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Molecules, Cells and Organisms > Prokaryotic Genetics (36-43) > Flashcards

Prokaryotic Genetics (36-43) Flashcards

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1
Q

Why are bacteria good model organisms?

A
  1. Haploid - see effect of mutation immediately
  2. Asexual reproduction - daughter cells have same properties
  3. Short generation time
  4. Easy to store
  5. Easy to genetically manipulate
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2
Q

What is the make-up of the bacterial genome?

A

A single circular, double stranded DNA chromosome
→ introns are rare
→ grouped in operon (related to same function)
→ often carry plasmids

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3
Q

How do bacteria reproduce?

A

Binary fission
→ asexual reproduction
→ cell elongates and content increased
→ DNA replicated and segregated
→ produces identical daughter cells

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4
Q

What are the growth requirements for E.coli?

A

Capable of synthesising all cellular components from simple inorganic nutrients and a carbon/energy source

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5
Q

What are auxotrophs?

A

Mutant organisms impaired in some metabolic capabilities

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6
Q

What are biosynthetic auxotrophs?

A

Require additional nutrients in order to grow
→ e.g. His- require histidine in its growth medium

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7
Q

What are catabolic auxotrophs?

A

Lost the ability to catabolism some carbon source
→ rarely a problem as glucose is often carbon source of choice
→ Ara- arabinose mutation - unable to grow on the monosaccharide arabinose (pointless using this as carbon source)

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8
Q

What type of catabolic auxotroph is often fatal?

A

Glucose catabolic mutants
→ glucose metabolisms is essential

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9
Q

When are conditional mutants lethal?

A

In repressive conditions
→ but not lethal in permissive conditions

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10
Q

What are temperature sensitive mutants?

A

Only grow at a permissive temperatures (30C for E.coli) and not at restrictive temperatures (37C for E.coli)

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11
Q

What did the Luria-Delbruck experiment predict?

A

Bacteria follow Lamarckian evolution
→ unlike ‘higher’ organisms
→ add toxic agent to bacterial culture and the entire culture becomes resistant

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12
Q

What was the conclusion from the Luria-Delbruck experiment?

A

Genetic mutations arise in the absence of selection pressure and are selected for by toxic agents
→ bacteria evolve as a result of mutation

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13
Q

What experiments determined bacterial evolution?

A

Luria-Delbruck, Newcombe and Lederberg and Ledeberg Experiments

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14
Q

How many substitutions does E.coli DNA polymerase make?

A

~once every 10^7 bases
genome is 5.4x10^6
→ after 2 generations 3 substitutions
→ if not recognised + repaired mutation is inherited

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15
Q

What are the 3 types of spontaneous mutation?

A
  1. Replication errors - wrong base pairs inserted by DNA pol
  2. Tautomers (isomers) - different H-bonding pattern, wrong base
  3. Base pair slipping - repeat nucleotides can cause frameshift mutations
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16
Q

What are mutagens?

A

Chemical or physical agents that cause damage to DNA
→ increase mutation rate
→ e.g. nitrous acid, reactive O species, UV light

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17
Q

What are intercalating agents?

A

Insert themselves into DNA between base pairs
→ usually flat multiple ring structures
→ distors helix
→ causes frameshift mutations

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18
Q

What are point mutations?

A

A change to one base pair
→ substitutions
→ insertion
→ deletion

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19
Q

What are the 2 types of DNA substations?

A
  1. Transitions (e.g. purine→purine)
  2. Tranversions (e.g. purine→pyrimidine)
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20
Q

What are the consequences of point mutations?

A

Protein coding parts: can affect sequence or regulation of translation

Promoter: can affect transcription

Non-coding: may have no consequence,

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21
Q

What types of mutations can substitutions leads to?

A
  1. Silent → no change
  2. Missense → change aa
  3. Nonsense → STOP codon
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22
Q

What type of mutation do insertions and deletions cause?

A

Frameshift mutations

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23
Q

What happens to proteins after mutations?

A
  1. Silent → nothin: genotype changes, phenotype doesn’t
  2. Missense → often nothing: genotype changed, phenotype may change
  3. Nonsense + frameshift → detrimental: genotype and phenotype changes
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24
Q

What are the types of large scale mutations?

A

Deletions
Inversions
Tandem repeats
Transposons

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25
Q

What is reversion mutation?

A

A point mutation resulting in the restoration of the original sequence

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26
Q

What is a suppressor mutation?

A

A second mutation resulting in the original phenotype being restored
→ e.g. salt bridge reversed stabilising protein

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27
Q

What is suppression of frame shift?

A

When a mutation restores the original frameshift

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28
Q

What is intergenic suppression?

A

A second mutation in a different gene to the original, that suppresses the phenotype of the first mutation
→ e.g. nonsense suppression

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29
Q

What are selectable phenotypes?

A

Drug resistance, phase resistance

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30
Q

How do you make a histidine auxotroph?

A
  1. Expose to a mutagen
  2. Grow in complex media to allow expression of phenotype
  3. Grow in minimal medium + penicillin
    → auxotrophs argent killed by penicillin’s they’re not grown
    4.. Plate on minimal medium + histidine and grow
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31
Q

What is phenotype lag?

A

The time between a genetic mutation and its phenotypic expression
→ bacteria phenotypes aren’t seen for several generations

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32
Q

What is cross feeding?

A

The exchange of nutrients between organisms
→ metabolic pathway blocked, metabolite accumulates, if it diffuses out another bacteria can take it up
→ both mutants can grow but are dependant on each other
→ phenotype becomes obvious once isolated

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33
Q

What is the Ames test?

A

Used to identify chemicals that are mutagenic (therefore carcinogenic)
→ assumes if a chemical is mutagenic to bacteria its also mutagenic to humans

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34
Q

How can you use biological assay in an Ames test?

A

(using a His auxotroph, doesn’t grow regularly)
Plate the same number of bacteria on plates with and without chemical being investigated
→ mutagenic - lots of reversions
→ not mutagenic - only a few reversions

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35
Q

What is a limitation of Ames testing?

A

Chemical itself may not be mutagenic, but a metabolite might be

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36
Q

What is an operon?

A

A group of genes regulated together under control of the same promoter
→ common in prokaryotes

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37
Q

What are housekeeping genes?

A

Genes that are constantly expressed as they are required for basic cellular function
→ e.g. genes involved in replication and transcription always need to be active

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38
Q

Why aren’t all genes always constitutively expressed?

A

Making RNA and protein is energy costly so genes are switched on and off according to the needs of the cell
→ e.g. switching to rich medium with aa now available means genes to make them are switched off to save energy

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39
Q

Is the lac operon constitutively transcribed?

A

No

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40
Q

What is diauxic growth?

A

Microbes presented with 2 carbon sources have bi-phasic growth with a lag phase in-between
→ carbon sources used consecutively not simultaneously

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41
Q

Why is a lag phase required in diauxic growth?

A

Time is needed for genes to be expressed and necessary proteins to be made after the initial carbon source (e.g. glucose) has run out

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42
Q

What do the lac genes encode?

A

lacY: β-galactoside-permease
lacZ: β-galactosidase (cleaves lactose disaccharide)
lacA: galactoside acetyl-transferase (transfers acetyl group to galactoside and glucosides)

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43
Q

How is the lac operon normally turned off?

A

A lac protein represses the operator preventing transcription of the upstream operon
→ RNA polymerase blocked

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44
Q

What is an inducer?

A

A molecule that turns genes on, disables the represser
→ for the lac operon allolactose is the inducer (similar to lactose but has 1-6 bond instead of 1-4)

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45
Q

How can allolactose formation be catalysed by β-galactosidase (LacZ) if the lac operon is repressed?

A

LacZ catalyses the splitting of lactose, even when the lac operon is repressed state there is still a small amount of transcription

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46
Q

How is the lac operon switched on?

A

Allolactose (rearranged glucose) binds to the lac repressor and makes it let go of the operator
→ RNA polymerase can now transcribe the operon

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47
Q

What is the purpose of catabolite activator proteins (CAPs)?

A

They bind to a region on DNA with cAMP just before the lac operon promoter to help recruit RNA polymerase

48
Q

When is the lac operon expressed?

A

When lactase is present and glucose isn’t

49
Q

What happens to cAMP at low levels of glucose?

A

cAMP attaches to CAP allowing it to bind to DNA
→ CAP helps recruit DNA polymerase to the promoter, resulting i high levels of transcription
→ the enzyme used to make cAMP is inhibited by glucose

50
Q

How does glucose suppress the lac operon?

A

Glucose inhibits adenylate cyclase, so no cAMP is made
→ CAP can’t bind so the lac operon is transcribed slowly

51
Q

What is bacterial transformation?

A

Induction of competence
→ the ability of a bacterial cell to take up extracellular (‘naked’) DNA from the environment

52
Q

What does bacterial transformation lead to?

A

Increasing genetic diversity and the spread of:
drug resistance, novel virulence factors, novel metabolic capabilities

53
Q

What are the 3 types of horizontal gene transfer?

A
  1. Bacterial transformation
  2. Bacterial transduction
  3. Bacterial conjugation
54
Q

Why does transformation occur at the entry to stationary phase?

A

At the stationary phase they starting to run out of nutrients and are at the risk of dying, so bacterial cells try to do something
→ quorum sensing: the ability to regulate genes based on population density

55
Q

What is the mechanism for competence?

A

Cells secrete ComX, cell density increases means more ComX
→ ComX binding with ComP leads to changes in gene expression, cells become competent

56
Q

How does bacteria know what DNA to take up and what to reject?

A

It recognises specific DNA sequences from the same species

57
Q

What is the mechanism of DNA uptake?

A
  1. DNA bind to surface protein on cell
  2. Single or double;e stranded DNA enters the cell
  3. Bind to competence-specific protein
    → recombination leads to new traits required
58
Q

What is transduction?

A

Genetic exchange in bacteria mediated by bacteriophages

59
Q

What is the lytic cycle with phages?

A
  1. Attachment
  2. DNA inserted into cell
    → replication, transcription and translation, new virions assembled
  3. Lysis and release of new virions
60
Q

What is the lysogenic cycle with phages?

A
  1. Attachment
  2. DNA inserted into cell and integrated into genome
  3. DNA stays there and is transmitted to daughter cells
61
Q

What is conjugation?

A

The process of moving genetic material (often plasmids) via direct cell-to-cell contact

62
Q

What are plasmids?

A

Small double stranded DNA section
→ mostly circular, can be linear
→ replicate individual of chromosomal DNA
→ do not have extra cellular form (like phages)

63
Q

What is an episome?

A

A special type of plaid that can integrate into the host genome

64
Q

What is the role of plasmids?

A

Carries non-essential but often highly useful genes for:
1. Antibiotic resistance
2. Virulence factors
3. Bacteriocins

65
Q

What are conjugative plasmids?

A

Plasmids capable of horizontal transmission
→ most plasmids themselves encode the genes that will allow transfer to other cells
→ some transfer only to same species

66
Q

What is a F pilus?

A

A thin flexible filament on the surface of bacteria that connects a mating pair
→ allows for the unidirectional transfer of DNA from donor to recipient
→ creates contact and pulls cells closer together

67
Q

How are plasmids transferred?

A
  1. The double stranded plasmids is nicked
  2. The nicked strand is unrolled and transferred
  3. Once transferred plasmid is made circular and other strand synthesised
68
Q

How is a plasmid copied?

A

Rolling circle replication (RCR)
1. One strand is nicked creating 5’ 3’ end
2. 3’ serves as primer for replication
3. Once a full round is synthesised old strand released and new strand ligated
4. Single strand circularised and replicated

69
Q

What is a high frequency recombination strain (hfr)?

A

Has f plasmid integrated into genome through recombination
→ they can transfer part of their genome to another cell

70
Q

How is the development of complex multicellular organisms possible?

A

Due to the capacity of cells to become specialised and communicate
→ functional units need structural integrity and to be able to receive and respond to stimuli

71
Q

What are the 4 essential processes of development determined by selective gene expression?

A
  1. Cell proliferation
  2. Cell specialisation
  3. Interactions with environment
  4. Cell movement and migration
72
Q

What is the shared sequence of cell development events common to all animals?

A

egg → cleavage (1st division) → gastrulation → germ layers

73
Q

What are the proteins important for multicellular development?

A

Cell adhesion and signalling transmembrane proteins

74
Q

What are the 2 types of cell adhesion molecules?

A
  1. Cadherins: mediate cell-cell adhesion
  2. Integrins: mediate interaction between cytoskeleton and extracellular matrix
75
Q

What are the 2 types of cell-cell anchoring junctions?

A
  1. Adherens junctions: actin filaments via cadherin proteins
  2. Desmosome junctions: intermediate filaments via cadherin proteins
    → connect with the intracellular cytoskeleton
76
Q

What are the 2 types of cell-matrix anchoring junctions?

A
  1. Actin-linked cell matrix adhesion: actin filaments via integral proteins
  2. Hemidesmosomes - intermediate filaments via integral proteins
77
Q

How do the differences in DNA regulatory proteins (transcription factors) and non-coding DNA (enhancers) lead to variant in body plan/shape/structure?

A

The same gene regulatory protien (transcription factors) in different organisms bind to different enhancer regions so different down stream protein transcription
→ leading to different environmental influences of cells

78
Q

How do differences in protein expression and cell-cell communication manifest into anatomical changes?

A
79
Q

What happens as embryonic development proceeds?

A

The embryo is divided into broad regions which become the future germ layers (mesoderm, ectoderm and endoderm)
→ the cells within these regions are more committed to their fate dependant on their spacial region

80
Q

What are the 2 stages of cell commitment?

A
  1. Specification: in a neutral environment can differentiate according to fate, in a different environment fate changes depending on cell signals
  2. Determination: cells can differentiate according to fate even if in a different environment (fully determined no matter what)
81
Q

What is induction?

A

Where a signal from one group cells influences the developmental fate of another
→ inductive signals have spacial and temporal influence

82
Q

How is cell fate determined by asymmetrical cell division?

A

Significant molecules (e.g. mRNAs) are differently distributed causing sister cells to be born different
→ changes protein production and function

83
Q

How is cell fate determined after symmetric cell division?

A

Sister cells become different as a result of influences acting on them after birth
→ extracellular influences determined by location and susceptibility to inductive signals

84
Q

What are HOX proteins?

A

Transcription factors that active or repress genes
→ determine the type of structures formed in particular segments

85
Q

Where are the animal and vegetal poles?

A

Animal pole - ectoderm layers
Vegetal pole - endoderm layers
→ contain differing selections of mRNAs providing polarity
→ before fertilisation there is already polarity - maternally derived

86
Q

What does fertilisation trigger in the polarity of cells?

A

Triggers cortical rotation 30° rotation
→ offsets the animal pole and location of important mRNA molecules
→ leads to asymmetry of mRNA

87
Q

What occurs after cortical rotations completed?

A

1h later cleavage follows
→ results in many small cells (blastomeres) without significant change in mass
→ first differences in cell fate
→ ectoderm, mesoderm and endoderm

88
Q

What is gastrulation?

A

early embryo development processes
→ embryo becomes hollow ball of cells (blastula)
→ blastomeres are predetermined to become 3 germ layers

89
Q

Why is a dorsoventral signal gradient created during gastrulation?

A

To control tissue pattern and coordinate gastrulation movement

90
Q

What happens during cell migration in gastrulation?

A

Cells are spatially rearranged some undergoing involution
→ cell shape also changes via convergence or elongation

91
Q

What is neurulation?

A

The initial stages of nervous system development
→ gives rise to the neural plate, neural tube forming the spinal cord and brain
→ as the central body is formed following gastrulation distinct mesoderm become apparent on either side of the body

92
Q

What are somites?

A

Precursor cell populations that give rise to vertebrae body plan
→ from vertebrates, ribs and muscle

93
Q

What are the chemical modifications in chromatin structure that can alter foetal programming?

A
  1. Methylation of the DNA
  2. Acetylation of histones
  3. miRNAs
94
Q

What happens after a seed is germinated?

A

The short emerges - enlargement of non-meristem cells followed by the shoot
→ rapid cell division of the apical meristems

95
Q

What are the 3 stages of plant morphogenesis?

A
  1. Cell division - meristem
  2. Cell growth - elongation (turgor pressure and orientation of cellulose fibrils)
  3. Cell differentiation - specialisation
96
Q

What is meristem tissue?

A

Undifferentiated cells capable of cell division
→ can differentiate into all other tissues and organs of the plant

97
Q

What are tissues?

A

Composed of cells that have a common embryonic origin
→ structure and properties influenced by cell-cell connections and the surrounding extracellular matrix

98
Q

What are the 4 tissue types?

A
  1. Connective tissue
  2. Epithelia
  3. Muscles
  4. Nerve
99
Q

What does a blastocyst consist of?

A

Zona pellucida: layer of 3 different glycoprotein, species specific
ICM: becomes the embryo
Trophoblast: becomes supporting tissue, placenta
Hypoblast: yolk sac
Epiblast: gastrulation and neurulation

100
Q

What is epithelia tissue structure?

A

Creates barriers, is abundant and widely distributed throughout the body
→ arranged in tightly packed continuous sheets
→ line internal and cover external surfaces
→ small gaps between cells to control what goes through layers
→ cells are Polaris and closely associated via cell junctions

101
Q

What are the major functions of epithelia tissue?

A
  1. Protection - waterproof skin
  2. Selective barriers
  3. Filtration - kidney
  4. Secretion
  5. Absorption
  6. Excretion - urine formation
102
Q

What are the 2 types of epithelial tissue?

A
  1. Covering and lining epithelium: controls transport
  2. Glandular epithelium: ability to secrete
103
Q

What is the function of epithelium tissue?

A

Bind, support, strengthen, provide integrity, insulate and compartmentalise
→ not present on body surfaces

104
Q

What is connective tissue composed of?

A
  1. Extracellular matrix: ground substance - water + GAGs and protein fibres - collagen, elastin reticular
    → ECM variation determines structure and function of connective tissue
  2. Cells widely spaced
105
Q

What are the types of connective tissue cells?

A

Loose and dense CT - fibroblasts
Cartilage CT - chondroblasts
Bone - osteoblasts
Liquid CT (blood tissue, lymph)

106
Q

What is muscle tissue comprised of?

A

Elongated cell muscle fibres - myocytes
→ electrical stability, contractibility, extensibility, elasticity

107
Q

What are the main types of muscles tissue?

A
  1. Skeletal
  2. Smooth
  3. Cardiac
    → some control automatic, other self contracting
108
Q

What are the functions of muscle cells?

A

Movement and locomotion
, maintenance of posture, controlled movement fo substances, thermogenesis

109
Q

What is the composition of skeletal muscle?

A

Long cylindrical fibres
→ striated due to overlapping fibrils of actin and myosin
→ develop from fusion of 100s myoblasts so multinucleated

110
Q

What is the composition of smooth muscles?

A

Short fibres tapered at each end
→ central oval nucleus
→ no overlap of filaments, non striated (smooth)
→ greater ability to stretch and recoil

111
Q

What are the 2 types of smooth muscle?

A
  1. Visceral: skin, stomach, intestines
    → several fibres innervated by one ANS synapse
    → connected by many gap junctions to spread action potential
  2. Multiunit: lung airways, artery walls
    → each fibre has one ANS synapse
    → not as closely associated, fewer gap junctions
112
Q

What is the function of tissue stem cells?

A

Form the basis for tissue homeostasis and repair
→ general maintenance + magnified cell proliferation the damaged

113
Q

What influences stem cell niche?

A

Th micro environment
→ change in environment causes change in cell fate
→ cell adhesion, endocrine signals, nervous stimulation, metabolic products

114
Q

What are the 2 essential stem cell properties?

A
  1. Self renewal: proliferate without any limit
  2. Potency/plasticity: how many different cell types?
115
Q

What are the types of stem cells?

A
  1. Totipotent - zygote
  2. Pluripotent - embryonic
  3. Oligiopotent - epidermal
116
Q

What are the fundamental extracellular signal molecules?

A
  1. Mitogens: remove the hand-brake on the cell cycle
  2. growth factors: increase cell mass
    3.Survival factors: suppression of apoptosis

Molecules, Cells and Organisms (5 decks)

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