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Edexcel A2 IAL Biology Topic 6 Immunity Infection and Forensics
Edexcel A2 IAL Biology Topic 6 Immunity Infection and Forensics
Survival
Topic 6: Infection, Immunity and Forensics
Decay and Decomposition
Microorganisms (fungi. bacteria, other decomposers) decompose organic matter and are an important
part of the carbon cycle. They secrete enzymes that decompose the dead organic matter into smaller
molecules during respiration. Scientists can estimate time of death of a body based on things like
degree of decay and this can give them a lot of information about the circumstances of the death.
All mammals produce heat from metabolic
reactions (respiration), so from TOD these
reactions slow down and eventually stop
causing body temperature to fall until it equals
the temperature of the environment.
Body
Forensic scientists know that the human body
Temperature
cools at a rate of 1.5-2.0°C per hour, so can
work out an estimate of TOD. Useful for first
24hrs post mortem.
Different conditions such as air temp, clothing,
body weight, body position, air movement, and humidity can affect cooling rate.
Muscles relax, then contract (rigor mortis), then relax again.
Rigor mortis (stiffening of the muscles) sets in about 2-6 hours after death.
Degree of
Occurs due to muscle cells becoming deprived of O2 and is affected by body
muscle
contraction composition and temperature. Respiration still occurs, but lactic acid is produced
due to anaerobic respiration. pH of the cell decreases due to lactic acid, inhibiting
(Rigor
Mortis) enzymes from working, Therefore no ATP is produced and bonds between actin
and myosin become fixed.
Small muscles in head contract first, large muscles in lower body contract last.
After death different microorganisms start colonising
the body. TOD can be estimated by type of insect
present in/on the body.
Identifying stage of lifecycle of the insects can help
estimate TOD. Different conditions affect an insect’s
Forensic lifecycle (drugs, humidity, oxygen, temperature).
entomology Flies are first (a few hours after death). Other
insects (beetles) arrive later.
Extent of Immediately after death, bacteria and enzymes start to decompose the body. This
decompositi extent of decomposition can be used to estimate TOD.
on Different conditions affect the rate of decomposition (e.g. temp, O2 availability).
Approximate time
Extent of decomposition
since death
Cells and tissues are broken down by the body’s own enzymes
Hours – a few days and bacteria that were present before death (autolysis). The
skin turns greenish (putrefaction at 36-72 hours).
Microorganisms decompose tissues and organs. This
Few days – a few
produces gases, which causes the body to smell and become
weeks
bloated. The skin begins to blister and fall off.
Tissue begins to liquefy and seep out into the areas around
A few weeks
the body. Gas is released and the body deflates.
Few months – a
Only skeleton remains.
few years
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Decades to The skeleton begins to disintegrate until there is nothing left of
centuries the body.
Types of organisms found in/on a body change over time. TOD can be
established from the stage of succession that the body is in. The stages are:
1. Immediately after death the body is most favourable to bacteria.
Stages 2. Bacteria decompose tissue making conditions favourable for flies and larvae.
(waves) of 3. Fly larvae feed on a dead tissue making conditions favourable for beetles.
succession 4. As the body dries out conditions become less favourable for flies, so they leave.
Beetles remain and decompose dry tissue, leaving only the skeleton.
The stages of succession of a dead body are affected by things such as location
of the body, left above/below ground, under water, sealed away, etc.
DNA Profiling
Forensic scientists use DNA profiling to compare samples of DNA from
crime scenes and possible suspects (to link them to crimes). DNA is
isolated from the collected samples, and each one is amplified using
PCR. PCR products are run through electrophoresis gel and the DNA
profiles are compared.
We inherit our DNA from our parents, ± half from each, so the more
bands of the two DNA profiles that match, the closer the relation
between the two people. In animals and plants, DNA profiling is used to
stop inbreeding which can cause health, productivity and reproductive
problems. Inbreeding decreases the gene pool of alleles; leading to an
increase in genetic disorders.
PCR
The Polymerase Chain Reaction (PCR) is used
to amplify DNA and make millions of copies of
specific regions of the DNA in just a few hours.
There are several stages:
1. A reaction mixture containing the DNA
sample, free nucleotides, primers (short DNA
sequences that are complimentary to DNA
adjacent to the STR) and the DNA polymerase
enzyme is made up.
2. The DNA mixture is heated to 95oCto break
down H bonds between the two strands of
DNA.
3. Mixture is cooled to 50-65oC so primers
(marked with fluorescent tags) can bind to
DNA strands.
4. Reaction mixture is again heated to 72oC so
the DNA polymerase can work.
5. DNA polymerase makes strands of new DNA
by complement strand synthesis and lines up
free DNA nucleotides alongside each template
strand. Two new copies of the fragment of
DNA are now formed and one cycle of PCR is
complete. Each cycle doubles amount of DNA
present in sample.
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6. The cycle starts again with the mixture being heated to 95oC and this time all four strands are used
as template strands.
Gel Electrophoresis
Once DNA has been amplified a florescent tag is added to the
fragments for viewing under UV light.
Gel Electrophoresis is then used to separate out the DNA fragments
according to their length:
1. DNA is placed into a well of gel and covered in a buffer solution so
that it conducts electricity.
2. An electrical current is passed through the gel – DNA fragments
are negatively charged and so move towards the positive
electrode.
3. Shorter fragments move faster and further through the gel;
fragments separate according to length.
4. The gel is viewed under UV light; DNA fragments appear in bands.
When two DNA profiles are the same they provide the same
bands at the same place.
Summary of forensics:
When: rigor mortis, decomposition, forensic entomology,
temperature
Who: personal ID, finger prints, dental records, DNA profiling
Infectious diseases can be transmitted and are caused by the spread of pathogens or natural flora
(bacteria on skin and gut) mutating and becoming pathogenic.
Bacteria:
Bacteria grow and reproduce in the body; producing toxins
which make people feel poorly.
Single celled, prokaryotic microorganisms (prokaryotic means
no nucleus) that lack membrane bound organelles.
Have a single strand of free floating DNA found in the
cytoplasm. Cytoplasm also sometimes contains plasmids
(small, circular loops of DNA).
Some have a flagellum to aid movement by rapid rotations
(e.g. sperm) – like a rudder.
Some have a slime capsule which protects them from attack
(e.g. phagocytosis by WBCs and blocks their receptors so
cells don’t recognise them as non-self).
Respiration occurs on folds of cell membrane called
mesosomes (which increase surface area).
Some have pilli (protein tubes) which help them attach to host
cells, and are also used for sexual reproduction.
Most bacteria are only a few micrometers long.
Bacteria cells have a plasma membrane (cell wall), cytoplasm
and ribosomes (produce proteins).
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Reproduce asexually by binary fission; replication of DNA,
they divide identically. They do not produce a spindle during
cell
division.
Bacteria can be cocci (spherical), bacilli (rod shaped), spirilli
(twisted) or vibrious (comma shaped).
Structure of Bacteria:
Plasma Membrane / Cell Wall: rigid wall Plasmids: additional hereditary material.
protects against rupture due to osmosis and Small rings of DNA present in cytoplasm of
keeps shape. some (not all) bacteria.
Cytoplasm: about 75% water. Contains Ribosomes: sites of protein synthesis, are
dissolved proteins (mainly enzymes), known as 70S ribosomes because they are
lipoproteins, sugars, amino acids, fatty acids, smaller than those in the cytoplasm of plant
inorganic salts, and the waste products of and animal cells, and fungi (called 80S
metabolism. ribosomes).
Slime Capsule: a layer or capsule made up Flagella: rigid protein strands that arise from
of materials that are laid down on the outer basal bodies in the plasma membrane in
surface of the wall. Capsules are firmly some bacteria. They bring about movement
attached, whereas slime layers may diffuse by rotating from their base, driven by the basal
into the surrounding medium. body.
Mesosomes: in-folding of the plasma Pilli: tiny tubular structures that arise from the
membrane found in some bacterial cells. In cell membrane of some bacteria. They enable
photosynthetic bacteria, they are where the bacteria to attach to surfaces and to other
photosynthetic pigments are housed. bacteria.
There are two types of bacterial cell walls, distinguished by Gram Staining.
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- Gram positive bacteria have a thick layer of peptidoglycan containing chemicals (acids). The crystal violet
in the stain binds to the acid & resists decolouring, leaving the positive PURPLE/BLUE in colour.
- Gram negative bacteria have a thinner layer of peptidogylcan with no teichoic acid.
- Any crystal violet which binda is readily decolourised & replaced with red safranine in the stain, so cells
appear RED in colour.
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between the two cells through which DNA is transferred to the recipient cell, similar to the
female cell
Beneficial Bacteria:
- Many bacteria in the body (skin and gut flora) are
beneficial, helping to break down food and keeping
pathogens at bay by outcompeting them. The normal
growth of bacteria on your skin or in your gut is referred to
as the ‘skin flora’ or ‘gut flora.’ Probiotic drinks and
foods contain cultures of these ‘good’ bacteria to help
support the normal healthy bacterial flora of the gut.
- Bacteria also play a vital role in the ecosystems of the
natural world. The majority of bacteria are decomposers.
They break down organic material to produce simple
inorganic molecules such as CO2 and H2O.
They release inorganic nitrogen which returns to the soil in the nitrogen cycle.
- Another important aspect of bacteria in the carbon cycle is the fact that some microorganisms
produce the enzyme cellulase. This enzyme breaks down the cellulose produced in plant cell
walls to give sugars which can then be used as food by a wide range of other microorganisms.
Viruses:
The smallest type of microorganism. They aren’t cells; they are nucleic acids
surrounded by protein.
Composed of a strand of viral DNA and
proteins enclosed in a capsid (viral protein
coat made up of individual capsomeres).
Sometimes have a lipid envelope
surrounding them (taken from a host cell; it
allows them to pass from cell to cell).
Contain a core of nucleic acid; viral genetic
material (DNA/RNA/single/double stranded)
to create proteins and reproduce.
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Viral RNA directs the synthesis of a special enzyme called reverse transcriptase which proceeds
to make DNA molecules corresponding to the viral genome.
Invade living organisms and manipulate the cells biochemistry to reproduce/create more viruses.
Have receptors on their surface to help them attach to hosts; each antigen (glycoprotein) only
attaches to a specific host membrane.
Smaller than bacteria.
Have no plasma membrane, no cytoplasm and no ribosomes.
There are very few drugs that can kill viruses – anti viral drugs.
How
viruses
enter a
cell:
- Some
enter cells by endocytosis and the host cell digests the
capsid releasing the genetic material.
- Some enter the cell by fusing the lipid envelope with the
phospholipid bilayer of a cell and releasing its contents
inside the cell.
Reproduction of Viruses:
1. If the virus contains DNA, the viral DNA is inserted into
the host DNA and can be replicated by DNA polymerase
and then used to make more viral proteins by protein
synthesis.
2. If the virus contains RNA, DNA reverse transcriptase is used to translate the RNA into DNA. The
DNA then inserts itself into the hosts DNA and the host cell creates viral proteins during protein
synthesis. This is called reverse transcription. The new viruses then exit the cell by exocytosis
and go on to infect other cells.
Viral infections are specific to tissues e.g. some viruses will only infect the respiratory tract.
Retroviruses:
Retroviruses have a more complex life cycle. Their genetic material is viral RNA and this cannot be
used as mRNA but is instead translated into DNA using reverse transcriptase (e.g. HIV).
1. The retrovirus attacks an animal cell. 3. Viral RNA is translated into viral DNA by
2. Viral RNA enters the host cell. This RNA reverse transcriptase in cytoplasm.
cannot be used as mRNA.
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4. Viral DNA is incorporated into the host DNA in viral genome RNA, mRNA and coat proteins.
the nucleus. It directs the production of new 5. New viral particles are assembled and leave
Barriers to Entry:
Pathogens are transmitted in a variety of ways:
- Open routes such as eyes, nose, ears, mouth, anus, penis, etc.
- Vectors: living organism that transmit infections from one host to another (e.g. mosquitoes –
malaria).
- Fomites: travelling by inanimate objects that carry pathogens from one host to another (e.g.
hospital towels and bedding).
- Direct Contact: shaking hands, direct contact of genital organs (e.g. gonorrhea, syphilis).
- Inhalation: coughing, sneezing, and talking release pathogen containing droplets which can be
inhaled (e.g. TB, influenza).
- Ingestion: contaminated food – the risk is greatest in raw or undercooked food (e.g. salmonella).
- Inoculation: directly through a break in the skin either through contaminated medical instruments or
shared needles in drug abuse. An infected animal may also bite or lick you. (e.g. HIV, rabies).
But there are several barriers which humans have to prevent entry and infection:
Stomach The acidic environment of the stomach kills most of the pathogens that enter through the
Acid digestive system; but some may survive and get passed into the gut wall.
A fibrous structural protein layer toughened by keratin that forms a physical barrier between
the pathogen laden environment and the blood rich tissues beneath the skin. The skin is made
Skin from 2 layers: the outer epidermis layer (provides a physical barrier to invading pathogens;
blood clots seal wounds, skin flora prevents colonisation of bacteria), and the inner dermis
layer.
Skin Flora Sebum (oily substance with a pH 3-5 which makes the skin acidic) contains chemicals which
inhibit the growth of microorganisms.
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Natural skin flora prevent disease by competing with pathogens for nutrients and space and
produce substances that inhibit the growth of other microorganisms. This restricts pathogens
from infecting the body.
Our intestines are naturally covered by harmless microorganisms called flora that compete
Gut Flora with pathogens for nutrients and space. This restricts pathogens from infecting the body.
Surfaces of internal tubes and ducts are more vulnerable than the skin; however these
epithelial layers also produce defensive secretions (e.g. mucus). Part of the non-specific
defense of the body.
Mucus contains lysozymes: enzymes which kill pathogens by destroying microbial cell walls.
Lysosomes Sebaceous glands secrete the enzyme lysozyme which is a natural antibiotic that destroys
bacterial cell walls.
Lysozymes are also present in tears; to keep eyes moist and protect them from entry of
pathogens.
- Saliva in the mouth has bacterial properties. Some polypeptides produced in the salivary glands
destroy bacteria while others slow down bacterial growth.
- Vomitting is effectively removing many of the microorganisms physically from the system when the
body is infected.
Immune Response:
There are 2 main types of white blood cells (WBC’s) involved in the immune systems;
1. Lymphocytes: agranulocytes made in bone marrow. Involved in specific immune responses.
- T cells: T lymphocytes, a type of lymphocyte found
in the blood and lymph. Mature and become active
in the thymus.
- B cells: B lymphocytes, a type of lymphocyte found
in the lymph and blood. Mature in blood.
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digest pathogens and any other foreign material in the blood and tissues. Phagocytes can
sometimes be seen as pus which may ooze out of the wound or it may be reabsorbed into the
body. There are two types of phagocytes:
- Macrophages: agranulocytes which move freely through the tissue after leaving the
bloodstream, make up about 4% of WBC’s. They accumulate at the site of infection to attack
invading pathogens.
- Neutrophils: granulocytes, make up 70% of the white blood cells.
Interferons: a group of chemicals produced when cells are invaded by viruses. Interferons are
proteins that inhibit viral replication within the cells. They bind to receptors in the surface membranes
on uninfected cells, stimulating a pathway which makes the cells resistant to infection by viruses by
preventing viruses reproducing.
The working of these cells depend on special proteins known as major histocompatibility complex (MHC)
proteins, which display antigens in the cell surface membranes. MHC proteins are the proteins that display antigens on the surface of cells to make them
antigen presenting cells.
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Activation of T cells by macrophages:
1. Phagocytes (macrophages) activate T cells by
binding of their antigens to complementary CD4
receptors on the T cells. Each T cell has a
different shaped receptor on its surface so
when it meets the complementary antigen it
binds to it, activating the T cell.
2. This causes the T cell to divide and differentiate
into other types of T cell. These include T
helper cells (secrete substances that activate B
cells, T killer cells, and macrophages), T killer
cells (attach to antigens on a pathogen-infected
cell and kill the cell), and T memory cells
(immunological memory; responsible for
secondary immune response).
B cell activation and plasma cells:
1. T helper cells activate B cells (WBC covered
with proteins - antibodies).
2. Antibodies bind to complementary antigens on
the pathogen to form an antigen-antibody
complex. Each B cell has a different shape
antibody on its surface that binds with its
complementary antigen. This together with
substances released from the T cells help
activate the B cells.
3. The B cell that is specific to the antigen (has a
specific antibody on its surface) engulfs the pathogen, fuses the vesicle with a lysosome and
digests the pathogen leaving behind the antigens. These antigens are presented on the surface of
the B cell.
T helper cells recognise the antigens and bind to them. They release cytokines which cause the
activated B cells to divide by mitosis and form clones called B memory cells and B effector cells.
4. The B effector cells differentiate into plasma cells and produce large amounts of antibodies which
circulate around the body in the blood and attack pathogens. Plasma cells secrete antibodies for
specific antigens on the surface of the pathogen to form antigen-antibody complexes.
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Antibodies: help to clear the body of infection; they do various jobs these include:
Agglutinating pathogens – they clump pathogens together to prevent them from functioning.
Neutralising toxins – antibodies bind to the toxins produced by pathogens. They prevent toxins
from affecting human cells, so the toxins are neutralised.
Preventing the pathogen from binding to human cells – antibodies bind to antigens on pathogens,
blocking the cell surface receptors so that pathogens cannot attach to a host cell.
Apoptosis: programmed cell death which occurs as a normal, controlled part of an organism's growth
or development.
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Immunity
The production of memory cells gives a person immunity; when a pathogen enters the body for the
first time, the antigens on its surface activate the immune system (slow primary immune response
in which B cells are made, producing antibodies needed to bind to the antigen and overcome
infection).
After exposure, both T cells (remember the specific antigen) and B cells (remember the specific
antibody required for the antigen) produce memory cells which remain in the body.
If the same pathogen enters the body again, the immune system produces a quick, stronger
secondary immune response in which B memory cells divide into plasma cells that produce the
right antibody for the antigen, and memory T cells divide into the correct type of T cell to kill the cell.
You can become immune to a specific disease in a number of ways:
Active immunity: Immune system makes its Passive immunity: You get given antibodies
own antibodies after being stimulated. made by a different organism.
Active Natural Immunity Passive Natural Immunity
When a baby/fetus becomes immune by receiving
When you become immune after catching the
preformed antibodies from the mother through the
disease; the body comes into contact with a
placenta or breast milk. Both provide temporary
foreign antigen and the immune system is
immunity until baby’s own immune system
activated. The body actively makes antibodies and
becomes active; not a long term solution as the
the pathogen is destroyed.
antibodies don’t live for long periods of time.
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HIV and TB
Over millions of years vertebrates have evolved better immune systems, but pathogens have also
evolved mechanisms to evade immune systems of hosts (evolutionary race). Two examples are:
Types of antiretrovirals:
Reverse transcriptase inhibitor: prevents viral RNA
from making DNA for integration into hosts genome.
Protease inhibitor: inhibit the proteases that catalyse
the cutting of larger proteins into smaller polypeptides
for use in the construction of new viruses.
Integrase inhibitor.
Fusion inhibitor.
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How does HIV cause AIDS?
1. gp120 receptors (glycoproteins located on HIV viruses) attach to CD4 receptors on T helper cell
membranes allowing the virus envelope to fuse with and invade the T helper cell.
2. Once inside the host T helper cell, the virus uses reverse transcriptase (enzyme) to reverse
normal transcription and manufacture DNA from the viral RNA template.
3. The virus then inserts viral DNA into the T helper c ells DNA using integrase (enzyme). Once HIV
genome is integrated into the host cells genome it uses the hosts protein synthesis mechanism to
produce new viral proteins.
4. The new viral proteins together with glycoproteins and nuclear material assemble into HIV viruses.
5. The new viruses bud out of the T cell, taking some of the host cell surface membrane with as their
envelope, killing the T helper cell as they leave.
HIV infected T helper cells will also be destroyed by T killer cells. Thus as the number of viruses
increases, the number of host T helper cells decreases causing macrophages, B cells, and T killer
cells to not be successfully activated, and therefore not function properly. The infected person’s
immune system becomes, so opportunistic infections occur.
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Protein Synthesis
Transcription Translation
1. RNA polymerase (an enzyme) attaches to the 1. Amino acids are joined together at the ribosomes
DNA double helix at the beginning of a gene. to make a polypeptide chain, following the
2. The H bonds between the two strands breaks. sequence of codons carried by the mRNA.
The strands separate and the DNA uncoils. 2. The mRNA attaches itself to a ribosome while
3. One of the strands is used as a template to transfer RNA (tRNA) carries amino acids to the
make an mRNA copy. This DNA template strand ribosomes.
is also called the antisense strand. 3. A tRNA molecule with an anticodon that is
4. The RNA polymerase lines up free RNA complementary to the first codon on the mRNA
nucleotides alongside the template strand. attaches itself to the mRNA.
Complementary base pairing takes place 4. A second tRNA molecule attaches itself to the
leaving mRNA as a reverse copy. next codon in the same way.
5. Once RNA nucleotides have paired up with their 5. Amino acids attach to the tRNA molecule by
complementary bases on the DNA strand they peptide bonds. The first tRNA molecule moves
join together forming an mRNA molecule. away, leaving an amino acid behind.
6. The RNA polymerase moves along the DNA, 6. A third tRNA molecule binds to the next codon on
separating the strands and assembling the the mRNA. Its amino acids binds to the first two
mRNA strands. and the second tRNA molecule moves away.
7. The H bonds between the uncoiled strands of 7. This process continues, producing a polypeptide
the DNA re-form once the RNA polymerase has chain, until it reaches a stop codon on the mRNA.
passed by and the strands coil back into a 8. The polypeptide chain moves away from the
double helix. ribosome and translation is complete.
8. When the RNA polymerase reaches a stop
codon, it stops making mRNA and detaches
from the DNA.
9. mRNA moves out of the nucleus via nuclear
pores and attaches to a ribosomes in the
cytoplasm.
Different codons code for different amino acids; this is the genetic code. In the genetic code each
triplet is read in a sequence, separating it from the triplet before and after it; the code is non-
overlapping as no base of one triplet contributes to part of the next triplet. There is a possible 20
amino acids from 64 possible codons; some amino acids have several codons coding for them.
DNA is copied into RNA (a single polynucleotide strand that contains a sugar (ribose) and uracil
(which replaces thymine)) for protein synthesis. The organelle needed for protein synthesis is found in
the cytoplasm (outside of the nucleus. DNA is too large to move out of the nucleus, so sections are
copied into RNA during transcription. RNA leaves the nucleus and joins onto a ribosome in the
cytoplasm where it is synthesised into a protein (translation).
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Genes contain sections that don’t code for
amino acids called introns (non-coding
regions of DNA).
Genes also contain sections that do code for
amino acids called exons (coding regions of
DNA). Introns are separated by exons.
During transcription both introns and exons
are copied, but the introns are removed by a
process called splicing which takes place in
the nucleus as a post transcriptional
modification. The exons can then be joined
together in different orders to form different
mRNA (template) strands during translation of
proteins. In this way, one mRNA gives rise to
more than one protein by post transcriptional
modifications.
mRNA tRNA
Carries the genetic code from DNA in the nucleus Carries the amino acids that are used to make
to the cytoplasm where it is used to make proteins proteins to the ribosomes.
during translation. It has an amino acid binding site at one end and a
mRNA is modified before it is translated. sequence of three bases at other end (anticodon).
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