BIOL1110 Genes to Organisms Lecture Notes PDF

**BIOL1110 -- Genes to Organisms** **Lecture 2** The Scientific Method - Scientific inquiry is the search for information and explanation. Investigation of the natural world by natural methods - Two types of scientific inquiry: Discovery science and hypothesis-based science - Disc...

**BIOL1110 -- Genes to Organisms** **Lecture 2** The Scientific Method - Scientific inquiry is the search for information and explanation. Investigation of the natural world by natural methods - Two types of scientific inquiry: Discovery science and hypothesis-based science - Discovery based science comes from the analysis of data - A hypothesis is a tentative answer or explanation to a well framed question which leads to predictions, hypothesis' must be testable/falsifiable, achieved through observations and performing experiments - Research can only support a hypothesis does not prove it, but you can refute a hypothesis - Observation -- hypothesis -- prediction -- experimentation -- refute or support hypothesis -- communicate Deductive/Inductive Reasoning - Deductive reasoning -- uses general principles to deduce the answer to specific questions - Inductive reasoning -- uses a series of examples from which to draw general conclusions - The problem of induction -- can we induce something that does not exist, scientists generally rely on disproving null hypothesis' Experimental Design - Variables features that vary in an experiment: - Independent variable (what the researcher changes) - dependent variable (what the researcher measures in response to the independent variable) - Control Some Words & Meanings - Law -- a generalisation about data; a statement of relationships between variables - Hypothesis -- conclusions based on prior experience, background, knowledge, observation and logic possess explanatory power - Theory -- broad explanations for a wide variety of phenomena supported by many lines of evidence **Lecture 3&4** DNA Biological Information - Genetic information must serve two basic functions: 1. Enable the growth, development & function of an organism 2. Needs to be passed on from one generation to another Charles Darwin - Voyage of the HMS Beagle around the world - The origin of species by means of natural selection 1. Evolution from common ancestor 2. Mechanism occurred via natural selection Evolution and Natural Selection - Darwin identified traits and species as heritable - Individuals and species with heritable traits best suited to the environment did better - Darwin proposed a process for change, he did not have an explanation for mechanism behind inheritance Gregor Mendel - Medel was an experimentalist who examined the scientific basis of inheritance using plant breeding - Worked on peas: many varieties, easy to breed, produce many offspring Mendel's Experiments - Mendel identified heritable characters that were masked in the F1 generation - Mendel could predict what the ratio of different characters would be - These heritable invisible factors were later called genes Johann Friedrich Meishcer - Biologist to first isolate 'nuclien' DNA and proteins from the nucleas - Buclien contained phosphorus and nitrogen Albrecht Kossel - Biochemist who identified the five compounds present in 'nuclien', Adenine, Cytosine, Guanine, Thymine, Uracil - Provided the DNA -- Deoxyribonucleic Thomas Morgan - In early 1900s morgan identified after multiple years of breeding fruit flys, variation in trait eye colour - Found that mating red(female) and white(male), fly eye colour followed mendelian inheritance - 3:1 (red: white) in F2 - But morgan also noted that all F2 females had red eyes while 50% of makes had red eyes & 50% white Chromosomes & Inheritance - In the late 1800s chromosomes had been discovered, flies have distinvt sex chromosomes, link between trait with sex evidence of chromosome inheritance, carries a specific factor DNA or Proteins? - Chromosomes were known to be made of DNA and proteins, which one is the element of heredity Frederick Griffith - Bacteriologist developing vaccines streptoccus pnemoniae two strains: Pathogenic, non-pathogenic - Demonstrated transformation experiment with mice injecting with pathogenic and non-pathogenic - Suggested it wasn't protein as they would denature with heat Oswald Avery - What is the transformation substance that is causing observation - Experiment -- killed s strain of bacteria using heat, the remaining debris had DNA, RNA and protein, and if u treat these with protease, DNAse and RNAse it would breakdown corresponding component, if you add protease or rnase youre left with both bacteria, if you use dnase youre left with just R bacteria - Concluded that the transforming substance was DNA Hershey & Chase - Worked on bacteriophages - Found that the sulphur or proteins were in the top part of the tube and the radioactive DNA found in the bottom with the bacteria - More evidence for DNA as the molecule of inheritance It's DNA - Molecule of inheritance, on chromosomes, contained four nucleiods Edwin Chargraff - DNA base composition changes with species - So DNA was not a tetranucleotide - Chargaff showed that the amount of A=T, G=C Wilkins & Franklin - Used X-ray diffraction to show DNA: 1. Was a long helical rod 2nm in diameter 2. Had regularity in its structure every 0.34nm and another every 3.4nm Watson & Crick - Used models consistent with all the data to determine the structure of DNA A Nature Paper & Nobel Prize - "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." - Watson and Crick - Discoveries concerning the molecular structure of nucleic acids and its significance Nucleic Acids - polymers consist of multiple repeating subcomponents - Nucleotides: repeating subcomponents that exist in a variety of forms rather than repeated monomer subcomponents - Polynucleotides: polymers consisting of multiple nucleotides Three Components of Nucleotides - Phosphate group -- links together in bonds - Sugar -- connects phosphate backbone with base - Nitrogenous base -- structure identifies nucleotides as G,T,A,C Nucleotides and bases - Nucleotides are the individual units of DNA - Deoxyribonucleic Acid - A DNA nucleotide is composed of a nitrogenous base, the sugar deoxyribose, and one or more phosphate groups. - The four bases in DNA are adenine, thymine, cytosine, and guanine. Adenine and guanine are purines, and cytosine and thymine are pyrimidines. - Adenine bind with Thymine (two H-bonds), Guanine bind with Cytosine (three H-bonds) Pyrimidines and Purines - Nucleotides come in two varieties: Pyrimidines (T and C) and Purines (A and G) - For double helix, Purine + Purine too wide, Pyrimidine + Pyrimidine: too narrow, Purine + pyrimidine consistent Directionality - Each strand has directionality - 5 to 3 direction for one and opposite 3 to 5 for other - Antiparallel two complementary strands running in opposite directions - The base sequence can vary but the other strand must be complementary Replication of DNA - Semiconservative model: new and old split even - Conservative: new and old seperate - Dispersive: new and old randomly distributed Divide and Conquer - Prokaryotes are single cells, cell division to reproduce, eukaryotes are muticellular - Cell division requires DNA replication Copying Mechanism - DNA Replication - base pairing is all important, C-G, A-T - but most chromatin is usually tightly wound around histones, need to unwind for replication Semi-conservative Replication - two strands of DNA are complementary, each strand acts as a template for building a new strand in replication - in DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules Proteins Involved in DNA Replication DNA Replication - replication begins at special sites called origins of replication, two DNA strands are separated opening up a replication 'bubble' - a eukaryotic chromosome may have hundreds or even thousands of origins of replication, proceeds in both directions from origin Stages of DNA Replication - Initiation: helix is unwound and open to enzymes (proteins), Helicases unwind the DNA strand - Elongation: DNA polymerases add nucleotides to the growing DNA strand - Termination: end point of replication Key Terms - RNA primer -- Short strand of RNA complementary to DNA & enables the binding of DNA polymerase, 5 -- 10 nucleotides long - RNA primase-- Enzyme which synthesizes RNA primers - Okazaki fragment-- Short, newly synthesized DNA fragments that are formed on the lagging strand - Leading strand-- DNA which is being synthesized in the same direction as the growing replication fork - Lagging strand-- DNA whose direction of synthesis is away from the replication fork Ligase-- Enzyme which joins together Okazaki fragments Antiparallel Elongation - Antiparallel structure of double helix affects replication, a new DNA can only elongate in the 5' to 3' direction Errors During DNA Replication - Errors occur at a rate of 1 in 10\^5 nucleotides - But, changes to the sequence (mutation) only occurs in around 1 in 10\^10 nucleotides - This is due to proof-reading and repair mechanisms - Errors that persist in DNA are called mutations Telomere Problem - Telomerase carries a short RNA template and adds complementary DNA sequence to the 3' ends of the chromosomes - Telomeres contain no genes but many non-coding short repeats, in humas the repeat is 5' -- TTAGGG-3' - Telomeres are repeated sequences at the end of chromosomes - Telomerase helps maintain the length of telomeres Mutations - Changes in genetic material of cell, are drivers of evolution/natural selection can be good/bad - Mutations can be small scale and affect one or fellow nucleoids or larger scale affecting sections of chromosomes - Can occur from mutagens: physical -- X-ray, UV rays, Chemical -- ethidium bromide, asbestos Point mutations can affect protein structure and function - Point mutations within a gene can be divided into two general categories: Base-pair substitutions, Base-pair insertions or deletions Chromosomal mutations: alterations in chromosome structure Breakage of a chromosome can lead to four types of changes in chromosome structure: - Deletion removes a chromosomal segment - Duplication repeats a segment - Inversion reverses a segment within a chromosome - Translocation moves a segment from one chromosome to another DNA Repair - There are many DNA repair proteins, over 100 in bacteria - Mismatch repair proteins remove and replace incorrect nucleotides - Nuclease -- protein that cuts out the incorrect nucleotide **Lecture 5&6** Genes & Genomes Brief History - Darwin 1853 possibly blending heredity, Mendel 1866 physical elements transmitted through parents, Morgan 1910 chromosomal theory of inheritance, Watson and Crick 1953 structure of DNA What is a Gene? - Genes are carried on chromosomes and DNA is the molecule of heredity - the basic and functional unit of heredity, it transferred from parent to offspring and determines some characteristics of the offspring - a distinct sequence of nucleotides forming part of a chromosome, the order of which determines the order of monomers in a polypeptide or nucleic acid molecule which a cell may synthesise - Genes produce proteins or RNA (messenger, transfer, ribosomal, non-coding) Central Dogma of molecular biology - DNA contains genes, genes can be copied to produce RNA, RNA can be translated to produce proteins, proteins perform the work inside the cell Gene structure: prokaryotes - Control regions -- determines when a gene produces proteins - Involves promoters - a region of DNA where transcription starts - Other regulatory regions - Prokaryotes read genes from an uninterrupted stretch of nucleotides Gene structure: eukaryotes - Control regions - Protein coding regions -- exons - Non-protein coding regions -- introns - Many eukaryotic genomes are primarily non-protein coding -- in humans \~1.5% DNA codes proteins, 8% regulatory Eukaryotes -- one gene many proteins - Alternative RNA splicing allows for more complexity Genomes - Genomes: the entire genetic complement of an organism - DNA sequencing has become faster and cheaper over the last decade - Gene density is higher in bacteria and archaea than eukaryotes Gene density - Prokaryotes and eukaryotes tend to have different numbers of genes per Mb of DNA -- lengths are different, prokaryotes genes are close together and even overlap, eukaryotes there is a lot of non-protein coding DNA - Prokaryotes have evolved to maximise the use of genomic territory -- protein coding regions are close and may even overlap - Eukaryotes have evolved other ways of generating complexity -- differences in gene expression, differential gene splicing, epigenetic factors Non-protein coding genes - Non-coding RNA -- tRNA, rRNA, IncRNA, siRNA - Pseudogenes -- non functional copies of normal genes - Introns with genes - Highly repetitive DNA sequences between genes -- satellites and microsatellites e.g. ATT ATT ATT - Large regulatory regions upstream and downstream of genes - Structural: forming critical regions within chromosomes -- centromeres and telomeres Sequencing Genomes - Sequences can be aligned using bioinformatic software - Range of different software's available Information from genomes - Personalised medicine - Omics profiles -  Comparative Genomics - Genome sequencing can provide detailed information about gene content and organisation in different species - Conserved regions of the genome can tell us about the selection on organisms to maintain phenotypes - Provide information about evolutionary relationships - Identify genes that give organisms unique characteristics - Can allow us to understand the mechanisms that underpin evolutionary change DNA Transcription RNA - Ribonucleic acid - Uracil replaces thymine - Mostly single-stranded (can fold on itself) - Less stable than DNA Flow of Information - DNA stores hereditary information -- how an organism looks and functions - Proteins are structural components of cells and are involved in how an organism function - Gene expression is the link between DNA and the synthesis of proteins (or RNA) Cookbook Analogy - DNA -\> Transcription -\> mRNA translation -\> Polypeptide/protein Transcription - Synthesis of RNA using DNA - Similar process to DNA replication - DNA replication -- DNA provides the template for the synthesis of the complementary DNA strand - Transcription -- DNA provides template for synthesis of complementary RNA strand Types of RNA - mRNA -- messenger RNA carries the message from DNA - rRNA -- ribosomal structural RNA that forms part of the ribosome - tRNA -- transfer RNA, structural RNA involved in the synthesis of amino acid chains Localisation in the Cell - bacteria -- no nuclei no RNA processing - eukaryotes -- transcription & RNA processing occurs in nucleus, translation occurs in the cytoplasm Template Strand - each gene is transcribed from one of the two DNA strands -- the template strand - the opposite strand can also act as the template strand - template strand is 3' to 5' Complementary Base Pairing - transcription is similar to DNA replication, involves complementary base pairing but thymine is replaced by uracil - like DNA, RNA synthesised in an antiparallel direction to the template strand - DNA template 3' AATCGATGC 5' - RNA 5' UUAGCUACG 3' - Transcription Coding Strand - The coding strand is identical to RNA (except for U) and is complementary to the template strand -- coding because nucleotide triplets (codons) code for amino acid - DNA template 3' AATCGATGC 5' - DNA coding 5' TTAGCTACG 3' - RNA 5' UUAGCUACG 3' - Coding strand = non- template strand - Non-coding strand = template Transcription - RNA polymerase -- separates the DNA double helix and adds RNA nucleotides - Like DNA polymerase and DNA replication, RNA pol can only add nucleotides in a 5' to 3' direction - Unlike DNA pol, do not need a primer for RNA polymerase to attach and add nucleotides - Only one RNA pol in bacteria - Multiple in eukaryotes (3 \ - Help facilitate export of mRNA out of the nucleus and into cytoplasm (where ribosomes are and where translation occurs) - Protect mRNA from enzymatic degradation - Help ribosomes attach to the 5' end of mRNA mRNA Splicing - Non-coding regions of primary transcript (pre-mRNA) removed - Exons (expressed) are coding - Introns (intervening sections) are non-coding - Hence coding sections are split into two sections - Proteins and small RNAs complex called the spliceosome recognizes and cuts out introns - After RNA splicing, mature RNA moves to Alternative RNA Splicing Why is it important to have introns? - Different exons spliced give rise to different proteins - In many cases, different exons code for the different domains in a protein - Exon shuffling may result in the evolution of new proteins Universal Information Flow - Almost universal information flow from bacteria to eukaryotes - More support for common ancestry of all life - Utility in biotechnology -- can put a gene like insulin from humans into bacteria to produce it in mass amounts Lecture 7 & 8 Translation - Conversion from nucleotides the "language" of mRNA, to amino acids, the "language" of proteins Codons: triplets of bases - There are 20 amino acids but there are only four DNA bases - The flow of information from gene to protein is based on a triplet code: a series of non-overlapping, three nucleotide words (codon) - All 64 codons were deciphered mid-1960s, 61 code for amino acids, 3 triplets signals "stop" end translation - One codon AUG is the universal "start" codon - The genetic code is redundant but not ambiguous; no codon specifies more than one amino acid, third codon position is called wobble DNA to Protein - DNA sequence of coding (sense, non-template) strand: 5' -- ATG TTA TAC CAC -- 3' - RNA sequence: 5' AUG UUA UAC CAC -- 3' - Proteins are chains of amino acids that fold into 3d structures Protein Back to DNA - Create one possible DNA sequence (both anti-parallel strands) for one combination of the mRNA, which makes the below protein sequence 1. Create the mRNA sequences first using the table 2. Include the 5' and 3' ends of each polynucleotide 3. Create DNA sequence from the mRNA sequence Evolution of the Genetic Code - The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals - Genes can be transcribed and translated after being transplanted from one species to another RNA Components of Translation - mRNA: a cell translates an mRNA message into protein with the help of transfer RNA (tRNA) - tRNA: molecules of tRNA are not identical: - each carries a specific amino acid on one end - each ahs an anticodon on the other end; the anticodon base pairs with complementary codon on mRNA - rRNA: ribosomal RNAs combine with proteins to form the site of translation -- ribosome Transfer RNA - a tRNA molecule consists of a single RNA strand that is about 80 nucleotides long - contains an amino acid attachment site and an anticodon that recognizes the complementary codon on the mRNA Binding of Amino Acids - matching the correct amino acid with a tRNA is performed by proteins called aminoacyl-tRNA synthetases - there are 20 different synthases one for each amino acid rRNA - like tRNA, rRNA is a structural molecule that folds on itself - rRNA is a component of the ribosome Ribosomes - ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis - the two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA) - a ribosome has three binding sites for tRNA: - the A site binds the tRNA that carries the net amino acid to be added to the chain - the P site holds the tRNA that carries the growing polypeptide chain - the E site is the exit site where discharged tRNA leave the ribosome - move through in order A-P-E Translation - the three stages of translation: 1. initiation 2. elongation 3. termination Initiation - the initiation stage of translation brings together mRNA, an intiator tRNA with the first amino acid, and the two ribosomal subunits -- forms the initiation complex Elongation - during the elongation stage, amino acids are added one by one to the preceding amino acid - each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation Termination - termination occurs when a stop codon in the mRNA reaches the A site of the ribosomes - the release factor causes the addition of a water molecule instead of an amino acid Polyribosomes - a number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome) - polyribosomes enable a cell to make many copies of a polypeptide very quickly Transcription and Translation - in Prokaryotes transcription and translation both occur in the cytoplasm (transcription in convoy and polyribosomes - in eukaryotes transcription and mRNA modification in nucleus translation into cytoplasm Functional Protein - folds -- amino acid sequence, has a 3d shape - post translational modification Proteins - the flow of information: DNA-\ (transcription/reverse transcription) RNA-\> (translation) Protein - make up more than 50% of dry mass for most cells RNA - messenger RNA (mRNA): the molecule into which DNA is transcribed takes the genetic information to the ribosome - Transfer RNA (tRNA): carries individual amino acids to the ribosome - Ribosomal RNA (rRNA): constituent of the ribosome along with the proteins Translation occurs at Ribosomes - Complex mixture of RNA proteins - Reads mRNA and recruits tRNA to add amino acids to growing polypeptide chain Enzymes - Analogous to lock & key mechanism - They are catalysts, selective acceleration of chemical reactions, catalyse hydrolysis of bonds in food molecules Defensive - Recognise and target foreign bodies like pathogens and target them for destruction - Protect against disease, create antibodies Storage - Source of nutrition, store amino acid - Casein is a protein milk major source of amino acids for baby mammals, plants have proteins in their seeds Transport - Carrying molecules, haemoglobin the iron containing protein of vertebrate blood, transports oxygen Hormonal - Allows different components (organs or tissues) of an organism to communicate, coordinates an organism's activities Receptor - Signals a response to a stimuli, receptors built into the membrane of a nerve cell detect signalling molecules released by other nerve cells Movement - Flagella, cilia & muscle, movement motor proteins are responsible for the undulations of cilia flagella actin and myosin proteins are responsible for the contraction of muscles Structural - Proteins that are responsible for structural support of various types oof protein Proteins Consist of Polypeptides - Polypeptides are polymers built from the 20 amino acids - A protein consists of one or more polypeptide, range from 10 to \>1000 amino acids in length Amino Acids - Amino acids are organic molecules with carboxyl and amino groups - Amino acids differ in their properties due to differing side chains called R groups - Every amino acid has the same basic structure Peptide bonds - Carboxyl and amino groups form peptide bonds to join amino acids together end to end Protein structure & Function - A functional protein consists of one or more polypeptides twisted folded and coiled into a three-dimensional shape - The sequence of amino acids determines the structure of a protein - Primary structure of a protein is its unique sequence of amino acids - Secondary structure consists of coils and folds into the polypeptide chain - Tertiary structure is their 3D shape and is determined by interactions among various side chains (R-groups) - Quaternary structure results when a protein consist of multiple polypeptide chains Chemical Bonds - Hydrogen bonds: hydrogen atom and an electronegative atom - Van der waals interactions: uneven distribution of electrons resulting in dynamic positive and negative charge which allows weak bonding between molecules - Ionic bonds: between a cation (positive) and an anion (negative) - Disulphide bonds: covalent bond between two sulphur atoms Protein Structure - Physical and chemical conditions can also affect protein structure - pH, salt concentration, temperature, or other environmental factors can cause a protein to unfold - this loss of native protein structure is called denaturation - a denatured protein is biologically inactive - Protein folding is important causes: alzheimers, diabetes, cardiac arrhythmias etc. **Lecture 9&10** Chaperons - Chaperone proteins aid in the correct folding of some proteins Protein Degradation - Proteasomes are giant protein complexes that bind protein molecules and degrade them Gene Expression - The genome contains all the information needed for the growth and development of individuals - Every cell contains the same genome - Gene expression -- different cell types - Gene expression is the use of DNA sequences to synthesise RNA and proteins - Some genes are expressed all the time (constitutive), while others are expressed only when needed (regulated) - It takes energy to produce proteins -- only produce those that they need at the time - Some proteins are always needed: housekeeping proteins -- e.g. ribosomal proteins - A cell can regulate the production of proteins by feedback inhibition or by gene regulation Responding to the Environment - Prokaryotes can regulate response: 1. Activity of first enzyme in a pathway is inhibited by the end product -- feedback inhibition 2. Genes coding in metabolic pathway are controlled -- gene regulation Operons - In prokaryotes genes are often arranged into operons - Several genes involved in the same biological process, under the control of a single promoter - All the necessary proteins are produced at the same time in response to the same stimulus - A cluster of functionally related genes coordinated by a single on-off "switch" - An operon is the entire stretch of DNA that includes the operator, the promoter and the genes that they control - The regulatory "switch" is a segment of DNA called an operator usually positioned within the promoter - The operon can be switched off by a protein repressor - The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase - Repressor protein is coded for by a regulatory gene located elsewhere in the genome (co-repressor is tryptophan) Repressible Operons - A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription - Repressible enzymes usually function in anabolic pathways - Their synthesis is repressed by high levels of the end product e.g. tryptophan synthesis Inducible Operons - An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns transcription off - Inducible enzymes usually function in catabolic (breaking down metabolites) pathways Their synthesis is induced by chemical signal (e.g. lactose) lac operon - Lactose: major sugar of milk - Lactose is an uncommon nutrient for bacteria - Enzymes for lactose metabolism are normally not expressed (they are turned off to conserve energy) - Cells use glucose for energy - Lactose is a disaccharide of glucose and galactose - Three enzymes are involved in the lac operon: 1. Permease -- allows lactose to enter bacterial cells 2. B-galactosidase -- breaks down lactose to glucose and galactose 3. Transacetylase -- unknown function but assists lactose breakdown - lac I (control gene) encodes the lac repressor protein when bound to DNA (operator), this protein prevents transcription at the lac operon - the inducer (a form of lactose) binds the repressor protein and inactivities it, which allows transcription of the lac operon Operons - both inducible and repressible operons involve the negative control of genes (via the repressor) - in contrast, a regulatory protein that switches transcription on represents positive control (e.g. cAMP receptor protein activity in lac operon) - glucose and lactose present, CRP inactive, reduced expression of lac operon - lactose present and no glucose, CRP active, high levels of lac operon transcription Regulation of transcription initiation - associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors (proteins) that help regulate transcription - control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types Eukaryotic gene transcription - proximal control elements are located close to the promoter - distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron Eukaryotic Control Regions - distal and proximal control elements Transcription factors - general transcription factors bind to TATA box within promoter, other proteins, transcription factors or RNA polymerase - only when the complete transcription initiation complex is assembled does transcription occur (i.e. RNA polymerase and transcription factors) - an activator is a specific transcription factor that binds to an enhancer and stimulates transcription of the gene - some transcription factors function as repressors, inhibiting expression Transcription Regulation - each enhancer has around 10 control elements - each control element binds one or two specific transcription factors - the combination of control elements is important in transcription regulation - appropriate activator proteins may only be present at a particular time or in a certain cell type Coordinated transcription - unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements - these genes can be scattered over different chromosomes, but each has the same combination of control elements - copies of the activators recognise specific control elements and promote simultaneous transcription of the genes Post-transcriptional Regulation - remember that mRNA only codes for a protein -- it is the protein that carries out the function - so after transcription we can have: alternative RNA splicing block translation with regulatory proteins that prevent attachment of mRNA to ribosome regulation of the post-translational modification of the protein Different Cell Types - during embryonic development a fertilised egg gives rise to many different cell types - cell types are organised successively into tissues, organs, organ systems, and the whole organism - gene expression orchestrates the developmental programs of animals - cell differentiation is the process by which cells become specialised in structure and function - differential gene expression results from genes being regulated differently in each cell type Stem Cells - a stem cell is a relatively unspecialised cell that can reproduce itself indefinitely and differentiate into specialised cells of one or more type - stem cells isolated from early embryo are called embryonic stem cells; these are able to differentiate into all cell types - the adult body also has stem cells, which replace non-reproducing specialised cells as needed - totipotent stem cells obtained from early embryos, spores and plant calluses - can give rise to a complete individual - pluripotent stem cells - can give rise to many different cell types, but cannot reproduce an entire individual - multipotent stem cell - gives rise to different cell types within tissues Prokaryote chromosomes and evolution - generally a single chromosome - lots of lateral gene transfer (plasmids and naked DNA) - evolution is more of a tangled bowl of spaghetti than a tree DNA - liner DNA (nuclear) - circular DNA (organelles) - in prokaryotes theyre found in a cytoplasmic region called the nucleoid. Prokaryotes also contain small circular pieces of DNA called plasmids - bacterial chromosomes are small (\`10,000 nucleotides each); - in eukaryotes chromosomes are found in the nucleus, mitochondria and chloroplasts - eukaryotic chromosomes are large (\`1 billion nucleotides in each chromosome) Mitochondrial DNA - high copy number - maternally inherited - high mutation rate - approx. 16.6kb in size - 13 genes/22 tRNA Chloroplast DNA - High copy number - Range from 80kb to 600kb - Inherited from a single parent (usually) Measuring DNA - The basic unit is a nitrogenous base: A,C, G or T - 1000 bases make up a kb, 1000000 a mb There are kilobase pairs and megabase pairs since DNA is a double stranded molecule - There are about 3000 mb in a human genome -- 2m in length What is a Chromosome - Linear DNA double helix around 1.5 x 10\^8 nucleotide pairs long in humans - Combination of DNA and lots of proteins Chromatin and Chromosomes - The uncondensed (chromatin) and condensed form (chromosome) of DNA Chromatids - Two sister chromatids (two halves of replicated chromosome!) join at the centromere to form a chromosome Chromosome Number - Human somatic cells have 23 pairs of chromosmes, total of 46 - Most eukaryotic chromosomes exist in an uncondensed state called chromatin (chromatin condenses into chromosomes during replication) Ploidy - Humans have 2n chromosomes (2x23 =46 chromosomes) - N haploid - 2n diplod - 3n triploid - Polypoid refers to more than two sets of chromosomes - Many plants exhibit polyploidy e.g. wheat is 6n Chromosomes/Structure - Autosomes -- 22 in humans - Allosomes = sex chromosomes -- X and Y in humans - In eukaryotes chromosomes usually have a centromere - Centromeres are not actually usually central, so we get A short arm (p) A long arm (q) - Genes can therefore be located to: a specific position on a specific arm, or a specific chromosome - E.g. TP53 is located at 17p13.1 - Chromosome 17 short arm, base pairs 7,668,401 to 7, 687, 549 Visualising Chromosomes - DNA is colourless - In order to look at chromosomes we must stain them - Karyotype: the number and appearance of chromosomes of eukaryotic cell Chromatin - Chromosomes are made up of chromatin -- DNA and proteins - Euchromatin is loosely-packaged chromatin and contains actively expressed genes - Heterochromatin contains unexpressed (inhibited or silenced) genes Chromatin Organisation - Euchromatin can be condensed into heterochromatin - Genes in condensed DNA are less likely to be expressed How is DNA Packaged? - In eukaryotes DNA is wound around proteins called histones - DNA + histones = nucleosome two of each of four histone proteins (H2A, H2B, H3 & H4) form a histone core - DNA wraps around the histone octamer (core) Model of Nucleosome - Nucleosome is the basic structural subunit of chromatin, consisting of approx. 146 bp of DNA and an octamer of proteins Chromatin Fibre - An electron microscope image of a condensed chromosome fibre, approximately fibre, approximately 30 nm thick Eukaryote Chromosomes and Evolution - Linear chromosomes - Having two copies of each gene allows for hidden variability - Some traits dominant over others -- such as brown eyes being dominant to blue - But if the environment changes, recessive traits may turn out to be valuable **Lecture 11&12** Cells - Evolution involves the replication and distribution of genes - The evolution of the cell allowed for continuity in gene transmission & "cooperation" between genes - Cell Theory: all organisms are made of cells, the cell is the most basic unit of life, all cells arise from pre-existing living cells Microscopy - Most subcellular structures, including organelles are too small to be resolved by a light microscope - Electron microscopy: transmission electron microscopy (TEM) -- sends an eletron beam through thin slice of speciemen (resolution approx. 0.05 nanometers) - Scanning electron microscopy (SEM) -- scans surface of specimen with an electron beam (resolution about 0.4 nanometres) Plasma Membrane - Is a selective barrier that allows passage for sufficient oxygen, nutrients and waste is a double layer of phospholipids Endomembrane System - Components of the endomembrane system include: - The nuclear envelope (membrane) - Endoplasmic reticulum (ER) - The Golgi apparatus - Lysomes - Vacuoles - The Plasma Membrane - These components are either continuous, or connected via transfer by vesicles Endoplasmic Reticulum - The endoplasmic reticulum (ER) accounts for more than half of the total membranes inmany eukaryotic cells - The ER membrane is continuous with the nuclear envelope - There are two distinct regions of ER: - Smooth ER, which lacks ribosomes Lipid synthesis Carbohydrate metabolism Detoxification of poison Calcium storage - Rough ER with ribosomes studding its surface Protein (glycoprotein) synthesis Membrane production Golgi Apparatus - The Golgi apparatus consists of flattened membranous sacs called cisternae - Functions: Modification of ER products Manufacture of certain macromolecules Packaging materials into transport vesicles Lysosomes - A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules - Lysosomal enzymes can hydrolyse proteins, fats, polysaccharides and nucleic acids - Some types of cell can engulf another cell by phagocytosis: Forms a food vacuole A lysosome fueses with the food vacuole and digests the molecules - Lysosomes also use enzymes to recycle organelles and macromolecules of the cell, a process called autophagy Peroxisomes - Peroxisomes are specialised metabolic compartments bounded by a single membrane - Peroxisomes produce hydrogen peroxide and convert it to water - Oxygen is used to break down different types of molecules -- oxidation Cytoskeleton - The cytoskeleton is a network of fibres extending throughout the cytoplasm - It organsises cellular structures and activities, anchoring many organelles - It is composed of three types of molecular structures: Microtubules Microfilaments Intermediate filaments - For support, mobility and regulation - The cytoskeleton helps to support the cell and maintain its shape - It interacts with motor proteins to produce motility - Inside the cell, vesicles can travel along 'monorails' provided by the cytoskeleton - Three main types of fibres make up the cytoskeleton: Microtubules are the thickest of the three components of the cytoskeleton Microfilaments, also called actin filaments are the thinnest components Intermediate filaments are fibres with diameters in middle range Microtubules - Microtubules are hollow rods about 25 nm in diameter and about 200nm to 25um - In many cells microtubules grow out from a centrosome near the nucleus - Functions of microtubules include Shaping the cell Guiding movement of organelles Separating chromosomes during cell division - Component of flagella and cilia - Motor proteins (dynein) 'walk' along the microtubule - Results in the flagella or cilia to bend Microfilaments - Microfilaments are rods 7nm in diameter, built as a twisted double chain of actin subunits - Function is to bear tension, resisting pulling forces within the cell - Forms a 3D network called the cortex to help support cellular shape - Interact with myosin to bring about movement Intermediate Filaments - Intermediate filaments range in diameter from 8-12 nanometres - They support cell shape and fix organelles in place - Constructed from a variety of different proteins - More permanent than microtubules and microfilaments Cell Division Overview - Duplicate DNA (the genome) - Move each copy of the genome to different ends of the cell - Split the cell into two daughter cells Types of Cell Division - Most cell division results in daughter cells with identical genetic information in the DNA - There are three types of cell division: Binary Fission: carried out by prokaryotic (and some eukaryotic) cells Mitosis: carried out by most eukaryotic cells, resulting in the information of identical daughter cells Meiosis: a special type of division producing non-identical daughter cells (gametes, or sperm and egg cells) Binary Fission - Prokaryotes double in size then divide into two cells - Occurs in some eukaryotes that undergo asexual reproduction, but mitosis is also involved Mitosis - Results in two cells which are identical (but not always) Meiosis - Production of egg and sperm cells - Produces four cells with shuffled DNA Mitosis Chromosomes Duplicate - In preparation for cell division, DNA is replicated, and chromosomes condense - Each duplicated chromosome has two sister chromatids attached along the way by protein complexes known as cohesins - Separate during cell division - The centromere (made upp of repitive DNA seuences) is the narrow 'waist' of duplicatred chromosome, where the two chromatids are most closely attached Cell Division - Not all cells divide - Some are terminally differentiated - Come are senescent - Many do divide - Developing embryos - Testes - Cancer cells - Tissue repair following a cut or grazing Senescence - Chromosomes end with telomeres - With every cell division telomeres get shorter - Eventually the cell no longer continues to replicate The Cell Cycle - The cell cycle consists of: Mitotic (M) phase (mitosis and cytokinesis) Interphase (cell growth and copying of chromosomes in preparation for cell division) - Interphase (about 90% of the cell cycle) can be divided into subphases: - G1 phase (first gap) -- function - S phase -- synthesis - G2 phase (second gap) - The cell grows during all three phases but chromosomes are only duplicated during the S phase - G0 phase: stasis - Interphase - G1 phase: growth - S phase: replication - G2 phase: growth - Mitotic phase: chromosome separation - Cytokinesis: cell separation Divisions of Mitosis - Mitosis is conventionally divided into five phases: 1. Prophase 2. Prometaphase 3. Metaphase 4. Anaphase 5. Telophase - P: Please M: make A: Another T: Twin - Cytokinesis is well underway by late telophase Interphase - Nuclear membrane exists - One or more nucleoli - Centrosome has duplicated (each contains two centrioles) - Chromosomes have duplicated but not yet condensed Prophase - Chromosomes condense - Nucleoli disappear - Sister chromatids visible (X-shaped chromosomes) - Mitotic spindle starts to form - Centrosomes move away from each other Prometaphase - Nuclear membrane breaks up - Each sister chromatid has a kinetochore - Some microtubules attach to the kinetochores - Other microtubules interact to lengthen the cell Metaphase - Centrosomes are at opposite poles of the cell - Chromosomes line up on the metaphase plate - Kinetochores on sister chromatids are attached to microtubules from opposite poles Anaphase - Sister chromatids break apart Each is now a chromosome - Chromosomes begin moving to opposite poles - Cell elongates Kinetochore microtubules - During anaphase, microtubules shorten at the kinetochore end (not spindle end) - Motor proteins involved in 'walking down' the microtubule Telophase - Two daughter nuclei form - Nuclear membranes form - Nucleoli appear - Chromosomes start to de-condense - Spindle microtubules break down The Mitotic Spindle - The mitotic spindle is an apparatus spindle is an apparatus of microtubules that controls chromosome movement during mitosis Microtubules - Microtubules are filamentous structures within cells - Aid movement, organization of cellular structure, intracellular transport, cilia and flagella and cell division - Made of proteins called tubulins (α and β) The Mitotic spindle - During prophase, assembly of spindle microtubules begins in the centrosome, the microtubule organising centre - Spindle fiers attach to a region of chromosomes called the kinetochores Cytokinesis - The actual process cell division - Cytoplasm starts dividing during telophase - In animal cells, cytokinesis occurs by a process known as cleavage, forming a cleavage furrow - During cleavage, microfilaments (actin) orchestrate the pinching of the cell into two - In plant cells, a cell plate forms during cytokinesis - The cell plate is formed from vesicles originating from the Golgi apparatus - A new cell wall is derived from the cell plate The importance of Mendel - Gregor Mendel was the first to apply a scientific approach to understanding the nature of inheritance - Mendel was a monk - Before Mendel, belied in blended inheritance and no understanding of the equal role of parents Darwin thought blended inheritance was probably true? But statistically this theory doesn't make sense - Mendel laid the foundation of the science of genetics (even before chromosome had been discovered) Gregor Mendel Experiments - Between 1856 and 1863, Gregor Mendel conducted experiments on garden peas to investigate heredity. He used a scientific approach involving experiments, data collection, and mathematical analysis to test his hypotheses. Mendel\'s key findings include: - He established true breeding lines of plants with distinct traits. - When crossing pure-breeding purple-flowered and white-flowered plants, only purple-flowered plants appeared in the first generation (F1). - However, when F1 plants were bred among themselves, both purple and white flowers appeared in the second generation (F2), in a 3:1 ratio. - This result contradicted the blending hypothesis and demonstrated that purple flower color is dominant while white flower color is recessive. - Mendel observed a consistent 3:1 ratio in the F2 generation for seven different traits he studied. Heritable Factors - Traits are encoded by heritable factors - Heritable factors are passed on to the next generation in defined ratios - These heritable factors were later called genes - The ability for factors to be passed on is called heredity - A gene determines a trait such as flower color in pea plants - A locus is the place on the chromosome where that gene is located - An allele is an alternative variant of a gene that produces a specific form of the trait such as purple flowers Principle of Dominance - Mendel dound that heterozygotes were all pruple this led to the principle of dominacnce - A dominant allele is expressed as a phenotype when only one copy is present - A recessive allele is only expressed when two copies of the recessive allele are present Mendel's Model - Genes are in pairs; different forms called alleles - Each gamete carries only one member of each gene pair; an organism inherits two alleles - Alleles separate equally into gametes: law segregation - There are dominant and recessive alleles Testcross to Determine Genotype - Purple colour phenotype can have different genotypes - Perform a testcross to determine the genotype based on the frequency of traits in the offspring Law of Independent Assortment Crosses of two traits - Crossing plants differing in two characters produced 1 phenotype in F1 and 4 phenotypes in F2 - Mendel recognised this 9:3:3:1 ratio - Law of independent assortment: different gene pairs assort independently in gamete formation Mendel - The traits he researched had only dominant or recessive alleles - One gene controlled each individual trait - Each trait had two alleles - The genes for the traits he studied were all on different chromosomes - None of the genes were on the sex chromosomes - The relationship between the genotype and phenotype does not always follow these rules Incomplete Dominance - If one allele is not able to completely mask another it is called incomplete dominance - For example if a true- breeding red snapdragon is bred to a true-breeding white snapdragon, the offspring - Incomplete dominance is not a result of blending as shown by F2 - Phenotype of heterozygote is intermediate between the two homozygotes - Results from a reduced amount of a protein product Codominance - Codominance occurs when both alleles are expressed in the heterozygote - In the human ABO blood group, alleles for A and B are codominant, and dominant to O - Blood type also demonstrates having more than two alleles for a character Some Genes Have Multiple Effects - When a single gene regulates multiple traits, this is called pleiotropy - For intake chickens with the frizzle gene exhibit frizzled feathers but also have defects in metabolism and other body functions Gene Products can Interact - Epistasis is when the effect of one gene is dependent on the presence of one or more 'modifier genes', the genetic background Effects of one gene may be masked or modified - Epistatic mutations have different effects in combination than individually Pedigree Analysis - A family pedigree investigates a family tree and describes the traits across generations - Can be used to investigate what the genotype of family members must be\\ Autosomal Dominant Pedigree - Affected individuals have affected parents - Likely to see affected individuals in every generation - Both males and females can be affected - As most genetic diseases are rare, affected people are most likely to be heterozygous Autosomal Recessive Pedigree - Affected individuals generally do not have affected parents - If a small family, affected people may be in a single generation - May see more affected individuals if parents are related - Both males and females can be affected Recessive Alleles & Carriers - Phenotypically normal heterozygotes can transmit the recessive allele to offspring - Referred to as carriers - Occurs in albinism and cystic fibrosis Sex Linked Traits - A woman is a carrier of an X-linked recessive allele for a disorder and her mate does not have it. All their boys will have 50% chance of inheriting the disorder. None of their girls will have it but half of them are likely to be carriers - If a man has an X-linked recessive disorder and his mate does not carry the allele for it, all their girls will be carriers. None of their boys will inherit the harmful allele Quantitative Characters - Polygenic inheritance is when a phenotype is determined by multiple genes Phenotype can be complex - We can use mendelian genetics to predict patterns of inheritance of characteristics caused by one or a few genes **Lecture 13 & 14** Somatic Cells & Gametes - Evry cell in humans have two copies of each chromosome Diploid number of chromosomes One from the mother and father - Gametes (egg and sperm cells): one set of chromosomes Haploid - Gametes unite at fertilization (sexual reproduction) to create a new embryo -- union of two haploid cells restores the diploid number Somatic cells - Humans have 23 pairs of chromosomes numbered in order of size - Only non-paired chromosomes are the sex chromosomes X and Y - Do not confuse paired chromosomes with sister chromatids prior to replication Meiosis from Diploid to Haploid - Like mitosis, meiosis is preceded by the replication of chromosomes - Meiosis takes place in two sets of cell divisions, called meiosis I and meiosis II - The two cell division result in four daughter cells, rather than the two daughter cells in mitosis - Each daughter cell has only half as many chromosomes as the parent cell Chromosome Replication - DNA replication produces chromosomes with two sister chromatids Meiosis I - In the first cell division (meiosis I), homologous chromosomes separate - Meiosis I result in two haploid daughter cells with replicated chromosomes Meiosis II - In the second cell division (meiosis II), sister chromatids separate - Meiosis II results in four haploid daughter cells The Stages of Meiosis - Meiosis I: Prophase I, Metaphase I, Anaphase I, Telophase I and cytokinesis - Meiosis II: " " - At the end of meiosis, there are four daughter cells, each with haploid set of chromosomes - each daughter cell is genetically distinct from the others and from the parent cell Mitosis v Meiosis - mitosis conserves the number of chromosome sets, producing cells that are genetically identical to the parent cell - meiosis reduces the number of chromosomes sets from two (diploid) to one (haploid), producing cells that differ genetically from each other and from the parent cell Crossing Over - an important aspect of meiosis is recombination parents' DNA is shuffled each gamete gets a different set of genes approximately 50% from mother and 50% from the father Homology - homology: similarities in DNA sequences due to common ancestry in this case the same genes are in the same regions of the chromosome - note: homologous does not mean identical you get one gene for eye colour from your mum and one from dad eye colour gene is on the same position on both chromosomes but they may be different alleles: e.g. one for brown eyes, one for blue Homologous Recombination - parental and maternal chromosomes line up at loci - chiasmata form at regions of homology - segments of DNA are exchanged Errors during Meiosis - terminology diploid: having two sets of chromosomes haploid: having one set of chromosomes polyploid: having more than two complete sets of chromosomes euploid: having an equal number of all the chromosomes of the haploid set aneuploid: having a different number of chromosomes than is usual - aneuploidy occurs when there is an error in meiosis most cases lead to miscarriage 1 in 160 babies have aneuploidy Most commonly trisomy 21, 18 and 13 Genetic Variation - mutations (changes in an organism's DNA) are the original source of genetic variation - mutations create different versions of genes called alleles - reshuffling of alleles during sexual reproduction produces genetic variation Origins of Genetic Variation - the behaviour of chromosomes during meiosis and fertilisation is responsible for most of the variation that arises in each generation - three mechanisms contribute to genetic variation 1. independent assortment of chromosomes 2. crossing over 3. random fertilisartion - mutation also contributes but is usually harmful Independent Assortment of Chromosomes - In independent assortment, each pair of chromosomes sorts maternal and paternal homologous into daughter cells independently of the other pairs - For humans (n=23) there are more than 8 million possible combinations of chromosomes Crossing Over - Crossing over produces recombinant chromosomes - Crossing over begins very early in prophase I, as homologous chromosomes pair up gene by gene (synapsis) - In crossing over, homologous portions of two non-sister chromatids trade places - Crossing over contributes to genetic variation by combining DNA from two parents into a single chromosome Random Fertilization - Random fertilisation adds to genetic variation because any sperm can fuse with any ovum - The fusion of two gametes produces a zygote with any of about 70 trillion diploid combinations Autosomal Pairs of Chromosomes carry the same series of genes - Autosomes carry the same series of genes along their length - Each autosome may carry a slightly different version of a particular gene (alleles) - Therefore, cells may carry two alleles of the same gene - Which allele is expressed by cell varies between different genes Cystic Fibrosis - Alleles are often generated from simple mutations - For example, cystic fibrosis (CF) - Involves mutant allele of a gene, CFTR on chromosome 7 - The normal CFTR protein controls the movement of chloride ions across the membranes of cells in the gut, lungs pancreas and liver - Mutant allele varies from normal allele by deletion of just one amino acid - Causes excess mucous production blocking ducts like bronchioles - Most patients die from lung infections Inheritance - Cystic fibrosis is a recessive disease - You need two copies of the mutant allele before you get the symptoms of the disease - One copy of the normal gene (+) produces sufficient normal protein to make cells function normally so that heterozygotes (+/cf) are normal Drawbacks to Sexual Reproduction - Significant investment of time and energy into getting mates and in making gametes - Sexual reproduction is often slower than asexual reproduction - Risk of sexually transmitted diseases - Random mixing of genes may lead to suboptimal results Genetic Variation and Evolution - Variation allows for adaption - Evolution occurs when Phenotypic traits are genetically encoded Genes are passed on to offspring Genes can vary Different genes have different effects on phenotype (fitness) Sexual reproduction is nearly ubiquitous - Nearly all eukaryotes reproduce sexually Except 22 fish, 23 amphibians and 29 reptiles - Sex evolved around one billion years ago Lecture 15 & 16 Chromosomes & Mendel's Laws - In Meiosis only one chromosome pair is randomly selected to be transmitted to offspring - This is the chromosomal basis of Mendel's principle of segregation - Different chromosomes are separated independently of each other in meiosis 1 - This is the chromosomal basis of Mendel's principle of independent assortment Genetics Depends on Probabilities - The probability of two independent events occurring is the product of their individual probabilities - E.g. chance of 2 heads on a coin toss is ½ x ½ = ¼ - Can be applied to probabilities of receiving 2 particular alleles from parents - Punnett square is used to work out these probabilities in genetics - The probability of two independent events occurring is the product of their individual probabilities - E.g. chance of 2 heads on a coin toss ½ x ½ = ¼ - Can be applied to probabilities of receiving 2 particular parents - Punnett square is used to work out these probabilities in genetics Testcross - What is the genotype of the purple plant? - To work out the genotype of an individual with the dominant phenotype, you cross it to an individual with a known genotype i.e. homozygous recessive - Identifying the genotype of one parent using a testcross Dihybrid Cross - Alleles at two independent genes assort independently - A double heterozygote can produce 4 different gametes - Multiply probabilities of having 2 independent alleles in gamete - Proportions 9:3:3:1 Morgan's Experiments - Thomas Hunt Morgan (1866-1945) - In the early 1900s morgan worked on Drosophila melanogaster - After multiple years of breeding, he identified variation in a trait -- eye colour - Eye colour followed mendelian genetics; 3:1 (red:white) in F2 - All F2 females had red eyes, while 50% of males had red eyes & 50% white eyes - As opposed to the genes that mendel studied (autosomes), eye colour is on the sex chromosomes X-linked Recessive Genes - Many genes unrelated to sex are carried on the X-chromosome - Fathers pass X-linked alleles to all daughters but none to sons - Mothers can pass X-linked alleles to both sons and daughters - More males than females have X-linked disorders - E.g. red-green colour blindness - Colour blind father cross with normal homozygous mother - Colour blind father will transmit mutant allele to all daughters and no sons - Males can not be carriers of recessive X-linked alleles - Carrier crosses with a normal colour vision male - 50% chance that daughters will be carriers - 50% chance son will have disorder - Carrier crosses with colour blind male - 50% chance each child will have the disorder - Daughters with normal vision will be carrier Human Pedigrees - In humans you cant set up crosses - Have to work from the observed phenotypes in a family to work out the mode of inheritance - Pedigrees are often of rare genetic disorders X-linked Recessive - Affected individuals most likely to be males - Disease generally passed through unaffected carrier mothers - Fathers cannot pass on X-linked diseases to their sons - Examples: haemophilia, Duchenne muscular dystrophy, colour blindness Autosomal Dominant - Affected individuals have affected parents - Liekyl to see affected individuals in every generation - Both males and females can be affected - As most genetic diseases are rare, affected people are most likely to be heterozygous - Examples: huntington disease, achondroplasia Autosomal Recessive - Affected individuals generally do not have affected parents - If a small family, affected people may be in a single generation - May see more affected individuals if parents are related - Both males and females affected - Examples: cystic fibrosis, albinism, phenylketonuria X Inactivation in Females - Because females have two X chromosomes, one is inactivated during the development of the embryo - Inactive X chromosome becomes a Barr body, and the genes are not expressed - Embryonic cells have a random mosaic of X inactivated chromosomes Linkage - The closer two genes are on a chromosome, the more likely they are together - Genes located near each other and are likely to be inherited together are linked - Linked genes deviate from Mendel's law of independent assortment - The closer two genes are on a chromosome, the more likely they are to be inherited together - Genes located near each other, and are likely to be inherited together are linked - Linked genes deviate from Mendel's law of independent assortment Benefits - No uncertainty in the taxonomy of organisms - Each species/group in this system is a taxon e.g. birds is the taxon aves Phylogenetic relationships - Darwin all organisms share a common ancestor - Like Linnaeus' system: the ancestors of closely related species in same genus) must be younger than ancestor of different genera - The relationships can be depicted as a tree - Phylogenetic trees are hypotheses of the evolutionary history of taxa Phylogenies - Phylogenies reflect patterns produced by evolution and reveal evolutionary relationships of organisms - Phylogenies model evolution using relationships, morphology, DNA - Lineage: series of organisms connected by genetic information passed from one generation to the next - Common ancestor: hypothetical organism that gave rise to different lineages - Sister taxa: two lineages that share a common ancestor not shared by other groups Phylogeny - Phylogenetic trees (phylogenies) can have many shapes Phylogeny Architecture - Tips (leaves): Terminal lineage on a phylogenetic diagram - Branch: a line on a tree diagram that represents a lineage - Node: a point on a phylogeny where one lineage splits into two lineages Interpreting Phylogenies - Patterns of descent, not phenotypic similarity - A taxon did not evolve from the species next to it, it evolved from a 'common ancestor' - Each generation there is an interbreeding population - At some point in time, an event may split the population into species - This means that the populations no longer have gene flow between them - Each population then begins as a reproductively isolated unit, where evolution is now independent for each unit - The time since divergence is represented by the branches on the tree - The nodes represent the last generation before the splitting event - The tips represent the current species - Which organism is more closely related to the lizard? The frog or the human? 1. Position of tips on phylogeny is not important; to understand relatedness, find the common ancestor 2. A phylogeny can be flipped around any node without changing relationships Common ancestry - Organisms share characteristics because of common ancestry - We can better understand a species if we know its evolutionary history - An organism is likely to share many of its genes, metabolic pathways, and structural proteins with its close relatives Taxonomy - Binomial nomenclature - Genus and species - Hierarchical classification system - Can be revised based on molecular evolution data Interpreting Phylogenies - Two different trees that show the exact same phylogenetic relationships - Same number of nodes (of common ancestors) in same order - Reinforces misconception -- some species are 'less evolved' or are the actual ancestors of living - More accurately reflects relationships among species Potential Trees - What if we had three taxa? - The number rapidly goes up with the number of taxa in the tree - 15 trees for four species 34,459,425 for ten species DNA mutations - Evolution in DNA is captured by changes (mutations) - DNA sequences are aligned to build phylogenies - Simarity of sequences reveals relationships between taxa - We use the changes, and the probability of those changes, to infer evolutionary relationships (phylogeny) DNA sequencing - Computer programs align sequences based on sequence similarity, considering deletions and insertions - The similarity between sequences is calculated which are used to infer phylogeny Methods of Tree-building - Maximum parsimony -- the tree with the least number of overall changes (mutations) that explains the relationship of taxa - Maximum likelihood -- finds the most probable tree given a model of DNA evolution Phylogeny and Characters - Character -- a feature (usually morphological) that can be used to differentiate between groups of organisms - Shared ancestral character -- a trait that originated in an ancestral organism - Shared ancestral character (homology): closely related anatomical structures sharing relative position in body that have the same surrounding elements - Originate and grow in the same embryonic tissues and develop in similar way - Non-homolhous = homoplastic characters e.g. skin & feathers - Shared derived character -- an evolutionary novelty within a clade - Tree output -- an organism that is closely related to but not part of the species being investigated (ingroup) Types of Phylogenies - Cladogram represents relationships of taxa, branch lengths are equal - Phylogram represents rate of genetic change (scaled branch lengths) between taxa - Chronogram -- calibrated to time (fossil record) Molecular Clocks - Measures the absolute time of evolutionary change based on regions of the genome that appear to evolve at constant rates - Assumption: number of nucleotide substitutions is proportional to the time that has elapsed since ddivergence time (common ancestor) - Calibrate against the fossil record - Use this to estimate dates of events not known from fossil records - But... does not give complete precision. It is an approximation Utility of Phylogenies - Uncover the evolutionary history of species - Identify novel and unique lineages - 13 samples of 'whale meat' purchased from Japanese fish markets - Sequenced part of the mitochondrial DNA (mtDNA) from each sample - Compared results with the comparable mtDNA sequence from known whale species **Lecture 17 &18** Populations and Gene Pools - Concepts: - A populations is a localized group of interbreeding individuals - Gene pool is the combinations of alleles in a population Remember the difference between an allele and a gene - Allele frequencies -- describe how often a certain allele is found in a certain population e.g. how many A vs. a in a single population Microevolutionary Change in Populations - Microevolution = changes in allele frequencies in a population Population not undergoing evolution lacks all drivers of evolutionary change: 1. Very large populations (no genetic drift) 2. No migration (lack of gene flow) 3. No mutations (no new genetic variation) 4. Random mating (no assortative mating) 5. No natural selection (equal fitness) Calculating Frequencies - Genotype and allele frequencies are proportions e.g. 3 dogs out of 5 pets, 3/5, 60% - genotype frequency is the number of individuals with a specific genotype, divided by the number of total individuals - allelic frequency is the number of a particular allele, divided by the number of alleles in all individuals