DNA Structure and Nucleotides

• Red dot points are syllabus points
• Black information is notes

Heredity

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

DNA Structure

• DNA is deoxyribonucleic acid, composed of nucleotide subunits arranged in a double helix.
• DNA stores inheritable information.
• The DNA molecule is very long, containing tens of thousands of base pairs.
• Each DNA strand runs anti-parallel to the other.
• Sides of the DNA ladder consist of alternating phosphate and sugar molecules.
• Rungs are made of nitrogenous bases held by weak hydrogen bonds.
• The weak hydrogen bonds can be easily broken during replication

Nucleotide

• Nucleotides consist of a five-carbon sugar, a negatively charged phosphate group, and a nitrogen base.
• Adenine pairs with Thymine, and Guanine pairs with Cytosine.
• Guanine and Cytosine are bound by 3 hydrogen bonds.
• Adenine and Thymine are bound by 2 hydrogen bonds.
• Purines (adenine and guanine) have a single sugar structure.
• Pyrimidines (thymine and cytosine) have a double sugar structure.

DNA Replication Process

• Helicase unwinds the parent DNA, creating a replication fork.

• Single-stranded binding proteins (SSB) coat the strands to prevent re-annealing.

• Primers (short DNA segments) begin the replication process, synthesized by RNA primase.

• DNA polymerase extends the nucleic acid chain.

• Free nucleotides attach to complementary bases from the nucleoplasm in the 5' to 3' direction, creating leading and lagging strands.

• The lagging strand comprised of Okazaki fragments.

• Ligase joins DNA strands together.

• DNA reforms and two identical daughter molecules are created.

• DNA occurs bound to proteins in chromosomes within the nucleus.

• It also exists as unbound circular DNA in the cytosol of prokaryotes, and in the mitochondria and chloroplasts of eukaryotic cells.

• A nucleosome is the structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around histones.

Relationship Between DNA, Genes, and Chromosomes

• Chromosomes and genes are composed of DNA.
• A chromosome is a long DNA strand wrapped around histones.
• A gene is a DNA segment encoding specific characteristics, and an allele is a specific form responsible for variation in traits.
• Genes have instructions for proteins, typically with two alleles.
• The position of a gene on a chromosome is called its locus.

DNA in Prokaryotes/Eukaryotes

• Prokaryotes have DNA in plasmids and in the nucleoid.
• In humans, DNA condenses into chromosomes.
• Eukaryotes: DNA is in the mitochondria, chloroplasts and nucleus.
• Prokaryotes: DNA located in the cytosol of the cytoplasm.

Chromosome Packaging and Structure

• Prokaryotes lack a nucleus and membrane-bound organelles, have a single circular chromosome, and may have plasmids.
• Eukaryotes have a nucleus and membrane-bound organelles, multiple linear chromosomes, and lack plasmids.

Nuclear DNA vs. Mitochondrial DNA

• Nuclear DNA is inherited from both parents.

• It is a linear shape present in low copy numbers.

• Mitochondrial DNA in inherited via maternal lineage

• It is a circular shape present in high copy numbers with random segregation.

• Proteins, are essential for cell structure and function.

• Structural proteins maintain cell wall shape.

• Examples of enzymes include Helicase and Amylase and Protein Carriers are also used

Protein Synthesis

• protein synthesis involves transcription and translation of a gene into messenger RNA in the nucleus, and translation into amino acid sequence at the ribosome.

Transcription

• Only the anti-sense (lagging) strand is transcribed in the nucleus of eukaryotes.
• Initiation: RNA polymerase attaches to the promoter region, unzipping DNA.
• Elongation: Messenger RNA is transcribed using DNA as a template; only one DNA strand (anti-sense strand, 3' end) is transcribed, resulting in single-stranded mRNA.
• Termination: Transcription stops when the sequence is reached; RNA polymerase detaches and releases mRNA.

Post Transcription

• mRNA is pre mRNA initially but is then removed by spliceosomes which leaves the coding extrons
• Methylated cap added to 5' end and adenine tail added to 3' end
• mRNA matures and leaves the nucleus.

Translation

• mRNA moves from nucleus to cytoplasm, binds to ribosome.
• tRNA brings amino acids to the ribosome, starting with the start codon AUG/Methionine.
• Each codon has 3 bases, coding for one amino acid.
• tRNA reads mRNA codon and contains an anti-codon.
• tRNA binds to ribosome, bringing amino acid until a stop codon is reached.

Amino Acids

• Amino acids join via polypeptide bonds to form polypeptide chain.
• The polypeptide chain travels to the endoplasmic reticulum in vesicle for folding into functioning protein.

DNA vs RNA

• Nucleic acids are genetic material.

• DNA carries the blueprint; RNA plays a role in making proteins.

• DNA is deoxyribonucleic acid found in the nucleus, mitochondria, and chloroplast, consisting of double-stranded thymine, adenine, cytosine, and guanine bases.

• RNA is ribonucleic acid found in the ribosome, consisting of single-stranded uracil, adenine, cytosine, and guanine bases.

• The genetic code is a triplet base code including coding and non-coding DNA, with many genes containing information for protein production.

• The DNA strand is only used by a small amount for RNA template this region is the gene

• A triplet base has 3 nitrogen bases, the codon

• tRNA has an anti codon complimentary to the mRNA section.

Ribosome Differences

• Prokaryote ribosomes have 2 unequal subunits and locate in mitochondria and cholorplasts, they are also smaller

• Eukaryote ribosomes have 2 subunits (40s and 60s) and are bound to the ER and free in the cytoplasm and are also bigger.

• The continuity of life requires replication of genetic material and transfer to the next generation through binary fission, mitosis, meiosis, and fertilisation.

Binary Fission

• Prokaryotes reproduce using binary fission with a single circular chromosome. Steps
• Replication of DNA.
• Each DNA copy reaches opposite ends of the cell membrane.
• Cells grows in size.
• Each copy of chromosome get duplicated to the other part of the cell.
• Cell then begins to separate pulling chromosomes and performing Cytokinesis
• Wall forms across the cell dividing it into 2 identitical cells

Mitosis

• Interphase: DNA replication occurs; DNA is not condensed into chromosomes.
• Prophase: where DNA condenses into visible chromosomes and spindle fibres appear.
• Metaphase: Chromosomes line up at the equator.
• Anaphase: Chromosomes are pulled to either side of the cell.
• Telophase: Cytokinesis; nuclear membrane reforms while 2 identical daughter cells get produced

Cell Cycle

• Cells spend most of their time in interphase
• Mitosis begins in M phase and ends in C phase.

Meiosis

• Prophase I: DNA condenses, homologous chromosomes pair, and crossing over occurs.

• Metaphase I: Homologous chromosomes line up at the equator.

• Anaphase I: Microtubules pull homologous chromosomes apart and move them to opposite ends.

• Telophase I: Spindle fibres break, new membrane forms, chromosomes uncoil, and cell divides.

• Prophase II: Chromosomes condense, and membrane breaks down while new spindles begin to form.

• Metaphase II: Spindle fibres attach and line chromosomes at the equator.

• Anaphase II: Sister chromatids are pulled, and cell elongates while chromatid becomes daughter cell chromosome.

• Telophase II: Sister chromosomes uncoil, and new nuclear membrane forms while the cells divide into haploid (gamete (n)) cells.

• Phenotypic expression relies on interaction of genes and environment.

Gene Expression

• Cells do not express all genes at the same time and only some produce protein syntheis
• EUKARYOTIC- Only 2% of human genome is transcribed, either as coding proteins (exons) or non-coding proteins (introns).
• DNA methylation, (attachment of methyl group to nucleotide/histone protein) prevents transcription.
• EPIGENETICS is Study where chemical modifications to gene function are studied but aren't due to DNA.

Environmental Influence on Gene Expression

• Gene expression affected by environment.
• Himalayan Rabbits: Temperature affects coat color. Warm areas switch C gene' on and but in cold fur is black
• Hydrangea: pH of soil: Soil high in pH result in red soil or neutral soil

Mutations

• Mutations in gene and chromosome can occur due to error

• Mutation is permanent change in DNA and/or envoronment.

• Physical Mutagens produce energy which also damages DNA.

  • Radiation with X-rays which causes loss of adenine/guanine bases and creates gaps which results in incorrect bases in DNA
  • UV Radiation that causes hydrogen to break causing thymine bases to bind
  • Nuclear radiaion that causes DNA strand breaks

• A chemical Mutagen causes additions, deletions, or susbtitutions in DNA

  • Alcohol cause DNA breaks that alter it
  • Ciggies
  • Mustard gas: causes guanine to be replaced by other bases

• Biological Mutagens damage cells and changes cells/DNA, sometimes DNA is inserted - e.g. Virus, Bacterium and Micro-organisms

• POINT MUTATIONS are Change in a DNA and/or bases - Difference between sequences are called single nucleotide polymorphism (SNP/snips)

• SUBSTITUTION where one nucelotide replaces another

• INSERTION/DELETION where a nucleotide gets added

• SILENT MUTATION where a coding results in the same original results

• MISSENSE MUTATION occurs when a nucleotide changes and affects the amino acids

• NONSENSE MUTATION when nucleotide results in a stop which leads to a incomplete protein

• MUTATIONS change protein structures and affects protein function

• FRAMESHIFT mutation affects CODONS downstream from mutation.

Effects of Mutation on Survival

• NEUTRAL if the Protein unaffected. ex. same amino acids
• DELETEROIUS which effects function of protein
• BENEFICIAL where allele mutations can affect other regions.

Chromosomal Mutations

• Changes structure of chromosome ex Double strands, rearrangement, loss of chromosome, or exposure to Mutagen
• DELETION where Chromosomes get broken at segments and ends in lost segments + has adverse effects/fatal
• DUPLICATION occurs when Extra copy of chromosomes is made and repeats sequences, normally harmful
• INVERSION when broken segments rotates 180 and rejoins, effect is normally less dramatic
• TRANSLOCATION is when a section of chromosome breaks but reattaches to another

###Variations in chromosomes

• MONOPLOIDY more Economical, + has harmful effects and deleterious with mutations can be masked better. Colonial insects like males that produce mitosis and Females that produce meiosis

• POLYPLOIDY is common in flowering plants, in humans its lethal

• Organisms can have sets of chromosomes.

• ANEUPLOIDY is characterized by addition/loss of chromosome from cell and it causes miscarriage

• Variations in the genotype of offspring happens due to meiosis where crossing over + is random + assortment of chromosomes + fertilisation and mutations

Processes that Causes Variation

• MEIOSIS independent assortment of Alleles

  • Exchange on alleles occurs

• FERTILISATION from maternal and parents

  • DNA seq changes

• MUTATIONS permanent

• Frequencies of Genotypes and phenotypes of offspring are determined

• This includes Alleles, Dominance, Autosmal and sex linked alleles and Polygenes

• ALLELE Each gene has normally 2 alleles that are similar

• 2 ALLeles are called Homozygous or Heterozygous

Mendelian Inheritance

• Pea model organism

• Traits include quick growth and hight seed rates

• Some tall plants have recessive trait

• Law that traits controlled by single gene has 2 genes per organism

• Purebreeding is when two parents always has offspring the same

• Law of dominance shows of certain trait that shows dominant ones

• Recessice only show when alleles present

• Independent assortment states get sorted into gametes

• INCOMPLETE DOMINANCE occures when a trait os nit dominant over its partners and expressed by mix in phenos example. crossing of flowers

• BLENDED DOMINANCE where alleles are fully expressed when are fully expressed Examples are white and red cattle that makes roan

Polygenes

• Traits conrolled by over 1 gene
• Can result multiple genes that effect phenotypes
• Example. Skin Colors

Multiple Alleles

• Alleles are more common amongst a pop and located on x/y chromo. that do not appear sexually in genders
• Heterozygous that only copy a gene instead of 2

X-Linked Recessive

• When a phenos is showed determined by the allele on the X chromo. but if males receive 1X from mom it affects the allele

• Punnett squares where we asses different color blinds

• Carries females expected to pass 50% alleles on the next generation regardless of sex

• All effected must have 1 carrier

DNA/RNA sequencing and Profiles.

• Dna Seq. enables mapping of special genomes and identifies unique genetic makeup
• DNA seq determines base paring from order in gene
• Genetic engineering is found in bacteria. in DNA form + Antibiotic resistance

RESTRICTION ENZYMES

• It is obtained from bacterias where cut dna in specific sites (Restriction site).
• There are sticky and Blunt ends in the cut.
• BLUNT ENDS is where cleaved fragments have no over hanging
• Sticky Ends cuts are asymetrical over haning bases.
• Uses of gel electrohporesis to make dna + molegules by moving them.

PCR- polymerase Chain reaction

• Amplifies Dna by use of tax polymerase and other nucleotides to make it

• MICROARRAY a tool to find specific gene expression that can lead to cause huntingdons

GENE Technology

• Clone or create a genome + farmaceuctal,s(insuline)
• where targeting DNA, bactiral transf., bacteria sel. Harvesting
• GMO and Transgenetics (genetically modifies species by additions/deletion)
• TRANSGENICS

GMO and TRANSGENICS

• A genetic code when it has modifications from another type of species'
• TRANSGENETICS is plants with bacteria + plasmids(crown gall)

CONTINUITY LIFE on Earth.

• Evolved from anearobic to aero. + provides o2 = photo synthase
• Types of evolutions which differ + is convergent. Convergent comes more alive
• Phylogenetic trees that include a branch which is morphology
• The evidence has to be shown when it comes more like dna
• Relative (sedimentary) dating.
• Absolute (radiometric) dating is relies on predictable decay
• Comparative anatomy, all that is similar suggests common ancestry
• ANALOGOUS STRUCTURE. + homologous

Comparative Emylography

• Vertebrates are some of the traits that a parent has. Ex. Gills/whale fin
• Selection from environment has adapted to selection
• All comes from natural (more offpsirng born than reproduce)

Sexual Selection

• Traits are inheritated by generations.

• Act Phenotypes.

• GENE FLOW are caused mutation with low population. Can be also caused by chance

• Bottleneck + Founder effect.

• SELECTIVE breeding in that new breeds have intentional reproduction of individuals with alleles

• This includes MICRO and Maro Evolution