ANSC20010 Genetics and Biotechnology Section 4 Spring Trimester 2023-24 PDF

ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 ANSC20010 Section 4: Molecular Genetics and Genomics Campbell 11th ed. Chapters 16 and 17 Electron micrograph showing DNA released from a bacteriophage (a type of virus which infects bacteria) 1 Biological organisms possess de...

ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 ANSC20010 Section 4: Molecular Genetics and Genomics Campbell 11th ed. Chapters 16 and 17 Electron micrograph showing DNA released from a bacteriophage (a type of virus which infects bacteria) 1 Biological organisms possess deoxyribonucleic acid (DNA) in the form of a genome that contains the genetic information 2 A modern description of genetics Biological traits are largely controlled by the genes that are encoded by the deoxyribonucleic acid (DNA) molecules that make up chromosomes in genomes. Modern description of genetics can be described as: “Genetics is the branch of science devoted to the study of the molecular nature of genes, including their DNA composition, how they control or contribute to a trait and how they are transmitted from parent to offspring.” 3 1 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Molecular genetics and DNA are central to biology Genetics is central to biology because genes and gene activity underlie all life processes. Genes (encoded by DNA):  Determine cell structure and function (tissue function).  Control an organism’s development from a single-celled zygote to a multicellular adult.  Regulate biochemical reactions that maintain the physiology of an organism over its lifespan.  Enable organisms to fight disease.  Are transmitted from parent to offspring. 4 The DNA Double Helix Discovery https://youtu.be/1vm3od_UmFg 5 Discovery that DNA is the genetic material (1944) Oswald Avery, Colin MacLeod and Maclyn McCarty Building on earlier work by Fred Griffith (1928), Avery, MacLeod and McCarthy showed that DNA from killed virulent Streptococcus pneumoniae bacteria could transform living non-virulent S. pneumoniae into the virulent type. They hypothesised that DNA rather than protein is the hereditary material of bacteria and proposed that was also the case for complex organisms. Their work was supported by many subsequent experiments and the Avery–MacLeod–McCarty experiment marked the birth of molecular genetics. 6 2 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The experiment performed by Fred Griffith (1928): genetic transformation of non-virulent bacteria In 1944, Avery, MacLeod and McCarthy showed that the transforming substance (“principle”) in Griffith’s experiment was actually DNA. 7 Avery–MacLeod–McCarty experiment (1944): supported the hypothesis that DNA is the genetic material in bacteria Avery McLeod McCarth y 8 Bacteriophage: a virus that infects and replicates inside bacterial cells 9 3 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Confirmation that DNA is the genetic material: The Hershey-Chase Experiment (1952) Martha Chase and Alfred Hershey 10 Confirmation that DNA is the genetic material The Hersey-Chase Experiment (1952) https://youtu.be/B1jDNSEnfIA 11 Deoxyribonucleic acid (DNA) is the genetic material DNA is a polymer: a large molecule that consists of smaller molecular subunits (monomers). The monomers in DNA are nucleotides:  A nucleotide is a nitrogenous base covalently attached to a pentose sugar and a phosphate group.  A chain of nucleotides is referred to as a polynucleotide. 12 4 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The chemical structure of a nucleotide 13 The structure of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Nucleotides join together to form long chains (polynucleotides). DNA is a double-stranded polynucleotide molecule. The pentose sugar in DNA is deoxyribose. There are four nitrogenous bases in DNA: Adenine (A), Thymine (T), Guanine (G) and Cytosine (C). RNA (ribonucleic acid) usually exists as a single-stranded polymer composed of a sequence of nucleotides. The pentose sugar group in RNA is ribose. The four nitrogenous bases in RNA are A, U (Uracil), G and C. 14 The chemical structure of a nucleotide 15 5 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Chemical structure of a single polynucleotide chain 16 Elucidation of the three-dimensional structure of DNA James Watson and Francis Crick (1953) 17 Elucidation of the three-dimensional structure of DNA James Watson and Francis Crick (1953) Rosalind Franklin (1920 – 1958) Photo 51: X-ray diffraction image of DNA 18 6 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The structure of deoxyribonucleic acid (DNA) 19 The structure of deoxyribonucleic acid (DNA) DNA is a right-handed double helix. The two polynucleotide strands are held together in the helical formation by hydrogen bonding between bases in opposing strands. The base-pairing is specific: Adenine = Thymine (two hydrogen bonds) Guanine ≡ Cytosine (three hydrogen bonds) The two polynucleotide chains run in opposite directions from one another (anti-parallel). There are 10 base-pairs per turn of the DNA double helix (3.4 nm). The order of a specific segment of ‘letters’ in a DNA molecule can specify genetic information in the form of a gene. 20 The directionality of a double-stranded DNA molecule 21 7 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The individual strands of a DNA molecule are complementary and are read 5‘ to 3' 5’-AGGCATCGTACTGAGACTAGCCTAGATTGCA-3’ 3’-TCCGTAGCATGACTCTGATCGGATCTAACGT-5’ Further information about the discovery of the structure of DNA: www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397 22 The complementary nature of double-stranded DNA and its information-carrying capacity: DNA unzipped https://youtu.be/qYsW0jIFH5A 23 Required properties of the genetic material 1) Replication 2) Functionality 3) Evolution 24 8 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Erwin Schrödinger and What is Life? written in Dublin during the Second World War Kincora Road Clontarf 25 Required properties of genetic material 1. Genotypic function: replication  The genetic material must store genetic information and accurately transmit that information from parents to offspring, generation after generation.  The genetic material must be replicated precisely during mitosis and meiosis. 2. Phenotypic function: gene expression  The genetic material must regulate the development of the phenotype of the organism.  The genetic material must dictate the growth and differentiation of the organism from the zygote to the mature adult. 26 Required properties of genetic material 1. Evolutionary function: mutation  The genetic material must be capable of undergoing change in the genetic information that it contains.  Variations in the genetic information enable adaptation of biological organisms to changing environments.  These variations (mutations) are required for biological evolution to occur. 27 9 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Replication of DNA Watson and Crick’s model for the structure of DNA immediately suggested the basic mechanism of DNA replication. “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” Nature, 1953 28 Overview of DNA replication A T C G T A A T G C C G T A T A G C A) Before replication: parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding. 29 Overview of DNA replication A T C G T A A T G C C G T A T A G C B) The first step in replication is separation of the two DNA strands. 30 10 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Overview of DNA replication old A T A T C G C G T A T A A T A T G C G C C G C G T A T A T A T A G C G C new old C) Each “old” strand acts as a template that determines the order of nucleotides along “new” complementary strands. 31 The molecular machinery of DNA replication Each new ‘daughter’ molecule consists of an ‘old’ strand and a newly synthesised strand: semi-conservative replication. A diploid mammalian genome contains approximately 6 giga base pairs (Gb) of DNA; therefore, remarkable speed and accuracy is required for DNA replication. A cell can copy all of this DNA in a few hours with an error rate of ~ 10-9. Extension of DNA at replication fork is performed by enzymes called DNA polymerases. 32 The molecular machinery of DNA replication 33 11 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The molecular machinery of DNA replication 34 The mechanism of DNA replication https://youtu.be/I9ArIJWYZHI 35 Required properties of the genetic material 1) Replication 2) Functionality 3) Evolution 36 12 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 How do genes function to direct biochemical and cellular processes? The structure, function, development and reproduction of an organism depends on which genes are expressed in each cell and tissue. Genes direct biochemical and cellular processes through their encoded products; a gene encodes either: 1. A polypeptide (a chain of amino acids that constitutes part of a protein) – most genes encode a polypeptide.  Some proteins are composed of a single polypeptide (e.g. lysozyme) while other proteins are composed of more than one polypeptide (e.g. haemoglobin). 37 Mammalian haemoglobin: composed of four globin protein subunits 38 How do genes function to direct biochemical and cellular processes? 2. A functional RNA molecule:  tRNA = transfer RNA  rRNA = ribosomal RNA  hnRNA = heterogeneous nuclear RNA  snoRNA = small nucleolar RNA (modification of rRNA)  miRNA and siRNA = microRNA and short interfering RNA (regulate expression of individual genes) Gene products are the link between genotypes and phenotypes. 39 13 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Functional RNA molecules 40 Overview of transcription and translation 41 Overview of transcription and translation Transcription, RNA processing and translation Polypeptide chain consisting of amino acids 1 2 Haemoglobin (multimeric protein) 3 4 5 6 Lysozyme (single polypeptide) 42 14 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Transcription and translation are the two main processes linking gene to protein The bridge between DNA and protein synthesis is RNA. Nucleic acids (polymers of A, C, G, T, or U) and proteins (chains of amino acids) are written in two different chemical languages. Transcription and translation convert DNA information into protein information. Transcription: synthesis of messenger RNA (mRNA) from DNA. Translation: synthesis of a polypeptide using information encoded in an mRNA molecule. 43 Transcription and translation are the two main processes linking gene to protein Eukaryotes: transcription occurs in the nucleus and translation in the cytoplasm. Only one DNA strand (the template DNA strand) is transcribed into mRNA. Transcription is carried out in the nucleus by an RNA polymerase enzyme. In eukaryotes, the primary RNA transcript is processed in various ways before it is exported from the nucleus as an mRNA molecule. Translation occurs in the cytoplasm of the eukaryotic cell and involves ribosomes, tRNAs, mRNAs and amino acids. 44 The genetic code: nucleotide triplets specify amino acids The mRNA is exported from the nucleus to the cytoplasm where it is translated by ribosomes. Translation: flow of information from gene to protein is based on a triplet code - trinucleotide “words” or codons. Translation: the mRNA triplet codons are decoded into a sequence of amino acids to form a polypeptide. Each codon specifies an amino acid according to the genetic code. 45 15 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 A simplified overview of transcription Template strand T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A Gene (DNA) Complementary strand Transcription (RNA polymerase reads off the template DNA strand in a 5’-3’ direction mRNA A U G A A G U U U G G C U A A mRNA leaves nucleus Nucleus Cytoplasm 46 RNA transcription from the template strand of DNA 47 RNA transcription from the template strand of DNA 48 16 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 RNA processing: eukaryote cells modify RNA after transcription The 5' end of the mRNA is capped with a modified guanine (G) nucleotide, which is termed a 5' cap. The 5' guanine cap protects the mRNA molecule and acts as an “attach here” signal for ribosomes during translation. A poly(A) tail is added to the 3‘ end consisting of 30-200 adenine (A) nucleotides. The non-coding introns are removed and the amino-acid coding sequences (exons) are joined together (RNA splicing). 49 Comparison of prokaryotic and eukaryotic gene structure Prokaryotic gene Regulatory region for transcription initiation Coding region Transcription termination signals Eukaryotic gene (generally much larger) Regulatory region for transcription initiation Transcription termination signals Exons (coding regions) Introns (noncoding - excised during RNA processing) 50 Transcription and RNA processing in eukaryotes 3' Human -globin gene [HBB] (DNA) 5' Promoter Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 Termination +1 (transcription start) Transcription Pre-RNA for human -globin polypeptide - 146 aa (part of haemoglobin) 5' 5' Cap Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 3' Poly(A) tail +1 51 17 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Transcription and RNA processing in eukaryotes Pre-RNA for human -globin polypeptide - 146 aa (subunit of haemoglobin). 5' Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 3' Poly(A) tail 5' Cap 1st amino acid 146 amino acid Introns excised and exons spliced together Mature mRNA 5' Cap 1 Leader (ribosome binds here) 146 Poly(A) tail Trailer 52 Mammalian haemoglobin: composed of four globin protein subunits 53 Translation and the synthesis of a polypeptide chain Translation is the RNA-directed synthesis of a polypeptide chain. Transfer RNA (tRNA) molecules transfer amino acids from the cytoplasmic pool to the ribosomes for incorporation into new polypeptide chains. The ribosome adds each amino acid to the growing polypeptide chain. There are 45 different tRNA molecules that link specific mRNA codons with a particular amino acid. The tRNA anticodon binds to mRNA and the bound amino acid is added to the polypeptide chain in sequence. 54 18 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 An overview of transcription followed by translation Template strand T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A U U G G C U A A Gene (DNA) Complementary strand Transcription and RNA processing mRNA A U G A A G U Nucleus Cytoplasm Translation Polypeptide Met Lys Phe Gly STOP 55 The twenty commonly occurring amino acids used by biological organisms 56 The genetic code: nucleotide triplets specify amino acids Redundancy of the genetic code Note that more than one codon sequence codes for the same amino acid. However, there is no ambiguity in the genetic code: e.g. GAA and GAG code for glutamic acid, but do not specify any other amino acid. 57 19 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The genetic code: nucleotide triplets specify amino acids https://youtu.be/rW8NKvQQ8P4 58 A typical transfer RNA (tRNA) molecule 59 60 20 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Gene expression – the pathway from gene to protein https://youtu.be/D3fOXt4MrOM 61 Required properties of the genetic material 1) Replication 2) Functionality 3) Evolution 62 Mutation and mutants in popular culture 63 21 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The molecular basis of mutation Mutations are changes in the genetic material of an organism. Point mutations are DNA sequence changes involving one or a few base pairs within the genome. Point mutations can occur anywhere in the genome. The genomic location of a point mutation can determine whether or not the mutation can affect phenotype. If the mutation occurs in non-coding DNA then it is unlikely to affect phenotype. If the mutation occurs in protein-coding DNA sequences (exons) then it can affect protein function and ultimately phenotypes. 64 The molecular basis of mutation T 65 Types of point mutations Point mutations can be divided into two main categories: 1. Base pair substitutions. 2. Base pair insertions or deletions (indels). Base pair substitution: replacement of one nucleotide and its partner on the complementary strand with another pair of nucleotides. Insertions or deletions (indels) : additions (insertions) or losses (deletions) of one or more nucleotide pairs in a DNA sequence. 66 22 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Base pair substitutions in protein-coding (exon) DNA sequences: silent mutations If a substitution occurs in an exon it can change the codon sequence of the mRNA. If the ‘new’ codon codes for the same amino acid as the ‘old’ codon this is called a silent mutation. Silent mutations reflect the redundancy of the genetic code. 67 The genetic code: nucleotide triplets specify amino acids Redundancy of the genetic code Note that more than one codon sequence codes for the same amino acid. However, there is no ambiguity in the genetic code: e.g. GAA and GAG code for glutamic acid, but do not specify any other amino acid. 68 Base pair substitution: silent mutation (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G U Lys U U G G C U Gly Phe A A STOP Silent substitution: no effect on amino acid sequence mRNA Protein A U Met G A A Lys G U U Phe U G G Gly U U A A STOP 69 23 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Base pair substitutions in protein-coding (exon) DNA sequences: missense mutations If the ‘new’ codon specifies a different amino acid this is called a missense mutation. Some missense mutations may have little effect on a protein as the variant amino acid may be chemically similar to the original amino acid. However, some missense mutations can result in the variant amino acid being chemically very different from the ‘old’ amino acid. These missense mutations can have a major effect on protein function and can affect phenotypes. 70 Base pair substitution: missense mutation (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G U Lys U U G G C U Gly Phe A A STOP Missense mutation mRNA Protein A U Met G A A Lys G U U Phe U A G C U Ser A A STOP 71 The twenty commonly occurring amino acids used by biological organisms 72 24 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 An example of a missense mutation: the sickle cell anaemia mutation in humans β-globin gene DNA Normal β-globin gene DNA sequence TGA GGA CTC CTC ACT CCT GAG GAG Mutated β-globin gene DNA sequence TGA GGA CAC CTC ACT CCT GTG GAG Transcription and translation Protein chain thr Normal red blood cells pro glu glu thr pro val glu Sickle-shaped red blood cells 73 74 Base pair substitutions in protein-coding (exon) DNA sequences: nonsense mutations If a substitution changes an amino acid codon to a stop codon this is termed a nonsense mutation. Nonsense mutations usually result in the formation of shortened (truncated) proteins, which are often non-functional. Nonsense mutations are often detrimental and can result in genetic disease. 75 25 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The genetic code: nucleotide triplets specify amino acids Redundancy of the genetic code Note that more than one codon sequence codes for the same amino acid. However, there is no ambiguity in the genetic code: e.g. GAA and GAG code for glutamic acid, but do not specify any other amino acid. 76 Base pair substitution: nonsense mutation (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G U Lys U U G G C U Gly Phe A A STOP Nonsense mutation mRNA Protein A U Met G U A G U U U A G C U A A STOP 77 Insertions and deletions (indels) An insertion or deletion (indel) occurring in exon sequences can alter the reading frame of the mRNA sequence. Reading frame: the sequential order of codons along an mRNA sequence. If an indel alters the reading frame of the mRNA sequence it is termed a frameshift mutation. All codons downstream of an indel will not be read properly and the resulting protein will have a very different amino acid sequence to the normal non-mutant amino acid sequence. Frameshift mutations involving numbers of nucleotides that are not multiples of 3 can have significant effects on the amino acid sequence. 78 26 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Base-pair insertion or deletion (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G U Lys U A U G A Met Protein G G C U Gly A A STOP U Frameshift deletion causing extensive missense mRNA U Phe A G U Lys U G G C U A A Ala Leu 79 Base-pair insertion or deletion (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G U Lys U U G G C U Gly Phe A A STOP Frameshift insertion causing immediate nonsense mRNA A U G U Met Protein A A G U U U G G C U A STOP 80 Base-pair insertion or deletion (occurs in DNA but mRNA and protein shown here) Wild type mRNA A U G A Met Protein A G Protein A U Met A G U U Phe U U G U G A G Gly G C Gly Phe Insertion or deletion of 3 nucleotides: No extensive frameshift mRNA U Lys U A A STOP G U U A A STOP 81 27 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Mutagens generate chemical and structural changes in DNA to produce mutations Spontaneous mutations (not caused by mutagens): errors during DNA replication, repair, or recombination can cause substitutions, insertions or deletions. However, mutagens can also cause mutations in DNA: physical and chemical mutation-causing agents. In the 1920s, Hermann Muller discovered the first mutagen when he used X-rays to obtain Drosophila melanogaster mutants (he worked initially in Columbia with Thomas Hunt Morgan and then in 1926 at the University of Texas he showed that X-rays induced mutations in D. melanogaster). Many other forms of radiation are also mutagens: radon gas, UV radiation (joins adjacent pyrimidines). 82 Mutagens generate chemical and structural changes in DNA to produce mutations Certain chemicals can also cause mutations: Base-analog mutagen: e.g. 5-bromouracil (incorporated into DNA instead of T and more prone to mispairing). Nucleotide analogs: e.g. AZT – used as a therapy for AIDS by slowing replication of HIV because virus polymerase incorporates AZT instead of T. Examples of chemical agents that modify DNA  Nitrous acid (HNO2).  Ethyl methanesulfonate (EMS).  Acridine (intercalation between base-pairs - frameshift). 83 Atomic gardening: using radiation to accelerate mutation rates to provide genetic variation for plant breeding Institute of Radiation Breeding, Japan www.naro.affrc.go.jp/archive/nias/eng/org/GR/IRB/index.html 84 28 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Atomic gardening: using radiation to accelerate mutation rates to provide genetic variation for plant breeding Deep red grapefruit: bred using gamma radiation-induced mutation 85 Microbial Evolution, and Growth Arena (MEGA) Rapid bacterial evolution across time and space http://news.harvard.edu/gazette/story/2016/09/a-cinematic-approach-to-drug-resistance/ https://youtu.be/plVk4NVIUh8 86 DNA and genomes 87 29 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 The horse genome: the complete complement of genetic material (DNA) DNA TGGGCATATA TTCACTAGCA TTACTGCCCT TGGTATCAAG GAGAAGACTC ACCCTTAGGC CTGTCCACTC CTCGGTGCCT CTGAGTGAGC TGGGACCCTT GGGAGAAGTA AAGTCTCAGG TTAATTCTTG AGTCAGGGCA ACCTCAAACA GTGGGGCAAG GTTACAAGAC TTGGGTTTCT TGCTGGTGGT CTGATGCTGT TTAGTGATGG TGCACTGTGA GATGTTTTCT ACAGGGTACA ATCGTTTTAG CTTTCTTTTT GAGCCATCTA GACACCATGG GTGAACGTGG AGGTTTAAGG GATAGGCACT CTACCCTTGG TATGGGCAAC CCTGGCTCAC CAAGCTGCAC TTCCCCTTCT GTTTAGAATG TTTCTTTTAT TTTTCTTCTC TTGCTTACAT TGCACCTGAC ATGAAGTTGG AGACCAATAG GACTCTCTCT ACCCAGAGGT CCTAAGGTGA CTGGACAACC GTGGATCCTG TTTCTATGGT GGAAACAGAC TTGCTGTTCA CGCAATTTTT TTGCTTCTGA TCCTGAGGAG TGGTGAGGCC AAACTGGGCA GCCTATTGGT TCTTTGAGTC AGGCTCATGG TCAAGGGCAC AGAACTTCAG TAAGTTCATG GAATGATTGC TAACAATTGT ACTATTATAC 88 Genome: the full complement of genetic material of an organism (human genome is shown) Gamete cell (haploid) Somatic cell (diploid) Haploid genome Diploid genome (two copies of the haploid nuclear genome) Nuclear Genome Mitochondrial Genome Nuclear Genome Mitochondrial Genome ~3.2 × 109 base pairs ~16,000 base pairs ~6.4 × 109 base pairs ~16,000 base pairs ~8,000 copies ~8,000 copies One copy of each autosome (22 in total) One copy of the X or Y chromosome 23 chromosomes in total Two copies of each autosome (44 in total) Two copies of the X or one copy of the X and Y chromosome 46 chromosomes in total Approximately 21,000 genes (one copy of each) Approximately 21,000 genes (two copies of each) 89 Genome size – standard units used in genomics Term Number of base pairs (bp) base pair (bp) one bp 1 bp kilo base pair (1 kb) thousand bp 1,000 bp 1 × 103 bp mega base pair (1 Mb) million bp 1,000,000 bp 1 × 106 bp giga base pair (1 Gb) billion bp 1,000,000,000 bp 1 × 109 bp tera base (1 Tb) trillion bp 1,000,000,000,000 bp 1 × 1012 bp 90 30 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Genomes: sizes and number of genes (www.ensembl.org) Genome Group Size (bp) Number of protein-coding genes Eukaryotic nucleus Saccharomyces cerevisiae Caenorhabditis elegans Arabidopsis thalania Homo sapiens Yeast Nematode Plant Mammal Prokaryote Escherichia coli Hemophilus influenzae Methanococcus jannaschii Bacterium Bacterium Bacterium Viruses T4 HCMV (herpes group) Bacterial virus Human virus ~172,000 (L/C) ~229,000 (L) 300 200 Eukaryotic organelles H. sapiens mitochondria Arabidopsis chloroplast Mammal Plant ~17,000 (C) ~154,000 (C) 37 128 12,162,994 (Linear) 103,022,290 (L) 135,670,229 (L) 3,381,944,086 (L) 4,738,834 (Circular) ~1,830,000 (C) ~1,660,000 (C) 6,590 20,447 27,416 20,364 4,236 1,703 1,738 91 The relative sizes of various genomes 92 Genome size in kilobases (kb) of DNA for various types of organism 103 104 105 106 107 108 103 104 105 106 107 108 Flowering plants Birds Mammals Reptiles Amphibians Bony fish Cartilaginous fish Echinoderms Crustaceans Insects Molluscs Worms Molds Algae Fungi Gram +ve bacteria Gram -ve bacteria Mycoplasma 93 31 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 Gene number is not necessarily correlated with organismal complexity: Crassostrea gigas genome >28,000 genes Barbecued Pacific Oysters with Wasabi Mustard Sauce Zhang G. et al. (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature advance online publication (20th September 2012). 94 Growth of GenBank and major genome milestones [doubling time ~ 12 months] 10 Pb 1 Pb 1996 Yeast, 14 Mb 6,231 genes 2001 Mouse, 3.0 Gb 20-25,000 genes 1998 Nematode,100 Mb 16,384 genes 2003 Human, 3.1 Gb 20-25,000 genes 100 Tb 2009 Cow, 2.9 Gb 20-25,000 genes 10 Tb 1 Tb 2014 Sheep, 2.6 Gb 20-25,000 genes 2012 Bactrian camel 2.38 Gb 20-25,000 genes 100 Gb 2000 Arabidopsis 117 Mb 20,000 genes 10 Gb 2009 Horse, 2.7 Gb 20-25,000 genes 1995 Haemophilus 1.8 Mb 1,709 genes 1 Gb 2013 Turkey, 1.1 Gb 15-20,000 genes 2004 Chicken 1.1 Gb 20,000 genes 100 Mb 2000 Fruit fly, 160 Mb 13,600 genes 10 Mb 2012 Pig, 2.8 Gb 20-25,000 genes 1 Mb 2013 Goat, 2.7 Gb 20-25,000 genes 100 Kb 1980 1985 1990 1995 2000 2005 2010 2015 2020 95 Accessing genome information and data Ensembl Genomes: ensemblgenomes.org http://ensemblgenomes.org 96 32 ANSC20010 Genetics and Biotechnology: Section 4 Spring Trimester, 2023-24 A single base pair substitution: also termed a single nucleotide polymorphism (SNP) 97 Analysis of SNPs can be massively parallel, automated and high-throughput Illumina® Bovine SNP50 BeadChip® ~55,000 SNP genetic markers that span the whole bovine genome [used for genomic selection programmes in dairy and beef cattle] 98 RTE Science Squad video on Genomic Selection https://youtu.be/GOP_AQt5ANo 99 33