BCHM 4360 EXAM II ACTUAL QUESTIONS AND

BCHM 4360 EXAM II (ACTUAL / ) QUESTIONS AND

VERIFIED ANSWERS 100% PASS

Describe the helix-turn-helix and its interaction with DNA. - -- -Answersw----DNA-binding motif that is common and found in many protein folds. It has the first helix and the recognition helix that fits in the major groove.

What is the homeodomain? - ---Answersw----common eukaryotic DNA binding domain that is a monomeric helix- turn-helix

Describe the structure of a zinc finger and how it interacts with DNA. - ---Answersw----~30 amino acids with an alpha helix and two beta strands around a central zinc ion. The zinc interacts with two cysteines and two histidines

What are the most common DNA-binding domains in the human genome? - ---Answersw----zinc fingers

Describe basic region-leucine zippers (bZIP) - ---Answersw-- --long alpha helices of about 60 amino acids, have hydrophobic leucine residues on the surfaces that zip together

Describe basic region-helix-loop-helix (bHLH) proteins - --- Answersw----four helices joined by a loop that fits in the major groove, region where the four helices interact is called the four-helix bundle 1 / 4

What kind of domain is the Trp repressor and what is its basic function? - ---Answersw----helix-turn-helix, prevents RNA Polymerase from accessing the promoter

What happens to the Trp operon when tryptophan levels are high? - ---Answersw----the tryptophan repressor binds to the Trp operator and blocks RNA Polymerase from binding

In low tryptophan, which two regions, or blocks, pair together to form a step-loop? - ---Answersw----2 and 3

In high tryptophan, which two regions, or blocks, pair together to form a Rho-independent terminator? - ---Answersw----3 and 4

What is another term for an intrinsic terminator? - --- Answersw----attenuator

Explain what Catabolite Activator Protein (CAP) does. - --- Answersw----Activates more than 100 bacterial promoters when carbon sources are low.

What is CRP? - ---Answersw----cAMP receptor protein

• / 4

What does glucose depletion lead to with regard to CAP/CRP?

• ---Answersw----increase in cAMP levels, binds to CAP and

increases its binding to DNA

What is the difference between class I and class II CAP? - --- Answersw----Class I, CAP binds upstream of the promter, Class II, CAP binding site overlaps RNA Polymerase binding site

Lactose binds to the lactose repressor, preventing it from binding. So when lactose is absent, what happens? - --- Answersw----the repressor binds to the lac operator and transcription is off

Low glucose, lactose unavailable, transcription? - --- Answersw----off

High glucose, lactose unavailable, transcription? - --- Answersw----off

Low glucose, lactose available, transcription? - ---Answersw- ---Strongly on, CAP binds to CAP operator, enhancing transcription

High glucose, lactose available, transcription? - ---Answersw- ---weakly on, CAP does not bind CAP operator, but repressor is not bound so weak transcription

• / 4

True or False: The spacing between -10 and -35 sequences can

vary - if it is very large, RNA Polymerase binding is weakened

• this is another layer of regulation. - ---Answersw----True

Describe the function of the MerR family regulators. - --- Answersw----Bind to DNA and change its conformation to change the -10 to -35 distance from 19 bases to 17 bases, allowing RNA Polymerase to bind more readily.

True or False: The RNA Polymerase holoenzyme that contains

sigma factor 54 needs to be activated by ATP hydrolysis to drive promoter opening. - ---Answersw----True

What does NtrC do? - ---Answersw----Activator in sigma factor 54 system that activates genes that are important for nitrogen metabolism

Describe how NtrC works with regards to activation. - --- Answersw----1. NtrC binds at enhancer elements and activates transcription when phosphorylated.

• Phosphorylation triggers oligomerization of NtrC, and

promotes interaction with the polymerase at the promoter.

• Oligomerization also stimulates its rate of ATP hydrolysis,

which helps promote formation of the open complex.

Describe how a two-component signal transduction pathway works. - ---Answersw----1. There is a sensor kinase and a response regulator (two components).

• / 4