DNA Replication: Semi-Conservative Replication

DNA Replication

• A DNA molecule replicates to produce two identical copies of itself
• New strands are produced matching the base sequence of existing strands
• The structure enables repeated replication for continuity of life across generations
• DNA replication is essential for reproduction and growth/tissue replacement

Semi-Conservative Replication

• DNA strands of the double helix separate
• Both original strands act as templates for new strand polymerization
• Nucleotides are incrementally added and linked to form new strands
• Replication fork is the active site of DNA copying
• Semi-conservative replication yields two DNA strands: one original and one new
• The template strand's base sequence determines the new strand's sequence
• Only complementary bases are added to the new strand

Complementary Base Pairing

• Complementary bases form hydrogen bonds, stabilizing the structure
• Base pairing ensure resulting DNA molecules are identical to the parent
• Base pairing ensures high degree of replication accuracy
• The base sequence can be checked, mismatches recognized, and errors corrected
• Genetic continuity between generations is explained

Helicase and DNA Polymerase

• Helicase is a ring-shaped protein that separates DNA strands for new strand formation
• Helicase breaks the hydrogen bonds between bases, unwinding and unzipping DNA
• DNA Polymerase assembles two new DNA strands using original strands as templates
• There is separate DNA Polymerase for each strand
• DNA Polymerase positions nucleotides
• Nucleotides are linked to the new strand with covalent bonds

PCR and Gel Electrophoresis

• Automated DNA replication is called DNA amplification
• PCR cycle steps are triggered by temperature changes
• During melting, heat breaks hydrogen bonds to separate DNA, Taq polymerase is not denatured
• With annealing, cooling allows primers to bind to the start of the selected base sequence
• Elongation involves optimal temperature for Taq to bind adjacent to primer and assemble new DNA strands
• Gel electrophoresis is used to separate DNA molecules by length
• Applying voltage across electrodes creates an electric field, causing charged molecules to move through the gel
• Smaller molecules move faster and further due to charges from phosphates towards positive anode

Applications of PCR and Gel Electrophoresis

• Used for coronavirus testing, which is highly sensitive and specific, but expensive
• DNA profiling distinguishes individuals using short tandem repeats (base sequences)
• Child, mother, and man profiles are compared in DNA profiling

Protein Synthesis - Transcription

• Transcription synthesizes RNA using DNA as a template
• RNA is single stranded, so transcription occurs along only one of two DNA strands
• Genes are transcribed repeatedly to provide multiple copies of a base sequence

Role of RNA Polymerase

• Binds to a site on DNA at the start of the gene being transcribed
• Unwinds DNA and separates it into a template and coding strand
• Moves along the template strand
• Positions RNA nucleotides on template strands with complementary bases
• Links RNA nucleotides via sugar-phosphate bonds for a continuous RNA strand
• Detaches assembled RNA and allows DNA to reform into a double helix
• Transcription stops at a sequence marking the gene's end
• The completed RNA molecule is then released
• RNA has a base sequence complementary to the template strand, identical to the sense strand of DNA

Base Pairing in Transcription

• Copying base sequences during transcription depends on complementary base pairing
• Complementary bonding forms between Cytosine and Guanine and between Uracil and Adenine
• Coding (sense) strand is DNA with the base sequence to be copied into RNA
• Template (antisense) strand is complementary to the sense strand
• Transcription of the template strand results in an RNA strand with the same sequence as the sense strand, except uracil replaces thymine

Gene Expression

• Gene expression is the process by which information carried by a gene has an observable effect on an organism
• The sequence of bases in genes does not determine the observable characteristics of an organism
• Most genes specify a sequence of amino acids in a polypeptide
• Proteins determine an organism's characteristics
• Transcription and translation are required to produce a particular polypeptide
• Transcription initiates gene expression and can switch genes on or off
• Only some genes are expressed in a cell at a given time

Translation

• Translation involves linking amino acids in the correct sequence to form a polypeptide
• The information for this process is encoded in the base sequence of an RNA molecule, copied from a gene
• RNA holds information as a genetic code
• Translation synthesizes a polypeptide from mRNA and happens in the cytoplasm
• Eukaryotes produce RNA in the nucleus, and it exits to the cytoplasm via nuclear pores

Role of mRNA, Ribosomes, and tRNA in Translation

• mRNA serves as a site for ribosome binding and a template for a.a. sequence with start/stop codons
• tRNA translates the base sequence of mRNA into the amino acid sequence
• tRNA has an anticodon at one end and an a.a. attachment point at the other
• Each tRNA has a distinctive shape
• Ribosomes form complex structures with a small subunit (mRNA binding site) and a large subunit (tRNA binding sites)
• tRNA anticodon's three bases must complement mRNA's codon for binding and amino acid delivery
• DNA is well-suited for data storage because it holds long sequences of bases

Genetic Code Specifics

• Data in DNA base sequences store the amino acid sequence of polypeptides
• Codon is a sequence of three mRNA bases coding for amino acid addition to the polypeptide
• Living organisms use a triplet code
• Degeneracy occurs when different codons encode the same amino acid
• Universality is that all living organisms and viruses use the same code

Stepwise Movement of Ribosome along mRNA

• mRNA attaches to the small subunit of the ribosome, then the large subunit with tRNA binding sites attaches
• mRNA is read in triplets (codons)
• tRNA with a corresponding anticodon attaches with an amino acid on top
• Another tRNA binds to mRNA via complementary base pairing
• The ribosome forms a peptide bond between amino acids, detaching that a.a. from the first tRNA, causing it to leave the ribosome
• Polypeptide chain continues to lengthen until a stop codon signals the polypeptide's release

Gene Mutation

• Gene mutation is a base sequence change
• Sickle cell disease is a single base substitution (GAG to GTG), and a new allele is formed
• The mutation can be inherited and affects hemoglobin molecules in low-oxygen tissues
• Hemoglobin molecules distort red blood cells into a sickle shape, causing blockages and damaging tissues and can result in anaemia

Types of Gene Mutation

• Substitution replaces one base in the coding sequence with a different base
• Insertion is when a nucleotide is inserted
• Deletion is when a nucleotide is removed
• Base substitutions in non-coding DNA have no effect
• Same-sense mutations change the codon for one a.a. to another one for the same amino acid
• Nonsense mutations change the codon to a stop codon
• Missense mutations alter one amino acid, having little effect if new a.a.s are similar
• SNPs can occur in non-coding regions and be associated with diseases and determine genetic predisposition

Insertion/Deletion Consequences

• Insertion and deletion consequences depends on if nucleotides are a multiple of 3
• AA sequence would be unchanged apart from the extra AA for insertion of a multiple of 3 nucleotides
• Insertion/Deletion leads to frameshift mutations that change the entire reading frame
• All insertions/deletions are likely to cause significant changes to the polypeptide structure and function and can introduce premature stop codons BRCA1 Codes for Tumour Suppressor
• BRCAI function is DNA repair to mend doublestrand breaks
• Mutation in this can mean an increased risk of other mutations because of lack of DNA repair

Mutation Timing and Types

• Mutations can occur anytime, especially during DNA replication
• Mutagens increase the frequency of mutation
• Chemical mutagens cause chemical changes in DNA (mustard gas)
• High-energy radiation breaks bonds in DNA strands/results in base substitutions

Random Mutations

• Mutations are random and can occur in any gene of any cell, due to no known mechanisms for making specific base sequence changes
• Living organisms cannot make specific beneficial mutations
• Germ cell mutations can be passed to offspring, located in testes and ovaries.
• Somatic body cells cannot develop into gametes
• Somatic cell has limited changes, lethal mutations only kill that cell to be get repcled.

Long Term Survival

• Long-term survival of a species would be threatened if no mutation ever occurred due to the need to evolve as the environment changes
• Mutation is original source of all genetic variation with geentic variation in a population

Cell Division (Cytokinesis)

• New cells form from division of pre-existing ones
• Cytokinesis divides cytoplasm to form two cells, differently in plant and animal cells
• In plants, a new cell wall forms across the cell equator via a middle lamella
• In animals, cytoplasm divides by plasma membrane movement and cleavage furrow formation
• Unequal division can produce small cells if enough organelles and nucleus is received
• 2 polar bodies in Oogenesis, Budding in Yeast

Mitosis and Meiosis

• Nuclear division occurs before cytokinesis
• Without nuclear division synthesis cannot occure and leads to limited lifespan
• Mitosis - continuity, same number of chromosomes and geentically identical
• Meiosis Changes and genetic diversity and halves chromosomes
• Replication of DNA, leads to duaghter cells receiving entire genome, recombination and condensation tightly in early mitosis and meiosis stages.

Chromosomes

• Made up of Condensed chromatids with seperate Identifiable features
• Chromatids are separated and move to ends
• Supercoiling helps chromosomes pack, wrapping double helix
• Microtubules + Motors move and extend towards equator
• Shortened chromatids are caused by kinetochore by removing tubulin unit from the ends

Mitosis and Meiosis Stages

• Mitosis has supercoiling chromosomes, microtubules growing. spindle microtubules grow and breaks membrane down
• Homologous Chrmosomes separate in A1
• Chromosomes condense, migrate, separate and then uncoil in genetically identical visible cell nucleus
• Kinetochres pulls choromosomes

Diploid Nucleus/Meiosis

• Diploid nucleus contains homologous chromosomes with the same genes (but different alleles)
• Without Meiosis, Number of Chromosomes would double every generation.
• Down syndrome happens if homologous chromosomes (21) fail to separate to same pool.
• Meiosis increases Combos of Alleles

Stages of Chromosome Pairing

• Homologous pair in P1 with growth for spindle microtubules
• Random pair with chromosomes on spindle fibres
• Each chromosome gets pulled until halving the number of chromatids

Water Potential

• Solvents Liquid made to dissolve substances
• Solutes Substances Dissolves
• Solvation Dissolving with hydrogen and negative polar
• Hypertonicity= HIGH
• Hypotonity= Very Low
• Isotonic == same

Animal Plasma

• Water movement bad for all animals
• Too much causes bursting
• Too less means crenation

Tissue Solutes

• Intravenous must be isotonic
• Tissues need it or slushy as well when it comes to transplant

Reproduction Asexual Vs Sexucal

• Asexual One Parent, NO meiosis. Offspring indentical
• Sexual Two Parents, YES meiosis, diverse offspring.
• Gametes needed to join to alleles
• fusion - mitosis to prevent change to chromosome

  Gamete Types:

• motile
• non motile All comes out with pollination sperm fertilization in Flowering Plants with mitosis and meiosis to make seed after.