DNA and proteins test

Genes

Chromosomes are essentially long, long, long, strands of DNA that are coiled multiple times around histones (eukaryotic cell). Sections of DNA with specific base sequences are called genes. A gene is a specific sequence of bases that code for a specific type of protein or RNA molecule. Genes code for proteins and RNA.

Protein synthesis

Life is a series of chemical reactions, therefore it's all to do with:
1. The random movement of molecules
2. The shape of proteins - enzymes

Importance of Complementary base pairing

1.The structure of DNA remains exact and orderly. Hydrogen bonding between the strands ensures the DNA molecule does not form an irregular structure.
2.The DNA molecule can store and transmit large quantities of (genetic) information as it is very large base pairing enables the strands to separate so the information can be used in replication and transcription.

RNA

RNA - ribonucleic acid is a polymer that codes and decodes genetic information. it includes different types, messenger rna (mRNA), transfer rna (tRNA) AND ribosomal rna (rRNA). DNA codes for RNA. RNA codes for proteins
Similar to DNA with the following differences:
•Single stranded
•Ribose sugar instead of Deoxyribose
•Contains the base Uracil (U) instead of Thymine (T)
•Shorter
Base pairing:
A-U
C-G

DNA in Prokaryotic cells

Bacteria cells, smaller than eukaryotic cells and more simple. Do not contain a nucleus.
Have a single, circular chromosome located in a region of cytoplasm called the nucleoid.
Do not have histones but have proteins that assist in organization.
May contain plasmids - small, extrachromosomal DNA molecule

DNA in Eukaryotic cells

Larger more complex cells found in plants, animals, fungi and protozoa. Have a nucleus and other organelles such as mitochondria and chloroplasts.
DNA is packaged into linear chromosomes found in the nucleus.
DNA is in the form of chromatin, the DNA is tightly coiled around globular proteins called histones.
Chromosomes become visible when the chromatin condenses before cell division.
DNA is also found in chloroplasts (plants) and mitochondria (plants and animals) the structure is similar to prokaryotic cells.

DNA Replication purpose

DNA contains the genetic information required to synthesise proteins that carry out life processes. DNA is passed on to daughter cells during cell division. The DNA in the parent cell needs to be replicated before cell division, to ensure each daughter cell receives an exact copy of the genetic information.

DNA replication steps

1. An enzyme called helicase unzips DNA along weak hydrogen bonds between complementary bases.
2. The bases along both sides of the DNA molecules become exposed.
3. The 2 exposed strands become templates for new strands to be built on.
4. Free floating DNA nucleotides dissolved within the cell randomly come into juxtaposition with their complementary partners by re-establishing the hydrogen bond. The result is a semi-conservative strand, half new DNA and half old DNA

Homologous chromosomes

Chromosomes in eukaryotic cells come in pairs called homologous chromosomes. One of each homologous pair (HP) comes originally from each parent
- Same length/size and contain genes that code for the same characteristic
- Are not genetically identical

Leading and Lagging strands

- The leading strand runs in the 5' to 3' direction. DNA polymerase builds the new strand in the 3' to 5' direction, by moving along the strand and adding bases continuously.
- The strand running from 3' to 5' is called the lagging strand because DNA polymerase only works by adding bases from 3' to 5' RNA primers need to keep being placed for the DNA polymerase to add the DNA bases in sections.

RNA Splicing

-In transcription the entire gene (exons and introns) is copied into messenger RNA (mRNA) molecule.
-This molecule is called pre-mRNA and needs to be modified.
•RNA splicing is the removal of introns from pre-mRNA forming mature - mRNA.
-The process is carried out by a protein-RNA complex called spliceosome.
-Mature-mRNA contains only exons and are translated into proteins

Transcription

The genetic code is copied from the gene (DNA) to messenger RNA (mRNA)
1. DNA polymerase unzips DNA at the site of the hydrogen bonds along the length of the gene.
2. The base sequence of the genes is exposed.
3. Free RNA nucleotides come into juxtaposition with their complementary base pairs.
4. RNA polymerase joins the complementary nucleotides together to form a single stranded molecule of messenger RNA (mRNA) (working molecule contains both introns and exons at this point)
5. mRNA is cut by enzymes to remove introns. Ligase enzymes join the exons together to form a working copy of mRNA that will be translated.

Messenger RNA (mRNA)

Synthesised during transcription, mRNA is the working copy of the gene. It enables a protein to be formed. It has the same sequence as the coding strand of DNA except it has Uracil instead of Thymine.

MRNA then travels to the ribosomes

Ribosomal RNA (rRNA)

Ribosomes consist of a small and large subunit.

The small subunit reads the mRNA and the large subunit joins the amino acids to form a protein.

Ribosomes are composed of rRNA (60%) and protein (40%)

The rRNA functions as an enzyme by catalysing the formation of the protein molecule

Transfer RNA (tRNA)

- A small RNA molecule that transfers amino acids to the ribosome during translation.
- tRNA molecules have an attachment site for a specific amino acid and a mRNA binding region called an anticodon.

Anticodon

Anticodons are a sequence of 3 bases which are complementary to the mRNA codon which codes for the attached amino acid.

Translation

The protein molecule is assembled using the genetic code on the mRNA
1. A mature mRNA molecule attaches to the small ribosomal unit of a ribosome.
2. A tRNA molecule transfers the first amino acid to the ribosome. Hydrogen bonds are formed between the tRNA anticodon and the mRNA codon
3. The mRNA molecule moves so that the next codon is now covered by the ribosome. A second tRNA transfers an amino acid to the ribosome. The large ribosomal unit catalyses a chemical reaction that joins the amino acids together.
4. The process is repeated until a stop codon is reached on the mRNA. The newly synthesized protein molecule then moves to the rough endoplasmic reticulum for modification.

Triplet

3 bases in a gene on DNA coding for an amino acid

Codon

Opposing 3 bases on mRNA coding for an amino acid

Template strand

Single strand of DNA from which a single stranded molecule of mRNA is made from in transcription.

Antibody

Provide protection against pathogens by binding to and neutralizing molecules called antigens found on the surface of pathogens.

The shape of an antibody is complementary to the shape of an antigen.

Activation Energy

-Chemical reactions involve the collision of two reactants.
-A successful collision results in the formation of products.
-A successful collision occurs when the reactants collide with a minimum amount of energy called activation energy.
-The amount of activation energy determines the rate of a reaction.
-Reactions with a high activation energy proceed slowly as fewer molecules posses the energy.
-Reactions with low activation energy proceed more rapidly as more molecules posses the energy.

Enzymes

- Enzymes catalyse reactions by binding with a substrate forming an enzyme-substrate complex and increase the rate of reactions in cells by lowering the activation energy
- Substrates bind to a specific region of the enzyme called the active site.
- The shape of the active site is complementary to the substrate.
- The unique 3D shape of the enzyme and its active site ensures that the enzyme binds to a specific substrate.

Factors affecting the rate of an enzyme catalysed reaction

The rate of an enzyme catalyzed reaction is dependent on physical and chemical factors including Temperature, pH, the concentration of enzymes, substrates and products and the presence of inhibitors.

How does temperature affect the rate of enzyme catalysed reaction?

- The rate of a reaction initially increases with temperature as the enzyme and substrate have more kinetic energy which increases the number of collisions between the active site and substrate.
- The reaction rate is greatest at the optimum temperature.
- The rate of the reaction decreases above the optimum.
- Above the optimum the 3D structure of the enzyme is altered.
- The attractive forces that maintain the tertiary structure of the enzyme are overcome and the enzyme is denatured.

How does pH affect the rate of enzyme catalysed reaction?

-Changes in pH affect the 3D structure of an enzymes and its active site which limits the formation of enzyme substrate-complexes and reduces the rate of reaction.
-The reaction is greatest at the optimum pH

How does Enzyme Concentration affect the rate of enzyme catalysed reaction?

-The reaction rate is low when enzyme concentration is low.
-The rate increases as enzyme concentration increases.
- The reaction rate becomes constant as the number of substrate molecules is less than the number of available enzymes.

How does Substrate concentration affect the rate of enzyme catalysed reaction?

-Reaction rate is low when substrate concentration is low. There are more enzymes than substrates.
-The rate of the reaction increases as substrate concentration increases as more substrates occupy active sites.
-The rate becomes constant as the number of enzymes is less than the number of substrates.

How does product concentration affect the rate of enzyme catalysed reaction?

-Some enzymes are inhibited when the concentration of products becomes too high in a cell.
-Example: enzyme hexokinase which converts glucose (substrate) into glucose-6-phosphate during respiration.

Enzyme Cofactors

-Small molecules or ions that activate enzymes or transfer important molecules to the active site.
Coenzyme: (Vitamins) bind temporarily with an enzyme and support its function.
Inorganic ions: (activators) inorganic metal ions, alter the charge of the active site which improves binding.
Prosthetic group: Bind permanently to an enzyme molecule.

Inhibitors

-Enzymes can be inactivated by the presence of an inhibitor.
-Inhibitors maybe reversible or irreversible depending on whether the binding is temporary or permanent.
Examples:
-Heavy metals: Mercury, lead, arsenic and cadmium bind to amino acids in primary structure, inhibiting formation of active site
-Cyanide: Prevents cells from producing ATP
-Glycophosate (herbicide): kills plants by inhibiting enzyme involved in amino acid synthesis.

Competitive inhibitor

A chemical structure that has a similar shape to a specific substrate molecule and can be therefore temporarily bind to it. This means that the substrate cannot bind it because the active site is blocked for some of the time. The effect of this is to slow the reaction down.

Non-competitive inhibitors

A chemical structures that attach to the enzyme at a site other than the active site. This causes the enzyme to become denatured and to no longer complementary its substrate. This will cause the chemical reaction that the enzyme catalyses to stop.

What is a mutation?

- A permanent change to the sequence of DNA bases. Can lead to alteration or absence of proteins and subsequent changes to the appearance of offspring (phenotype)
- Mutations occur during cell replication, which occurs before cell division
- Impacts include genetic diseases if a specific protein is not produced. Cancer if a gene responsible for the formation of a protein which controls the cell cycle is involved

Point mutation

- A change in the nucleotide base at a single point on a gene is sufficient to cause a change in both the mRNA codon sequence and the primary structure of the protein.

inversion (point mutation)

Inversion of adjacent nucleotides

Deletion (point mutation)

A nucleotide base has been deleted from gene

Insertion (point mutation)

A nucleotide base has been inserted

Substitution (point mutation)

A nucleotide has been substituted for another.

Missense (gene mutation)

Results in a different amino acid being coded for which alters primary structure.

Samesense (silent) (gene mutation)

Results in the same amino acid being coded for which does not change primary structure.

Nonsense (gene mutation)

Results in changing to a stop codon. Prevents protein synthesis and results in a non-functioning protein

Frameshift (gene mutation)

- Insertions and deletions usually cause major changes in the mRNA sequence as all of the codons are affected and there may be many amino acids changed.
- These changes prevent the protein from folding into a shape that is biologically active

Chromosome Mutations

- A change in the number or structure of chromosomes in a cell
- Caused by errors that occur during cell division (DNA replication, mitosis and meiosis)
- Chromosome mutations can affect the whole chromosome. Affecting hundreds or thousands of genes.
- Usually result in significant phenotypic changes, they may affect multiple genes.

Translocation (chromosome mutation)

Genes are exchanged between non-homologous chromosomes(not a pair). Occurs during meiosis

Duplication (chromosome mutation)

A gene maybe replicated more than once creating extra copies of a gene on a chromosome.

Deletion (chromosome mutation)

A gene can be removed at any location on a chromosome causing a loss of genetic material

Inversion (chromosome mutation)

A section of a chromosome breaks off, inverts and rejoins the chromosome.

Aneuploidy

A chromosome mutation that causes individuals to have an abnormal number of chromosomes.
e.g. Klinefelter (males have an extra x chromosome)
Turner syndrome (females have an extra x chromosome)
Down syndrome (an additional chromosome 21)

Polyploidy

Individuals have more than two sets of chromosomes in a cell. Common in plants, seen in some amphibians and fish.

Mutagens

Mutagens are environmental factors which increase the rate of mutation.

Ionising radiation (mutagen)

Breaks bonds in DNA causing both gene and chromosomal mutations.
Examples: Alpha, beta and gamma radiation
X-rays

Non-ionizing radiation (mutagen)

Causes adjacent thymine bases to form chemical bonds, causes gene mutations.
Example: UV radiation

Mutagenic Chemicals (mutagen)

React with and change the molecular structure of DNA. Cause point mutations. Some chemicals stimulate oncogenes causing uncontrolled cell division.
Examples: Nitrous Acid, Nicotine and Food preservatives

Virus (mutagen)

Initiate uncontrolled cell division by inserting oncogenes into the genome.
Example: HIV-1, papilloma

Somatic mutation

Somatic cells include all the body cells except germ cells (sperm and eggs)
- Occur in body cells in all organs except reproductive organs
- Are often localized in one organ or tissue type
- Are not inherited
- Affect the individual in which mutation occurred

Germinal mutation

Germ cells differentiate into gametes (sperm and egg cells)
- Occur in germ cells in the reproductive organs
- Are passed on when germ cells differentiate into gametes
- Are inherited and maybe expressed by offspring
- Found in every cell of the offspring
- Generally do not cause changes to phenotype of the individual in which the mutation occurred

Somatic mutations and cancer

Somatic mutations in proto-oncogenes cause cancer tumours. The cancerous cells have unregulated cell division, they divide rapidly forming a mass of identical cells (primary tumour). Primary tumours can become mobile (metastasis) and spread if not treated.

Mutation and genetic variation

- Genetic variation is important as it allows for changes in the genotype of populations.
- Different forms of the same gene are called alleles, e.g. different blood type in humans
- New alleles arise from existing ones through spontaneous and induced mutations.

What is biotechnology?

-The science of modifying existing biological processes in living things to produce useful products.
-Genetic engineering, involves manipulation of the genes in organisms to make useful products such as therapeutic drugs and proteins.
-Involves a range of techniques

Restriction Enzymes

- Used to remove a target gene from one organism (target organism) and inserting into the genome of a suitable host.
- Restriction enzymes are used to cut the DNA at specific locations called restriction sites.
- Some restriction enzymes cut straight across the enzyme and create blunt ends with no exposed bases. Others cut in an offset way to create sticky ends with exposed bases.
- The genome of the target organism is sequenced before restriction enzymes are added. This is to identify restriction sites either side of the target gene.
- There are many restriction sites in the organisms genome. The restriction enzyme cuts the DNA at all restriction sites creating restriction fragments that vary in length.
- Restriction fragments are separated by gel electrophoresis.
- Separated fragments are transferred to a nylon membrane and immersed in a solution containing gene probes.

Gene probes

-Single stranded DNA or RNA molecules with a nucleotide sequence that is complementary to the nucleotide sequence of the target gene.
- The gene probe contains radioactive or fluorescent particles that emit radiation, allowing for detection of the probe when it is bound to the target gene
- The probe and target gene are then visualised using autoradiography.
- PCR is use to increase the number of copies of the gene

Recombinant DNA

- This stage involves using a vector to insert the target gene into the genome of the host.
- The widely used vectors are plasmids which are small, circular DNA molecules in bacteria and yeast.
- Plasmids are isolated from the host bacteria and are cut open using the same restriction enzyme used to remove the target gene.
- The restriction enzyme produces sticky ends on both the plasmid and target gene. This allows the target gene to form hydrogen bonds with complementary bases on the plasmid.
- Enzymes called ligases join the target gene to the plasmid forming recombinant DNA.
- Bacterial plasmids contain genes that confer resistance to some antibiotics. Insertion of the target gene will often disrupt one of these resistance genes.

Bacterial transformation

- The process where recombinant DNA is mixed with the cells of a host such as bacteria or yeast.
- Electroporation, which involves shocking host cells with electrical energy to form holes in the cell membrane through which plasmid DNA can enter the cell.
- Host bacterial cells containing the recombinant DNA can be identified using growth mediums containing different antibiotics.
- Host cells containing recombinant DNA will grow on ampicillin but not tetracycline due to insertion of target gene,
- Bacteria containing the target gene are called transcribed. These cells are transferred to a growth medium where they multiply producing millions of daughter cells which contain the gene.
- The product protein is isolated and purified e.g. Insulin

Viral Vectors

- Viruses can be used as vectors due to their ability to transfer genetic material to a host.
- The target gene is inserted into the viral genome, the virus is then used to infect the host cells causing the target gene to be incorporated into the hosts genome.

CRISPR

-Originated from bacteria, used in defence against viruses called bacteriophages.
- CRISPR sequences are found in a region of the bacterial genome called the CRISPR array and function to destroy viral DNA that has been encountered before.

CRISPR array

The short palindromic repeat sequences in a CRISPR array are separated by spacers (short sequences of nucleotides) which are removed from the bacteriophage and inserted into the genome of the bacteria to help prevent reinfection.
Spacers are cut and inserted by
Cas proteins

Cas proteins

- Enzymes that breakdown nucleic acids (DNA and RNA)
- Used by bacteria to create a new spacer by removing DNA from a bacteriophage and inserting into a CRISPR array, as well as breaking down invading viruses.

CRISPR/Cas system

- Used to insert and remove sequences of nucleotides from living things.
- The manufactured guide RNA (gRNA) has a nucleotide sequence complementary to the target DNA
- gRNA bonds with the target DNA and cas9 cuts the sugar-phosphate backbone at specific locations.
- The genome is edited by either removing or inserting nucleotides

Benefits of CRISPR/Cas

- Genomes edited quickly, multiple genes can be edited simultaneously
- Inexpensive
- Highly specific and accurate
- The gRNA can be altered to be complementary to any nucleotide sequence

Limitations of CRISPR/Cas

- Mutations in the target nucleotide sequence reduce effectiveness
- Cuts made by Cas 9 can be repaired before gene inserted
- May cause unwanted cuts if the target nucleotide sequence occurs more than once

Applications of CRISPR/Cas

- Agriculture: insert genes into plants that confer disease resistance
- Biotechnology: modified the genomes of yeast to synthesise
hydrocarbons that are used to make plastics
- Research: Modify nucleotide sequences in target genes to study the effect of a mutation on genetic disease.
- Gene therapy: Remove mutations from genes to minimise the risk of diseases such as cancer.
- Immunology: to remove viral DNA from the genome of an infected host which can minimise infection rates in humans

Concerns with CRISPR/Cas

-Accidental or Deliberate release: Viruses are used as vectors to insert the CRISPR/Cas9 into cells of a target organism. An airborne viral vector could escape the laboratory and enter the human population.
-Off-target editing: CRISPR can edit the genomes of organisms in unwanted locations producing harmful mutations.
- Designer Babies: Concerns about using CRISPR to edit germ cells in human embryos to remove gene mutations.Could be used to produce genetically superior humans

Protein Design

- Development of new proteins molecules to control biochemical processes in cells for applications including biomedical research, medicine and technology.
- Involves the use of a computer software to predict the 3D structure of the protein from its amino acid sequence.
- The designed proteins may then be synthesised using biotechnology techniques.

Application of Protein design

- Enzyme design: used in commercial applications, industry
- Studying protein-protein interactions: look at proteins involved in disease. Design a protein to bind to inhibit disease causing protein
- Development of new materials: Design proteins with desirable characteristics e.g. high tensile strength
- Targeted Chemotherapy: proteins attach to the membrane of cancer cells where they attract immune cells that destroy the tumour.

Biosensors

Receptor proteins, antibodies or enzymes that detect chemical substances in their environment by binding with target molecules.
Applications:
- Medical: monitoring blood glucose levels in diabetics
- Environmental: detecting pesticides and river water contaminants
- Food quality: Detection of contaminants in food products

Coding Strand

The strand of DNA which has the correct sequence to produce a protein, the same as the mRNA strand

Amino acids

Proteins are made from a specific sequence of amino acids. There are 20 different types of Amino Acids. Amino Acids have three distinct chemical groups:

Protein structure levels

primary, secondary, tertiary, quaternary

Peptide Hormones

Hormones regulate physiology and behaviour in a multicellular organism by facilitating communication between cells.

Hormones are released from endocrine glands and travel in the circulatory system to target cells.

Examples include: insulin, glucagon, and ADH

The hormones bind to receptor proteins in the membrane and cytoplasm of target cells. The shape of the receptor protein is complementary to the shape of the hormone.

Silencing Genes

-Genes which are turned off (silenced)
-Involves adding or removing chemical groups from DNA or the histone proteins associated with DNA (in chromatin) in eukaryotes.

Environmental factors of epigenetics

-Factors such as diet and drug use can cause epigenetic changes such as DNA methylation which can alter gene expression.
-Pre-natal exposure to famine and drug use can cause epigenetic changes linked to chronic diseases and behaviour disorders

Epigenetics and disease

-Studies suggest epigenetic factors are involved in auto-immune disorders such as multiple sclerosis, type 1 diabetes and rheumatoid arthritis.
-Causes the T-cells to attack the target organ

Amount of Chromatin remodelling

-Decreased histone acetylation creates more heterochromatin which can silence tumour suppressor genes.

-Increased histone acetylation creates more euchromatin which activates proto-oncogenes

Amount of DNA Methylation

-Decreased DNA methylation can activate proto-oncogenes and trigger unregulated cell division.

-Increased DNA methylation can silence tumour suppressor genes and trigger unregulated cell division

DNA profile table

Data from an STR electropherogram can be displayed in a DNA profile table. The numbers in the table are the allele values which identify the number of repeats in the STRs on the alleles of an individual at a certain loci.

Issues in collecting genetic information

-Potential for discrimination
-Ownership
-Privacy and confidentiality
-Emotional impact on the individual
-Impact on family members
-Impact on children
-Social implications
-Impact on reproductive choices
-Limitations
-Inaccuracies
-Reliability

Epigenetics and cancer

-Cancer is caused by unregulated cell division which can result in the formation of tumours.
-Two genes are important in preventing cells from becoming cancerous:

Proto-oncogene - Promotes cell division

Tumour suppressing gene - inhibits cell division and tumour development

Epigenetics and Development

-Epigenetic factors are passed on to daughter cells during cell division.
-Epigenetic factors are crucial for the development of specialized cells in multicellular organisms.
-E.g. a liver cell contains genes which are switched on and off. When the cell divides each daughter cell has the same genes switched on and off.

STR electropherogram

-A graphical representation of a DNA profile showing the location of STRs on certain chromosomes
-Two peaks shows the individual is heterozygous at these loci, due to maternal and paternal chromosomes having different short term random repeat sequences. D8S1179 13 repeats and 16 repeats
-One peak at D7S820 shows the individual is homozygous, STR is same length in maternal and paternal chromosomes

Epigenetics and inherited characteristics

-Genes that are silenced in sperm and egg cells are silenced in the offspring (zygote).

Importance of Epigenetics

-Affect the phenotype of the cell without changing the underlying DNA sequence.
-Allows the development of complex multicellular organism made of specialized cells, tissues and organs from a single celled zygote.
-Epigenetic factors can be inherited

STR analysis

-STR (short tandem repeats)
-Scientists have found several loci in the human genome where STR's are commonly found
-The number of STR repeats is highly variable, which allows forensic scientists to compare DNA from two individuals.

DNA Profiling procedure

1.The DNA is extracted from sample (clothing, surface, weapon or directly from person)
2.The extracted DNA is cut by restriction enzymes which cut the sugar phosphate backbone at specific locations. Restriction enzymes cut DNA at locations adjacent to a minisatellite or microsatellite. The products are called restriction fragments.
3. Restriction fragments are then separated using electrophoresis.
4. DNA is transferred to a nylon membrane.
5. The nylon sheet is immersed in a solution of labelled DNA molecules called probes. The DNA sequence of the probe is complementary to the minisatellite or microsatellite under analysis. Probes generally contain a radioactive element. Excess probes are washed away.
6. X-ray film is placed over the nylon sheet. The film is exposed to radiation regions where radioactive probes have bonded with microsatellites and minisatellites. The DNA profile is displayed as a autoradiograph

Euchromatin v's Heterochromatin

Non-coding RNA (ncRNA)

-A small RNA molecule that is transcribed from DNA but not translated into a protein.
-Control gene expression

Micro RNA (miRNA) - Bond with complementary bases on target mRNA molecules
Small interfering RNA (siRNA) - Prevent translation by causing mRNA to be degraded after transcription
Piwi-interacting RNA (piRNA) - RNA interacts with piwi proteins which bonds with and degrades target mRNA molecules after transcription
Long non-coding RNA (lncRNA) - Regulate the activity of proteins involved in transcription of genes

Epigenetics

-Heritable changes in gene expression in eukaryotic cells
-gene expression (switching on or off genes) is regulated by epigenetic factors such as:

Epigenetic factor - Gene switched off (silenced) - Gene switched on (active):
Histone acetylation - less - more
DNA methylation - less - more
Chromatin remodelling - Heterochromatin - Euchromatin
Non-coding RNA (ncRNA) - re miRNAs, piRNAs and siRNAs - Less miRNAs, piRNAs and siRNAs

Basis of DNA Profiling

The genome of an individual contains exons and intron. Introns contain repetitive sequences of bases called tandem repeats.

Variable Number Tandem Repeats (VNTRs) are tandem repeat sequence that vary in length and chromosome location.

Two examples:
Minisatellites: tandem repeat sequences between 10-70 bases in length
Microsatellites: tandem DNA sequences that are less than 10 base pairs in length.

Due to their different size the VNTRs move at different rates through the gel. Larger VNTRS move slower.

The likelihood of two individuals having the same VNTRs is very low as these nucleotide base sequences vary in both length and number of tandem repeats.

Chromatin remodelling

-Chromatin is a mixture of DNA and histone proteins which makes up chromosomes.
-DNA molecules are negatively charged due to the presence of phosphate groups.
-Histone proteins are positively charged (due to R groups on amino acids), this property attracts DNA, forming firmly packed heterochromatin.
-Negatively charged acetyl groups attach to histones neutralizing them and weakening bonds between DNA and histones forming loosely packed euchromatin.
-DNA in heterochromatin is inaccessible to RNA polymerase and cannot be transcribed.
-Addition of acetyl groups (acetylation) to heterochromatin causes remodelling to euchromatin.
-DNA in euchromatin is accessible to RNA polymerase and can be transcribed.
Heterochromatin ≠ transcription
Euchromatin \= transcription

DNA Profile

A DNA-based pattern composed of a series of bands corresponding to DNA fragments of different sizes.

Also called a DNA fingerprint

Used in forensic science, paternity and ancestor testing and genetic screening.

Half of the bands in a DNA profile come from the mother (maternal) and half from the father (paternal)