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LF104 - Molecules, Cells and organisms > Lectures 1-10 > Flashcards

Lectures 1-10 Flashcards

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Organic Chemistry 101 flashcards
1
Q

What type of organisms are prokaryotes?

A

Bacteria

Archaea

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2
Q

What type of organisms are eukaryotic?

A

Fungus

Animal

Plants

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3
Q

What causes sickle cell anemia?

A

Mutant haemoglobin

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4
Q

What causes the swiss cheese phenotype and what is the result of this?

A

A mutant phospholipase

Causes brain cells to commit suicide

Adult brain is full of holes

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5
Q

What causes obesity, as tested in mice and why does this occur?

A

Hormone leptin is missing

Causes loss of a cell signalling pathway

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6
Q

What are sugars and what is their function in cells and organisms?

A

Polysaccharides

Energy source, making nucleotides and forming polysaccharides

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7
Q

What is the molecular formula for monosaccarides?

A

(CH2O)n

where n = 3 or more

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8
Q

What cause the differences between alpha and beta glucose?

A

Differ due to mutation

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9
Q

What form do a- and B- glucose chains interchange by?

A

Linear form

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10
Q

What is glycogen?

A

Multibranched a-glucose

Polysaccharide

Energy storage in animals, fungi, bacteria (universal)

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11
Q

What is cellulose?

A

B-glucose molecules linked to form fibres

Give structured cell walls in plants

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12
Q

What is B-glucose polymerised into?

A

Long linear chain

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13
Q

What is the function of fatty acids in the cell and organism?

A

Energy - fatty acids

Structure - membranes

Action (catalysis, communication)

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14
Q

What is a lipid?

A

Water insoluble molecule that is soluble in organic solvents

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15
Q

What is the structure of a fatty acid?

A

Carboxylic acid group one end

Methyl group the other end

Long aliphatic chain (saturated or unsaturated)

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16
Q

What is the difference in the appearance and structure of a saturated and unsaturated fatty acid?

A

Saturated: no double carbon bond - straight

Unsaturated: double carbon bond - kinked

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17
Q

What are 2 examples of steroid hormones?

A

Oestrogen: prepares for ovulation, falling levels triggers ovulation

Progesterone: thickens mucus wall

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18
Q

How many common amino acids are there?

A

20

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19
Q

What is the standard structure of an amino acid?

A

Central alpha carbon
Basic amino group (NH2)
Acidic carboxylic group (COOH)
Hydrogen
Side chain - R group

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20
Q

What is the common charge of an amino acid when in the correct pH?

A

Positively charged

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21
Q

Why is valine insoluble?

A

The side chain on the amino acid has no solubility

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22
Q

What is another phrase for hydrophilic and hydrophobic?

A

Hydrophilic: water-loving

Hydrophobic: water-fearing

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23
Q

What is polarity when referring to macromolecules?

A

A sense of direction

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24
Q

What is the polarity in proteins?

A

Read from amino to carboxyl

N terminus to C terminus

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25
Q

What are chaperones when associated with proteins?

A

Making sure other proteins can fold properly, action molecules

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26
Q

What are the functions of nucleotides in cells and organisms?

A

Action and storing genetic information

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27
Q

What is the polarity in nucleotides?

A

ready from 5’ to 3’

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28
Q

What are the 3 main domains of life?

A

Bacteria

Archaea

Eukaryotes

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29
Q

When was there estimated to be a common evolutionary ancestor between all organisms?

A

3.5-3.8 billion years ago

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30
Q

What is phylogeny?

A

Relationship between organisms

Visual representation of the evolutionary history of populations, genes or species

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31
Q

What are the 3 types of evidence to construct phylogeny?

A

Morphology

Molecular evidence

Fossils

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32
Q

What are homoplastic traits?

A

Traits that are similar for reasons other than inheritance from a common ancestor

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33
Q

What are synapomorphies?

A

Derived form of a trait shared by a group of related species

Shared derived characteristics

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34
Q

How is molecular evidence used to construct a phylogeny tree?

A

Take DNA of modern animals and compare to others to see how similar it is to another animal

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35
Q

Who classified the diversity of life and when did they do it?

A

Linnaeus

1700s

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36
Q

What are the tips in a phylogenetic tree?

A

The terminal ends of an evolutionary tree

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37
Q

What are nodes?

A

Points in a phylogeny where a lineage splits

Branching point

Represents where populations became genetically isolated

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38
Q

What are clades?

A

Single branches - an organism and all its decedents

All organisms that share a common ancestor

Set of hierarchically nested groups

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39
Q

What is morphology and how is it shown in a phylogenetic tree?

A

Study of size, shape and structure of organisms

Each own characteristic shows a separate trait

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40
Q

What are characters in the study of evolution?

A

Heritable aspects that can be compared

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41
Q

What are taxa in the study of evolution?

A

Group of organisms that form a cohesive taxonomic unit

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42
Q

What is homology?

A

Similarity of traits in different species resulting from their inheritance from a common ancestor

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43
Q

What is the first principle of phylogenetic inference?

Assumes similar features are…

A

homologous until shown otherwise

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44
Q

What is the second principle of phylogenetic inference?

Doesn’t use shared ancestral features but..

A

uses shared derived features

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45
Q

What are autapomorphies?

A

Unique morphological features

Do not provide useful grouping information

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46
Q

Why might microorganisms share genes?

A

Due to horizontal gene transfer

Where genetic material other than other than from parents to offspring is transferred to another organism

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47
Q

When was Darwin’s theory of evolution?

A

1859

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48
Q

What can phylogeny be used for?

A

Used to identify source of viruses

Date of disease onset

Track viral evolution

Identify modes of potential transmission

Organize knowledge of diversity

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49
Q

How do you know if organisms are more closely related in a phylogenetic tree?

A

Taxa that diverged from each other more recently

Have more character states in common

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50
Q

How can timing be estimated within phylogeny?

A

Combing phylogenetic morphological evidence with fossils

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51
Q

What are branches?

A

Lineages evolving connecting other branching events

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52
Q

What are internal nodes?

A

Occur within phylogeny, represent ancestral populations or species

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53
Q

What is a cladogram?

A

When phylogenetic tree shows only relationship among species

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54
Q

What does monophyletic mean in phylogeny?

A

Group of organisms that form a clade

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55
Q

What does polyphyletic mean in phylogeny?

A

Taxon that doesn’t include common ancestor of all members of the taxon

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56
Q

What does paraphyletic mean in phylogeny?

A

Group of organisms that share a common ancestor although the group doesn’t include all the decedent of that common ancestor

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57
Q

What is an outgroup?

A

Group of organisms outside of monophyletic group

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58
Q

What is homoplasy?

A

Character state similar not due to shared descent

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59
Q

What is convergent evolution?

A

Independent origin of similar traits in separate evolutionary lineages

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60
Q

What is evolutionary reversal?

A

Describes reversion of a derived character state to form resembling its ancestral state

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61
Q

What is parsimony?

A

Selection of alternative hypothesis

Require fewest assumptions or steps

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62
Q

What is polytomy?

A

Internal node of phylogeny with more than 2 branches

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63
Q

What is a consensus tree?

A

Combining hypotheses

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64
Q

What is exaptation?

A

Trait that initially carries out one function and its later co-opted for a new function, original function may be lost

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65
Q

What does LUCA stand for?

A

Last universal common ancestor

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66
Q

What are the 3 major divisions or domains of life?

A

Bacteria
Archaea
Eukaryotes

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67
Q

When was the last LUCA?

A

3.5-3.8 billion years ago

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68
Q

How are the 3 major divisions or domains of life identified?

A

Based on comparison of ribosomal RNA

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69
Q

Who established the 3 domains of life and when?

A

Carl Woese and George Fox

1977

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70
Q

Who revised the ‘web of life’ and when?

A

W Ford Doolittle

2000

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71
Q

How did W. Doolittle revise the ‘web of life’?

A

Domains of life are based on horizontal gene transfer

Through the sharing of genes

A community rather than a single origin

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72
Q

In what ways are eukaryotes similar to archaea?

A
  1. Proteins involved in cytokinesis
  2. Cell shape determination
  3. Protein recycling
  4. Membrane remodelling (cellular compartmentalisation)
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73
Q

What was previously understood about similarities between archaea and eukaryotes?

A

Features used to be unique to eukaryotes ONLY

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74
Q

What is the most modern view of the ‘tree of life’?

A

Hug et al

2016

Based upon the sequences of 16 ribosomal proteins, extensive mapping

Eukaryotes are group that has arisen from archaea

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75
Q

When was Einstein’s Theory of General relativity?

A

1915

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76
Q

What is the general relativity theory?

A

Gives the simplest description of cosmology that is consistent with all known experimental and observational data

Consistent across all known data

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77
Q

Why is Einstein’s work under scrutinity?

A

Echoes of gravitational waves when black holes fuse

Suggests there is a structure to the event horizon of a black hole

(Einstein suggest nothing should be found there)

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78
Q

What is the movement of information to understanding science starting with Mythos and then Logos?

A

Mythos: stories of gods and heros
Logos: dominated by rational thinking
- lack of evidence for claims

  1. Science is performed in a naturalistic framework
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79
Q

What are the fundamental principles of science?

A
  1. Science is performed in a naturalistic framework
  2. Experimental/ observational support is required
  3. Proceed with the simplest explanation consistent with all the data
  4. Inductive reasoning allows you to draw conclusions
  5. Compile and disseminate your knowledge
  6. Accept uncertainty
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80
Q

Who stated that a hypothesis must be supported by experiments based on evidence?

A

Alhazan

c965-c1040

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81
Q

What is Occam’s razor?

A

Take the simplest possible view that aligns with data

Supported by Einstein - make simple but no simpler

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82
Q

What is the principle of Parsimony?

A

Theories should explain and predict with the fewest assumptions

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83
Q

What percentage of papers are rejected?

A

80%

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84
Q

What must happen before work is published?

A

Scientists describe their approaches, observation and conclusions in sufficient detail allowing others to extend or repeat them

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85
Q

What must happen before work is published?

A
  1. Scientists describe their approaches, observation and conclusions in sufficient detail allowing others to extend or repeat them
  2. Papers are submitted to journal
  3. Papers returned for improvement
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86
Q

What is the idea of falsification with science?

A

Science is a set of ideas about how the universe works

Science has an in-built self correcting mechanisms

We can never be certain that new data will not change out ideas - all science is theory

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87
Q

What is evolution?

A

The genetic content of a population changes over time

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88
Q

What is microevolution?

A

Changes in allele frequencies in a population of a species over time

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89
Q

What are the 3 main mechanisms of microevolution?

A

Natural selection

Genetic drift

Gene flow

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90
Q

What is macroevolution?

A

Changes at or above the level of the species

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91
Q

What was the second voyage of HMS Beagle?

A

5 year journey but 3 years on land

Darwin - Galapagos Islands

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92
Q

What ideas influenced Darwin?

A

Economic population (population growth and food supply)

Naturalistic framework

Observations and prior knowledge

Combination of all factors contributes to natural selection

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93
Q

Who tested Darwin’s postulates hypothesis?

A

Rosemary and Peter Grant

1976-1978

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94
Q

How did Rosemary and Peter Grant test Darwin’s first
and second postulate?

A

Off coast of Ecuador in the Galapagos islands

Finches show variation in beak length so all captured and measured

Variation to support: parents with small beaks have offspring with shallow beaks, parents with deep beaks tend to have offspring with deep beaks

Large genetic component - heritable component with beak length

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95
Q

How does Rosemary and Peter Grant’s experiment support Darwin’s third postulate about reproduction not being random?

A

Individuals that reproduce the most are those with the most favourable variations

Beak depth increased, deeper beaks can cracker harder seeds which is advantageous

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96
Q

How does Rosemary and Peter Grant’s experiment support Darwin’s second postulate about some variation being heritable?

A

Variation to support

Parents with small beaks have offspring with shallow beaks, parents with deep beaks tend to have offspring with deep beaks

Large genetic component to determine beak length

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97
Q

How does Rosemary and Peter Grant’s support Darwin’s first postulate about variety within species?

A

Medium ground finches showed variation in beak depth

98
Q

How has genetic variation been shown in the Chernobyl nuclear disaster with frogs?

A

Melanin protects against ionising radiation

Brighter frogs in background radiation areas
Darker frogs in high radiation conditions

99
Q

What is the conclusion about Darwin hypothesis and microevolution?

A

Populations adapt genetically to the environment

Microevolution by natural selection is a theory

100
Q

What is genetic drift?

A

Changes in allele frequencies in a population

101
Q

What percentage of genes are protein coding genes?

A

1.5%

102
Q

Why are mutations not always acted upon?

A

As many are not in coding genes

(only 1.5% of protein coding genes in the genome)

Mutations from natural selection not acted upon

103
Q

What are overall trends in natural selection and allele fixation?

A

Dominant: rapid rise as seen in both heterozygote and homozygote

Recessive: slower rise - only visible in homozygotes so fixation takes longer

104
Q

How can genetic drift occur by sampling error?

A

Not every sperm contributes to next generation

Massive attrition occurs due to death

Sampling error is causing evolution to happen rapidly

105
Q

How did Richard Lenski measure long term evolution?

A

E. Coli grown in medium with glucose and citric acid for carbon source

Sub-cultured every day for 30 years, every 75 days samples taken and frozen as fossil records

3 flasks developed mutations and some cells affected DNA repair mechanisms causing mutant streams

106
Q

How did citrate used in aerobic conditions evolve in Lenski long term experiment?

A

Citric receptor only expressed in anaerobic conditions

In aerobic conditions transporter is not expressed so E.Coli cannot utilise external citrate as an energy source

Gene is duplicated by mutation causing strains being able to utilise citrate as well as glucose as energy sources

107
Q

What is gene flow?

A

The movement of alleles between previously separate populations

108
Q

How can alleles move by gene flow?

A

Migration of adults and subsequent mating

Movement of gametes and subsequent fertilisation

Alleles migrating from one area to another and finding mating success

109
Q

What are the 3 main mechanisms to gene flow?

A
  1. Genetic drift removes genetic variation within demes - causes differentiation between demes
  2. Gene flow introduces new alleles into demes within a metapopulation - can cause genetic homogeneity between demes
  3. Selection and reproductive isolation
110
Q

What is a deme?

A

A sub-population

111
Q

What is a meta-population?

A

Overall population

112
Q

What is a species (at eukaryotic level)?

A

A population of organisms that can potentially or actually interbreed, giving viable fertile offspring

113
Q

How is each species defined?

A

Defined on looks and how they act

Not breeding behaviour

114
Q

What is the argument about tree frogs and chromosomal duplication with species?

A

Instant speciation occurred when a treefrog failed to sort its 24 chromosomes during meiosis, generating a new species

Identical in size, shape and colour to original but has 48 chromosomes and a different mating call

Gene exchange has occurred

115
Q

What is the example of the tube mosquito with species differentiation?

A

Mosquitos adapted to having mice as host

Originally eggs lay in open spaces, multiple genetic changes to host on mammals

Londoners hid in tubes during blitz and caused the plague

116
Q

How is the ‘Big Bird Lineage’ an example of macroevolution?

A

Immigrant bird found female partner

2 of the hybrid offspring mated together to produce fertile offspring

117
Q

Who produced the first complete genome sequence of any organism?

A

J. Craig Venter

118
Q

How many base pairs were sequenced by J. Craig Venter?

A

1.8 million

119
Q

When was the full human genome sequenced?

A

2003

120
Q

When was all human genome set to be sequenced by?

A

Between 2008-2015

1,000 genomes project - describe all human genetic variation

121
Q

When could gene mapping be done with detecting the likelihood to diseases?

A

2012-2018

122
Q

On what date was the first draft of the complete genome sequence reported?

A

14th April 2003

123
Q

What are the goals of the human genome project?

A
  1. Identify all genes
  2. Determine sequences
  3. Store information
  4. Improve tools for analysis
  5. Transfer related technologies
  6. Address ethical, legal, social issues
124
Q

When identifying genes how many were expected and how many were found?

A

100,000 genes expected

20,000 found found

Only 1.5% of our genome is protein coding

125
Q

How big is the haploid human genome?

A

3,2000,000,000 bp

(3.2 x 10^9)

126
Q

What is a chromosome fusion event?

A

2 chimp chromosomes fused in man

127
Q

What are the benefits to human genome project?

A

Understanding our evolutionary history
(Human and chimpanzee genomes can be compared to identify genes that contribute to uniquely human traits)

Personalised medicine
(AI that plans how to treat people based on their genome)

To identify functions of all our genes
(Medicine can become predictive, preventative, personalised)

128
Q

When was there a genomic test for breast cancer risk?

A

2019

129
Q

What are the ethical or legal issues associated with the human genome project?

A

Could be refused employment

Could be denied employment

130
Q

What is the central dogma of molecular biology?

A

Describes the transfer of information from DNA via an RNA intermediate to protein

Information cannot be transferred back from protein or nucleic acid

Recognised DNA replication and RNA replication also transfer information

131
Q

Who published The Central Dogma and when?

A

Francis Crick

1958

132
Q

What are the 5 steps to the Central Dogma of molecular biology?

A
  1. DNA replication
  2. Transcription
  3. Translation
  4. RNA replication
  5. Reverse transcription
133
Q

Who was Gregor Mendel and what was he known for?

A

Demonstrated the inheritance of certain traits follow particular patterns

Referred to the laws of Mendelian inheritance

The Father of Genetics - naturalistic framework

134
Q

Why did Mendel work with peas?

A

They produce large numbers of offspring

They have a relatively short generation time

Both self-fertilisation and cross-fertilisation are possible

Pure-breeding lines with contrasting features were available

135
Q

What was Mendel’s experiment with peas?

A

Monohybrid cross - plants with green peas crossed with those with yellow
Only yellow seeds produced (called a dominant trait)

Yellow offspring (Heterozygous) mixed with pure green
Peas were mixture of green and yellow (1:1 ratio)
Called a recessive trait

136
Q

What was the explanation to Mendel’s first law of inheritance?

A

Each individual has 2 factors for each trait, one from each parent

If the 2 factors are identical, the individual is homozygous for the trait

If the 2 factors have different information, the individual is heterozygous

Alternative forms of a factor are called allelomorphs (alleles)

137
Q

What is the Law of Segregation?

A

2 coexisting alleles of an individual for each trait segregate during gamete formation so that each gamete gets only one of the 2 alleles

Gametes fuse randomly so there is a discrete inheritance of a trait than than a blending

138
Q

When was the chromosome theory of inheritance and who by?

A

1902

Walter Sutton

139
Q

What was the chromosomal theory of inheritance?

A

Sex was determined via chromosome-based inheritance

Proposed Mendel’s factors were carried on chromosomes

140
Q

How was sex-linkage detected?

A

1910, Morgan

Wild-type fruit flies have red eyes but some of his mutant flies has white eyes

Red-eyed females were crossed with white-eyed males = gave all red-eyed offspring

White-eyed females crossed with red-eyed males gave red-eyed females and white-eyed males

Results were influenced by sex of parents - concluded genes for eye colour was carried on the X chromosome

141
Q

What was Garrod’s ‘inborn errors of metabolism’?

A

Each case an inheritable factor for a metabolic step was defective

Albinism: lack of pigment
Alkaptonuria: individuals secrete homogentisic acid into their urine, which goes black following exposure to air

142
Q

Why did Beadle and Tatum use red bread mould in their experiment?

A

Grows rapidly on a very simple medium containing only salts, C and N

143
Q

What was Beadle and Tatum ‘one gene-one enzyme’ experiment?

A

Hereditary diseases are ‘inborn errors of metabolism’ is correct

  1. Mutagenesis: took haploid and illuminate it
  2. Grow all survivors in complete medium
  3. Identify mutants: every survivor transferred to minimal medium, failure to grow identified a potential nutritional requirement
  4. Identify nutritional requirement: growth on minimal medium containing amino acids identifies a requirement for an amino acid
  5. Identify arginine auxotrophs
144
Q

What is a auxotroph?

A

A mutant that requires a particular additional nutrient

145
Q

What is a prototroph?

A

The normal strain which does not require that nutritional supplement

146
Q

What was Beadle and Tatum’s key steps to their experiment in 1941?

A
  1. Illuminate and breed sample
  2. Transfer some of complete to minimal medium
  3. Work out whether it has required amino acids
  4. Test each one for the specific amino acid
147
Q

What did Beadle and Tatum identify when testing the arginine auxotrophs?

A

If the auxotroph came from different asci, they would probably have different mutations

If the auxotroph came from one ascus, they have the same mutation

148
Q

How does complementation work in Beadle and Tatum’s experiment?

A

As the heterokaryons both contain nuclei, each cell can perform combine phenotypes - each defect complements the other

Suggests they isolated 3 classes of mutants defective in arginine biosynthesis

149
Q

What other functions do enzymes perform?

A

Structural and immunological functions

150
Q

Why did the one gene-one enzyme hypothesis change and what did it change to?

A

One gene-one protein

Some proteins are not enzymes but perform other functions (structural, immunological)

Multiple genes for a pathway

151
Q

What did Friedrick Miescher discover in 1869?

A

Found the ‘nuclein’ which contianed C, N and H prtiens but was rich in phosphorus with no detectable sulphur

Proposed that the nuclein might be the basis of heredity

152
Q

Who discovered transformation in 1928?

A

Frederick Griffith

Showed bacterial transformation (bacteria changes its form and function through the action of a transforming principle or transforming factor)

153
Q

What is the Griffith experiment (1928) - first control?

A
  1. Mouse injected with living R cells
  2. Mouse remains healthy
  3. Living R cells can be recovered from mouse heart tissue

= R cells survive in mice, but do not cause pneumonia, R cells are non-pathogenic

154
Q

What is the Griffith experiment (1928) - second control?

A
  1. Mouse injected with living S cells
  2. Mouse contracts pneumonia
  3. Living S cells can be recovered from mouse heart tissue

= S cells survive in mice, and cause pneumonia, S cells are pathogenic

155
Q

What is the Griffith experiment (1928) - third control?

A
  1. Mouse injected with heat-killed S cells
  2. Mouse remains healthy
  3. No living streptococci can be recovered from mouse heart tissue

Only living cells are causing disease

= Dead S cells do not cause pneumonia

156
Q

In the Griffith experiment, what is the experimental arm?

A
  1. Mouse injected with mixture of heat-killed S cells and living R cells
  2. Mouse dies
  3. Both R and S cells can be recovered from mouse heart tissue

= An S cell transforming principle that survives heat treatment has altered some of the R cells

157
Q

Who did work finding the transforming principle and when?

A

Avery, MacLeod and McCarthy

1944

158
Q

What was the Avery, MacLeod and McCathy experiments?

A

Formal evidence that DNA is a transforming factor

  1. Living S cells in a flask and boiled to kill cells
  2. Only soluble extract remains, split into 3 and mixed with protease, RNase or DNase enzyme treatment

Protease: transformation of R cells to S cells - protein is not the hereditary material

RNase: S and R cells = still transformation - cannot be RNase

DNase: no DNA - lost during transformation

= DNase destroys the transforming principle

159
Q

What is another piece of evidence conducted in 1944 with the Avery, MacLeod and McCarthy experiment?

A

Purifying DNA from S cells resulted in transformation of some R cells to S cells

Definitive evidence that DNA is the hereditary material

160
Q

Who was A. Hershey and what did he do?

A

1952: protein is not the hereditary material

1969: gained Nobel prize for discoveries but did not mention Martha Chase (research assistant) in his acceptance speech

161
Q

What is the structure of a T2 phage?

A

DNA - hereditary information, tightly packed

Inside icosahedral head, attached to a core

Surrounded by a sheath

Attached to base plate with tail fibres emerging

162
Q

What is the state of phage research from 1948-1952?

A

Taking E.Coli and infecting with T2 causes attachment mediated by the fibres

Phage particles remain attached to the bacterium, heads appear empty forming ‘ghosts’

Bacterium burst open exposing new viruses

163
Q

What did Martha Chase experiment with the state of phage research in 1952? (Hershey-Chase experiments)

A

Phage protein labelled radioactively
Sulphur: present in proteins, not DNA
Phosphorus: present in large amounts of nucleic acid

Grow bacteria and infect, when burst spin out dead and non-infected cells leaving a suspension of radioactive phage

Next generation are radioactive - confirms DNA is genetic material, only when labelled with phosphorus

164
Q

Who was Phoebus Levene and what theory did he propose? (1909)

A

Tetranucleotide theory

Showed each building block of DNA is a nucleotide:

Phosphate group linked to a deoxyribose sugar, linked to nitrogenous base

165
Q

What sugar is used in DNA and RNA?

A

DNA: pentose (5C) deoxyribose
RNA: pentose (5C) ribose

166
Q

What is the difference in structure between ribose and deoxyribose molecular structure?

A

Hydroxyl group in ribose on 2’

Hydrogen in deoxyribose on 2’

167
Q

What bases are purines?

A

Adenine

Guanine

168
Q

What bases are pyrimidine?

A

Cytosine

Thymine

Uracil

169
Q

What are nucleosides and where/what is the bond?

A

Sugar and base

Glyosidic bond: between C-1’ and N-9 (purine) or N-1 (pyrimidine)

170
Q

What are nucleotides and where/what is the bond?

A

Phosphorylated nucleosides

Ester links: between sugar C-5’ group and the phosphate

171
Q

What forms do nucleotides come in?

A

All come in mono, di and tri phosphate form

172
Q

What kind of molecule is DNA?

A

Polynucleotide with polarity

173
Q

What is the polarity associated with DNA?

A

Phosphodiester bond links the 3’C of one nucleotide to 5’ of the next

Base sequence is written and read 5’ to 3’

Polarity at the 5’ phosphate end –> 3’ hydroxyl end

174
Q

How did Levene ‘tetranucletoide model’ not support Avery et al?

A

Showed how DNA was simple and repetitive and could not be the genetic material

Not believed to be transforming principle

175
Q

Who was Erwin Chargaff and what did he propose?

A

Nucleotides in DNA should be present in equal proportions

(If Levene was correct)

%T = %A = %G = %C

176
Q

How did Chargaff show Levene to be incorrect?

A

Measured concentrations of each of 4 nitrogenous bases in different organisms

Different organisms had different DNA constitutions

Reality: %T = %A and %G = %C

177
Q

What did Linus Pauling say about DNA? (1951)

A

Described the alpha helix

Basic structure present in many proteins

Used X-ray crystallography - so shape must be helical

178
Q

How does an X-ray crystallography indicate the helical structure of DNA?

A

Crystalline target molecule diffracts X-rays

Causes exposed patches on photographic film

Resulting diffraction pattern is unique

179
Q

What did Huygens show with the ‘Wave theory of light’?

A

When light passes through a small opening, a wave front is propagated on the other side, single spot appears on a screen

Wider slit, all points across the slit act as point source - results in single slit diffraction pattern on screen

2 slits causes interference - causes double slit interference pattern on screen

With a diffraction grating the pattern becomes much sharper

180
Q

What did Augustin Fresnel extend the ‘Wave theory of Light’ concept?

A

Showed diffraction occurred around a solid object with the same width as a slit

Replacing slit with object of same size causes the same results

181
Q

What are the spatial relationships with the light theory?

A

Features that are close produce widely separated reflections

Features that are distant produce closely separated reflections

Vertical grids = horizontal spots
Grid = cross

182
Q

What did Maurice Wilkins do?

A

Stretched DNA and air dried it

Allowing for stretching into long fibres and mounting in front of X-ray source

183
Q

What was Maurice Wilkins produce?

A

1950 - Produced X-ray diffraction of dried DNA

High resolution

Without clear model in mind - too difficult to interpret

184
Q

What was Gosling and Franklin B model of DNA?

A

1952 - Used hydrated DNA after 100 h of exposure

Cross is unmistakable - DNA must be helical

185
Q

Who proposed the triple helical model of DNA?

A

Linus Pauling

Triple helix 3-strand model, with bases pointing outwards

(supported by Watson and Crick)

186
Q

What did Watson, Crick and Wilkins propose?

A

Double helix 2-strand model, with the bases pointing inwards

187
Q

What was each turn of the DNA helix measured to be?

A

3.4nm

(Spots far apart give features that are close together)

188
Q

How many bases were there thought to be per turn of the DNA helix?

A

10 bases per turn

(More distant the spots, smaller the actual distance in the target)

189
Q

What was the measured diameter of DNA to be?

A

2nm

Calculated using degrees of rise within the ‘X’

190
Q

Why did Pauling model of DNA fail?

A

(triple helix)

The negative charges of the stacked phosphate groups would repel each other and destabilise the molecule

  • Sugar phosphate backbone must be compressed together
191
Q

How did Watson’s deduction support Chargaff rule?

A

2 purines = too wide for DNA

2 pyrimidines = too narrow for DNA

= A must pair with T
= G must pair with C

192
Q

What was Watson and Crick’s model in 1953?

A

Made DNA with metal scraps, almost 2m tall

Watson: specific A/T and G/C pairing scheme

Crick: idea of antiparallel strands

Everything clicked into place beautifully

193
Q

What are 6 key features of Watson-Crick model?

A
  1. Right-handed (clockwise) double helix
  2. The strands are anti-parallel 5’ –> 3’ and 3’–> 5’
  3. Sugar-phosphate backbones are on the outside of the helix, bases oriented towards the central axis
  4. Complementary base-pairing - bound by weak hydrogen bonds
  5. Base pair distance (10.5 bp per turn, helix turn = 3.6nm
  6. major and minor grooves - backbone not equalling spaced causing grooves
194
Q

How many bonds does A-T have?

A

2 hydrogen bonds

195
Q

What are the other structural variants of DNA?

A

A-DNA: occurs in low hydration conditions (uncertain whether this occurs)

B-DNA: most structurally stable

Z-DNA: taken up physiologically by stretches of alternating pyrimidines and purines

196
Q

Who established the directionality of DNA synthesis?

A

The Okazaki

197
Q

What is the leading and lagging strand?

A

Leading: synthesised continuously - same direction as the replication fork

Lagging: synthesised discontinuously - 5’to4’ synthesis proceeds in the opposite direction

198
Q

What are Okazaki fragments?

A

Small fragments of strand on the lagging strand only

Consequence of synthesis of new DNA in one direction only

Occur away from replication fork

199
Q

Why is there no 3’to5’ synthesis of DNA?

A

One nucleotide removed leaving 5’ phosphate but a triphosphate is required

No high energy bond can be cleaved, no reaction can be processed

High energy bond required for incorporation of nucleotide

200
Q

What is the life cycle of a M13 bacteriaphage?

A

Injection via the pilus

Single stranded DNA is replicated and becomes double stranded

Packed into fresh phage and secreted

201
Q

What did Okazaki and Kornberg discovery with the beginning to DNA replication?

A

DNase cannot completely destroy Okazaki fragments

Primer for an Okazaki fragment is RNA, not DNA

Little pieces of RNA, 10-12 bases long were left

202
Q

How are RNA primers synthesised?

A

DNA primase is a rifampicin-sensitive DNA directed RNA polymerase

Synthesizes an RNA primer to initiate DNA synthesis on lagging strand

RNA polymerases don’t require a primer

203
Q

How is the lagging strand synthesised?

A
  1. New RNA primers are synthesised by DNA primase
  2. DNA Pol III extends RNA primer using dNTPs to make Okazaki fragments on lagging strand
  3. As replication fork separates fork separates more DNA, new primers are laid down by DNA primase
  4. Old primers erased by 5’to3’ exonuclease
  5. Gap sealed with DNA ligase, joining Okazaki fragment to growing chain
204
Q

How is the Okazaki fragment joined by DNA ligase?

A

DNA ligase uses ATP, releasing pyrophosphate and attaching AMP to 5’ phosphate of downstream fragment

AMP released, phosphodiester bond formed between 3’ -OH of upstream Okazaki fragment and 5’ phosphate of downstream fragment

Sealing needs ATP
New bond seal gap

205
Q

What is the clamp holder?

A

Hold 2 molecules of Pol III

Has helicase and DNA primase

206
Q

What is leading strand synthesis?

A
  1. DNA helicase unwinds DNA helix, separating strands
  2. DNA primase synthesises DNA primer on leading strand template
  3. Primed duplex is captured by Pol III
  4. New clamp halves maintain in clamp holder

5.Clamp holder transfers 2 halves of B-clamp to Pol III

  1. Helicase continues to unwinds, and Pol III replicates the leading strand continuously
207
Q

What is processivity?

A

Measure of an enzyme’s ability to catalyse consecutive reactions without releasing substrate

208
Q

What is particular of Pol III?

A

Has low processivity

Can only make short stretches of DNA before it falls off DNA

209
Q

What is the process of lagging strand synthesis?

A
  1. DNA primase produces RNA primer
  2. Primed duplex is clamped by Pol III forming loop
  3. Helicase continues to unwinds, Pol III extends new primer on lagging strand until Okazaki fragment has been pulled back to Pol II
  4. Lagging strand and template are unclamped
  5. DNA primase primes the lagging strand template
  6. DNA Pol I and DNA ligase repair the gap
  7. Process restarts by clamping new lagging strand primer
210
Q

Why does DNA Pol III have to have low processivity?

A

If it was a highly processive enzyme, it could not release the new Okazaki fragment easily

211
Q

Does DNA Pol I have low or high processivity?

A

Low

212
Q

When can stem-loop structures be formed?

A

When DNA is denatured and fails to re-anneal properly

213
Q

What is SSB and what is its importance?

A

Single stranded DNA binding protein

DNA replication required a supporting cast of SSB

It protects the ssDNA from base pairing and from nuclease

Being displaced by Pol III and replaced as the helix is unwound

214
Q

Why is most DNA negatively supercoiled?

A

Easier to replicate

Topoisomerases are used to regulate the degree and type of supercoiling

Arises from unwinding of DNA

215
Q

How is overwound positively supercoiled DNA turned into underwound negatively supercoiled DNA using Type II topoisomerase?

A
  1. Topo II binds to the positive supercoil
  2. Binding and then cutting BOTH strands of DNA
  3. Brings coil forward and re-ligates it causing negative supercoil
216
Q

How is negatively supercoiled DNA relaxed using Type I topoisomerase?

A
  1. Topo I binds to negative supercoil
  2. Cuts one DNA strand
  3. Causes DNA to unwinds and re-ligates it causing relaxed DNA
217
Q

How is bacterial DNA polymerisation bi-directional?

A

2x Pol II complexes enter DNA at an origin of replication

Proceeds in both directions at the same time

Topo IV separates the catenated daughter chromosomes by a double stranded break and relegation

218
Q

How quickly do eukaryotic DNA Pols polymerise at?

A

50 nucleotides per second

219
Q

Why do chromosomes get shorter with each replication?

A

When DNA polymerase falls off and Okazaki fragments are left so they can join

Primers are erased and gap is filled by DNA polymerase and repaired by DNA ligase on leading strand

Gap on lagging strand cannot be filled by DNA polymerase as there is no primer

220
Q

How is telomerase a reverse transcriptase?

A

Telomerase provides an RNA template to synthesise a DNA copy of the template at the 3’ end of the parental lagging strand template

Telomeres are build of repetitive motifs

221
Q

Where is telomerase active?

A

Some germline cells

Epithelial cells

Haematopoietic cells

and in >90% of cancer cell lines
- responsible for immortal phenotype of cancer cells

222
Q

Who determined the order of nucleotides in pieces of DNA?

A

Gilbert and Sanger

223
Q

What does Sanger sequencing rely on?

A

The incorporation of dideoxynucleotides into newly replicated DNA

224
Q

What is a dideoxynucleotide?

A

Terminator

Lacks a 3’ hydroxyl so is a terminator of chain extension

Allows no more nucleotides to be added

225
Q

What is needed for Sanger’s dideoxy sequencing method?

A

Single stranded template DNA

Primer complementary to template

DNA polymerase

Pool of normal deoxynucleotides

Small proportion of radioactively-;abelled ddATP

226
Q

What is the practice of the Sanger sequencing method?

A
  1. Add template + primer + DNA Pol I + dNTPs
  2. Add appropriate ddNTP
  3. Separate nested fragments on basis of size by electrophoresis
  4. Autoradiograph and read sequence from bottom upwards
  • Looking for competition between normal nucleotides and incorporation of added product
227
Q

What is the process of automates dideoxy sequencing?

A
  1. Template + primer + DNA Pol + all dNTPs + all fluourescent ddNTPs in one tube
  2. Dye present in each synthesized fragment corresponds to dye attached to dideoxynucleotide that terminated the synthesis of that particular fragment
  3. Pass nested product through an electrophoretic system and read with lasers
228
Q

Who discovered the PCR?

A

Kary Mullis

229
Q

What did Mullis say were the components of PCR?

A

Template dsDNA with target area

2 specific oligodeoxynucleotide primers

dNTPs

Buffer and MgCl2

Taq polymerase

230
Q

Why is Taq polymerase useful?

A

Thermal stability of Taq DNA polymerase

231
Q

What is the method of PCR?

A
  1. Heat to 94 degrees to denature DNA and cause H bonds to break
  2. Cool down (45-65 degrees) to allow primers to anneal
  3. Warm again to 72 degrees to allow primers to be extended

Repeat 30 times

232
Q

What happens in cycle 1 of PCR?

A
  1. Target DNA is denatured
  2. Reaction is cooled, allowing primers to anneal to their complementary sequences
  3. Reaction is raised to 72 degrees, allowing Taq polymerase to extend the primers
  4. Products of cycle 1 can now act as substrates for cycle 2
233
Q

How does PCR have both specificity and sensitivity?

A

Specificity provided by primers:
- Complementary to opposite strands with 3’ ends pointing towards each other

Sensitivity: one target molecule can be amplified to >10^9 molecules in just a few hours, product in one acts as template for next

234
Q

Why do the regions defined by primers increase exponentially?

A

Starting DNA and hybrid duplexes also acts a templates for more PCR amplification

Expect >10^9 molecules of product from each starting target DNA after 30 cycles

235
Q

What are the applications of PCR?

A

Medical-genetic purposes

Analysing pregnancy tissue for pre-natal genetic screening

Archaeological and ancient DNA sources

Use PCR to alter a DNA sequence

Forensic applications

236
Q

How were the sequencing on archaic hominin genomes useful?

A

Found Europeans and Asians have 4-5% of their genes derived from Neanderthals

Gene flow can be detected from Neanderthals into modern humans

(later version: Europeans share 2% of DNA with Neanderthals)

237
Q

What did Green et al study with sequencing of archaic hominin genomes?

A

Nuclear DNA was amplified from fossil Neanderthal bones from Croatia

Compared DNA from modern humans

238
Q

What new type of human was found in 2021?

A

Eurasian human

Dragon Man

239
Q

What is the application of PCR with mutations?

A

Mutations can be introduced into amplified DNA by engineering one or more mismatches in a primer close to its 5’ end

240
Q

What is a VNTR?

A

Variable number tandem repeat

Short run of repeated nucleotides sequences

Found on many chromosomes, show variation in length between individuals

241
Q

How can a VNTR be used for personal or parental identification?

A

Each VNTR can act as an inherited allele

Number of repeats is variable

Individuals inherit a different variant of each VNTR locus from mother and father

Different sized fragments can be separated electrophoretically

242
Q

What is an example of VNTR analysis in practice?

A

CODIS: combined DNA index system, operated by FBI

STR: short tandem repeat, particular form of VNTR

Multiplex PCR is performed using specific primers for 13 different VNTRs on different chromosomes

LF104 - Molecules, Cells and organisms (12 decks)

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