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Flashcards in Transcription and Translation Deck (57):
1

What is a central dogma?

The central dogma of molecular biology describes the flow of genetic information in cells from DNA to messenger RNA (mRNA) to protein

2

Describe the difference between the C4 (4th carbon) in ribonucleic acids and deoxyribonucleic acids.

RNA has ribonucleic acid which has an OH group on the 4th carbon whereas deoxyribose has no OH and is only a H attached to the C4

3

Describe the process of DNA transcription.

-INitiation
-Elongation
-Termination
-RNA polymerase attaches to a recognition site
-Binding causes the double helix to unwind, forming a transcription bubble
-Complementary bases pair up
Nucleotides linked to the three prime end of the growing RNA molecule
-RNA polymerase dissociates one the terminator sequence has been reached

4

What causes torsional strain on the DNA during transcription?

DNA leaves the RNA polymerase at an angle which causes a torsional strain

5

What is the function of the 'flap' in RNA polymerase?

Flap is a door at the back of the enzyme to stop the RNA falling out of place whilst it is still being synthesised

6

What is the rudder in RNA polymerase?

Mechanism to steer the DNA through, base by base

7

What are the 5 subunits of bacterial RNA polymerase? What does each do?

-Sigma- initiation of transcription

-Omega-function under dispute

-Alpha- promotes binding

-Beta- binds nucleotides and allows ribonuceotides come in through the 'tunnel' by which they must enter

-Beta'- template binding, holding on to the DNA

8

What is meant by the 'core enzyme' with respect to RNA polymerase?

When the sigma subunit leaves the holoenzyme

9

Describe what occurs in the initiation stage of transcription.

-Cosensor sequences at the -10 and -35 positions are recognised
-Recognised and bound by a subunit of RNA polymerase
-Base pairs separate here

10

What is meant by a co-sensor sequence?

'Boxes' such as the -10 and -35 boxes which are regions upstream of transcription which are recognised by NRA polymerase during initiation (which have positions of about 10 and 35 base pairs away from the promoter region)

11

What is meant by a consensus sequence?

'Boxes' such as the -10 and -35 boxes which are regions upstream of transcription which are recognised by NRA polymerase during initiation (which have positions of about 10 and 35 base pairs away from the promoter region)

12

What direction does transcription occur in?

5' to 3' direction

13

When is the sigma factor of RNA polymerase ejected?

Sigma factor gets ejected once the formation of RNA is underway (not needed after the first stage)

14

How can RNA polymerase get away with having a proof reading activity that is not as effective as DNA polymerase?

It is not as important if there are a few mistakes made by RNA polymerase because if there is a faulty transcript the error will not be perpetuated many times and also it will more likely lead to a non functional enzyme or a piece of RNA that cannot be translated

15

Describe the two different processes of termination in transcription.

Rho independent (intrinsic termination)
-Many A's on DNA complementary base pair to many U's on RNA
-Hairpin loop forms
-Makes RNA polymerase dissociate by affecting the active site so it can no longer hold onto the RNA


Rho dependent termination
-Rho is a helicase which moves behind RNA polymerase
-When a hairpin loop forms and the polymerase reaches it, it stalls and the rho protein catches up
-Rho breaks the bonds between the UUUU and AAAA (etc) sequence
-RNA released form active site

16

Give examples of catabolic and biosynthetic operons.

Catabolic- lac operon

Biosynthetic- tryptophan operon

17

What happens to the lac operon in the presence of lactose (if no glucose is present)?

It gets switched on.

18

What is a sigma factor?

It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. ... Once initiation of RNA transcription is complete, the sigma factor can leave the complex.

19

What are the two monosaccharides that from lactose?

Galactose and glucose

20

Which enzyme cleaves lactose?

Beta galactosidase, breaks the glycosidic bond.

21

Which enzyme neutralises toxic sugars accidentally made by beta galactosidase?

Transacetylase

22

What is lacI?

The repressor which is bound to the promoter for the lacZYA operon

23

What is lacZYA?

A set of 3 genes in the lac operon that are transcribed if lactose is present. They code for 3 different enzymes/proteins which allow lactose to be taken up and used by the bacterium.

24

What is lacY?

A gene encoding beta-galactoside permease, which is a membrane bound protein that transports beta-galactosidase into the cell.

25

What is lacA?

A gene that encodes a protein called Beta-galactoside transacetylase. This enzyme transfers an acetyl group from acetyl-CoA to the Beta-galactoside. (Neutralises toxic sugars made by betagalactosidase).

26

What is lacO?

It is the operator

27

What is lacO?

It is the operator. The repressor from the transcription of lacI is bound at lacO.

28

What is the inducer in the lac operon model?

Alloactose is the inducer molecule in the lac operon.

29

How is allolactose (the inducer in the lac operon model) formed?

Lactose passively diffuses into the cell and is converted to allolactose by the few betagalactosidase molecules that are present.

30

How is allolactose (the inducer in the lac operon model) formed?

Lactose passively diffuses into the cell and is converted to allolactose by the few betagalactosidase molecules that are present.

31

What is meant by the 'promoter' in the lac operon?

A region where RNA polymerase attaches when the genes are to be transcribed however it is blocked through steric hinderance by the repressor attached to the operator if lactose is not present.

32

What role is played by cAMP in the lactose operon?

-If glucose is present, there is not much cyclic AMP produced
-When glucose is present a phosphate is transferred from PEP to Hpr and then to IIA then to IIB then the membrane protein IIC which allows glucose to enter the cell and phosphorylates it as it moves into the cell. IIA has no phosphate so can’t activate adenylate cyclase to produce cAMP so no cAMP is produced (aka if glucose is present, it gets phosphorylated instead producing cAMP).

33

How does cAMP aid transcription?

cAMP binds to CAP (catabolic activator protein) protein which can bind to DNA.
-CAP binds to CAP binding site in the promoter region and allows transcription to occur even more (even faster transcription of operon).

34

How does CAP allow a transcription bubble to form?

The CAP forces the DNA to bend around the CAP protein which opens up the DNA so the transcription bubble can occur.

35

How does the protein IIA reduce the chance that the lactose operon will be switched on if glucose is present?

IIA regulates lactose pores to stop lactose getting in if glucose is present.

36

What is PEP?

-Phosphoenol pyruvate
-An intermediate in glycolysis which carries a high energy phosphate group which is transferred to the glucose phosphotransferase system in order for glucose to be phosphorylated and prevent cAMP forming and the lac operon being transcribed.

37

Briefly describe the tryptophan operon.

-Tryp is a co-repressor which binds to a repressor to form a holo-repressor which attaches to the operator and blocks RNA polymerase, this occurs in high tryp environments.

38

What is meant by negative control of the lac operon?

When the regulatory protein (that binds to the operator to either switch on or switch off the operon) is a repressor and the operon transcription is switched OFF.

39

What is meant by positive control of the lac operon?

When the regulatory protein is an activator. (e.g. CAP cAMP complex required to bind for transcription to occur).

40

What does constitutive mean (e.g. in the example of a lacI- gene being constitutive)?

Always expressed.

41

What does IIA do?

When glucose is present, it becomes dephosphorylated and inactivates adenyl cyclase which is the enzyme that produces cAMP.

42

What is adenyl cyclase?

The enzyme that produces cAMP during a cyclisation reaction.

43

Describe the two types of positive and negative control:

Positive:
-Induction
-Repression

Negative:
-Induction
-Repression

Positive induction- letting the activator work

Positive repression- preventing the activator from working

Negative induction- preventing the repressor from working

Negative repression- allowing the repressor to work

44

What do the 3 structural genes code for in the arabinose operon?

-Kinase
-Isomerase
-Epimerase

45

What are alternative sigma factors?

Sigma factors bind to RNA polymerase, there are different sigma factors which can attach to ensure different genes are transcribed.

Sigma factors are sub units of RNA polymerase that detach once the polymerase has attached and started transcription.

46

Name two ways in which bacteria control the termination of transcription. Describe how they work. (Use example of tryp operon)

Attenuation- in the leader sequence, there are three partially overlapping regions which are capable of forming stem loops. If there is lots of tryp present, stem loops one and three will form (only stem loop 3 is a terminator, the other two are just regions capable of forming stem loops). If there is little tryptophan present, the RNA polymerase will stall in the stem loop section 1 and will allow stem loop two will form and as it overlaps with stem loops one and three, the terminator will not form and transcription will not be terminated so the 5 structural genes for the tryp operon will be transcribed.

Antitermination- RNA pol moves along the promoter and when it reaches the antitermination site it picks up the antiterminator protein and brings it along with it. Having the antiterminator protein allows Pol termination signal 1 and keep transcribing the next block of genes until it reaches terminator 2, which it obeys

47

Describe the structure of ribosomes in bacteria and in eukaryotes (Hint: S number)

Ribosomes have two subunits: one large and one small.

Bacteria: 70S ribosome composed of 30S and 50S subunits

Eukaryotes: 80S ribosome composed of 40S and 60S subunits

48

What are ribosome subunits made of?

Ribosomal RNA (rRNA) and protein

49

What is the 'S' unit used to describe the size of ribosome subunits?

Svedberg units. Used to describe the rate at which particle sediments (moves to the bottom) of a liquid when centrifuged.

-The units don't add up because the S number depends on size, shape and density!

50

What is the active site of a ribosome called? What is it made from? What is the position of the active site?

Peptidyl transferase. Made from rRNA, not the protein. Positioned at the interface between the two subunits.

51

What do these do?
-Elongation factor 1A
-Elongation factor 1B
-Elongation factor 2

-Elongation factor 1A-loads tRNA with amino acid onto A site
-Elongation factor 1B-recycles EF1A after its used its energy from GTP
-Elongation factor 2-checks that translocation is successful and moves everything along by one space each time.

52

How does a release factor work in the ribosome?

-Release factor recognises stop codons and when it occupies the A site, it ends extension of the chain

53

What is a phage?

Nucleic acid + coat (capsid)

54

What are the lysogeny and lytic phases in bacteriophage lambda?

* Lysogeny
* DNA integrates into host chromosome and replicates along with host chromosome
* Lytic
* New phage is made, host is killed to allow bursting out, lots of new viruses made
* Induction event allows you to go from dormant stage into lytic stage- requires plasmid popping out of chromosome and becoming a plasmid again

55

What do the early and late genes do in bacteriophage lambda?

* Early genes must be switched on for viral proteins to be produced (proteins to kill host AND build new phages)
* Late genes switched on to allow cell lysis to release new viruses

56

Why do turbid plaques occur with respect to bacteriophage lambda?

When the host has been partially lysed (both lysogeny and lytic pathways occurring)=plaque

57

Why do clear and turbid plaques occur?

Clear-when lytic pathway occurs as they lyse the cells and release the contents.

Turbid-phage isn’t in the lytic phase because the plaque becomes occupied by lysogenic bacteria that do not lyse the bacteria.