte Essential function in nerve transmission Essential in water reabsorption in loop of Henle and collecting duct

Question 37

Potassium ions

Answer 37

An electrolyte Essential in nerve transmission Essential in water reabsorption in loop of Henle and collecting duct Used in plant guard cells as part of the stomatal opening mechanism

Question 38

Hydrogen ions

Answer 38

Common bonds in biochemical molecules Involved in ATP formation Involved in the control of blood pH and in the transport of carbon dioxide

Question 39

Ammonium ions (NH4+)

Answer 39

An intermediate ion in the deamination of proteins

Question 40

Nitrate ion (NO3-)

Answer 40

Nitrogen source for green plants to manufacture proteins | It is the form taken up from soil

Question 41

Hydrogen carbonate (HCO3-)

Answer 41

Involved in carbon dioxide transport in the blood, with H+

Question 42

Chlorine ion

Answer 42

The shift of chloride ions into and out of red blood cells maintain pH balance during carbon dioxide transport

Question 43

Phosphate (PO43-)

Answer 43

as phospholipids, phosphates form part of cell membranes Forms calcium phosphate, an important constituent of bone for giving strength Constituent of ATP and nucleic acids

Question 44

Hydroxide (OH-)

Answer 44

One of the important ions in bonding between biochemical molecules

Question 45

Biosensors

Answer 45

Offer methods for obtaining quantitative results Is very precise and accurate analytical device. Converts biological response into an electrical signal using a highly specific and stable enzyme.

Question 46

Hydrophobic and hydrophilic interactions

Answer 46

If a protein is hydrophilic or hydrophobic depends on the R groups of the amino acids. Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecule shielded from the water in the cytoplasm.

Question 47

Breakdown of peptides

Answer 47

The enzyme, protease reverse peptides back to their constituent amino acids. A water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid groups.

Question 48

Insulin

Answer 48

Globular protein Hormone involved in the regulation of blood glucose concentration Transported in the bloodstream so need to be soluble. Also need to fit into specific receptors on cell-surface membranes to have their effect and therefore need to have precise shapes.

Question 49

Keratin

Answer 49

A group of fibrous proteins present in hair, skin and nails Contains a large proportion of the sulphur-containing amino acid, cysteine. This results in many strong disulphide bonds (bridges) forming strong, inflexible and insoluble materials. More disulphide bonds, less flexible the keratin molecule is

Question 50

Elastin

Answer 50

Fibrous protein found in elastin fibres Present in the walls of blood vessels and in the alveoli of the lungs- they give these structures the flexibility to expand when needed, but also to return to their normal size. Is a quaternary protein made from multiple tropoelastin molecules.

Question 51

Two types of nucleic acids

Answer 51

DNA (deoxyribonucleic acid) RNA (ribonucleic acid) These are polynucleotides

Question 52

What is the monomer molecule of a polynucleotide

Answer 52

Nucleotide

Question 53

What is the structure of nucleotide structure

Answer 53

Phosphate group Pentose sugar molecule Organic nitrogenous base

Question 54

What sugars do DNA and RNA have

Answer 54

DNA has deoxyribose | RNA has ribose

Question 55

Examples of Purines

Answer 55

Adenine Guanine Both purINEs have INEs in them

Question 56

How many rings do Purines have

Answer 56

Purines | Have two rings

Question 57

Examples of pyrimidines

Answer 57

Thymine Cytosine URACIL (only exists in RNA) pYrimidines have a Y in their names (except uracil)

Question 58

How many rings do pyrimidines have?

Answer 58

One ring

Question 59

What are bonds between the components in a nucleotide

Answer 59

Phospho-diester bonds form between the phosphate groups and the pentose sugars. Glycosidic bonds form between the pentose sugars and the organic nitrogenous base. Both of these are covalent bonds, formed by condensation reactions. Two condensation reactions occur- one between the sugar and phosphate group and another between base and sugar; thus forming two water molecules

Question 60

What is called the backbone of a DNA

Answer 60

The sugar-phosphate formation in a strand of DNA is known as the sugar-phosphate backbone.

Question 61

What structure does DNA have

Answer 61

A double-stranded helix

Question 62

What is different about the polynucleotide strands

Answer 62

They run in opposite directions- they are antiparallel | The DNA molecule twists to form the double helix structure

Question 63

What bond holds the two strands of DNA together

Answer 63

Hydrogen bonds 3 between G and C 2 between A and T The importance of the base pairing is that the molecule becomes very stable and is always the same width along the chain, because the bases hold the backbones the same distance apart.

Question 64

Why do the base A pair up to T and G to C

Answer 64

Purine bases and pyrimidine bases have complementary shape | This is known as complimentary base pairing

Question 65

There is 30% of Guanine in the DNA strand. How much Adenine is there?

Answer 65

If there is 30% of Guanine, there will also be 30% of Cytosine. This is because they pair up. There always be equal number of complimentary bases in a DNA strand. So, 30 + 30= 60% 100-60= 40% 40/2= 20% There will 20% of Adenine and 20% of Thymine

Question 66

At what phase of cell division, does DNA replicate itself?

Answer 66

Interphase

Question 67

What is DNA replication

Answer 67

Semi-conservative

Question 68

How does semi-conservative replication work

Answer 68

DNA first unzips and unwinds while breaking the hydrogen bonds between the bases. The enzyme Helicase is involved in the process of separating the two polynucleotide strands of DNA . These then act as template for the formation of a new molecule of DNA. Free floating nucleotides in the nucleus arrange themselves opposite the exposed complimentary bases of the DNA templates as the two polynucleotide strands separate. The enzyme, DNA polymerase catalyses the condensation reaction to covalently bond each nucleotide to the adjacent one along the sugar-phosphate backbone. The pentose sugars and the phosphate group forms the covalent bond, phosphodiester bonds.

Question 69

What is the result of semi-conservative replication?

Answer 69

By the end of the replication there are two identical DNA polymers. With each strand bonded with its complimentary strand.

Question 70

The four main differences between DNA and RNA

Answer 70

DNA's sugar molecule is deoxyribose RNA's sugar molecule is ribose The nitrogenous bases in a DNA strand are AGCT The nitrogenous bases in a RNA strand are AGCU There are two DNA strands There is always one single RNA strand There is only one type of DNA There are three types of RNA

Question 71

Other differences between DNA and RNA (only refer to these when the question is worth more than 4 marks)

Answer 71

DNA are bigger polymers DNA is also more stable DNA is only found in the nucleus whereas RNA is present in nucleus and cytoplasm. DNA has many base pairs but in RNAs, some bases are paired and some aren't

Question 72

Similarities between DNA and RNA

Answer 72

Made up of nucleotides Phosphodiester bonds form between each nucleotides by condensation reaction, forming a polymer (nucleic acid) Order of nitrogenous bases form code on the nucleic acid.

Question 73

3 types of RNA and their location

Answer 73

mRNA (messenger RNA) Made in the nucleus, travels to cytoplasm tRNA (transfer RNA) Cytoplasm rRNA (ribosomal RNA) In ribosomes Free in cytoplasm or attached to RER

Question 74

What are ATP and ADP

Answer 74

These are phosphorylated nucleotides Comprise of ribose (pentose sugar) adenine (an organic nitrogenous base) and inorganic phosphates. They are energy storage molecules where the energy can be released by breaking the bonds between phosphates. ATP has 3 phosphate groups and ADP has 2 phosphate groups

Question 75

Structure and function of ATP and ADP

Answer 75

ADP + phosphate group = ATP This is formed by a condensation reaction ATP - phosphate group (+ energy released) = ADP This is formed by hydrolysis ATP is the universal energy currency of all living organisms.

Question 76

Analogy for ATP and ADP

Answer 76

ATP is a like a charged battery which releases energy. However, when it breaks the bond between its third phosphate group, it turns into a dead battery (ADP) The phosphate group acts as a charger

Question 77

What is DNA- nucleic acid

Answer 77

The nucleic acid forms when two polynucleotide chains join together, by hydrogen bonds between nitrogenous bases, to form a double-stranded molecule.

Question 78

What is the gene

Answer 78

DNA is an extremely long molecule that codes for numerous proteins. Each short length of DNA known as gene is a sequence of bases that code for the amino acids making up a single protein. Because no two proteins are the same length, the length of the gene also varies.

Question 79

why could there be several triplets coding for the same amino acid

Answer 79

There are 20 different amino acids and 64 different combinations of triplet codes, therefore some triplets code for the same amino acid. This is known as the degenerate code. Ex: serine is coded by 6 triplets.

Question 80

What is the advantage of an amino acid being coded by multiple triplets

Answer 80

The advantage of having different codes for the same amino acid is that if a mutation causes a base to change, the triplet may still code for the same amino acid and therefore not change the protein produced.

Question 81

Examples of amino acids that only have one base triplet that code for

Answer 81

Methionine- AUG (this starts the amino acid chain) Tryptophan AGT, GAT and AAT code for full stops signalling the end of the message.

Question 82

Protein Synthesis- Transcription

Answer 82

In a gene that codes for a protein, one of the DNA strands is called a coding strand and the other is a template strand When this protein needs to be made, RNA polymerase unzips the DNA by binding it its strand. Then RNA polymerase then moves along the template strand in the 3' to 5' direction. As it moves along it pairs free RNA nucleotides with complementary nucleotides on the DNA template strand. These RNA nucleotides covalently bond through condensation reaction to form phosphodiester bonds. This creates a polynucleotide chain growing in the 5' to 3' direction, known as mRNA. So the mRNA and the coding DNA strand will have the same sequence of nucleotides- except uracil instead of thymine

Question 83

Translation

Answer 83

The mRNA leaves the nucleus through the nuclear pore, and travels to the ribosomes in the cytoplasm, or in the ER. These then sit on a ribosome, exposing its base triplets otherwise known as codons. Free floating tRNAs in the cytoplasm have a specific amino acid molecule at one end and a sequence of three bases (known as anticodon) at the other. These anticodons code for the amino acid attached to the tRNA on one end; and are also complimentary to the codons on the mRNA. The correct anticodon binds with its complimentary codon in the mRNA in the P site of the ribosome. Note that the E,P and A sites of the ribosome are formed when the two subunits (small subunit of 30s and large subunit of 50s) join. Another tRNA fills in the A site and its anticodon binds with the codon. The amino acids at the opposite end form peptide bonds. The tRNA on the P site detaches the amino acid from its structure and moves to the E site (which is next to the P site) and leaves. Simultaneously the tRNA in the A site with two amino acids shift to the P site. Another tRNA follows and fills in the A site. Its anticodon binds with the codon on the mRNA. Then the chain of two amino acids on the tRNA (in the P site) form another peptide bond with the amino acid on the tRNA (in the A site). This goes on until a stop codon is reached. Note that the ribosome moves; not the mRNA strand.

Question 84

What enzyme is responsible for forming the peptide bonds

Answer 84

Peptidyl transferase

Question 85

How does a stop codon work

Answer 85

When the stop codon is reached while forming the peptide chain, it is thought that there are two possibilities that occur at this time. First being that the anticodon of a tRNA with no amino acid molecule attached to it, binds with the codon. Thus stopping the chain. Second possibility is that no tRNA binds with the codon. So, this isn't translated.

Question 86

What happens after the peptide chain has been formed

Answer 86

These then are packaged off as transport vesicles to the Golgi Apparatus. Here they are modified (folded into its specific tertiary or quaternary structure). They enter the Golgi Apparatus through a process called exocytosis. This is when the vesicle fuses to the membrane of the Golgi Apparatus. After they are modified, they are sent off as secretory vesicles from the cis network of the golgi body. They travel through cytokinesis and fuse to the cell surface membrane by exocytosis. After it has been modified, it is send off as a secretory vesicle; which travels through cytoskeleton to the cell surface membrane and fuses to it through exocytosis.

Question 87

Features of DNA compared to features of RNA- information code

Answer 87

DNA: The base sequence is a code used to build proteins RNA: It copies the DNA code by hydrogen bonding RNA nucleotides to the DNA bases and forming a chain of mRNA

Question 88

Features of DNA compared to features of RNA- | Replication

Answer 88

DNA Each DNA molecule has one of the old polynucleotide chains (template strand) and one new chain (coding strand). It is replicated by semi-conservative replication. RNA transcription

Question 89

Features of DNA compared to features of RNA- size of molecule and information stored

Answer 89

DNA- Large amounts of information can be stored because the strand is extremely long. RNA- molecules are shorter because small amount of information is copied each time

Question 90

How is DNA chain held together (mark scheme)

Answer 90

``` Phosphodiester bonds between the phosphate and sugar Hydrogen bonds between the bases Purines to pyramidines 3 H bonds between C and G 2 H bonds between A and T ```