Introduction, evolution and genomes Flashcards
Who presented the 1909 tetranucleotide theory?
Phoebus Levene
What did Phoebus Levene show in 1930?
showed that each building block of DNA is a nucleotide
Which carbon is deoxygenated on deoxyribose?
C 2 prime
Purine bases?
Adenine and Guanine
Pyrimidine bases?
Thymine and Cytosine
What is a nucleoside?
Base and the sugar
Where is the glycosidic bond in a purine nucleoside?
C-1’ and N9
Where is the glycosidic bond in pyrimidine nucleoside?
C-1’ and N1
Nucleoside + Phosphate group?
Nucleotide
Where are the ester links found in a nucleotide?
sugar C-5’ and phosphate
Why is C-5’ phosphorylated in a nucleotide?
Provides the genetic information with directionality so it can be read
How to name a nucleotide?
2’ -deoxy(base)- 5’(mono/di/tri)phosphate
e.g. 2’ -deoxyadenosine-5’ triphosphate (dATP)
What does the phosphodiester bond link?
Links 3’C of one nucleotide to 5’C of next nucleotide
Why is it important for the phosphodiester bonds to link 3’C and 5’C?
For the DNA molecule to have polarity and directionality
What is found at the 5’ end of the DNA chain?
Phosphate group
What is found at the 3’ end of the DNA chain?
Hydroxyl group
What is included in the phosphodiester bond?
Phosphate group and 2 ester links joining the 5’C and 3’C on the sugars
In which direction is DNA made?
from 5’ to 3’ end
What was the tetranucleotide model? (1930)
4 nucleotides in a ring with the bases pointing outwards
Conclusion of the tetranucleotide model?
DNA was simple and repetitive and could not be genetic material
Levene’s nucleotide ratio prediction?
T = A = G = C (25% each)
What is the basis of Chargaff’s rules?
T = A and G = C
Who discovered x-ray crystallography?
Linus Pauling - discovered protein alpha helix in 1951
How does X-ray crystallography work?
X-ray shot at crystallised molecules, rays are diffracted and reflected in photographic film - reflections form patterns and we can use trig to identify the distance between the crystallised molecules + the molecule
What is a single slit diffraction pattern?
When is wider within opaque board, multiple waves of propagated light, causing more patterns to appear on the film
ONLY ONE SLIT
What do 2 slits in the opaque board do with the reflection pattern on the film?
Diffraction patterns interfere - resulting in a complex double slit interference pattern (multiple blobs)
What does diffraction grating do? (Using a grid with more slits)
Produces a sharper image, reducing the intermediate peaks - easier to calculate how far apart the slits are (if light wavelength is known)
Why do reflections from a helix form a cross?
Helix similar to using an angled grid, which produces a crossed image.
When was photo 51 produced?
1952 by Rosalind Franklin
What did photo 51 show?
A cross was produced - meaning that DNA must be helical (helical objects produce crosses by diffraction)
Features of B-DNA?
Right-handed helix, most structurally stable form physiologically
Features of A-DNA?
right-handed helix, only in low hydration conditions, no physiological equivalent
Features of Z-DNA?
left-handed, found physiologically, stretches of alternating pyrimidines and purines
Why was Linus Pauling’s model rejected?
Bases pointed outwards and phosphate groups faced inwards. Phosphates would repel each other = destabilise molecule
Key ideas of Watson and Crick model?
Specific pyrimidine + purine pairing (A/T and G/C), antiparallel strands - all clicked together
6 features of Watson and Crick model?
Right-handed double helix, antiparallel nucleotide chains (one reads 5’-3’, other 3’-5’), Sugar-phosphate backbone + bases face inwards, C+G and A+T form weak hydrogen bonds, B-DNA 10.5 base pairs per turn each turn 3.6nm and base pairs 0.34nm apart, contain major and minor grooves
Why does DNA have major and minor grooves?
sequence-specific DNA-binding proteins interact with major grooves (backbones get in the way of the space in minor grooves) - don’t interact with minor grooves
1902 Archibald Garrod proposal?
An inheritable factor for a metabolic step was DEFECTIVE (caused heritable diseases e.g. albinism, where gene controlling production of pigment was defective)
what was the 1941 Beadle and Tatum experiment?
generating mutants of neurospora crassa with different altered steps in biochemical pathway to work out how to produce defects in metabolic pathway
What is the life cycle of Neurospora crassa?
haploid ascus spores from 2 different matting types (e.g. A and a) germinate and form 2 diff haploid vegetative mycelia. they asexually regenerate more haploid mycelium as conidiospores regerminate.
2 vegetative mycelia of 2 different mating types (a and A) fuse to form a binucleate heterokaryon, a + A nuclei fuse in pairs forming a diploid phase, meiosis + mitosis forming 8 ascus spores.
Features of neurospora crassa cell?
Haploid, but multinucleate
Key features of vegetative mycelia?
they are haploid but MULTINUCLEATE, can constantly asexually regenerate from condiospores
What else can vegetative mycelia do?
haploid cells of opposite mating types can fuse together and form binucleate heterokaryote. Nuclei fuse, meiosis and mitosis to produce 8 asci spores
What is an auxotroph?
A mutant which requires a particular additional nutrient to grow and reproduce
What is a prototroph?
normal strain which doesn’t require any additional nutritional supplement
Step 1 of Beadle and Tatum’s 1941 neurospora experiment.
Created arginine auxotrophs of Neurospora crassa (mating type a, arg- allele) and mated with mating type A, agr+ (protoroph). Their nuclei fused, meiosis and mitosis 8 offspring. Created rare ascus spore with mutants in arginine biosynthesis.
Step 2 of Beadle and Tatum’s experiment
1) Dissect individual neurospora ascospores
2) Transfer to culture tube containing complete medium (medium including all nutrient for growth)
3) Grow colonies of asci
4) Discard tubes with no growth (faulty)
ALL TUBES WITH ASCI WILL HAVE GROWTH AS MEDIUM RICH WITH NUTRIENTS
Step 3 of Beadle and Tatum’s experiment
Surivours transferred onto minimal medium. Asci with mutated arg- allele will fail to grow - shows need for additional nutritional requirement (auxotroph). arg+ will grow (prototroph)
Step 4 of Beadle and Tatum’s experiment
Identifying the nutritional requirement needed for the mutated asci to grow- tubes with minimal + aa, minimal, minimal + vit, complete. Growth on minimal + aa showed that amino acids were required for growth of auxotrophs.
Step 5 of Beadle and Tatum’s experiment
Adding 20 aa to tubes to identify the nutritional requirement required by the auxtroph - growth on arginine proved that it was the nutritional requirement for growth
What is complementation?
Heterokaryons contain nuclei which have 2 different mutations but lead to the same product. (e.g. one mutation has a defect in step 1, so cant produce intermediate, second mutation can’t produce product from intermediate
2 diff mutations affect 2 diff steps - but work together to reform the biosynthetic pathway from reactant to product
Why is the discovery of complementation important?
Shows that there is a gene controlling each step in defective metabolism - Garrod was correct
Importance of complementation?
Can generate a whole biosynthetic pathway from partial pathways as long as they’re in the same cell
Complementation and Beadle + Tatum’s results
They had isolated 3 classes of mutants which were defective in arginine biosynthesis (3 diff arg auxotrophs) where different genes present controlled whether arginine could be produced from precursors and if growth occurred.
1869 Miescher’s discovery?
substance he called ‘nuclein’ rich in phosphorous and no sulphur - was convinced it was a different protein.
proposed that nuclein was basis of heredity
What did Griffith discover in 1928?
Demonstrated bacterial transformation - bacteria changes its function via a transforming principle.
Summary of Griffith experiment
R pneumonia cells = non-pathogenic
S cells = pathogenic
injection of dead S cells and living R cells into mice killed them, showing that dead S cells -> R cells -> living S cells, killing mice
1944 Avery et al. experiment summary
Living S cells killed by heat, soluble S cell extract added to living R cell extract. added protease, RNase and DNase as enzyme treatment.
protease + RNase tubes had both R and S cells - showed that there was transformation
DNase tube had R cells only = NO TRANSFORMATION, TRANSFORMATION FACTOR DESTROYED, DNA = TRANSFORMATION PRINCIPLE
Effects of Avery et al. experiment?
No one believed them - everyone thought protein was hereditary material
T2 bacteriophage content (1942-1952 knowledge)?
50% protein 50% DNA - role they played in infection unknown
T2 infects E coli. , after infection heads form ghosts
How was phage labelled in 1952 Hershey Chase experiment?
PROTEIN: Phage grown in medium with radioactive 35S - labelling phage proteins, DNA: phage grown in medium with radioactive 32P - labelling phage DNA
Results of 1952 Hershey Chase experiment?
E Coli infected with both radioactive sulphur and phosphorous labelled phages. After infection, ghosts and unabsorbed phages discarded. Once lysis of e coli., 2nd gen virons released still radioactively labelled with P, meaning that DNA must be genetic material - 2nd gen of S labelled phages weren’t labelled.
When was the first draft of the human genome sequenced?
2003
Who produced the first complete genome sequence?
J. Craig Venter 1995 - of Haemophilus influenza
What were the goals of the human genome project?
identify all genes in human DNA, determine sequences of DNA base pairs making up the genome, store information in databases to compare with other organisms (evolutionary)
How many protein-coding genes do humans have?
1.5% of our genome is protein coding
How big is the haploid human genome?
3.2 x 10^9 base pairs
What are the benefits of the human genome project?
- To understand our evolutionary history - find sustained similarities. e.g. human and chimp genes compared to identify genes that contribute to unique human traits.
- Personalised medicine - if you have genetic information of patients you can predict which specific people will benefit from a drug
Benefits of improved genetic screening?
Identify the function of our genes (and variant forms in individuals) which can make medicine predictive, preventative and personalised
When was the genomic test for breast cancer risk made available?
2019
Ethical problems associated with the human genome project
Employer refusing to hire people based on genetic disorders
Insurance refusal to some people
Who came up with the Central Dogma of Molecular Biology?
Francis Crick, 1958
What did Crick’s dogma of molecular biology entail?
-DNA makes RNA makes protein
-Recognised DNA replication during cell division and RNA replication
-proposed route from RNA to DNA (retroviruses)
-states that once DNA got into a protein it can’t get out again
What is the modern interpretation of the Central Dogma of Molecular Biology?
1) DNA can be replicated in cell division
2) DNA info can be transcripted into RNA
3) RNA can be translated into protein
4) RNA can be replicated (RNA viruses)
5) RNA can be copied into DNA (reverse transcription in retroviruses)
What was Mendel’s First Law of Inheritance?
the Law of Segregation - if alleles for each trait from parents are identical - individual homozygous, if not, heterozygous
Why did Mendel work with peas?
Produce large numbers of offspring
Short generation time
Self-fertilisation and cross-fertilisation possible
Simple tools needed
Mendel’s ratio observations?
3:1
What did Morgan suggest in 1910?
Genes for certain traits can be carried on sex chromosomes - sex linked genes, where females have to receive two copies of each X-linked gene to express phenotype(XX)
Who redefined evolution and when?
1973, Theodosius
What was the redefined evolution meaning?
A change in allele frequency within a gene pool
What were Darwin’s postulates?
1) variation exists within a species
2) some of this variation is heritable
3) reproduction is not random - more reproduction = more favourable variation
How was variation within a species proved?
1976 Rosemary and Peter Grant measured beaks of offspring from breeding birds with differently sized beaks. Results showed that there was a range of beak size - normal distribution curve
Variation is heritable - proof?
both parents small beak = offspring small beak.
large genetic component to determination of beak depth
strong correlation between parent + offspring beak size
Reproduction isn’t random - proof?
Drought caused seeds to become larger, harder. Offspring after drought had a higher proportion of larger beaks.
selection for birds with larger beaks - selection drives evolution
Conclusion of proving Darwin’s postulates?
Populations can adapt to the environment genetically - microevolution by natural selection is a fact
What is genetic drift?
Any deviation from expected levels of reproduction due to sampling error
Changes in allele frequency due to chance events
What is fixation?
Proportion of allele relative to another rises to 100%
What effect do mutations have on species?
They can increase or decrease fitness, but mostly have little effect
Cannot be acted on by natural selection
Change allele frequency - evolution absence of selection
How does genetic drift lead to fixation?
Due to chance events, proportion of DOMINANT advantageous allele rises very quickly, fixation - removing disadvantageous alleles
recessive advantageous allele slow natural selection action, but after some time it rises and fixation
Experiment to prove mutations change in populations by genetic drift?
Richard Lenski 1988 - 2 strains of E coli, 35 year long experiment.
Findings: One flask became able to use Citrate as C source for aerobic resp. = selective advantage to grow faster. E Coli. normally only use citrate anaerobically - speciation?
Constant dilution = strain lost Cit + gene
What is gene flow?
Movement of alleles between previously separate populations by:
-migration of alleles + mating
-movement of gametes (pollen) + fertilisation
What are 3 microevolution mechanisms?
Genetic drift, Gene flow, Selection + reproduction isolation
All lead to speciation
What is a species?
Population of organisms which are able to interbreed, giving fertile offspring
