kevin (L1-4)

Question 1

constitutive expression

Answer 1

genes that are always expressed

Question 2

general transcriptional mechanisms

Answer 2

these are the mechanisms used for the control of gene expression. there are 2:
INDUCTION - the switching on of genes when they are required
REPRESSION - the switching off of genes when they are not required

Question 3

operon

Answer 3

many genes being transcribed together from a single promoter
An operon is regulated like it was a single gene
Have a linked function and produce a polycistronic mRNA (where more than one gene is expressed in the same mRNA strand)

Question 4

repressors

Answer 4

Repressors are regulatory proteins which prevent transcription when bound to the DNA

(Regulatory proteins are often converted between inactive and active states by binding of small molecules (effectors like inducers and co-repressors))

Question 5

activators

Answer 5

Activators (apoinducers) are regulatory proteins which activate transcription when bound to the DNA

(Regulatory proteins are often converted between inactive and active states by binding of small molecules (effectors like inducers and co-repressors))

Question 6

regulons

Answer 6

Genes associated with a particular physiological function may not be in just one operon
These operons may be controlled by a single regulatory protein – together they are called a REGULON
The phosphate or PHO regulon consists of >80 genes in many operons, all are controlled by one regulatory protein

Question 7

global control / global regulation system

Answer 7

often an organism needs to regulate many genes associates with different metabolic functions in response to a single environmental factor.
Control systems that operate on such a wide basis are known as GLOBAL CONTROL or GLOBAL REGULATION SYSTEMS

Question 8

diauxic growth

Answer 8

If both glucose and an alternative carbon source is available the glucose is used first - Diauxic growth (when 2 carbon sources are being utilised in succession not at the same time)

Question 9

catabolite repression

Answer 9

Glucose represses the synthesis of enzymes that metabolise less preferred carbon sources

Question 10

lac phase in an e coli’s diauxic growth

Answer 10

When the cells run out of glucose there is a very rapid induction of the enzymes of lactose metabolism. We enter the lac phase, and the e coli switches its genes and proteins it’s producing to utilise the second carbon source, lactose

Question 11

lac Z

Answer 11

gene that encodes β-galactosidase, which cleaves β-galactosides into monosaccharides

Question 12

lac Y

Answer 12

gene that encodes β-galactoside permease, a cytoplasmic membrane protein which transports β-galactosides into the cell

Question 13

laz A

Answer 13

gene that encodes β-galactoside transacetylase, which is thought to detoxify toxic β-galactosides by acetylation

Question 14

promoter

Answer 14

lacP, where RNA polymerase bind

Question 15

operator

Answer 15

lacO, where the lac repressor binds

Question 16

cap site

Answer 16

where the cAMP acceptor protein (CAP; also called the catabolite repression protein, CRP) binds

Question 17

adenyl cyclase

Answer 17

ATP is converted to cAMP by the enzyme adenyl cyclase
When glucose is present adenyl cyclase is inactive
Once glucose is used up adenyl cyclase becomes active and makes cAMP

Question 18

Insertion vectors

Answer 18

Non-essential DNA has already been removed at a specific restriction site and DNA can be cloned and inserted into this site

Question 19

Replacement vectors

Answer 19

Non-essential ‘stuffer’ DNA is replaced with new non-coding DNA to be cloned

Question 20

fosmids

Answer 20

fosmids are large plasmids based on the F plasmid with cos-sites, lacZ and a T7 promoter added. (they can be used for us to fit in a lot of dna).

The cos-sites allow the vector to be packaged into λ phage particles for transfection into E. coli
Up to 40kbp (+8kbp of vector) can be packaged into each phage particle

Question 21

plasmid/phage cloning mix

Answer 21

Once a fosmid is transfected into an e coli cell, they are maintained in the cell as a plasmid.
This is a mix between plasmid and phage cloning.

Question 22

fosmids and cosmids

Answer 22

If you remove everything but its essential parts, you can create a plasmid vector (fosmid or cosmid) that allows you to produce bigger fragments of dna. These are engineered molecules (originally come from an F plasmid) that were engineered to have cos sites (at the end of a lambda phage, which allow it, when the dna is put into an e coli cell, to circulise itself).
So the 2 cos sites bind to each other to produce a very large 50kbp plasmid.

Question 23

ti plasmid

Answer 23

The Ti plasmid is found in the plant pathogen Agrobacterium tumefaciens and causes tumours (crown galls) on plants
Only a specific portion of the Ti plasmid is transferred into the plant cell and is then integrated into the plant genome to damage those cells

Question 24

BACs

Answer 24

BACTERIAL ARTIFICIAL CHROMOSOMES (BACs) – can carry up to 300 kbp of cloned DNA
Some vectors that can take very large fragments have been dubbed “artificial chromosomes”

(Based on the F plasmid they often carry selectable markers and their screenable marker is the lacZ gene)

Question 25

YACs

Answer 25

YEAST ARTIFICIAL CHROMOSOMES (YACs) are based on real yeast chromosomes and in order to replicate they must contain origins of replication, a centromere and telomeres
They are engineered to carry specific selectable and screenable markers and are often circularised by having a linker joining the 2 telomeres

Question 26

addiction cassettes

Answer 26

Low copy number plasmids encoded mechanisms called addiction cassettes that ensure that even if a plasmid-free cell is produced, it quickly dies

produces a very stable mRNA of a lethal membrane protein, also makes a ncRNA, a highly unstable anti-sense RNA molecule that binds to mRNA to prevent translation of lethal mRNA

Question 27

the non coding rna: rhyB

Answer 27

involved in controlling iron use
- IRON AVAILABLE
Global regulator FUR binds Fe2+ and represses ryhB (RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting)
All iron-requiring proteins are made
Any free iron is bound to these proteins
- IRON NOT AVAILABLE
FUR stops repressing ryhB
RyhB ncRNA binds to mRNA of nonessential iron needing proteins which degrades

Question 28

Positive interactions

Answer 28

toxic product of one organism may be substrate for another

Question 29

quorum sensing in Staphylococcus aureus

Answer 29

• P2 promoter constitutively expresses the proteins AgrA, B, C and D
  AgrD – Autoinducing peptide (AIP)
  AgrB – Transmembrane protein, secretes mature AIP
  AgrC – AIP receptor, binds AIP then phosphorylates AgrA
  AgrA – Response protein, activates P3 producing RNAIII
• At low cell density concentration of AIP is low
  AgrC inactive so no phosphorylation of AgrA to activate P3 and produce RNAIII
  Cell expresses many surface adhesins, which enhances biofilm formation
• As biofilm matures cell density and so AIP concentration rise
  At a threshold, AIP activates enough ArgC which phosphorylates ArgA
  ArgA-P then activated P3 to produce RNAIII (which acts as a regulatory RNA controlling many genes)

Question 30

five stages of biofilm development

Answer 30

1. Initial attachment – flagella, type I pili
2. Irreversible attachment – LPS, Type IV pili
3. Maturation I – micro-colonies, produce aliginate, repress flagella
4. Maturation II – Quorum sensing
5. Dispersion – release planktonic cells

Question 31

sigma factor

Answer 31

σ22 is encoded by algT, in the aliginate synthesis operon