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EOM 1 - Test 2 > Miles - Biochemical Control and Gene Regulation I, II, III > Flashcards

Miles - Biochemical Control and Gene Regulation I, II, III Flashcards

1
Q

How does substrate concentration or availability effect pathway?

A

For many enzyme, Km=physiological concentration–this will keep First Order and respong best to change in Substrate. Cofactors and compartmentalization lso play a role.

In higher organisms can also change quantity and efficiency of enzymes via regulation. (Feedback, inhibition, activation by proteolysis, +/- Phosphate)

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2
Q

What is difference between prokaryote and eukaryote regulation?

A

Prokaryotes: Gene expression is temporally separated, transcription and translation are coupled

Eukaryotes: Gene expression is temporally and spatially separated. Transcription in nucleus, translation in cytoplasm.

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3
Q

How does regulation of gene expression control enzymatic processes?

A

Housekeeping: Trancribed in fixed amount, required at all times

Growth Medium: Made is low amounts in response to medium, higher when stimulated

Biosynthesis: Made when endproduct is not present in growth medium, repressed if end product is available

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4
Q

What type of system is the lac operon an example of?

A

Inducible Enzyme System

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5
Q

During induction of the Lac Operon, what occurs in the following media situations:

Glucos

Lactose

Glucose + Lactose

A

Glucose = DownDownDown

Lactose = UpUpUp

Glucose + Lactose = Up

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6
Q

What occues when glucose is in the media for the Lac Operon?

A

Repressor bind to operator to block transcription—NEGATIVE CONTROL

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7
Q

What occurs when lactose is in the media for the Lac Operon?

A

Inducer binds to repressor to release from operator, RNA polymerase proceeds;

At low glucose cAMP is high and binds to CAP protein, which binds to CAP site—increase RNA polymerase binding to promoter.

Positive Control.

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8
Q

What occurs when Glucose and Lactose are present in the medium for the Lac Operon?

A

Inducer releases the repressor from the operator, however cAMP is high, so no CAP-cAMP complex forms. Catabolite Repression.

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9
Q

What occurs during a Lac-I mutation?

A

Repressor unable to bind operator, constitutive gene expression

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10
Q

What occurs during a Operator locus mutation in the Lac Operon?

A

Operator sequence can bind repressor–constitutive expression

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11
Q

Describe the Jacob and Monod model of enzyme repression?

A

f the end product is available from the medium, them enzymes of the biosynthetic pathway are not made. If the end product is absent from the medium then the enzymes are made.

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12
Q

What type of regulation is usually used in the anabolic pathway?

A

Derepression

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13
Q

What must a repressor have complexed to it in order to gain affinity for the operator?

A

Corepressor

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14
Q

What is the result if end product is not available in Jacob Monod model?

A

All enzymes are coordinately de-repressed (they are made)

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15
Q

Attenuation

A

Premature termination of mRNA synthesis

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16
Q

What is the difference in prokaryotic attenuation vs Operon model?

A

Regulation at variable termination, NOT variable initiation.

Occurs at transcription level

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17
Q

Attenuation;

High AA Concentation =

Low AA Concentration =

A

High = mRNA synthesis is terminated to prevent enzyme synthesis

Low = mRNA synthesis is completed

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18
Q

How is attenuation regulated?

A

Secondary structure forming at 5’ end of nascent mRNA; depends on rate of movement of first ribosome to translate message

Histidine Operon is example

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19
Q

How is the Histidine Operon model regulated?

A

Attenuation (variable termination)

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20
Q

What are the five levels of regulation?

A
  1. Genome
  2. Transcription

Post Transcription:

  1. RNA processing and export
  2. Translation
  3. Post-translation
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21
Q

What type of chromatin is subject to DNase I cutting?

A

Euchromatin

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22
Q

What are possible control points for gene expression in eukaryotes?

A

Environmental and Differentiation

It’s a long list, each has their own notecard.

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23
Q

X Chromosome Inactivation

A

Occurs in females, one X chromosome is methylated and turned off

24
Q

Lyon Hypothesis

A

Methylated section of chromosomes are Barr bodied, not identical in all cells

25
Q

Imprinting

A

Normal process, inactivation of certain genes from each parent in the autosome–happens in normal people when both genes aren’t needed

26
Q

When is the gene inactivated during imprinting?

A

Inactivated via methylation during gametogenesis

27
Q

Prader-Willi

A

Silenced Maternal, deleted Paternal;

Small hands/feet, obesisity, mental retardation

28
Q

Angelman

A

Silenced Paternal, Deleted Maternal; behavior disorders, seizures

29
Q

Is HbS a quantitative or qualitative “problem”?

Thalassemia?

A

HbS = Qualitative; make Hb, just incorrectly

Thalassemia = Quantitative, under production

30
Q

How are lymphocytes regulated during differentiation?

A

Specific chromosomal regions may be activated by translocation (gene rearrangement)

31
Q

What is a control point for RBC regulation?

A

Specific chromosomal materia is lost during development, or gene deletion.

It kicks out the nucleus.

32
Q

Xenopus cells have 900 RNA genes, what control point is this an example of?

A

Gene Reiteration, presence of many identical copies permits high rate of transcription

33
Q

Gene Amplification

A

Exception to adult eukaryotes having same genome. Select cells make a lot of the same gene. Can be a problem in DHFR amplification in methotrexate resistant cancer cells.

34
Q

Trancription Factors

What can activated transcription of genes?

A

Allow turn on/off transcription via Trans Regulators binding at enhancer.

Steroid Hormones

35
Q

How do steroids activate transcription of genes?

A
  1. Enter cells, interact with steroid hormone receptor
  2. Normally inactive–binding activates
  3. Receptor+Transcription Factor translocates to nucleus, activates genes
36
Q

What type of control is the acetylation of histone an example of?

A

activation via transcription factors

37
Q

Alternative Splicing

A

Allows coding of different proteins from same mRNA strand, example are antibodies.

38
Q

What will the composition of antibodies be for:

Membrane Bound

Secreted

A

Membrane = Hydrophobic

Secreted = Hydrophilic

39
Q

Where must mRNA be transported for translation? What implication does this have on regulation?

A

Must be transported to cytoplasm; dictates rate of synthesis of new RNA molecule of given protein

40
Q

What does the length of Poly-A tail have to do with control points for regulation?

A

Add stabilization, this is example of regulation through finite “life” for a cell

41
Q

What does the Ferritin/Transferrin regulation represent an example of?

A

Rate of translation

42
Q

Ferritin/Transferrin:

Low Iron

High Iron

A

Low Iron = Low Ferritin Binding, High Transferrin Import

High Iron = High Ferritin Binding, Low Transferrin Import

43
Q

RNA Interference (RNAi)

A

Small pieces of RNA can bind 3’ untranslated region

44
Q

Micro RNA (miRNA)

A

Imperfect match inhibits translations

45
Q

Short Interfering RNA (siRNA)

A

Exact match, leads to mRNA degradation, used in lab to block protein synthesis.

46
Q

HAT

A

Acetylation of lysine residues on Histones

= gene expression, reduces positive charge on tail and decreases affinity for negatively charged DNA

47
Q

HDAC

A

Removes acetylation from Histones, lowers chromatin activity

48
Q

DNA Methylation

A

Methylantion of cytosine residues favors inactive chromatin

49
Q

De Novo Methylation enzymes?

A

Methyltransferases - DNMT3A, DNMT3B

50
Q

Maintenance DNA Methylation Enzyme

A

DNMT1

51
Q

Demethylation of DNA enzymes

A

DNA demethylase

52
Q

What type of structure are steroid hormone receptors?

A

Zinc Fingers

53
Q

Zinc Finger

A

Zinc molecule subunit held together by cysteine and histidine

= transcription factor

54
Q

Helix-Turn-Helix

A

Two alpha-helices separated by a bend in chain, one helix binds the other stabilizes

55
Q

Leucine Zipper

A

Formed by interaction b/t two polypeptide chains w/reguarly spaced leucine residues, causing helices to wrap around eachother

56
Q

What are two types of things that can effect epigenetics?

A

Histone Mods/DNA Methylation

Diet

57
Q
A

EOM 1 - Test 2 (18 decks)

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