bacteria (completed)

structure of bacteria [10]

• bacteria chromosome

• plasmid

• starch granule

• 70s ribosome

• cytoplasm

• cell membrane

• peptidoglycan cell wall

• capsule

• fimbria

• flagellum

bacteria chromosome structure and where its found [3]

• ds circular DNA form looped domains by associating with DNA binding proteins

• then supercooling form highly condensed DNA

• found in nucleoid region

how does the F plasmid differ from the bacteria chromosome [2]

• F plasmid has significantly fewer base pairs

• F plasmid contains non-essential genes such those that confer advantages like anti-biotic resistance unlike bacteria chromosome which codes for essential genes like enzymes for cell metabolism

what is the structure and role of the F plasmid [5]

• small circular autonomously replicating DNA molecule

• F factor on the F plasmid codes for proteins necessary for the formation of sex piles and subsequently the mating bridge

• to allow conjugation to occur between bacteria

• allow bacteria genes to be transferred between bacteria increase genetic variation between bacteria

• containing genes which confer advantages such as antibiotic resistance

outline the process of bacteria conjugation [3]

• sex plus of F bacterial cell makes contact with F- cell and retracts bringing F- cell closer for mating bridge to be formed between both cells

• one of the 2 strands of plasmid DNA is nicked and transferred from the F+ cell to the F- cell through the mating bridge via the rolling circle mechanism and the other DNA strand is used as a template for elongation

• the single stranded F plasmid DNA circularised in the F- cell and is used as a template to synthesise a complementary strand for the ds F plasmid FNA resulting in a F+ cell

what methods give rise to genetic variation in bacteria genomes [3]

• conjugation

• transformation

• transduction (general or specialised)

describe the rolling circle DNA replication process [5]

• one strand of the ds circular DNA is nicked by nuclease, breaking the phosphodiester bond

• the 3’OH end elongated by DNA polymerase using intact stand as a template

• newly synthesised strand displaces the 5’ end of the nicked strand and transferred to the recipient bacterium via the mating bridge

• upon completion of 1 unit length of the plasmid, another nick occurs to release the original strand which recircularises

• for the synthesis of complementary DNA strand to form ds F plasmid

outline the process of bacteria transformation [3]

• fragments of foreign naked DNA from lysed bacteria cells in the surrounding medium are taken up by bacteria cells by cell surface proteins

• foreign DNA is incorporated into bacteria chromosome via homologous recombination (crossing over at homologous regions)

• if the foreign DNA contains a different allele that is now expressed in the bacteria cel, the bacteria cell has transformed

outline the process of general transduction [4]

• phage infects a bacterium, injecting viral genome into host cell

• bacterial DNA degraded into small fragments, which may be randomly packaged into a capsid head during spontaneous assembly of new viruses

• upon cell lysis, defective phage infects another bacterium and inject bacteria DNA from the previous hose cell into new bacterium

• foreign DNA can replace homologous regions in recipient cell chromosome if homologous recombination occurs which may express different allele from the previous host

outline the process of specialised transduction [5]

• temperate phase infects a bacterium, injecting viral genome into the host cell

• viral DNA is integrated into bacteria chromosome forming a prophage which mat be improperly excised to include adjacent segments of bacterial DNA during induction event

• bacterial DNA may be packaged into a caps hear during spontaneous assembly of new viruses

(last 2 points same as general transduction)

• upon cell lysis, defective phage infects another bacterium and inject bacteria DNA from the previous hose cell into new bacterium

• foreign DNA can replace homologous regions in recipient cell chromosome if homologous recombination occurs which may express different allele from the previous host

benefits of conjugation for the recipient bacteria [2]

• gain new alleles that when expressed allow it too survive in a different environment, antibiotic resistance

• use of new resources like metabolites

difference between pathways for repressible operons and inducible operons [2]

repressible is associated with anabolic while inducible is associated with catabolic pathways

state the preferred respiratory substrate [1[]

glucose over lactose

define operon [2]

• a cluster of functionally related genes under the control of the same promoter and operator

• allowing functionally related proteins synthesised together via translation of polycistronic mRNA

define promoter [4]

• GTF and RNA polymerase binding site for the formation of TIC to initiate transcription

• has critical elements

• TATA BOX (precise location of transcription start site where GTF binds)

• CAAT and GC BOX (improve efficiency of promoter)

define operator [1]

repressor protein binding site, prevent RNA polymerase from binding to the promoter, prevent transcription

define polycistronic mRNA [2]

• messanger RNA containinig base sequences coding for amino acids for several proteins

• contain many start (AUG) and stop (UGA, UAA, UAG) codons depending on number of polypeptides (3 sets for lac, 5 sets for trp)

define structural genes [1]

• gene that codes for protein product the forms part of a structure of has an enzymatic function in a metabolic pathway

define regulatory genes + examples [3]

• codes for protein involved in regulating expression of structural genes

• not found within operon but diffusible operator to exert its effect

• CAP and repressor

define effector and 2 examples [3]

• a small molecule that binds to a specific protein, causing a conformation change and this regulating biological activity of the protein

• allolactose in lac operon (inducer)

• tryptophan in trp operon (corepressor)

advantages of operons [4]

• allow functionally related proteins synthesised at the same time

• economical use of energy and resources, expressing genes only when needed

• allow bacteria respond rapidly and appropriately to changes in the environment

• give them selective advantage over those who cant

Lac operon structure [3SG, 1 RG, 2P, 1O, I] INDUCIBLE OPERON

structural genes:

• lac Z → beta-galactosidase (hydrolyse lactose to 1. glucose and galactose / 2. allolactose)

• lac Y → permease (facilitate movement of lactose into the cell)

• lac A → transacetylase

regulatory gene:

• lac L → lac repressor (bind to DNA binding site of operator and allosteric site of allolactose)

promoter:

• RNA polymerase binding site

• Catabolite activator protein (CAP) binding site

operator: (overlap with promoter)

• lac repressor binding site

inducer:

• allolactose

Trp operon structure [5SG, 1RG, P, 1O,C] REPRESSIBLE OPERON

structural genes:

• trp E, D, C, B, A → code for enzyme in tryptophan biosynthesis pathway

regulatory gene:

• trp R → trp repressor (bind to DNA binding site of operator and allosteric site of tryptophan)

promoter:

• RNA polymerase binding site

operator: (overlap with promoter)

• trp repressor binding site

corepressor

• tryptophan

negative regulation [1]

lac operon turned OFF by repressor protein in the absence of lactose

positive regulation

lac operon turned ON by CAP protein in the presence of glucose

lac operon (NO lactose and glucose) - just talk abt lactose

OFF

• regulatory gene lacl constitutively transcribed to produce lac repressor protein

• lac repressor protein in active form binds to the operator via the DNA binding site

• in the absence of lactose, repressor protein remains active binds to the operator prevent RNA polymerase from accessing the promoter

• preventing the transcription of structural genes

lac operon (YES lactose NO glucose)

ON

• presence of lactose, a few molecules of lactose enter the cell with the help of permease

• lactose converted to allolactose by beta galactosideas

• allolactose (inducer) binds to the allosteric site of the repressors, repressor becomes inactive as the DNA binding site of the repressor conformation altered and cannot bind to the DNA binding site of the operator as its tertiary structure altered and no longer complementary

• RNA polymerase can access and bind to the promter to initiate transcription of structural genes

• structural genes transcribed as a single polycistronic mRNA coding for 3 different proteins to be translated together

• absence of glucose, cAMP levels increase

• cAMP bind to the allosteric site the CAP forming CAP- cAMP complex, activating CAP which binds to the CAP binding site within the promoter

• this increase the affinity of promoter region of RNA polymerase, increase frequency of transcription of lac operon structural genes

lac operon (NO lactose YES glucose)

OFF

• regulatory gene lacl constitutively transcribed to produce lac repressor protein

• lac repressor protein in active form binds to the operator via the DNA binding site

• in the absence of lactose, repressor protein remains active binds to the operator prevent RNA polymerase from accessing the promoter

• preventing the transcription of structural genes

• presence of glucose, cAMP levels low

• catabolite activator protein (CAP) not activated as few cAMP bound to CAP

• hence no CAP binding to CAP binding site in the promoted and no up regulation of transcription of lac operon

lac operon (YES lactose and glucose)

OFF

• presence of lactose, a few molecules of lactose enter the cell with the help of permease

• lactose converted to allolactose by beta galactosideas

• allolactose (inducer) binds to the allosteric site of the repressors, repressor becomes inactive as the DNA binding site of the repressor conformation altered and cannot bind to the DNA binding site of the operator as its tertiary structure altered and no longer complementary

• RNA polymerase can access and bind to the promter to initiate transcription of structural genes

• structural genes transcribed as a single polycistronic mRNA coding for 3 different proteins to be translated together

• presence of glucose, cAMP levels low

• catabolite activator protein (CAP) not activated as few cAMP bound to CAP

• hence no CAP binding to CAP binding site in the promoted and no up regulation of transcription of lac operon

to memorise about glucose

U glucose → D cAMP

D glucose → U cAMP

what happens to the gnome of bacteria during binary fission [5ed]

• bacteria genome made upon of DNA replicates by semi-conservative replication

• DNA unzipped by helices by breaking the hydrogen bonds between the bases of 2 strands

• each parental strand serve as a template for synthesis of daughter strand

• free deoxyribonucleotides CBP with bases on parental strand

• DNA polymerase catalyse formation of phosphodiester bonds between adjacent nucleotides

describe hoe binary fission produces genetically identical bacteria [6]

• DNA replication begins at the original of replication DNA unzipped by breaking hydrogen between base pairs of 2 strands forming a replication bubble

• DNA replicate by semiconservative replication each original strand used as template for synthesis of complementary daughter strand by CBP

• 2 newly formed ori move to opp poles of the cell and attach to plasma membrane

• cell elongate to prepare for division

• DNA circular with no free ends and 2 daughter molecules interlocked with completion of replication

• enzyme topoisomerase cut, separate and reseal 2 DNA molecules

• invagination of plasma membrane and the deposition of new cell wall eventually divide parent cell into 2 daughter cells

COMPARISON: binary fission vs mitosis

COMPARISON: transformation vs general transduction vs specialised transduction vs conjugation

COMPARISON: viruses vs bacteria

COMPARISON: pro genome vs euk genome [6]

effect of a mutation of a single structural gene and on the other structural genes [2]

• truncated of non-functional protein coded for the mutated structural gene

• the other proteins still produced as they are translated indecently as they each have their own start and stop codon on the polycistronic mRNA

describe mutation of lac l gene and its effect [5]

• mutation of the gene results in a different mRNA transcribed and thus different amino acids translated, defective lac repressor

• causing a conformation change DNA binding site of the repressor, bind reversibly to the operator

• also causes a change in the allosteric site of the repressor, cannot bind to the inducer (allolactose) to become inactivated, remain bounded to the operator

• lac operon permanently switched off

• no structural genes transcribed thus levels of lactose etc same

why is it lactose not broken down immediately even though glucose is absent [1]

time is needed for the transcription of lac Z and subsequent translation to produce beta-galactosidase for lactose to be broken down

why regulatory gene located far away but can still regulate operon expression [1]

• the repressor protein coded by regulatory gene can diffuse to the location of the operator to bind and exert its effect

trp operon (high tryptophan) [4]

• trp repressor protein synthesised in inactive form

• as tryptophan accumulates, it acts as a corepressor and binds to the allosteric site of the repressor, changing its conformation to be active

• active repressor bind to operator, prevent binding of RNA polymerase to the promoter

• prevent expression of operon

trp operon (low tryptophan) [2]

• trp repressor protein synthesised in active form and unable to bind to the operator

• RNA polymerase can bind to the promoted and allow expression of operon

COMPARISON: how DNA arranged in pro vs euk genome

euk:

• DNA coils around histone proteins to form nucleosome

• follow by coiling around itself to form solenoids

• supercoiling of the loops consider into metaphase chromosome

pro:

• associated with relatively fewer proteins (histone-like proteins) to form loops

• super coiling cause further compaction

how are lac and trp operon similar [4]

• both consists of several genes under control of single promoter

• both have operator region for binding of active repressor to prevent transcription

• genes coding for functionally related proteins synthesised together as a unit

• operon produces a polycistronic mRNA with several start and stop codons

COMPARISON: lac and trp operon