Topic 1: DNA and Proteins Flashcards

Question

Describe the nature of DNA in prokaryotic cells.

Answer 1

In prokaryotic cells, DNA is free-floating, drifting around the cytosol of the cell. It is also circular.

Answer 2

DNA is also unbound and circular in the chloroplasts and mitochondria of eukaryotic cells.

Answer 3

A karyotype is a picture made up of images of a cell's chromosomes, the photos are taken during cell division and are ordered in their homologous pairs and in size order.

Answer 4

When a cell divides, it copies its DNA before dividing, allowing each daughter cell to receive a copy. In sexual reproduction, each individual receives half of a parent's genetic material.

Answer 5

Weak hydrogen bonds so they can be easily broken for new strands to be synthesised along the exposed bases. Complementary base pairing allows for new strands to be synthesised that are perfectly accurate complementary strands.

Answer 6

Universal. The complementary base pairing system and method of DNA replication applies to all life on earth.

Answer 7

DNA replication is described as a semi-conservative process as it produces two daughter DNA molecules from one parent DNA molecule, and each daughter DNA molecule inherits one strand of DNA from the parent molecule and has one newly synthesised strand, conserving some of the parent DNA molecule in each daughter DNA molecule.

Answer 8

DNA helicase enzyme.

Answer 9

DNA is unzipped in DNA replication to expose the bases of the two DNA strands, allowing for new strands to be formed by attaching to them, following the complementary base pairing system.

Answer 10

DNA polymerase enzyme, starting from the 3' direction.

Answer 11

Most of the chemical compounds that make up a cell are manufactured by the cell itself.

Answer 12

Each manufacturing process in producing chemical compounds for a cell requires many chemical reactions, each step being catalysed (caused or accelerated) by a specific enzyme.

Answer 13

Enzymes are protein molecules made from one or more polypeptide chains

Answer 14

No. There are many protein molecules in cells that are not functiona (i.e., enzymes), but are instead structural, such as keratin (found in hair, nails) and collagen (found in tendons, ligaments).

Answer 15

DNA is unable to leave the nucleus, however, protein synthesis requires the help of ribosomes, which are located in the cytoplasm. So, DNA transcribes a copy of its information, making an mRNA strand, so that the genetic code can be taken out of the nucleus for protein synthesis.

Answer 16

The genetic code of DNA codes for enzymes, which direct the metabolism of the cell (the chemical reactions that take place)

Answer 17

Transcription is the process by which a working copy of DNA is produced (an mRNA strand) and occurs in the nucleus.

Answer 18

First, the enzyme RNA polymerase unzips the relevant region of the DNA molecule. The enzyme then attaches free-floating RNA nucleotides to the exposed bases of one of the DNA strands, the template strand (also called the non-coding strand), to produce a single strand of messenger RNA (mRNA). Whilst following complementary base pair rules when joining free-floating nucleotides, the base thymine is replaced with uracil, which bonds to adenine instead. After being produced, the mRNA stand then peels off and enters the cytoplasm via a nuclear pore, carrying the code outside the nucleus. The DNA then zips up again.

Answer 19

DNA polymerase is an enzyme used to attach free-floating nucleotides to exposed DNA strands during DNA replication to produce a strand of DNA. RNA polymerase has the same function but also unzips part of the DNA molecule and is used during transcription To produce an mRNA strand. RNA polymerase also attaches the nucleotide base uracil instead of thymine to the exposed bases.

Answer 20

The start codon (TAC) indicates the beginning of a gene on a DNA molecule.

Answer 21

The mRNA strand produced in transcription is identical to the strand of DNA that did not act as the template strand, the non-template strand, which is called the coding strand. (Identical except the mRNA replaces thymine with uracil and ribose sugar).

Answer 22

Translation is the process that occurs when the mRNA strand from transcription moves outside of the nucleus and into the cytoplasm. In the cytoplasm, the mRNA strand attaches to a ribosome on the rough endoplasmic reticulum. tRNA molecules then begin to bring in specific enzymes to the ribosome, matching up their anti-codons (exposed base triplets on one end of the molecule) with their corresponding complementary codons on the mRNA strand with the help of the ribosome which acts as a site where the tRNA and mRNA are brought together. As more tRNA molecules bring in more amino acids, the amino acids join with a peptide link, forming a polypeptide chain, and then the tRNA molecules are released, having completed their function, delivering their amino acids. When the ribosome reaches the end of the mRNA strand and the polypeptide chain of amino acids has been completed, it breaks away from the ribosome and folds into its final protein shape, ready to carry out its function.

Answer 23

Translation is the process where a protein (polypeptide chain made up of a chain of amino acids) is produced. It occurs in the cytoplasm, specifically in ribosomes, which the mRNA strand attaches to. It is located on the rough endoplasmic reticulum.

Answer 24

Ribosomes themselves are made up of RNA and proteins. The RNA in ribosomes is a special type produced in the nucleolus, a region in the nucleus. It is called ribosomal RNA (rRNA)

Answer 25

Base triplets called codons, each one coding for a specific amino acid. There are also codons for 'start' and 'stop', indicating the beginning and end of the instruction for the synthesis of a protein.

Answer 26

Transfer RNA (tRNA) is another type of RNA that is about 80 nucleotides long and is folded into a t shape. At one end there is an exposed triplet of bases, an anticodon, and at the other end a specific amino acid is attached.

Answer 27

tRNA molecules bring their specific amino acids to the ribosome in translation, matching up with the complementary codon on the mRNA with the help of the ribosome, which acts as the site where the tRNA and mRNA are brought together.

Answer 28

As more tRNA molecules bring in more amino acids, the amino acids join with a peptide link, forming a polypeptide chain, and then the tRNA molecules are released.

Answer 29

When the ribosome reaches the end of the mRNA strand and the polypeptide chain has been completed, it breaks away from the ribosome and folds into its final protein shape, ready to carry out its function.

Answer 30

1. Initiation - the use of the start codon AUG. 2. Chain elongation - the building of the amino acid sequence (polypeptide chain) from the codons. 3. Termination - the completion of the mRNA sequence with one of the step codons, UAG, UAA, or UGA. The polypeptide chain is completed and released. All three stages require energy and enzymes.

Answer 31

Having one nucleotide base (A,U,C,G) code for one type of amino acid would mean only four different amino acids could be designated out of the 20 amino acids that make up proteins. Having triplets of nucleotide bases code for an amino acid allows for 64 combinations, more than enough to code for each amino acid, even allowing for some 'punctuation marks' and some amino acids being coded for by more than one codon.

Answer 32

An exon is a DNA sequence that is translated ('expressed') into proteins, called a coding sequence. An intron is a sequence that is transcribed but then edited or spliced out of the mRNA before translation, called a non-coding sequence. Their key difference is that the exons contain genetic code used in translation to form a polypeptide chain, while introns are only transcribed and spliced shortly after as they do not contain any genetic information for protein synthesis.

Answer 33

Introns are common in more complex eukaryotic cells, which have many introns. They are more uncommon in more simple eukaryotic cells, which have hardly any introns in their DNA, and they are even rarer in prokaryotic cells.

Answer 34

Macromolecules are big molecules. Proteins are macromolecules made up of one or more polypeptide chains.

Answer 35

Polypeptide chains are polymers made up of amino acids joined by peptide bonds.

Answer 36

Carbon, hydrogen, nitrogen, oxygen, and some sulfur (CHNO and some S)

Answer 37

Only 2 of the 20 amino acids contain sulfur, and not every amino acid sequence must have these amino acids, so not every protein may have sulfur.

Answer 38

The number of amino acids ranges from 20-1000s, each ordered with a unique sequence of amino acids. The possible combinations of proteins with these two criteria is seen as almost limitless.

Answer 39

The sequence of amino acids of a polypeptide chain determine the way the polypeptide chain will fold up after it is made, giving it a specific 3D shape. This shape determines how the protein functions. This folding must be very precise to achieve specific shapes.

Answer 40

Primary, secondary, tertiary, and quaternary.

Answer 41

The first level of the structure of a protein is the primary structure, the sequence of amino acids in the polypeptide chain/s. Its structure is determined by the sequence of bases on the mRNA strand that codes for its amino acid sequence. The mRNA base sequence is determined by the sequence of bases on the DNA that was transcribed.

Answer 42

The second level of the structure of a protein is the secondary structure, the coiling or folding of sections of the polypeptide chain. These sections are alpha-helices and beta-pleated sheets. Its structure is determined by its primary structure, which determines the positions of the hydrogen bonds that produce the coils and folds.

Answer 43

The third level of the structure of a protein is the tertiary structure, the 3D shape of the entire polypeptide chain. Its structure is determined by its primary and secondary structures. Disulfide bonds and hydrogen bonds play an important role.

Answer 44

The fourth level of the structure of a protein is the quaternary structure and consists of two or more polypeptide chains. Not all proteins have a quaternary structure, as many are made up of one polypeptide chain.

Answer 45

Fibrous proteins - long and narrow strands - have a structural role, they ARE something. Globular proteins - more compact and round shape - have a functional role, they DO something.

Answer 46

Structural - in hair and nails (keratin), ligaments (collagen). Catalyse reactions - enzymes (e.g., polymerase). Transport - carrying oxygen (haemoglobin). Defence - antibodies produced by white blood cells (immunoglobulins). Coordination - hormones (e.g., insulin)

Answer 47

Some types of proteins are enzymes, some hormones, receptor proteins and antibodies. The specific structure of proteins allow for them to all have different functions.

Answer 48

Some, but not all, hormones are made of protein. Hormones are chemical messengers that are secreted into the blood and transported around the body; however, a particular hormone will only produce an effect in cells, tissues, or organs that are 'tuned in' to that hormone by having receptors (signal-receiving molecules) with shapes complementary to part of the hormone molecule These structures are called target cells, target tissues, and target organs An example of a protein hormone is insulin, which regulates blood sugar levels

Answer 49

Cell receptors are special protein molecules that send and receive signals. Protein receptor molecules are found in cells and allow for hormones to bind to them. The region of the receptor molecule that has a shape complementary to that of a specific hormone is called the binding site.

Answer 50

Antibodies, called immunoglobulins, are protein molecules that bind to antigens (cells that the body does not recognise), stopping them from functioning in order to protect the body. A 3D region on the antibody called the antigen site allows for this to occur.

Answer 51

Proteins work because of their 3D shape, examples including enzymes, some hormones, receptor proteins, and antibodies, all of which require a specific structure to carry out their functions. Many genetic diseases are due to the person's cells producing proteins which have an abnormal 3D structure, such as sickle-cell anaemia, Tay-Sachs diseases and cystic fibrosis.

Answer 52

An enzyme is a globular (has a functional role) protein, catalysing the reactions of a cell.

Answer 53

Enzymes are specific for a particular reaction, meaning that every step in a metabolic pathway (a sequence of chemical reactions in a cell) is catalysed by a different enzyme.

Answer 54

Enzymes are specific for particular reactions due to their specific 3D structures, determined by the different levels of protein structure.

Answer 55

An active site is a region on an enzyme that is specific to each enzyme with a specific shape. It allows for the enzyme to bind with its specific substrate (a molecule an enzyme reacts with), which will only happen if the shape of the active site is complementary to the shape of the substrate.

Answer 56

Any small change in the structure of the active site on an enzyme may stop the enzyme from binding to its specific substrate, meaning the enzyme loses its ability to catalyse the reaction.

Answer 57

Majority of enzymes catalyse reactions within cells and are called intracellular, however some enzymes, although produced by cells, act outside cells and are called extracellular enzymes.

Answer 58

There are two theories of enzyme action (the actions of enzymes to catalyse chemical reactions): Lock and key interaction/model: Active site of enzyme has a shape that exactly matches the substrate so that they fit like a lock and key. Induced fit model (current main theory): The substrate binds to the active site of the enzyme, forming an enzyme substrate-complex. When the two join together, the site changes its shape to produce a 'close fit' to the substrate. The enzyme-substrate complex then undergoes the reaction far more easily than the substrate would have if there were no enzyme present. The products are produced and break away from the enzyme, leaving the enzyme free to be reused to repeat the process. It is called the induced-fit model as the change in the active site shape is induced (changed in response to) the substrate binding.

Answer 59

It is called the induced-fit model as the change in the active site shape is induced (changed in response to) the substrate binding.

Answer 60

Activation energy is the energy required for a chemical reaction to start. It can be compared to the match that lights the wood of a bonfire, starting the fire up.

Answer 61

Enzymes work by lowering the activation energy needed to start chemical reactions, speeding up the rates of chemical reactions occurring.

Answer 62

Enzymes are able to lower the activation energy required in a chemical reaction in one of the following ways: Bringing the reactants together in the correct orientation, so that they react more easily and reducing the energy they need to come together in the right orientation to react. Binding to a substrate molecule in a way that puts strain on its chemical bonds, making it more likely to react. This accelerates the reaction as less energy is required to break these bonds. Making the reaction happen in several steps, each of which requires only a small amount of activation energy. A different, specific enzyme controls each step.

Answer 63

Enzymes are sensitive to changes in their immediate environment due to their protein nature. Their activity is affected by the temperature, level of acidity (pH), and the presence of chemical inhibitors. Different enzymes operate best at different temperatures and pHs.

Answer 64

When the temperature exceeds the optimal temperature range of an enzyme, the shape of the enzyme is denatured (altered), including the active site, causing it to lose its ability to catalyse reactions. When the temperature drops below the optimal range, the rate at which substrate molecules collide with active sites lessens (more heated particles move faster, colliding more), decreasing the rate of reaction. When the temperature exceeds an enzyme's optimal temperature range, its shape will alter. This is known as the enzyme denaturing, and results in a change in the active site, meaning that it is no longer able to bind to its specific substrate and hence can no longer carry out its function of catalysing reactions.

Answer 65

When the pH level goes outside the optimal pH range of an enzyme, the enzyme will be denatured (altered), including the active site, causing it to lose its ability to catalyse reactions, similar to altering the temperature.

Answer 66

Enzymes may be inhibited (prevented from reacting) by certain chemicals called inhibitors. If an inhibitor were to bind permanently to an enzyme, then the enzyme would be rendered completely ineffective, being unable to catalyse reactions. There are two types of inhibitors: Competitive inhibitors - compete with the substrate for the active site, blocking it Non-competitive inhibitors - bind elsewhere on the enzyme, not blocking the active site, but distort the shape of the enzyme so that the active site no longer has a shape complementary to the substrate

Answer 67

For the same concentration of enzymes, increasing the concentration of reactant (substrate) molecules will increase the rate of reaction until all of the active sites on the enzyme molecules are occupied. Then, the rate of reaction will remain constant as all the active sites are saturated.

Answer 68

For the same concentration of reactant (substrate) molecules, increasing the concentration of enzyme molecules will increase until there are no more substrates for enzymes to bind to.

Answer 69

A metabolic pathway is a series of chemical reactions that occur in a specific sequence of many steps.

Answer 70

Some advantages of having metabolic pathways taking place in regulated steps are: The cell can exert greater control as each step uses a different specific enzyme They can be stopped at certain steps by inhibiting the corresponding enzyme so that intermediate products can be used elsewhere by the cell. The cell releases energy more gradually. A portion can then be trapped to be used in other processes. Having multiple enzymes can also speed up the overall reaction rate.

Answer 71

If chemical reactions in a cell occured in one big step, there would be an instantaneous release of a large amount of energy as heat, which could burn the cell. Having metabolic pathways in smaller steps allows for a more gradual release of this energy, keeping the cell safer.

Answer 72

A genotype of an organism is a set of genes responsible for a specific characteristic.

Answer 73

A phenotype is the result of a gene being expressed (transcribed and translated into a functioning protein), and refers to the physical, biochemical, or physiological characteristics of an organism.

Answer 74

The phenotypic expression of a gene refers to the physical, biochemical, or physiological features that it (the gene) produces.

Answer 75

Some examples of the phenotypic expression of genes are: Physical - hair colour Biochemical - blood type Physiological - muscle tissue elasticity

Answer 76

The expression of genes to form polypeptide chains involves transcription and translation. On the other hand, the expression of genes to form polypeptide chains involves transcription only.

Answer 77

The expression of genes can be regulated at its transcription or its translation.

Answer 78

Long-term regulation of gene expression is more likely to occur at the transcription stage, whereas regulation requiring a more immediate response is likely to occur at the translation stage.

Answer 79

A transcription factor is a regulatory protein (product of a gene) that controls gene expression, thus affecting the phenotypic expression of genes.

Answer 80

A promoter region is a specific site on a DNA molecule that allows for proteins to bind to them to start the transcription of its specific gene.

Answer 81

Some transcription factors can switch genes 'on' by binding to the promoter region of a gene, these are activator transcription factors. Other transcription factors can turn genes 'off' by blocking the attachment of RNA polymerase to the DNA, preventing transcription, and these are called repressor transcription factors.

Answer 82

Transcription factors can be activated by specific hormones, meaning that gene expression can be determined by the presence (or absence) of certain hormones.

Answer 83

Transcription factors can be activated by specific hormones, meaning that gene expression can be determined by the presence (or absence) of certain hormones. These hormones enter the cell and bind to a protein receptor molecule to form a hormone-receptor complex, which activated proteins that are transcription factors.

Answer 84

Some proteins can prevent translation by binding to mRNA, preventing its translation and hence the expression of the gene. Also, small interfering RNA (siRNA) can cut mRNA after transcription, preventing it from being translated

Answer 85

Environmental factors can affect protein synthesis and this changes the phenotypic expression in an organism. Examples of factors and effects on the phenotypic expression are: Increased UV exposure - change in skin colour Malnutrition - reduced body size

Answer 86

A zygote is a single cell formed by the union of a sperm and an egg and is the basis of all the cells of a sexually reproducing organism.

Answer 87

As a zygote begins to divide, creating more cells, these cells begin to differentiate.

Answer 88

Cell differentiation is the process by which unspecialised cells develop a range of differing shapes, structures and functions through controlled gene expression, becoming specialised.

Answer 89

Through cell differentiation, cells can become specialised. This is possible as not all genes of a cell are expressed: certain genes in these cells are active or switched on, whilst others are inactive/silent or switched off.

Answer 90

Tissues are made up of cells of like form and function, examples include muscle tissue, made up of muscle cells, and nerve tissue, made up of nerve cells.

Answer 91

The genes expressed in a cell produce specific proteins that determine the final structure and function of the cell.

Answer 92

Cells that are not specialised are known as stem cells, and can be useful in repairing faulty or damaged tissue in patients as they can take on any function.

Answer 93

DNA methylation is the addition or removal of a methyl group from a cytosine nucleotide by the enzyme DNA methyltransferase. Methylation silences a gene by inhibiting the function of RNA polymerase Demethylation activates a gene, allowing for transcription to occur.

Answer 94

It is difficult for transcription to occur in condensed DNA as transcription factors are unable to bind to promoter regions as they are buried in histones.

Answer 95

Histone acetylation can cause changes in how tightly DNA is coiled around histones, therefore affecting gene expression. Acetylation can cause DNA to loosen, allowing for transcription factors to bind to promoter regions and allow for genes to be expressed. Deacetylation causes the DNA to tighten around the histones, inhibiting gene expression by blocking the promoter regions.

Answer 96

Epigenetics refers to the heritable phenotypic changes that DO NOT involve alterations in the DNA sequence, but instead involves the switching on and off of genes.

Answer 97

Epigenetics involves the processes of DNA methylation and histone acetylation.

Answer 98

The processes of DNA methylation and histone acetylation are both epigenetic modifications (epi = above, so modification above/on the gene).

Answer 99

Some epigenetic markers are the methyl groups and acetyl groups from methylation and acetylation (which are epigenetic modifications).

Answer 100

The epigenome of a cell is comprised of all the epigenetic markers attached to the genome of that given cell.

Answer 101

Epigenetic markers can be passed on from one generation of a cell to the next through cell division. This is important as when an embryo is developing a liver cell (for example), when that cell undergoes division, the daughter cells must be identical, with the same genes being activated and silenced, so these epigenetic factors that determine this must be passed on. When a sperm and an egg cell combine to form a zygote, many of the epigenetic markers on their DNA are removed, although some can remain, influencing the gene expression of the offspring.

Answer 102

The genome of identical siblings and clones should stay the same (although they may vary slightly due to mutations). The epigenome of identical siblings (or clones) can differ over time as they are exposed to different environmental factors that cause epigenetic changes, causing their phenotypes to become different over time.

Answer 103

DNA methylation can be influenced by environmental factors such as: Temperature Oxygen levels Humidity Light cycles These can all trigger DNA methylation, impacting gene expression and hence the phenotypic expression of genes

Answer 104

DNA methylation can be influenced by lifestyle factors (the same meaning as environmental basically) such as: Diet Exercise Stress Drug use Infectious agents These factors can influence DNA methylation and hence impact gene expression and their phenotypic expression.

Answer 105

Epigenetic factors can silence or activate genes that should not normally be silenced/activated, causing abnormal proteins to be produced, or no proteins of that type at all.

Answer 106

Cancer is a genetic disease where the genes which usually control cell division have been disrupted, leading to uncontrolled cell division. This forms tumours, which disrupt local tissues, leading to tissue damage.

Answer 107

Genes that control cell division are: Proto-oncogene - promotes cell division Tumour suppressing gene - inhibits cell division Demethylation of proto-oncogenes can activate them and initiate unregulated cell division. Methylation of tumour suppressing genes can silence them, initiating unregulated cell division as there is nothing to stop it.

Answer 108

Mutations are permanent changes in the DNA sequence of genes. They can occur spontaneously or be induced.

Answer 109

Mutations can occur: During DNA replication During cell division (mitosis and meiosis) By exposure to certain factors

Answer 110

Mutations can occur spontaneously, such as attaching the wrong base to a DNA strand in DNA replication. Cells do have a mechanism for correcting such errors, but even so, some may remain.

Answer 111

DNA mutating during DNA replication could result in a different amino acid sequence being produced when this mutated strand is used for protein synthesis, which can change the 3D structure of the protein, which can impact the function of the cells and possibly the whole organism.

Answer 112

Some types of mutations are: Point mutation of DNA base sequence (substitution) Frame shift of DNA base sequence (insertion or deletion) Chromosomal mutations where parts of or whole chromosomes are involved

Answer 113

A point mutation is a change in a single base pair in a DNA sequence and affects the way just one codon is read.

Answer 114

The effect of a point mutation can range from no effect to lethal, because altered the altered codon may code for: The same amino acid, as there can be more than one codon that does for an amino acid, so the mutation has no effect. An amino acid with similar properties to what the original would have had, meaning the protein would still fold in a similar way, so the mutation could have less of an effect.

Answer 115

A frame shift mutation is the insertion or deletion of a base pair in a DNA sequence and affects the whole sequence and how it is read, as every codon is changed from that point on.

Answer 116

A frame shift mutation has a dramatic effect on the protein as many amino acid changes occur in the DNA sequence during translation, resulting in a completely different polypeptide chain and hence a different protein.

Answer 117

An example of a genetic disease caused by mutation is sickle cell anaemia, which results from the production of abnormal proteins due to just one nucleotide change out of the hundreds that code for the protein.

Answer 118

A chromosome mutation is the mutation of a segment of DNA on a chromosome, resulting in a change in parts of the chromosome, or even whole chromosomes. Segments of/whole chromosomes can mutate in various ways.

Answer 119

Some examples of chromosomal mutations are: Duplication - where extra copies of genes in one chromosome are created. Deletion - some of the DNA of a chromosome breaks off Inversion - a broken chromosome segment gets inversed (reversed) and put back on the chromosome Translocation - when a fragment from one chromosome breaks off and attaches to another chromosome

Answer 120

In meiosis, chromosomes group up in homologous pairs, which can be pulled apart to different cells abnormally, resulting in daughter gamete cells receiving fewer or extra chromosomes. An example is Down Syndrome, where a person has an extra chromosome.

Answer 121

Mutations can be induced by various environmental factors including: High energy radiation (e.g., X-rays and ultra-violet) Mutagenic chemicals, a common source of these is cigarette smoke Viruses - if some of the viral DNA of a viral infection becomes incorporated into the host cell DNA, it can cause mutations

Answer 122

Mutations that occur in somatic (body) cells will be confined to the individual organism in which they occur, affecting particular locations, but cannot be passed on genetically. However, if mutations occur in germ cells (cells that produce gametes), then there is the potential for them to be passed on to the next generation.

Answer 123

Mutations that are inherited via gametes result in nucleotide sequence changes in the offspring. This will result in different codons, which code for a different sequence of amino acids resulting in a polypeptide chain that could fold into a different 3D structure. This could result in an abnormal protein that cannot function, or no protein being produced at all, resulting in the organism expressing different characteristic/s. As the mutation affected the zygote of the cell, it would go on to affect the somatic and germ cells of the individual and so it might be able to pass it on to its offspring as well.

Answer 124

To extract DNA from cells, the cell membrane needs to be broken to release the content of the cells Enzymes are used to remove histones and other proteins from the DNA The DNA can then be isolated by treatment with ethanol, or by centrifugation

Answer 125

DNA can be isolated from even a single cell and then amplified (copied) to the point where there is enough to analyse and sequence it DNA isolated and amplified this way can then be used in forensic science and genetic engineering

Answer 126

Polymerase chain reaction (PCR) is a process used to amplify (copy) samples of DNA

Answer 127

The technique of PCR heats the sample DNA molecule being amplified to 95deg, which causes the hydrogen bonds holding its two strands together to break, separating them. The strands are then cooled to 55deg, but do not bond back together, but rather to DNA primers. Primers are very short stretches of DNA that are complementary to the ends of the DNA strands being copied. These strands then act as templates for DNA polymerase to synthesise new strands along the exposed bases when the sample temperature is increased to 72deg. However, since enzymes are proteins, they will denature at such high temperatures, and so special DNA polymerase from bacteria that live in high temperatures is used, Taq polymerase. Many copies of the primer are included in the mixture of free nucleotides, Taq polymerase, and the original DNA molecule to increase the chance that each single strand will bind to the primer instead of its other strand. The Taq polymerase enzyme then brings these free nucleotides to bind to the single strands of DNA, resulting in two double strands instead of one. If the solution is cooled and warmed many times, the original DNA will turn into thousands of accurately copied strands, and all you have to do is keep the free nucleotides and primers in excess.

Answer 128

Overall, PCR can be summarised in three main steps: Denaturation - heating the DNA to 95deg so the strands separate Annealing - cooling the DNA to 55deg to allow the primers to bind Extension - reheating to 72deg to allow Taq polymerase to bring free nucleotides into place in a complementary fashion and extend the DNA strand.

Answer 129

Primers are responsible for preventing the two strands of a DNA molecule binding back together during PCR. They also act as a starting point for the Taq polymerase enzyme to begin DNA replication.

Answer 130

Different length DNA fragments are analysed using gel electrophoresis - a process that separates them according to their size. The DNA samples are placed into wells at one end of a block of gel, such as agar, which has electrodes at each end, with the negative electrode being by the wells. When the current is turned on, the DNA fragments, which are negatively charged, move towards the positive electrode, with the smaller fragments moving faster than the longer fragments as the longer ones find more difficulty moving through the gel.

Answer 131

Once DNA fragments are separated on the gel during gel electrophoresis, a dye can be added that binds to the DNA and fluoresces under UV light, producing visible strips called bands. Each band contains thousands of DNA fragments of the same length that have travelled to the same position.

Answer 132

Capillary electrophoresis uses the same concept as electrophoresis, but is faster and more efficient. Instead of using a block of agar, the DNA is passed through a capillary tube containing the agar. The end nucleotide of each DNA fragment is labelled with a fluorescent dye, each colour responding to the nucleotide. A current is applied, and the DNA fragments move through the capillary tube, and a laser reads the dyed fragments as they passed, producing an electropherogram.

Answer 133

While normally in PCR, Taq polymerase attaches normal free nucleotides until the entire double helix is completed, this would not help in determining the DNA sequence. Modified nucleotides are added into the mixture, which can bind to the DNA strands like normal nucleotides, but prevent Taq polymerase from adding further nucleotides, so the process of DNA replication stops as soon as the modified nucleotide was in place. There are four types, one for each of the bases A, T, G, and C

Answer 134

To sequence the DNA bases of a sample, the following process is followed: Four test tubes with copies of the same DNA fragments are set up and filled with different modified (and normal) nucleotides, each tube having a different modified nucleotide that stopped the further attachment of nucleotides. The lengths of DNA strands formed in each test tube are analysed using gel electrophoresis, which can then determine the nucleotide sequence based on their relative positions.

Answer 135

Analysis of DNA is known as DNA profiling and identifies the unique genetic makeup of individuals.

Answer 136

The non-coding regions of a person's DNA, introns, are analysed for genetic markers that vary between individuals. Genetic markers include sequences called variable number tandem repeats (VNTRs). The frequency of various non-coding repeats is characteristic of an individual just like a fingerprint.

Answer 137

A short tandem repeat (STR) is a type of VNTR (hence a type of genetic marker) 2-8 base pairs long. The number of repeats present at a STR locus (location) varies from person to person and may vary within an individual. They are often used more for analysis as analysing them takes much less time and provides greater certainty of identification than other VNTRs.

Answer 138

Each person has two copies, alleles, of each STR locus, one maternal copy of the chromosome and the other on the maternal copy. A person may have the same or different number of repeats at each STR locus on their maternal and paternal chromosomes. The two genotypes can be expressed by the allele values, which are two separate numbers for each allele, or one number if the person is homozygous. The number of repeats at each locus can be used to distinguish people.

Answer 139

DNA for DNA fingerprinting can be obtained from any cell with a nucleus such as blood, and skin.

Answer 140

DNA profiling produces a picture of some of the base sequences of an individual which can be used for comparison with others. The 'picture' is on a band on a gel or electropherogram or a table of data.

Answer 141

The STR fragments from DNA samples can be isolated using restriction enzymes, and then amplified using PCR. Gel electrophoresis can then be used to analyse the fragments, as different individuals have different numbers of STRs in a region, so they will be different lengths. These lengths can be compared to lengths of fragments from other peoples' DNA, since every individual has a unique banding pattern.

Answer 142

When STR fragments undergo PCR and capillary electrophoresis, the DNA profile created shows the number of repeats on the maternal and paternal alleles of a person at different STR loci (locations). Two peaks for one locus shows the number of repeats on a person's paternal and maternal chromosomes, but one peak means that both these alleles contain the same number of repeats. The individual is homozygous for the number of repeats of that particular STR at that particular locus.

Answer 143

DNA profiles can be used in forensic testing in criminal cases and paternity testing.

Answer 144

Forensic scientists can create DNA profiles using DNA from a crime scene, the victim, and the suspects, and can compare them to each other to determine guilt or innocence. If the number of STR repeats at various STR loci of a suspect are identical to the DNA of the crime scene, it can be linked to them as evidence.

Answer 145

DNA profiles can be used to determine the father of a child by comparing the DNA of the child, the mother, and possible fathers. A child's genotype at a given STR locus is a combination of their mother's and father's, inheriting one copy of each chromosome from each parent.

Answer 146

Another type of genetic marker in DNA are single nucleotide polymorphism (SNP). SNP are positions every 100-300 base pairs of both coding and non-coding DNA sequences were one nucleotide is different. The number of SNPs a person has can determine how related they are to someone. SNPs can also serve as genetic markers of disease-causing alleles, which can help scientists determine the probability of a person developing a particular genetic disease.

Answer 147

A concern is the way that people may use genetic information. If it became possible to inexpensively sequence DNA, companies such as life insurance may be able to test your DNA for genetic faults without consent or knowledge. This could lead to discrimination between people with a high risk for genetic diseases.

Answer 148

The current cost of collecting and storing genetic information is still quite expensive. Genetic testing is only accessible to developed countries.

Answer 149

Some religions and cultures may not see the uses of genetic information as natural, for example they may see the ability to predict diseases as unnatural. Results from genetic testing of certain ethnic groups may reveal information such as a higher chance for a disease, which could lead to stigmas and victimisation.

Answer 150

Biotechnology is the science of modifying existing biological processes in living things so we can create products that are more useful. Genetic engineering is an area of biotechnology which involves altering the genetic instructions of cells. It essentially involves combining DNA in test tubes (in vitro), and then inserting the recombined DNA into cells where it can be expressed via protein synthesis.

Answer 151

One type of genetic engineering involves removing a target gene (gene of interest) from one organism and inserting it into the genome of a suitable host.

Answer 152

A probe is a short single stranded DNA or RNA molecule that is complementary to a gene of interest designed to locate and reveal its position on a genome. They are also radioactively or fluorescently labelled to reveal their location.

Answer 153

Probes are mixed with DNA fragments that contain a gene of interest, which are then heated, separating the strands. The probes swill then bind to the genes of interest when the strands are cooled down, revealing where they are as they are labelled.

Answer 154

Restriction enzymes are enzymes whose active sites bind to a particular sequence of DNA roughly 4-6 nucleotides called restriction sites. There are many known restriction enzymes, each with a particular sequence that they can bind to. Once bound to the sequence they cut the sugar phosphate backbone. Some cut straight across the two strands of the double helix, leaving 'blunt' ends, while other restriction enzymes cut diagonally and leave some of the nucleotides from each strand unattached, resulting in 'sticky' ends. They can come together in a complementary fashion to form recombinant DNA

Answer 155

A vector is a vehicle for transferring DNA and can include plasmids and viruses. They are able to insert target genes into a host cell once they have been isolated.

Answer 156

Many bacteria contain plasmids, small rings of DNA separate from the bacterial chromosome. They can be isolated from the bacterial cells and cut open with a specific restriction enzyme. By using the same restriction enzyme that cut the DNA fragment being combined, they will have the same sticky ends and so will be able to bind together in a complementary fashion. The enzyme ligase then joins them together forming recombinant DNA.

Answer 157

Recombinant DNA is first mixed with host cells such as bacteria or yeast. Electroporation is then used, shocking the host cells with electricity to create holes in the cell membrane so the plasmid DNA can enter. These bacteria containing the target genes on recombinant DNA are described as transformed.

Answer 158

Viruses are non-living protein coats which contain a DNA or RNA genome. The genome codes for the proteins used to make more viruses and virus genomes. Viruses can also be used as vetors as they can transfer genetic material to a host. The target gene can be inserted into the virus, which can insert it into a host cell.

Answer 159

Transgenic refers to an organism whose genome has been altered by introducing (transferring) foreign genes.

Answer 160

Transgenic animals are most commonly produced using microinjection. DNA can be directly inserted into a single fertilised egg cell using a fine needle and a microscope. They are usually inserted into the nucleus of a fertilised embryo, so that it becomes incorporated into its genome and will divide into every cell of the organism.

Answer 161

Transgenic plants can be creatged by: Taking plasmids called Ti plasmids from the bacteria Agrobacterium Inserting the target gene into the Ti plasmid, creating recombinant DNA (using restriction enzymes and all that jazz, iykyk) Reinserting the recombinant DNA into the Agrobacterium cells, which can then infect plant cells, causing them to grow tumours containing the target gene. The cancer cells can then be harvested and cultivated in a lab to form plants, transgenic plants, that will express the newly inserted gene.

Answer 162

Clustered regularly interspaced short palindromic repeats.

Answer 163

Some bacteria are able to protect themselves from invasion by viruses by storing part of the viral DNA in CRISPR arrays along its DNA and using it to recognise the viral DNA to destroy it. These short nucleotide sequences removed from viruses and incorporated into the genome are called spacers, which separate CRISPR arrays. Spacers are cut and inserted into the bacterial genome by Cas proteins (CRISPR associated proteins). They are able to break down nucleic acids, for example the Cas9 enzyme is able to make an RNA copy of viral DNA spacers, using it as a guide (guide RNA) to locate the viral DNA so that it can cut it, destroying the viral DNA.

Answer 164

CRISPR-Cas9 is a biotechnology where Cas proteins are programmed to edit genomes, removing and/or replacing genes. Cas9 proteins can be used to cut DNA at a specific location when given a synthetic guide RNA molecule. gRNA is synthesised to have a nucleotide sequence that is complementary to the target DNA. It bonds to the DNA via complementary base pairing, and Cas9 cuts the DNA at the specific location. Repair enzymes then use another gene added along with the gRNA and Cas9 as a template to repair the break, resulting in an altered DNA sequence.

Answer 165

Protein design is the science of developing new protein molecules to control biochemical processes in cells for applications such as medicine, research, and technology. Uses computer software to design a 3D protein structure and determine its amino acid sequence to achieve that specific shape. These designed proteins can then be synthesised for applications such as: Proteins in vaccines that bind to viruses or bacteria, making them ineffective. Targeted chemotherapy, designing proteins that prevent tumour growth by interfering with target molecules needed for replication. Proteins that change colour or glow when they detect specific molecules.