How do enzymes work and what is the role they play in the process of metabolism?

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TAQ1

If a DNA sequence gives rise to the following RNA fragment AUG-CGU-AAA-GCA-GAG-GGA-CAA-UAA

1 – How has this been formed from the DNA strand? (150 words)

2 – How is this RNA then transformed into a protein? (150 words)

1 – The enzyme RNA polymerase has synthesised this RNA fragment from a template strand of DNA. Transcription factors inserted RNA polymerise between the strands of DNA, which then uncoiled and unzipped a small portion of the double helix. Travelling the length of the transcription unit, the RNA polymerase broke the weak hydrogen bonds holding the nucleotide subunits together. The exposed bases then attached to their complementary nucleotide bases which had entered the enzyme through the intake hole, creating this strand of messenger RNA (mRNA). RNA nucleotide bases differ from DNA bases in one respect: DNA is made up of Cytosine (C), Guanine (G), Adenine (A) and Thymine (T), but as RNA’s oxygenated sugar units do not bind to Thymine, it is replaced by Uracil. The Cytosine bases bonded with Guanine bases, and Adenine bases with Uracil, thus the DNA template which gave rise to this RNA fragment was: TAC-GCA-TTT-CGT-CTC-CCT-GTT-ATT. The resulting strand of RNA then detached from the single DNA strand.

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160 words

2 – The newly-formed strand of mRNA is transported to the cytoplasm through the nuclear pore complex. Here it enters organelles called ribosomes, which hold the mRNA in place – triggering the approach of a tRNA carrying the first amino acid. Each of the triplet codes (codons) on the mRNA template must match up with their exact complementary triplet (anticodon) on the tRNA. The next tRNA pairs up the anticodon for the subsequent mRNA triplet, and so on – from the start codon to the stop codon. Peptide bonds join the amino acid carried by each tRNA with its neighbouring amino acid, creating a long chain (polymer) which separates from the ribosomal fragments when the process is complete, whereupon a protein has been synthesised. The unique sequence of the hundreds of amino acids in the polymer determines the three-dimensional shape of the protein, and that shape determines the protein’s function.

146 words

TAQ2

Part 1 – Discuss the work of the Austrian Monk Gregor Mendel. Your work should include Mendel’s rules of inheritance (200 words)

Gregor Mendel’s Law of Segregation resulted from his monohybrid cross experiments, where he cross-fertilised pea plants with specific characteristics to examine how they passed on their traits to subsequent generations. For instance, by crossing pure red-flowered plants with pure white-flowered, he found the first generation of offspring were all red, but one in every four of the second generation were white-flowered. Identifying such patterns in offspring phenotypes, Mendel’s hypothesis stated that, through meiosis, individuals inherit two separate, randomly-selected alleles (hereditary factors) for every trait, one from each parent. These alleles are dominant or recessive, which influences how the offspring express that trait.

Mendel also experimented with dihybrid crosses to see whether separate genetic traits affect one another. Discovering that all four phenotypes were produced in the same ratio (9:3:3:1) when cross-breeding round, wrinkled, yellow and green seeds led to the second of his most important rules. The Law of Independent Assortment states that the alleles of different genes are selected entirely independent of one other during gamete formation. Thus, for instance, there is no relation between a person’s ear shape and eye colour.

Although Mendel’s work was disregarded during his lifetime, Mendelian inheritance became properly recognised in the early 1900s and he is now known as the father of modern genetics.

211 words

Part 2 – In humans there is a gene that controls formation of muscles in the tongue allowing people with those muscles to roll their tongue and those without to be unable to do so. This gene is expressed as a dominant gene. Using a Punnett diagram as part of your answer, discuss the children of a homozygous non tongue roller (recessive) and a heterozygous roller and what proportion of children they would have (100 words)

A homozygous tongue-roller has two recessive genes (rr) while a heterozygous roller has one dominant and one recessive (Rr). Analysing a monohybrid cross, we can assume that if they had four children, two would be tongue-rollers and two would not. As the Punnett diagram demonstrates, the second parent’s single dominant gene ensures their children would have a 50/50 chance of being rollers; the first parent’s two recessive genes – combined with the second parent’s single recessive gene - would give a 50/50 likelihood of being rr. None of their children could be a homozygous tongue roller (RR).

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rr x Rr

r

r

R

Rr

Rr

r

rr

rr

107 words

Part 3 – There is a chemical called Phenylthiocarbamate which some people can taste and others can’t due to their genetics, the ability to taste the chemical is a dominant trait. Using a Punnett diagram discuss how two heterozygous parents would have children that can taste and those that cannot and the proportions (100 words)

As both heterozygous parents would have one dominant gene and one recessive, they would both be Pp. The Punnett diagram shows that, if they had four children, three-quarters of them would be able to taste Phenylthiocarbamate. One child would inherit two dominant genes (PP) and two children could be expected to inherit one dominant and one recessive gene (Pp) – all three of whom would therefore be able to taste the chemical. In only one instance would two recessive genes (pp) be passed down, leaving that child unable to taste PTC.

Pp x Pp

P

p

P

PP

Pp

p

Pp

pp

101 words

Part 4 – Suppose a woman who is both a homozygous tongue-roller and a non-PTC-taster marries a man who is a heterozygous tongue-roller and is a heterozygous PTC taster. If these parents have plenty of children so that they had 16 in all, how many of those would you expect in each class? (100 words)

The woman’s genotype is RRpp; the man’s is RrPp. The woman’s alleles give just one potential parent gamete - Rp - since she is homozygous in both. The man’s alleles give four potential gametes (RP, Rp, rP, rp) as he is heterozygous in both. The Punnett diagram reveals a 1:1 phenotype ratio among their offspring: eight children would be tongue-rollers and PTC-tasters; eight would be tongue-rollers and non-PTC tasters. No offspring would be non-tongue-rollers due to the mother’s dominant homozygous genes.

RP

Rp

rP

rp

Rp

RRPp

RRpp

RrPp

Rrpp

Rp

RRPp

RRpp

RrPp

Rrpp

Rp

RRPp

RRpp

RrPp

Rrpp

Rp

RRPp

RRpp

RrPp

Rrpp

105 words

TAQ3

Complete a table similar to the one below (300 words)

Lipids

Carbohydrates

Proteins

Chemical structures

Carbon, hydrogen

and oxygen

Carbon, hydrogen

and oxygen (1:2:1)

Amino acid polymers joined by peptide bonds. Every acid has an amine group (NH2) consisting of two hydrogens, a nitrogen atom and a carboxylic group (COOH). Each acid’s unique side chain determines its chemical properties.

Roles in nature

Fats store energy by converting excess fatty acids into fat cells. This adipose tissue acts as both thermal insulator and shock absorber.

Cell walls are made up of phospholipids. In the lipid bilayers, hydrophilic phosphate heads line up on the outside to protect the hydrophobic fatty acid tails from the surrounding water, creating the membrane.

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Cholesterol is one of the important steroids in the body, giving essential fluidity to the cell wall.

Energy creation (especially for the brain and central nervous system): glucose is necessary for the production of ATP.

Energy storage: starch stores energy in plants; glycogen stores energy in animals.

Structure: carbohydrates help form cell walls in bacteria, plants (cellulose) and animals.

Cell-cell recognition: carbohydrates attached to proteins (glycoproteins) and coating cell surfaces can facilitate cell-cell recognition and signalling.

A protein’s primary structure is the unique sequence of amino acids in its polypeptide chain; the way that chain then folds after synthesis (e.g. into a helix or a beta pleated sheet) is its secondary structure. The final 3D shape (usually globular or fibrous) of the polypeptide chain bonded to other secondary structures is its tertiary structure; if a protein is made up of more than one major polypeptide chain folded together, this is its quaternary structure.

This vast range of potential structures and behaviours means proteins serve a huge number of functions. Examples include: defence (antibodies protect the bodies from disease); structural support (collagen supports body tissues and makes skin waterproof); transport (membrane gateways ferry ions into or out of cells); communication (insulin regulates blood sugar levels); catalysts (enzymes speed up chemical reactions) and storage (ferritin stores iron).

322 words

TAQ4

How do enzymes work and what is the role they play in the process of metabolism? (300 words)

Enzymes are biological catalysts which speed up and control chemical reactions within an organism. They do this by reducing the amount of activation energy needed to carry out a reaction. The hollow in an enzyme’s surface – caused by the way it folded into its tertiary or quaternary structure – is known as its active site. Only the specific molecule with which the enzyme can react (known as the substrate) is able to fit the active site in order to bind. Due to this lock and key model, if the wrong substrate (‘key’) tries to enter the active site, it will not fit and may even jam the ‘lock’ – although very occasionally, the active site will alter shape to allow a competitor substrate to fit it (this is known as induced fit).

Catalase is an enzyme found in the cells of most organisms exposed to oxygen. When the substrate hydrogen peroxide (H2O2) enters the active site, the enzyme pulls on it to lower its activation energy, allowing the chemicals to break apart into water and oxygen. Catalase can do this millions of times in a very short space of time because, like all enzymes, it is not used up or permanently changed by the reaction process. This particular catalytic process protects tissues from being damaged by peroxide, a by-product of metabolism.

Metabolism is the name for the thousands of chemical reactions of a cell. These reactions can be either anabolic (synthesis) or catabolic (degradation). In catabolic reactions, such as the example above, enzymes break down macro molecules into their smaller component parts. Where the enzyme joins two simple substances together, this is an anabolic reaction. In anabolism, the active sites are located next to each other so that the two substrates can bond during catalysis.

293 words

TAQ5

There are two major pathways involved in the production of energy within the cell. What are they and how do they link to each other? (300 words)

All living cells need to respire, as this releases energy (in the form of ATP). Both of the two major pathways release ATP from the breakdown of glucose; however one does this in the presence of oxygen, the other when there is not enough oxygen.

Aerobic respiration involves three metabolic processes to create energy from glucose and oxygen. In the cell’s cytoplasm, glycolysis first breaks the six-carbon glucose molecules into two three-carbon pyruvate molecules and two molecules of ATP, as well as two NADH molecules. The pyruvate is then converted into acetyl-CoA in the mitochondrial matrix. During the Krebs cycle, this acetyl-CoA is broken down further to give off carbon dioxide and produce two more molecules of ATP, as well as adding energy to NADH and FADH2. In oxidative phosphorylation, the high-energy electrons in NADH and FADH2 are transferred to the inner mitrochondrial membrane where an electron transport chain enables the release of energy in the form of about 32 ATP molecules.

Cells constantly use aerobic respiration, but when not enough oxygen is present (e.g. during strenuous exercise), anaerobic respiration is needed. Both respiratory pathways start with glycolysis, which releases two ATP molecules. But in the absence of oxygen, the NAD molecule is restored to its oxidised state through lactic acid fermentation, instead of in the mitochondria. The enzyme lactate dehydrogenase transfers the NADH’s hydrogen molecule to the pyruvate molecule, creating a lactate molecule and regenerating NAD+ to constantly repeat the glycolysis process, making two ATP molecules every time. Lactic acid eventually becomes toxic and is painful if it builds up in the muscles, so we breathe heavily after physical exertion as oxygen is needed to break the acid down; the amount needed is called the ‘oxygen debt’.

Anaerobic respiration (which all takes place in the cytoplasm) only releases around 5% of the energy released per glucose molecule during aerobic respiration, because the breakdown of glucose is only partial.

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