DNA Structure and Heredity

• Red dot points indicate syllabus points.
• Black information represents notes.

Heredity

• Structural properties of DNA, including nucleotide composition, pairing, and hydrogen bonds, allow for replication.

DNA Structure

• DNA is deoxyribonucleic acid.
• DNA consists of nucleotide subunits arranged in a double helix.
• It holds inheritable information.
• DNA is a very long molecule with 10,000's base pairs.
• Each DNA strand runs anti-parallel
• Its ladder-like structure features sides with alternating phosphate and sugar molecules and rungs of nitrogenous bases held by weak hydrogen bonds for easy breaking during replication.

Nucleotide

• Nucleotides have 3 components: a 5-carbon sugar, a negatively charged phosphate group, and a nitrogen base.
• Adenine pairs with Thymine, and Guanine pairs with Cytosine.
• Guanine + cytosine have 3 hydrogen bonds
• Adenine + thymine have 2 hydrogen bonds
• Purines include adenine and guanine, they have a single sugar structure.
• Pyrimidines include thymine and cytosine, they have a double sugar structure.

DNA Replication Process

• Enzyme helicase unwinds parent DNA.
• Double-stranded DNA unwinds at the replication fork.
• Strands are coated in a protein (SSB) to stop them from re-annealing.
• Template strand nucleotides are exposed and unpaired.
• Primers (short DNA segments) are needed to start replication process.
• Primers synthesized by the enzyme RNA primase
• DNA polymerase extends nucleic acid chain.
• Free nucleotides attach to complementary bases from the nucleoplasm.
• Synthesis occurs in the 5' to 3' direction, creating a leading and lagging strand.
• Ligase joins DNA strands together.
• DNA rezips and 2 identical daughter molecules are created
• DNA is a helical double-stranded molecule bound to proteins in chromosomes within the nucleus.
• DNA also exists as unbound circular DNA in the cytosol of prokaryotes, and in the mitochondria and chloroplasts of eukaryotic cells.
• Nucleosomes are structural units of eukaryotic chromosomes, consisting of DNA coiled around a core of histones.

Relationship Between DNA, Genes, and Chromosomes

• Chromosomes and genes are composed of DNA.
• Chromosomes are long DNA strands wrapped around histones.
• A gene is a short DNA segment encoding a specific characteristic.
• An allele is a specific form of a gene responsible for trait variations.
• Genes provide instructions for proteins.
• Most genes have 2 alleles.
• Locus is the position on the chromosome

DNA in Pro/Eu Karyotes

• In prokaryotes, DNA is in plasmids (extra DNA) and in the nucleoid region.
• In humans, DNA condenses into chromosomes.
• Eukaryotes have DNA in mitochondria, chloroplasts, and the nucleus.
• Prokaryotes have DNA in the cytosol of the cytoplasm.

Differences and Similarities of DNA Packaging

• Prokaryotes: No nucleus, no membrane-bound organelles, a single-stranded chromatid molecule, a circular shape, plasmids in the nucleoid region, and one chromosome.
• Eukaryotes: Has a nucleus and membrane-bound organelles, a double-stranded chromatid molecule, a linear shape, no plasmids, located in the nucleus, and multiple chromosomes.

DNA in Nucleus

• Nucleus DNA: Inheritance from both parents, a linear shape, and low copy number.
• Mitochondria DNA: Maternal lineage, a circular shape, and high copy number with random segregation.
• Proteins, including enzymes and structural proteins, are essential for cell structure and function.
• Proteins are essential to cell/organism function and structure.
• Structural proteins are used in the cell wall to maintain shape.
• Enzyme Examples: Helicase unwinds DNA, Amylase breaks down glucose into simple sugars and Protein Carriers are required in active transport.
• Protein synthesis involves transcription and translation of a gene into messenger RNA in the nucleus, and translation into an amino acid sequence at the ribosome.

Transcription

• Only the anti-sense (lagging) strand is transcribed.
• Transcription takes place in the nucleus of eukaryotes.
• Initiation: A protein (RNA polymerase) attaches to the promoter region, and DNA is unzipped to expose nucleotides.
• Elongation: Messenger RNA is complementary transcribed using DNA as a template, only one DNA strand is transcribed (anti-sense strand, 3' to 5' end), and mRNA is single-stranded.
• Termination: Transcription stops when the termination sequence is reached and RNA polymerase detaches from DNA, and mRNA is released.

Post Transcription Changes

• mRNA is initially pre-mRNA until the spliceosome removes non-coding introns and leaves coding extrons.
• A methylated cap is added to the 5' end.
• An adenine tail is added to the 3' end.
• mRNA is now mature and ready to leave the nucleus.

Translation

• mRNA moves from the nucleus to the cytoplasm and binds to a ribosome.
• tRNA brings amino acids to the ribosome.
• Begins with the start codon AUG/Methionine.
• A codon is a set of 3 bases, one codon codes from one amino acid.
• tRNA reads the mRNA codon and contains an anti-codon.
• tRNA binds to the ribosome and brings the amino acid until the stop codon is reached.

Amino Acid

• Joined by polypeptide bonds to form a polypeptide chain.
• The polypeptide chain travels to the endoplasmic reticulum in a vesicle for final folding to become a functioning protein.

DNA vs RNA

• DNA vs RNA: Nucleic acids are the genetic material of all organisms, DNA carries blueprints for assembling proteins, and RNA plays a role in making proteins.

• Nucleic Acid

• DNA: Deoxyribonucleic in Nucleus, mitochondria, chloroplast, double stranded with Thymine, Adenine, Cytosine, Guanine bases, long.

• RNA: Ribonucleic in Ribosome, single stranded with Uracil, Adenine, Cytosine, Guanine bases, short.

• The genetic code is a triplet base code that includes coding and non-coding DNA.

• Contains information for protein production

• Only a small amount of a DNA strand is used for an RNA template; this region is a gene.

• A triplet base has 3 nitrogen bases; this is a codon.

• tRNA has an anti-codon that is complementary to the mRNA section.

• DNA STRAND: AGC TAT CGA GTC AAA

• mRNA: UCG AUA GCU CAG UUU

• Anti codon (tRNA): AGC UAU CGA GUC AAA

Ribosome Differences in Eu/Pro Karyote

• Prokaryote Ribosome: 2 unequal sub units in Mitochondria + chloroplast, smaller than eukaryote ones.
• Eukaryote Ribosome: 2 sub units as well (40s and 60s) are Bound to ER and lose in cytoplasm, bigger then prokaryote ones.
• Continuity of life requires the replication of genetic material and its transfer to the next generation through processes including binary fission, mitosis, meiosis, and fertilization.

Prokaryotes and Binary Fission

• Prokaryotes reproduce using binary fission with a single circular chromosome.
• Replication of DNA occurs.
• Each DNA copy attaches to opposite ends of the cell membrane.
• The cell increases in size.
• Each copy of the duplicated chromosome attaches to a different part of the cell.
• The cell begins to pull apart separating the chromosome (cytokinesis).
• A wall forms across the cell and divides it into 2 identical cells.

Mitosis

• Occurs in Interphase where DNA replication occurs, and DNA is not condensed into chromosomes.
• In Prophase, DNA condenses into visible chromosomes, and spindle fibers appear.
• During Metaphase, chromosomes line up at the equator.
• In Anaphase, chromosomes are pulled apart to either side of the cell.
• Telophase: Cytokinesis occurs, the nuclear membrane reforms, and two identical daughter cells are produced

Cell Cycle

• Cell spends majority of time in interphase.
• During S phase DNA is replicated before cell division.
• Mitosis starts in M phase + ends in C phase.

Meiosis

• Prophase I: DNA condenses into chromosomes and homologous chromosomes pair and cross over.
• Metaphase I: Homologous chromosomes line up at equator.
• Anaphase I: Microtubules (spindle fibers) pull homologous chromosomes apart and move to opposite ends of cell.
• Telophase I: Spindle fibers broken up, the new nuclear membrane forms, chromosomes uncoil and cell divides.
• Prophase II: Chromosomes condense, nuclear membrane breaks down and new spindles form at right angles.
• Metaphase II: Spindle fibers line attach to chromosomes and line at equator.
• Anaphase II: Sister chromatids pulled to opposite ends, cell elongates and a chromatid becomes a daughter cell chromosome.
• Telophase II: Sister chromosomes uncoil, the new nuclear membrane forms, 2 cells divide again to form new haploid cells (gametes (n)).

Gene Expression

• Phenotypic expression of genes depends on the interaction of both genes and the environment.
• Cells do not express all genes in their genome at the same time.
• Some genes are active (produced via protein synthesis), while others are inactive or switched off.

Eukaryotic

• Only 2% of the human genome contains genes that are transcribed.
• Coding proteins are exons.
• Non-coding proteins are introns.

DNA Methylation

• Attaching a methyl group to a nucleotide/histone protein.
• DNA methylation prevents genes from being transcribed.

Epigenetics

• The study of chemical modifications to gene function that are not due to DNA sequence changes.

Environmental Influence on Gene Expression

• Gene expression can be influenced by environment.
• Himalayan Rabbits: Temperature affects fur color; in warm areas, the 'C gene' is switched on, but in colder extremities, the fur is black.
• Hydrangeas: pH of soil, flowers are blue in acidic soil and red in neutral/basic soil.
• Mutations in genes and chromosomes can result from errors in DNA replication or cell division or damage by physical or chemical factors in the environment.
• Mutation: a permanent change in DNA structure, which can be caused by environmental factors.

Mutagens

• Physical Mutagen: produces energy which damages DNA.. - Radiation (X-Ray): causes the loss of adenine/guanine bases creating gaps, incorrect bases inserted during DNA replication. - UV: hydrogen bonds along the DNA strand are broken, causing adjacent thymine bases too bond. - Nuclear Radiation: causes breaks in the DNA strand.
• Chemical Mutagen: causes substitution, addition, or deletion of a base - Alcohol: causes DNA breaks which permanently alters it. - Mustard Gases: causes guanine to be replaced by other bases.
• Biological Mutagen: damages cells and changes DNA, and some insert fragment of their own vaccinations. - Virus - Bacteria: no actual DNA changes but causes genes to switch on/off.

Point Mutations

• Occurs when a base change results in the same codon coding for the same codon.

• Change in a DNA sequence at one point or base with a difference between sequences in nucleotides at 1 position called single nucleotide polymorphism (SNP/snips).

• Substitution: Occurs when one nucleotide is replaced by another

• Insertion/Addition: Addition of one or more nucleotides.

• Deletion: Loss of nucleotides.

• Silent Mutation: Occurs when a base change results in the same codon coding for the same codon as the original codon.

• Missense Mutation: Arises when a single nucleotide changes the codon and therefore the amino acid.

• Nonsense Mutation: Occurs when a single nucleotide mutation results in a stop codon, an incomplete polypeptide.

Effects of Mutation on Survival

• Mutations change protein structures, this has an affect on protein function.

• Neutral: Protein product is unchanged, same amino acid is used, correct protein made, and no effect on survival.

  • Disrupts the function of the protein, incomplete or non-functional protein, and affects ability to carry out the process and survive.
  • Gene mutation leads to a new allele, and the new allele is beneficial to survival
  • Increases the chance of survival.

Chromosomal Mutations

• Changes the structure of the chromosome.
• Double stands, re-arrangement of broken segments, and loss of part of the chromosome.
• Naturally occurring (meiosis) and exposure to a mutagen.

Deletion

• The chromosome undergoes double stranded breaks at 2 locations.
• Results in a lost segments.
• Effect: fatal, survivors have adverse effects.

Duplication

• An extra copy is made of a section of chromosome + inserted into the same/other chromosome.
• Causes gene sequences to be repeated many times.
• Effect: usually harmful, sometimes advantageous.

Inversion

• A chromosome breaks in 2 places, the middle segment rotates 180* before rejoining
• Reserves gene sequence.
• Effect: less dramatic than other mutations, often causes non-disjunction in meiosis.

Translocation

• A section of one chromosome breaks off and is reattached to another one.
• Effect: normal control over genes as section is lost

Variations in Chromosome Number

• Monoploidy: more economical, mutations more harmful. Example: Often in colonial insects, males are monoploid (1n), gametes are made by mitosis, females are diploid, gametes are made by meiosis, and males are produced by parthenogenesis.

• Polyploidy: common for flowering plants to have increased size and better hardiness, but is lethal in humans and causes reduced fertility.

• If gametes aren't haploid resulting in some diploid, some none

• Diploid fuse with haploid to form (3n) or 2 diploid fuse (4n).

• Organisms can have extra sets of chromosomes.

Aneuploidy

• The addition or loss of a chromosome from a cell, causing miscarriage.
• Instead of chromosomes in meiosis separating into each cell, they go into one cell.
• 2 types of gametes are produced: 1 has 2 copies of a chromosome, the other has 0 (disjunction).
• Disjunction can occur in the 1st/2nd meiotic division.

Variation in Genotype

• Variation in the genotype of offspring results from the processes of meiosis, including crossing over and random assortment of chromosomes, and fertilization, as well as mutations.

• Meiosis: Independent Assortment of Alleles: Homologous chromosomes separate independently of each other during meiosis I, which forms random combinations of chromosomes and creates novel combinations.

• Meiosis: Crossing Over: The exchange of alleles between homologous chromosomes results in a new combo of alleles and different alleles create new genotypes.

• Fertilization: The fusion of gametes from maternal and paternal parents combines genetic material from 2 individuals and new genetic combinations M/paternal alleles in new genotype.

• Mutation: A permanent change in DNA sequence results in variation and is the ultimate source of new alleles.

Alleles

• Each gene usually has 2 alleles.
• 2 identical alleles (GG/gg): homozygous
• 2 different alleles (Gg): heterozygous
• Individuals receive one gene from each parent and are then paired.

Mendelian Inheritance

• Chose peas as a model organism and created purebreeding tall/short plants.

• Peas are good as have quick growth + high seed rate.

• Then he breed them with others to see how they inherited traits.

• Found that tall peas always had a hidden recessive trait.

• In second self-fertilization, the hidden recessive form appeared in some peas in F2 (3 tall pease to 1short).

• Also found inheritance of different traits were independent .

• Theory that traits are controlled by single genes, each organism has 2 copies of each gene .

• Purebreeding 2 pure parents will always have offspring the same as themselves .

• Law of dominance: mating between 2 organisms of different traits, offspring exhibits only 1 parent (dominant alleles).

• Recessive traits only show when both alleles are recessive.

• Law of independent assortment: alleles of 2 or more genes get sorted into gametes independently of one another .

• The allele a gamete receives for 1 gene doesn't influence the allele received for another gene .

• Law of segregation: when gametes are formed, each one receives 1 gene copy which is selected randomly .

• Heterozygous: produces G and g gametes .

• Cross test: used to determine if organism with dominant phenotype is homo/hetero.

• Mono hybrid: when parents of 2 different genotypes at a locus breed to create hybrids like (Gg) .

• Incomplete dominance: when one trait is not fully dominant over its partner.

  • Expressed by mixing of phenotypes → Red flower x white flower = pink flower

• Blended dominance: both alleles in a genotype are fully expressed in the heterozygote.

Polgenes

• Similar to incomplete dominance but it has bits of both phenotypes → Red cattle x white cattle = roan cattle.
• Characteristics controlled by more than one gene and are poly genetic and transmitted through poly genetic inheritance. Happens when a single characteristic is controlled by the alleles of 2 or more genes interacting with one another .
• Results in an expression of multiple genes -> range of phenotypes Continuous variation: showing a range for phenotypes, variations controlled by 2 or more genes (skin colour).
• Discontinuous variation: only 1 gene involved, results in small number of phenotype (hair line).

Multiple Alleles

• Usually only 2 alleles present for 1 gene, multiple alleles is 3+ in a gene within a population.

• When more than 2 genes types can occupy a locus.

• Human blood type: alleles IA, IB, \ IA, IB are codominant and ii is recessive.

• 2 O parents must have O child.

• 1 A parent + 1 O parent can have a couple of types of children but depends on if A parent is homo/heterozygous.

• If it's hetero they can have O blood group kiddies.

Sex Linked

• Genes located on X or Y chromosome: X/Y linked.
• Genes on sex chromosome don't appear equally in both sexes. Hemizygous: only having a single copy of a gene instead of 2 which is all genes on the male's X chromosome.
• Gametes have 22 autosomal chromosomes and one X and X/Y (males), females have XX’s.

X-Linked Recessive

• When recessive phenotype is determined by and alleles on the X chromosome.
• Males receive 1 X from their mother, inheriting 1 affected gene in will result in them being affected.
• Males with recessive allele: Always express phenotype (only have 1 X chromosome).
• Males show X-linked recessive more than females. Males with X-linked disease can't pass it onto sons as they inherit the Y chromosome only which is uneffected.
• Affected males can have affected daughters if mothers passes the recessive X-linked gene as well Example: haemophilia, colour blindness .
• Females with recessive allele: only express when both X chromosomes have affected allele, If the female if heterozygous (Gg) they are a carrier.
• X-Linked Dominant: Similar to recessive in that heterozygous females always show the phenotype.
• Affected males don't pass affected alleles to sons but will pass them to all daughters.

Pedigrees

• Shows genetic history between

• Graphic representation showing the pattern of occurrence in a family.

• Autosomal Dominant Both males and females are affected equally.

• All affected individuals have 1 affected parent 2 affected parents can have unaffected children.

• Autosomal Recessive Both males and females are affected equally. Two unaffected heterozygous parents can have affected offspring, and two recessive parents only have recessive offspring.

• DNA sequencing enables mapping of species genomes, and DNA profiling identifies the unique genetic makeup of individuals.

• DNA sequencing vs DNA profiling: Sequencing determines the order of base pairing or nucleic acid sequence in DNA to help identify specific genes.

  • Sequencing Uses: Gene probes
  • Profiling: is the analysis of the DNA and identifies species or individuals and uses gel electrophoresis

• Genetic engineering / Plasmids (vectors): found in bacteria. Extra chromosomal DNA.

• Often carry useful genes for traits like antibiotic resistance

• Easily copied and transferred between bacteria in conjunction. Can be picked up from the environment if they are encountered by the bacteria in the transformation is needed.

• Vector: an instrument/organism used to transfer genes between organisms, Restriction enzymes (endonucleases):

• How do they get the enzymes? Isolate them from bacteria .

• They are a natural defence against viruses in bacteria, they act as molecular scissors.

• Cut DNA at specific sites known as restriction sites (no longer than 6 bases) .

Blunt and Sticky Ends

• Blunt ends: Created when the cleaved fragments have no overhanging bases and rarely used in biotech as DNA bonds are weak.

• Sticky ends Cuts are asymmetrical that create over, the hanging bases on fragments and are useful in biotech as DNA bonds are strong

• Complementary DNA fragments are joined with DNA Ligase which acts as a molecular glue.

• Polymerase Chain Reaction technique used to amplify (copy) large quantities of DNA, copies DNA at an exponential rate, each cycle takes 1-3 mins, uses tag polymerase, was isolated from themophyllic, function function at high temperatures with no denaturing, polymerase Uses : DNA, nucleotides, primers, tag polymerase.

• PCR process:

  • Denaturation: the mixture is heated to 95°C, the DNA denatures and separates to be single stranded.
  • Annealing: temperature is adjusted at 50°C-60°C, primers are attached to single stranded DNA
  • Extension, at a temperature changed to 72°C, initiates taq polymerase to start adding free nucleotides to single stranded template DNA.

• Repeat the process about 30 times and creates millions of copies of a DNA sample . How to calculate amount of DNA in copies → 1 strand produces 2 copies, 10 cycles = 2 to the power of 10 = 1024 DNA

• Gel electrophoresis Uses gels to separate molecules by moving them in an electric field and separating molecules based on sizing . DNA prepared by cut with restriction enzyme + amplified with PCR . Agarose gel covered in buffer solution. DNA mixed with a loading dye is done to make it visible for spotting. DNA is loaded into wells of the gel. A negative electrode is placed near wells, a positive electrode is placed at the other end. DNA fragments have a negative charge resulting in them to flow positive towards an end. Big fragments move slowly + less, small fragments move quickly + further DNA fragments separate producing a DNA profile. Banding patterns are then analyzed

Uses

(child is a mix of maternal/paternal -DNA so 50% of bands will be shared with mother/father) DNA identification

• Forensic appliances ( crime scenes banding has to be an exact match for suspect +DNA sample).
• Conservation by ( identification of endangered species and from their illegal trade.
• Identification of mutations and Specific alleles.
• DNA microarrays are purposed to determine gene expression If gene is switched on and transcribed or switched off.
• Gene-probe in a tool that’s searches for a for a specific region within a genome for example it finds the, gene in DNA that causes Huntington's disease

Advantage

• Allows large number of genes to be screened simultaneously.
• It helps identify mutations by determining the nucleotide sequence to see where differences are
• Micro array Uses Can identify diseases like breast cancer genes or interesting in D and mutation 2.

Process

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• 1. Cutting + pasting DNA Target genes are isolated then cut out using restricting enzymes- Bacterial plasmid cut open Using same restriction enzyme DVA ligase Ligates the target gene into plasma

Clone & Creation

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