INTRODUCTIONS AND NUCLEIC ACIDS

Impact of Genetics: In the field of

1. Agriculture Aims: a) Increase food yields b) Increase resistance to pests and diseases c) Increase nutrient value d) Production of drugs and useful products for humans Approaches: a) Traditional approach: Selective breeding - Select high quality parents to be crossed to produce high quality generations Disadvantages: Long time for high quality generations Bad characteristics might be passed on too b) Modern approach: Gene modification - Select genes for certain characteristics and applied it to the object (plants/animals) 2. Medicine Roles: a) Characterisation of genetic diseases: better understanding of genetic diseases characters to find a way to avoid or cure b) Increase knowledge of other human diseases c) Improve diagnostics (identification of diseases) and therapeutics (cure of diseases) d) Development of novel, safe recombinant vaccines: combine genes from one organism to another. E.g. Human insulin genes get combined to yeast to produce more insulin. e) Future widespread use of gene therapy: isolation of gene and insert genes to patients. 3. Society Roles: a) Initiation of business ventures in biotechnology industry: companies market pharmaceuticals and diagnostic tests, or that provide services such as DNA profiling, contribute to worldwide economic growth b) Provide evidence based on analysis of DNA: test for paternity, convict guilty and to exonerate innocent of crimes, to authenticate claims to inheritances, and to identify the dead.

Model Research Organisms: Organisms commonly used in Genetics

Smallest organisms are the easiest organisms to study their genetics.

(1) Bacteriophages (T-even, , M13) - Have relative simplicity: smallest bacteriophages have just a handful of genes; largest bacteriophages have a couple of hundred genes Role: Study the basic genetic processes. (2) Bacteria (Escherichia coli) - Can be cultured in the laboratory on a simple medium - Amenable to all sorts of biochemical analyses - Mutant strains with different growth requirements can be isolated easily Role: Discovery of the mechanisms of DNA replication and the process of transcription and translation. (3) Yeast (Saccharomyces cerevisae) - Can be cultured on simple media in the laboratory - Large number of cells can be obtained from a single mother cell in just a few days - Mutants strain with different growth characteristics can be readily isolated Role: Used in kitchens as a leavening agent for making bread (4) Plants (Pisum sativum - pea and Arabidopsis thaliana) - Relatively short generation time - Self-fertilizing species - Different strains can be cross-fertilized in the laboratory to produce hybrids Role: Genetic analysis of Arabidopsis thaliana is providing a framework to understand how genes function in important food plants, which lead to a wealth of information about plant development, disease resistance, photosynthesis, cold tolerance, etc. (5) Worms (Caenorhabdits elegans round worm) Reproduce quickly and prolifically Can be reared easily on agar plates seeded with E. coli bacteria as food Short life cycle (3 days) Hermaphroditic (have both sperm and egg) without self-incompatibility hence allows self-fertilization - Transparent body Role: Transparent body allows researchers to watch cells dividing and moving from time when egg is fertilized. Hence, allows researchers to trace the formation of tissues and organs over the course of development.

(6) Insects (Drosophila melanogaster fruit fly) - Easy to rear in laboratory - Relatively short life cycle (10 days) - Reproduces prolifically Role: Anatomical complexity of Drosophila provides geneticists with the opportunities to study how genes control the formation of body parts. It also allows them to investigate the life cycle from fertilized egg into embryo and eventually into an adult. (7) Mammals (Mus musculus mouse) - Can be subjected to genetic experimentation - Genetic investigations of human own species Role: Mice have been used to study health and disease, effects of drugs, chemicals, foods, etc relevant to human health. Used in comparative genomics with human that provides a way of ascertaining which sequences are functionally important. (8) Humans (Homo sapiens) Role: Growing human cells in culture, this can be manipulated in all sorts of experiments. DNA cloning - isolation segments of human DNA and propagate them inside E. coli cells.

Progression in genetics studies of humans: Bacteria >> Yeast >> Worms >> Mammals (mouse) >> Apes >> Humans

3 General Areas of Genetics and Areas Covered

(1) Classical Genetics a) Mendels principles b) Meiosis and mitosis c) Sex determination d) Sex linkage e) Chromosomal mapping f) Cytogenetics (chromosomal changes) (2) Molecular Genetics a) Structure of DNA b) Chemistry of DNA c) Flow of Genetic Information: Transcription d) Flow of Genetic Information: Translation e) Control of gene expression f) DNA mutation and repair g) Extrachromosomal inheritance: DNA which is not parts of chromosomes E.g. Prokaryotes: Plasmid DNA; Eukaryotes: Mitochondrial DNA (3) Evolutionary Genetics a) Quantitative genetics b) Hardy-Weinberg equilibrium c) Assumptions of equilibrium d) Evolution e) Speciation

Properties and Functions of Genetic Material

(1) Must carry information (genetic information) for the cell to function: Genes have genetic information with codes that code for proteins. (2) Allow control and regulation of protein production: Control of gene expression whether to switch genes on/off. Regulates amount of protein products to be produced. (3) Allow faithful copying of genetic information (replication) during the cell growth: increase in cell number achieved by mitosis due to the replication of genetic information. (4) Allow slight changes (mutability) over many generations to account for evolution: slight changes that are beneficial over many generations result to evolution.

DNA (Deoxyribonucleic Acid)

A. DISCOVERY Year 1868 1910 1950 1952 1953 Discovery Johann Friedrich Miescher first studied and discovered DNA; found nuclein with large amount of nitrogen and phosphorous Phoebus Levene showed DNA contained 4 different nitrogenous bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C) with sugars and phosphate. Erwin Chargaff studied the percentage of nitrogenous bases present in DNA: %A = %T and %G=%C Rosalind Franklin and Maurice Wilkins proved DNA has helix shape by X-Ray crystallography James Watson and Francis Crick presented the DNA model

B. REPRESENTATION Shown as line with specific length E.g. 500 nucleotides in length Length may be in bases (b; kb; mb etc) or base-pairs (bp; kbp; mbp etc) Sequence of nucleotides often shown as letters representing each base sequence E.g. 5 --- TACCACGTGGACTGA --- 3
C. (1) (2) STRUCTURE DNA composed of repeating subunits called nucleotides Each nucleotide is composed of: (a) a phosphate group (b) a five-carbon deoxyribose sugar or pentose (c) a cyclic nitrogenous base 2 Types of nitrogenous bases: (a) Pyrimidines Contain single ring structure Includes Thymine (T) and Cytosine (C) (b) Purines Contain double ring structure Includes Guanine (G) and Adenine (A) Nucleotides joined together in long chain forming polynucleotide by Nucleotide Polymerisation

(3)

(4)

Formation of Polynucleotide: (1) Formation of Nucleoside :: 1st Carbon atom of pentose sugar is joined to the Nitrogen atom of nitrogenous base through the N-glycosidic bond (2) Formation of Nucleotide :: Nucleoside joined to a phosphate group at 5th carbon atom of pentose sugar (3) Nucleotide Polymerisation :: Nucleotides join by condensation reaction resulting to the loss of H2O :: Covalent link between 3 hydroxyl (OH) group and 5 phosphate of adjacent nucleotides forms phosphodiester bond
(5) (6) DNA consists of two strands which are complimentary. In pairing, pyrimidine in one chain is always paired with purine in the other chain. Two DNA strands held together by hydrogen bonds between each base of one strand and an associated base on other strand.

AT

CG

(7) (8) (9) (10)

(11) (12)

(13)

As individual hydrogen bonds are weak and easily broken, it eases separation of DNA strands during various activities. However, strengths of hydrogen bonds are additive, and the large numbers of hydrogen bonds holding the strands together make the double helix a stable structure. Two chains spiral form a pair of right-handed helices. Two chains comprising one double helix run in opposite direction; antiparallel. Thus, if one strand is aligned in 53 direction, complementary strand must be aligned in 35 direction. Sugar phosphate backbones are located outside the DNA molecule with 2 sets of bases projecting toward the center. Phosphate group give the molecule large negative charge. Bases occupy planes that are approximately perpendicular to long axis of the molecule and are therefore, stacked one of top of another like a pile of plates. Hydrophobic interactions and van der Waals forces between the stacked, planar bases provide stability for the entire DNA molecule. Distance from phosphorus atom of backbone to center of axis is 1nm. Thus, width of the double helix is 2nm. The spaces between adjacent turns of the helix form 2 grooves with different width: (a) Major groove a wider groove (b) Minor groove a more narrow groove The double helix makes one complete turn every 10 residues measured 3.4nm.

RNA (Ribonucleic Acid)

A. STRUCTURE (1) RNA composed of repeating subunits called nucleotides (2) Each nucleotide is composed of: (a) a phosphate group (b) a five-carbon deoxyribose sugar or pentose (c) a cyclic nitrogenous base (3) 2 Types f bases: (a) Pyrimidines - Contain single ring structure - Includes Uracil (U) and Cytosine (C) (b) Purines - Contain double ring structure - Includes Guanine (G) and Adenine (A) (4) Single stranded genetic material B. DIFFERENCES BETWEEN RNA & DNA Sugar DNA Deoxyribose sugar RNA Ribose sugar

Bases

Adenine, Thymine, Guanine, Cytosine Structure Single stranded polynucleotide; folds to form loops

Adenine, Uracil, Guanine, Thymine Double helix made of 2 antiparallel polynucleotide chains

C. TYPES OF RNA
(1) Messenger RNA (mRNA) - Carries information necessary for protein synthesis from the DNA to the ribosomes. (2) Transfer RNA (tRNA) - Small RNA molecules that function as adaptors between amino acids and the codons in mRNA during translation. (3) Ribosomal RNA (rRNA) - Structural and catalytic components of the ribosomes, the intricate machines that translate nucleotide sequences of polypeptides. D. TYPICAL RNA SIZES Type Sedimentation Coeff. Length Prokaryote Eukaryote Prokaryote Eukaryote 5S 5S 120 b 5.8 S 16 S 1540 b 18 S 23 S 2800 b 28 S 90 b 0.1 kb Remark Eukaryotes rRNA has more coefficient of sedimentation than of prokaryotes. Eukaryotes tRNA is slightly bigger than of prokaryotes. Eukaryotes mRNA is more varied than of prokaryotes.

rRNA

tRNA

mRNA

500b-6000b 0.5kb-17kb

S: Svedberg unit Length of mRNA varies because it carries code for different types of proteins. As proteins complexity varies, length of mRNA varies. The more complex proteins have longer mRNA.

E. CODING OF INFORMATION (1) DNA STRAND: 3 --- TACCACGTGGACTGA --- 5 (Template; anti-sense; non-sense; non-coding strand) 5 --- ATGGTGCACCTGACT --- 3 (Complementary; sense; coding strand) (2) mRNA STRAND: usually runs from 5 to 3 direction 5 --- AUGGUGCACCUGACU --- 3 (3) PROTEIN: first amino acid has NH2 while last amino acid has CO2H NH2 Met Val His Leu Thr ----- CO2H Central Dogma: DNA RNA Protein (1) Flow of information can only go in one direction (2) Does not work in viruses because some viruses are RNA. Therefore, only applied to prokaryotes and eukaryotes. *Central Dogma of Viruses: RNA DNA Protein