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Stage 2 Biology > Topic 1 - DNA and Proteins > Flashcards

Topic 1 - DNA and Proteins Flashcards

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1
Q

How is DNA interpreted?

A

5 prime to 3 prime.

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2
Q

How is DNA structured in eukaryotes?

A

DNA is found in structures called chromosomes. Eukaryotic DNA is linear and located in the nucleus.

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3
Q

What happens to the structure of eukaryotic DNA when undergoing replication?

A

When undergoing replication, the DNA condenses into a thicker rod (x-shape) due to being bound to a protein called histones. When condensed, the DNA wraps around these histones, which then wrap around each other, to form the DNA-protein complex called chromatin.

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4
Q

How is DNA structured in prokaryotes?

A

Prokaryotic DNA is a single circular chromosome which floats freely in the cytoplasm. The chromosome is not bound by a protein.

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5
Q

What does mitochondria and chloroplast DNA resemble?

A

Mitochondria and chloroplast have their own DNA that resembles prokaryotic DNA.

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6
Q

What is a gene?

A

A gene is a distinct sequence of DNA that codes for the production of a protein or RNA molecule.

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7
Q

Describe DNA structure.

A

DNA is composed of 2 complementary strands, twisted into a double helix structure. The backbone of the ladder is made of alternating Deoxyribose (sugar) and phosphate groups. Attached to the sugar groups are nitrogenous bases (Adenine, Thymine, Guanine, Cytosine), which form the “rungs” of the ladder. These bond in a complementary manner (A->T and G->C) and connect through hydrogen bonding, completing the “rung”.

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8
Q

What is the function of DNA?

A

The full amount of DNA carried in chromosomes is called the genetic code. It contains the instructions for how the cell functions. DNA is hereditary and passed down generations in all organisms.

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9
Q

What is RNA and how is it different from DNA?

A

RNA is a nucleic acid, like DNA, but it has some differences:
- sugar is Ribose, instead of Deoxyribose (one additional oxygen)
- single-stranded
- uses Uracil instead of Thymine, to pair with Adenine
- not confined to the nucleus

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10
Q

How does DNA replication work?

A

DNA helicase separates the DNA strands by breaking the hydrogen bonds between nucleotides. Free nucleotides then bind to their complement pairs on the separated DNA strands, and are joined by DNA polymerase to form the sugar-phosphate backbone. This process is semi-conservative as it produces DNA with one original strand and one newly composed.

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11
Q

What is a codon?

A

A packet of 3 nucleotide pairs is called a DNA triplet; the mRNA transcription of this triplet is called a codon.

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12
Q

What is a locus?

A

Each gene has a specific location on a specific chromosome, called a locus.

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13
Q

How do cells use protein shape?

A

The biological function and ability to interact with other molecules is entirely dependent on protein shape. Receptors have distinct shapes that are complementary to the protein, enabling interaction.

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14
Q

What are enzymes?

A

Enzymes are protein molecules produced by the cell and that catalyse chemical reactions within the cell.

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15
Q

What do enzymes do?

A

Enzymes increase reaction rates by lowering activation energy for the reaction. They also provide the correct orientation for substrates.

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16
Q

Phenotype VS genotype.

A

Phenotype describes physical characteristics, whilst genotype is the name given for the genetic expression. Alterations to the phenotype can occur without affecting the genetic base, but some environmental pressures may affect both the phenotype and genotype.

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17
Q

What are alleles?

A

Genes have different variations called alleles, explaining how phenotypes can skip generations.

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18
Q

What are the steps for protein formation? And what are proteins composed of?

A

Proteins are made of amino acids joined together. DNA —transcription—> RNA —translation—> Protein

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19
Q

What are the four protein structures during protein synthesis?

A

The sequence of amino acids determines the structure the protein will form. Primary structure is the unfolded chain of amino acids. Secondary structure is the coiling and folding between different parts of the polypeptide chain. Tertiary structure is the overall 3D shape of the entire peptide chain from other secondary interactions. Quaternary structure is the bonding between different polypeptide chains.

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20
Q

What is transcription?

A

Transcription is the process where a complementary section of a gene is created as RNA in order to construct a protein.

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21
Q

How does transcription work?

A
  1. A specific gene, containing the DNA sequence (instructions) for protein creation, is unzipped by DNA helicase.
  2. The two strand separate and, starting with the codon TAC, complementary free nucleotides align with the DNA template strand (expect Uracil is bonded to Adenine, instead of Thymine).
  3. The RNA polymerase enzyme links the nucleotides together into a single strand of mRNA.
  4. The mRNA leaves the nucleus via a nuclear pore and enters the cytoplasm.
  5. The two DNA strands are rejoined into a double-helix by DNA ligase enzyme.
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22
Q

What is the difference between the template and the coding strands?

A

The template strand is the one that mRNA copies in a complementary manner. The coding strand is not copied but it is the same as the finished mRNA (excluding the Uracil/Thymine swap).

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23
Q

What is the process of translation?

A

The mRNA constructed from transcription leaves the nucleus via a nuclear pore and enters the cytoplasm. It then finds a ribosome, the site for protein production. Each codon on the mRNA codes for a particular amino acid. These amino acids are brought to the ribosome by transfer RNA (tRNA). Attached to the other end of each tRNA is an exposed tripled of bases that are complementary to each codon (anticodon). As the mRNA is translated, the tRNA brings the corresponding amino acids and they are joined by part of the ribosome to form a polypeptide chain. The “used” tRNA are released to collect another amino acid.

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24
Q

What is transfer RNA (tRNA)?

A

tRNA are the carriers of amino acids. tRNA are approximately 80 nucleotides long and are folded into a clover-leaf shape. On one end of the tRNA, there is an exposed triplet of bases that is complementary to each codon (anticodon). Attached to the other end is the corresponding amino acid.

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25
Q

Which codon does the ribosome look for to begin translation?

A

AUG

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26
Q

What determines protein structure and how?

A

The sequence of amino acids determines the way the protein will form. The long chains of amino acids fold up and form chemical bonds, giving the protein a 3D shape. Excluding rare mistakes or external influences, a particular type of protein will always form the same shape - due to the secondary bonds associated with the sequence of amino acids.

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27
Q

How does substrate-enzyme binding work (induced fit model)?

A

The distinct shape of the protein stipulates its function, meaning enzymes can only do what they are made to do. Enzymes are globular proteins with a region specifically designed for binding, called the active site. The shape of the substrate and active site are complementary. When the enzyme and the substrate join, the substrate induces the enzyme to change shape slightly for a more exact fit. This is called the induced fit model. The movement and tighter fit causes more interactions between the enzyme and the substrate, prompting quicker conversion of the substrate into products.

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28
Q

What are the factors that affect enzymes?

A

Temperature, pH and presence of chemical inhibitors.

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29
Q

How does temperature affect enzymes?

A

Most human enzymes have an optimum temperature of 37 degrees Celsius. Low temperatures cause slower interactions between enzymes and substrates. Whilst higher temperatures can denature the active site of the enzymes, meaning the substrate and enzyme are no longer complementary and cannot bind.

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30
Q

How does pH affect enzymes?

A

Extremely pH conditions can break the hydrogen bonds holding the enzyme together, causing it to denature (change shape) and no longer contain an active site that is complementary to to substrate - meaning they cannot bind.

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31
Q

How does the presence of inhibitors affect enzymes?

A

Competitive inhibitors are other substrates of a similar shape that attempt to bind to the active site on an enzyme, preventing the enzyme from being able to catalyse its respective substrate. Non-competitive inhibitors inhibit the substrate from binding by attaching to a different site on the enzyme, and causing it to change shape. Thus, the active site is no longer complementary to the substrate, and cannot bind.

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32
Q

How do concentration of reactants and enzymes impact reaction rate?

A

If the concentration of substrate is increased, the reaction rate will also increase until all enzymes are being used - when the trend will become linear. Likewise, larger number of enzymes will increase the reaction rate until all substrate molecules are bound.

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33
Q

What are some examples of environmental factors influencing phenotype?

A
  • UV
  • temperature
  • oxygen levels
  • diet
    E.g. increased UV exposure, causing a change in skin colour. Malnutrition, causing a reduced body size.
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34
Q

How does DNA methylation work?

A

Methyl groups (CH3) attach to the cytosine nucleotides on the gene. This causes transcription factors and enzymes to be unable to “read” the DNA, meaning the gene cannot be transcribed. This results in the protein not being produced and the effect of the gene not being expressed. De-methylation is the removal of methyl groups from the cytosine nucleotides, and will cause more expression of the gene.

35
Q

How can changes in DNA methylation cause cancer?

A

Epigenetic modifications such as the methylation of suppressor genes and the de-methylation of promotor genes for cell division can lead to cancer. Suppressor genes reduce cell division, meaning the methylation of them will prevent transcription of the gene and cell division will no longer be controlled as the effect of the gene is not expressed. Expressor genes increase cell division, meaning the de-methylation of them will enable transcription and cell division will no longer be controlled as the effect of the gene is expressed. Uncontrolled cell division leads to cancer.

36
Q

How does histone modification work (methylation and acetylation)?

A

Histones are proteins that provide structural support for chromosomes. Methyl groups result in a stronger attraction between histones. This makes it more difficult for transcription factors to get in, decreasing the expression of the gene. Acetylation results in looser packing of histones. This makes it easier for transcription to occur, increasing the expression of the gene.

37
Q

What are mutations and how do they usually occur?

A

Mutations are changes in DNA sequence. Mutations in genes and chromosomes can result from errors in DNA replication or cell division, or from damage by physical or chemical factors in the environment.

38
Q

What are the factors that increase mutation rate?

A
  • ionising radiation
  • mutagenic chemicals
  • viruses
39
Q

What are restriction enzymes (RE) and restriction sites?

A

Restriction enzymes are proteins that come from bacteria, that cut DNA at highly specific regions. The sequence of bases recognised by the enzyme, approx. 4-6 nucleotides, is called the restriction site.

40
Q

What is a probe?

A

A probe is a short piece of single-stranded DNA or RNA. It is radioactively labelled and is complementary to the isolated gene, allowing it to bind.

41
Q

How do inherited diseases work?

A

Some diseases have a genetic base, meaning they are contracted via the inheritable genetic material. Generally, these diseases require two alleles of the affected gene to express themselves in the phenotype.

42
Q

What is PCR used for?

A

Polymerase chain reaction (PCR) is a commonly used technique to multiply pieces of DNA by several orders of magnitude.

43
Q

Describe the process of PCR.

A
  1. The DNA to be replicated, complementary DNA primers, free nucleotides, and heat tolerant DNA polymerase are added to the PCR machine.
  2. The DNA is heated, disruption the hydrogen bonds and separating DNA strands.
  3. The temperature is lowered to allow the annealing of primers to complementary DNA strands.
  4. It is heated again to allow DNA polymerase to create a new complementary DNA strand.
  5. The DNA strand is elongated to its maximal.
  6. The temperature is lowered for an indefinite time for long term storage of the reaction.
  7. The process is repeated to increase the amount of DNA produced.
44
Q

What are the ethical considerations surrounding DNA profiling, specifically electrophoresis?

A
  • costs money to collect, analyse and store genetic information
  • social debate surround who has access to the stored genetic information
  • could create a segregated society
45
Q

What are the gene insertion methods?

A
  • gene gun
  • agrobacterium
  • electroporation
  • viruses
  • liposomes
  • microinjection
46
Q

How does the gene gun work?

A
  1. Inert particles like gold or tungsten are coated with the gene of interest.
  2. It is then fired at high pressure into the cells to be transduced.
  3. Some particles will enter the cells and some of these will incorporate the new gene into the genome.
  4. These cells then express the desired protein (or develop the desired qualities).
47
Q

How does electroporation work?

A

A short electric shock is applied to the plasma membrane of a cell. This creates tiny holes through which particles containing the desired gene can pass, transducing the cell.

48
Q

How does microinjection work?

A

The gene of interest is inserted into the nucleus of a fertilised ovum. This is done using an extremely find glass micropipette, which is inserted through the plasma membrane and nuclear membrane. The organism will then express the gene of interest.

49
Q

What does CRISPR stand for?

A

Clustered regularly interspaced short palindromic repeats.

50
Q

How do liposomes work for gene insertion?

A

Liposomes fuse with the plasma membrane and deliver DNA payload into the cell.

51
Q

How does agrobacterium work?

A

The Ti plasmid is removed from the bacteria and the gene, and mixed together. The plasmid is returned to the bacteria, and the bacteria is used to infect the plant. It inserts the Ti plasmid into the plant cells, which divide rapidly to produce a tumour. The tumour is then harvested, cut up, and used to produce plants that now have the gene as part of the genome.

52
Q

How does DNA extraction work?

A

To extract DNA from cells, the membranes have to be disrupted first. Histones and other proteins are then removed. The DNA can then be isolated by treatment with ethanol or by centrifuging.

53
Q

What is DNA electrophoresis?

A

The different lengths of DNA pieces, cut up by restriction enzymes, are analysed using gel electrophoresis. This is a process that separates them according to their size, creating a DNA “finger print”.

54
Q

How does DNA electrophoresis work?

A

DNA samples are placed into wells and electricity is pumped through. DNA is slightly negatively charged, so it is attracted to the positive electrode. Smaller pieces of DNA travel further, whilst bigger pieces get stuck in the gel. This creates a unique DNA “finger print”.

55
Q

What are electropherograms and how do they work?

A

Electropherograms work in the same manner as electrophoresis. The difference is that the end nucleotide of each piece of DNA is labelled with a fluorescent dye (different colour for each base). The DNA fragments pass through a capillary tube containing the gel, and a laser reads the dyed fragments as they pass. This creates a graph called an electropherogram.

56
Q

How are electropherograms read?

A

Each coloured peak represents one of the four nucleotides and the size of the peak indicates the strength of the signal given off from the laser, as it hits the DNA fragment.

57
Q

How do viruses work for gene insertion?

A

The replication portion of the virus genome is removed. The virus is inserted into the gene of interest. The virus is still as efficient at infecting cells only now it contains the instructions to produce the desired protein, but without replicating. Virus transfection efficiency is the greatest of all vectors.

58
Q

How do base sequences help determine how closely related species are to each other?

A

Organisms which are closely related should have similar or even identical amino acid sequences, as they code for protein production. As the sequence of amino acids is determined by DNA sequence, the similarity between the arrangement of bases can distinguish organism relation.

59
Q

What is cellular differentiation?

A

Cellular differentiation is the changing or specialising of cells into different roles by turning genetic information “on” or “off”.

60
Q

What is DNA profiling and how does it work?

A

DNA profiling is the identification of individuals by their respective DNA profiles. Variable number tandem repeats (VNTRs), also known as “junk” DNA as they do not code for anything, are removed using restriction enzymes. These are amplified with PCR and then analysed using gel electrophoresis, which separates them according to size resulting in bands of DNA in gel.

61
Q

How does CRISPR-Cas9 work?

A

Guide RNA, complementary to the non-functioning gene, would need to be produced and loaded onto the Cas9 enzyme. The Cas9 was then introduced to the target cells to locate the gene of interest. It does so by aligning the guide RNA with the DNA until a complementary match is found. The Cas9 then cuts the DNA at this specific site, deactivating the gene and its expression. The gene could not be edited if required by either modifying, deleting or inserting new sequences.

62
Q

Where does transcription and translation occur?

A

Transcription occurs in the nucleus. Translation occurs at ribosomes within the cytoplasm.

63
Q

State the subunits that make up enzymes.

A

Amino acids.

64
Q

What do restriction enzymes leave and how it that used?

A

Restriction enzymes are proteins that come from bacteria, that cut DNA at highly specific regions - restriction sites. They are used in biotechnology to cut out specific DNA, and leave “sticky” ends for joining.

65
Q

Why are heat resistant DNA polymerase enzymes used in PCR?

A

Heat resistant DNA polymerase enzymes must be used in the PCR process as they can withstand the extreme temperatures required to disrupt the hydrogen bonds to separate DNA strands. This is important to allow the annealing of primers and free nucleotides. DNA polymerase that are not heat resistant would denature when exposed to the high temperatures in PCR, and would be unable to function.

66
Q

For a gene modification to be inherited, which cells must it be inserted into?

A

Somatic cells are all body cells that are not reproductive, whereas germline cells are sex cells. Any gene changes or insertions that are done to somatic cells only impact that organism. Gene modifications done to germline cells will be inherited and present in the DNA of all cells in the zygote.

67
Q

Why is complementary base pairing important in protein synthesis?

A

Complementary base pairing is required during protein synthesis to ensure that the correct amino acid is added. tRNA are the carriers of amino acids and have an exposed triplet of bases (anticodon) that are complementary to the codons on the mRNA. To obtain the required amino acid, complementary base pairing is needed between codons and anticodons.

68
Q

How do epigenetic modifications affect gene expression?

A

Epigenetic modifications, such as methylation/de-methylation and acetylation, do not involve changes to the underlying DNA sequence - a change in phenotype without a change in genotype. This switching “on” or “off” of genes affects how the cell responds, in order to express or repress the production of certain proteins.

69
Q

How are genes located?

A

Genes are located by probes. A probe is a short piece of single-stranded DNA or RNA. It is radioactively labelled and is complementary to the isolated gene, allowing it to bind.

70
Q

How is gene expression impacted by environmental factors?

A

Environmental factors such as diet, exercise, temperature and oxygen levels can impact which genes are expressed, thus, impacting the organism’s phenotype. These factors can influence which genes are turned “on” or “off”, in order to express or repress the production of certain proteins. Changes to wrapping of DNA around histones, caused by these environmental factors, leads to less expression of the more closely wrapped DNA and more expression of the looser wrapped DNA.

71
Q

Explain how the deletion of bases can result in a change to the structure of the resultant protein.

A

The deletion of nucleotide bases will cause the DNA sequence to change. This means that the DNA triplets will be different, resulting in different codons on the transcribed mRNA sequence. These codons correspond to specific anticodons and, thus, specific amino acids. The amino acid sequence determines the bonding and structure of the resultant protein. Therefore, the deletion of bases will result in a different amino acid sequence - changing the structure of the resultant protein.

72
Q

What is the SHE concept of application and limitation?

A

Develop solutions and discoveries, sustainability action, evaluation economic, social, cultural and environmental impacts. Explanations and predictions, with beneficial or unexpected consequences that may cause public debate.

73
Q

What is the SHE concept of influence?

A

Advances in science to influence other areas of science, technology, engineering and maths.
Influenced by social, economic, cultural and ethical considerations.

74
Q

What is the SHE concept of communication and collaboration?

A

Clear communication, international conventions, review and verification of results. Collaboration between scientists, governments and agencies.

75
Q

What is the SHE concept of development?

A

Complex scientific model/theory development. New technologies to improve efficiency of procedures, data collection and analysis, and modification of replacement of models/theories.

76
Q

What are designer proteins? Examples and their applications.

A

Designer proteins are a new branch of genetic manipulation where the particular folding structure of a protein is calculated. By coding the amino acid sequences, proteins with specific functions can be created. Some designer proteins include:
- vaccines (binds to viruses/bacteria, preventing it from working)
- protein spheres (like liposomes that deliver payloads to cells)
- channel proteins (regulate movement of substances through the membrane)
- proteins that glow when they detect specific molecules

77
Q

How are genes cloned using bacterial plasmids?

A

DNA ligase incorporates the gene of interest into the bacterial plasmid, and then rejoins them into rings. The new plasmids are introduced to a bacterial colony which are taken up under appropriate conditions. The reproducing bacteria now also reproduce the gene of interest.

78
Q

How are genes isolated using antibodies?

A
  1. Create the radioactively labelled antibody that is complementary to the isolated protein.
  2. DNA from the cell is cut up into fragments and incorporated into bacteria cells.
  3. Some bacteria will take up the DNA fragments and express the proteins related to those genes.
  4. The labelled antibody is then introduced to the bacteria.
  5. The bacteria that have taken up the gene will be labelled, whilst the remainder will not.
  6. The labelled bacteria can then be analysed.
79
Q

What is biotechnology and how does it work?

A

Biotechnology is the combination of DNA from different species to obtain benefits. This technology is able to read DNA codes and pinpoint sections to work with. These can be cut out of the whole DNA segment by restriction enzymes, leaving sticky ends for joining.

80
Q

What are epigenetics?

A

Epigenetics are heritable changes in gene expression that do not involved changes to the underlying DNA sequence. Essentially a change in phenotype without a change in genotype, which affects how cells read the gene. Epigenetics basically means change “after” and are caused by environmental factors.

81
Q

What are transcription factors and how do they work?

A

Transcription factors are regulatory proteins that control gene expression. Some switch genes “on” by binding to promotor regions on the DNA. Other turn genes “off” by repressing the RNA polymerase attachment to the DNA, preventing transcription. Transcription factors can be activated by certain hormones, meaning gene expression can be determined by the presence or absence of this hormone.

82
Q

How do mutations affect somatic VS germline cells?

A

If mutations occur in somatic cells, they will only affect the individual organism. If mutations affect germline cells, then it may be passed on to subsequent generations. Germline cell mutations will affect the zygote and, therefore, will appear in all cell DNA within the new organism.

83
Q

Exons and introns within a gene.

A

EUKARYOTES ONLY - prokaryotes do not have introns.
All of the DNA in a gene is transcribed to mRNA. Some of that mRNA is not required to make the final protein. The coding parts of a gene that are turned into protein are called exons. Non-coding parts of a gene are called introns. The mRNA produced from a gene includes introns in its RNA sequence (primary RNA). The mRNA has introns removed prior to translation. The exons are spliced together by a protein complex that removes introns in the nucleus, to form mature mRNA.

84
Q

What are translation factors and how do they work?

A

Some proteins can prevent binding to mRNA. Small interfering RNA (siRNA) can also cut mRNA after transcription, bind directly to DNA and/or attract other molecules to transcription and translation sites - preventing translation from occurring.

Stage 2 Biology (4 decks)

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