Bacteria

Question 1

Structure of bacteria

Answer 1

1. small and unicellular/prokaryotic
2. lacks true nucleus and membrane-bound organelles
3. smaller 70s ribosomes
4. peptidyoglycan cell wall
5. chromsome …
   - made out of circular, double-stranded DNA
   - lacks introns
   - has genes which are grouped into operons where multiple genes come under control of 1 promoter
   - for packing, it is wound around histone-like proteins to compact DNA into looped domains -> supercoiling for further compaction
6. contains plasmid(s)

Question 2

Types of peptidyoglycan cell wall (gram staining test)

Answer 2

• gram-positive:
  (a) thicker peptidyoglycan cell wall
  (b) which helps to track crystal violet dye from being washed away, thus staining the cell wall violet
• gram-negative:
  (a) thinker peptidyoglycan cell wall
  (b) causing crystal violet dye to be easily washed away, thus cell wall is not stained violet

Question 3

Plasmids

Answer 3

• small, circular, double-stranded extrachromosomal DNA
  
  • contain beneficial genes which confer beneficial traits such as
    (a) antibiotic resistance,
    (b) toxin synthesis and
    (c) enzyme production
  • capable of independent replication as it has its own oriR

Question 4

Differences between plasmids and chromosomes

Answer 4

1. size
   - plasmids: small
   - chromosomes: larger in size
2. genes and their use
   - plasmids:
   (a) contain beneficial genes
   (b) which confer beneficial traits such as antibiotic resistance, toxin synthesis and enzyme production
   - chromosomes:
   (a) contain genes essential for survival
   (b) such as genes essential for production of enzymes for metabolism

Question 5

Description of peptidyoglycan cell wall

Answer 5

(a) polysaccharide strands consisting of alternating monosaccharide subunits, NAM and NAG,
(b) joined via peptide cross-links between adjacent NAM residues

Question 6

Transformation in prokaryotes (form of genetic exchange)

Answer 6

1. naked DNA fragment is released when donor bacterial cell lyses
2. competent recipient bacterial cell takes up DNA fragments via competence factor
3. homologous recombination occurs
4. to allow for incorporation of donor cell’s DNA into recipient cell’s bacterial chromosome

=> increase in genetic variation
as this results in diff combos of specific genes in prokaryotes

Question 7

Transduction in prokaryotes (form of genetic exchange)

Answer 7

1. bacteriophage injects its DNA into bacterial host cell

2a. EITHER (generalised)
host bacterial chromosome is degraded, and a small random fragment of the host DNA is accidentally incorporated/packaged into phage capsid
2b. OR (specialised)
prophage is imprecisely excised upon induction and takes with it a small portion of bacterial DNA adjacent to prophage insertion site

3. resultant phage infects another bacterial cell, and homologous recombination occurs
4. to allow for incorporation of donor cell’s DNA into recipient cell’s bacterial chromosome

=> increase in genetic variation
as this results in diff combos of specific genes in prokaryotes

Question 8

Conjugation in prokaryotes (form of genetic exchange)

Answer 8

1. F+ donor cell uses a sex pilus to attach to a recipient F- cell and establish a temporary cytoplasmic mating bridge
2. The sugar-phosphate backbone of 1 strand of the F plasmid is nicked by endonuclease
3. Nicked DNA strand moves to F- cell through cytoplasmic mating bridge
4. Each parental strand becomes a template, in both donor and recipient cells
5. For the synthesis of a complementary daughter DNA strand, catalysed by DNA pol

=> increase in genetic variation
as conjugation allows F- to become F+ cell,
gaining the F plasmid which
contains beneficial genes which e.g. confers antibiotic resistance

Question 9

Fate of transferred DNA

Answer 9

• (for transformation and transduction) recombined with bacteria chromosome
• (for a transformation and transduction) replicates with bacterial chromosome /
  (for conjugation) replicates by itself
• (for all 3) expression of the genes in DNA

Question 10

Binary fission (reproduction in bacteria)

Answer 10

definition:
2 equal-sized genetically identical daughter cells are produced from a single parent cell

process:
- bacterial chromosome attaches to cell membrane
- semi-conservative DNA rep occurs
- where the 2 DNA strands separate at oriR, forming a replication bubble
- and replication bubble grows bidirectionally away from single oriR until bacterial chromosome is replicated fully

• the 2 bacterial chromosomes attach to cell membrane at 2 different sites of attachment
• cell elongates and 2 chromosomes move apart
• septum develops
• as cell membrane invaginates
• cell is eventually split into 2 genetically identical daughter cells by cytokinesis

Question 11

How binary fission is critical for abundance of prokaryotes

Answer 11

• simpler process, and thus can occur at faster rate
  -> ref to ability to double in number every 20 mins or so
• small size of genome, thus DNA can be replicated faster to produce daughter cells
• faster rate of evolving gives more opportunity for mutation to occur to give rise to beneficial alleles
• since prokaryotes are unicellular, each daughter cell is a new organism

Question 12

How horizontal gene transfer give rise to abundance of prokaryotes

Answer 12

• cause advantageous/beneficial genes to be spread throughout the population
  -> ref to examples of beneficial genes,
  such as genes which gives it ability to survive in extreme habitats (e.g. Taq)
• which allow prokaryotes to inhabit and exploit a wide range of envts

Question 13

regulation of gene expression in prokaryotes

Answer 13

• lack of chromatin level of control
  -> much less complex packing and folding of DNA
• transcriptional control present,
  where repressor molecules bind to operator
• no control over individual genes
  -> related structural genes are grouped together into operons (under the control of same promoter)
• lack of post-transcriptional modification and translational control
  -> transcription and translation occurs simultaneously

Question 14

how cell theory applies to prokaryotes

Answer 14

• cell theory states that a cell is the smallest unit of life
• and all bacteria are unicellular living organisms which can
  take in raw materials
  / extract useful energy from raw materials and synthesise its own molecules
  / grow in an organised manner
  / respond and adapt to the external envt
• cell theory states that all cells come from pre-existing cells
• and bacteria reproduces by binary fission

Question 15

description of lac operon (transcriptional control)

Answer 15

Usually,
1. lac repressor is in active conformation
2. and binds to operator sequence as it has a complementary conformation
3. thus RNA pol is prevented from binding to promoter and transcription cannot take place
4. thus operon is switched off
5. and hydrolysis of lactose cannot occur as B-galactosidase is not produced

However, when lactose enters the cell,
1. it forms allolactase, which functions as an inducer
2. and binds to lac repressor
3. changing it to its inactive conformation, which cannot bind to operator
4. thus RNA pol can bind to promoter, and transcription can take place
5. operon is switched on
6. and hydrolysis of lactose by B-galactosidase occurs

Question 16

basis of inducible operon

Answer 16

usually codes for
(1) enzymes involved in catabolic pathways,
(2) and is normally not transcribed (i.e. “off”).
(3) It is turned on
(4) by substrate of enzyme,
(enzyme) coded for by structural genes,
(5) which acts as an inducer

Question 17

structural features of mRNA transcribed from operon

Answer 17

• polycistronic mRNA (i.e. coding regions for multiple different genes on 1 mRNA)
• multiple start and stop codons (or Shine-Dalgarno sequences), one pair for each gene
• no 5’ cap and 3’ poly (A) tail
• no introns

Question 18

description of trp operon

Answer 18

Usually,
1. trp repressor is in inactive conformation
2. and cannot bind to operator as it does not have a complementary conformation
3. thus RNA pol can bind to promoter, and transcription can take place
4. operon is switched on
5. and synthesis of amino acid tryptophan takes place

However,
1. tryptophan accumulates and functions as corepressor
2. and binds to trp repressor,
3. changing it to active conformation, which can bind to promoter
4. thus RNA pol is blocked from binding to promoter, and transcription cannot take place
5. operon is switched off
6. and there is no synthesis of tryptophan

Question 19

basis of repressible operon

Answer 19

usually codes for
(1) enzymes involved in anabolic pathways,
(2) and is normally transcribed (i.e. “on”).
(3) It is turned off (repressed)
(4) by accumulation of pdt, coded for by structural genes,
(5) which functions as corepressor

Question 20

differences between structural and regulatory genes

Answer 20

• (pdt) regulatory gene codes for a transcription factor (e.g. repressor protein)
  while structural gene codes for a structural protein (e.g. enzyme)
• (function of pdt) transcription factor controls expression of structural genes
  while structural gene …

note: state in context if possible!
- for trp operon,
transcription factor -> repressor protein
structural protein -> enzyme,
which is involved in synthesis of aa tryptophan
- for lac operon,
transcription factor -> repressor protein
structural protein -> enzyme,
which is involved in hydrolysis of lactose

Question 21

significance of trp operon

Answer 21

• trp operon is turned off when tryptophan level is high
  => save resources for the cell

Question 22

trend in growth / pop size of bacteria when grown in a medium with both glucose and lactose

Answer 22

• trend: population (or any other indicator of growth) increases initially, then levels off, increases again, then levels off again
• 1st increase: glucose is preferentially used as a respiratory substrate, to provide ATP of binary fission of bacteria
• 1st levelling off: glucose was depleted,
  and lac operon was turned on such that lactose could be hydrolysed into glucose and galactose
  (no glucose -> no available ATP for binary fission -> no growth / increase in pop size)