Midterm 2

Question 1

(CENTRAL DOGMA OF BIOLOGY)

DNA Replication

Answer 1

Duplicates the DNA molecule so its encoded information can be passed on to the next generation.

Gene Expression to Transcription copies the information in DNA to RNA then Translation interprets the information carried by RNA to synthesize the encoded protein.

Question 2

In prokaryotes

Answer 2

• coupled transcription-translation
• transcriptional unit: operon (from promoter to termination signal)
• polycistronic mRNA

Question 3

Coupled transcription-translation

Answer 3

-Translation occurring before end of transcription.

Question 4

Polysome:

Answer 4

several ribosomes translate the same RNA at the same time

Question 5

Expenses

Answer 5

-presence of a particular compound stops endogenous synthesis of that compound fueling, biosynthesis and polymerization are tightly controlled –> This saves energy__> by sensing the environment or adapting to the environment

Question 6

Inducible enzymes

Answer 6

These enzymes are not routinely produced, but mechanisms can turn expression on for as long as needed, for example when the enzyme’s substrate is present.

Question 7

Repressible enzymes

Answer 7

These enzymes are routinely produced, but mechanisms can turn expression off for as along as necessary for example when the enzyme’s product is present in sufficient quality.

Question 8

(Action of enzymes)

Enzyme

Answer 8

A molecule (generally a protein) with catalytic activity, speeding up the reaction of conversion of a substrate to a product.

Substrate binding to enzyme leads to change in enzyme shape

Question 9

Regulation by repressors

Answer 9

Repressor is a regulatory protein that blocks transcription by binding the operator .

Question 10

(Regulation by repressors)

Induction

Answer 10

look at desktop image

Question 11

(Regulation by respressors)

Repression

Answer 11

look at desktop image

Question 12

Regulation by activators

Answer 12

Activator is a regulatory protein that enhances transcription by enabling RNA pol to bind to the promoter.

Question 13

Allosteric regulation, “ other shape”

Answer 13

an allosteric protein has an :

• active (catalytic) site
• alloseric (effector, regulatory ) site

in an allosteric enzyme:

• active site: binds to S and converts it to P
• allosteric site: occupied by a small (effector) or big (modulator) molecule, which is not a substrate

Question 14

Regulation and its may modes of action

Answer 14

1. ) promoter recognition
2. ) transcriptional repression
3. ) transcriptional activation
4. ) transcriptional enhancement
5. ) regulatory sRNA
6. ) DNA supercoiling
7. ) Translational repression
8. ) attenuation
9. ) messenger stability
10. ) proteolysis

Question 15

(complex responses)

Stimulon

Answer 15

Genses that are up-regulated or down-regulated as a group, upon response to a stimulus–> monitoring the transcriptome and monitoring the proteome —> synthesis/activation of dozens/hundreds of proteins.

Question 16

(Above the operon)

The operon

Answer 16

prokaryotic unit of transcription.

Question 17

(Above the operon)

The regulon

Answer 17

in dependent operons controlled by the same regulator, a group of genes regulated by the same environmental signal, repressor or activator. (such as arg regulon of E.coli)

Question 18

(Above the operon)

The modulon, sometimes referred to as the global regulatory system

Answer 18

a higher hierarchy, including operons from different regulons.
(ex: catabolite repression system through CAP/cAMP, stringent response system)

Question 19

Sensing the environment

Answer 19

Stress- extreme conditions are not stress by sudden change is!

This includes: 
pH
Temperature
Redox potential 
light 
osmolarity
individual nutrients (organic and inorganic) 
presence of toxic substances

two-component signal transduction/regulatory system

• signal transduction
• regulatory cascades
• multicomponent regulatory systems.

Question 20

The stationary phase RpoS regulon

Answer 20

sRNAs - regulators of translation initiation

sRNAs serve as integrators of signals –> specific response

Question 21

Chemotaxis

Answer 21

survival: away of toxins
growth: towards nutrients
virulence: colonization
communal: aggregation

taxis

to chemicals ---- chemotaxis
to oxygen --- aerotaxis
to pH  -- pH taxis
to magnetic force --- magnetotaxis
to temperature --- thermotaxis
to light --- phototaxis

Question 22

Chemotaxis circuit

Answer 22

look at adapting to environment slides #7

Question 23

Movement

Answer 23

counterclockwise coherent —> run which is no change in direction

clockwise incoherent –> tumble which is change in direction

Question 24

The global control system of carbon catabolite repression of the lac operon

Answer 24

Glucose is easiest sugar to catabolize

If glucose is present, lac is not transcribed due to inactivation of CAP

The catabolite activator protein CAP, (also called CRP, cAMP receptor protein)

High glucose–> low cAMP –> CRP/CAP inactive

Does not bind operons –> low level of lac transcription

lactose induces transcription by pulling the Lacl repressor off

glucose prevents transcription by pulling the CAP activator off.

Question 25

The tryptophan attenuator

Answer 25

attenuation regulation:
Trp presence, tryptophanyl-tRNA Trp leader, trpL gene

Stem loop structures in attenuator region

Question 26

Microbe metabolism

Answer 26

Microbial metabolism

• catabolism
• anabolism

Energy sources
-phototrophy
-lithotrophy
-organotrophy
Cellular energy 
Key catabolic pathways
-fermentation
-respiration
Carbon assimilation
-heterotrophy
-autotrophy
Central and auxiliary metabolic pathways.

Question 27

Building the cell

Answer 27

Catabolism
-chemical processes to break down molecules for energy

Anabolism
-Chemical processses to use energy to build cell components

Metabolism

• All chemical processes in the living organism
• Balance between catabolism and anabolism.