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Biochem Block 3 > Gene Expression > Flashcards

Flashcards in Gene Expression Deck (76):
1

Gene expression

-multi step process that ultimately result in the production of a functional gene product
-RNA or protein

2

Housekeeping genes

-involved in basic cellular functions that are REQUIRED reguardless of the cell type or environmental cues
-constitutively expressed and not regulated

3

Regulated genes

-required only in certain cell types and/or certain conditions
-subject to control mechanisms
-determine when and what genes are expressed

4

How many levels of regulation of gene expression do prokaryotes have?

-1
-transcription only
-DNA is transcribbed into mRNA then, directly into a protein

5

How many levels of gene expression regulation are present in eukaryotes and what are they?

-5
-transcriptional
-post transcriptional
-translation
-post translation
-epigenetics

6

Epigenetics

-nothing changes to DNA, just accessibility
-euchromatin and heterochromatin

7

Why are Eukaryotes more regulated than prokaryotes?

-we have more differentiated types of cells
-transcription and translation are in different locations in eukaryotes

8

Where does transcription, translation, and post-translational regulation occur in eukaryotes?

Transcription: nucleus
Translation: cytosol
Post-translation: golgi

9

transcription regulatory molecules for prokaryotes

-repressors and activators

10

Repressor

-suppress the transcription of a gene

11

Activator

-increase the transcription of a gene

12

repressible operon

-transcription is usually on, but it can be repressed
-structural genes are on unless inhibited

13

Inducible operon

-transcription is usually OFF, but can be stimulated
-structural genes are usually off

14

What are the two regions in an operon?

-control region and structural genes

15

Control region

-controls ALL genes in the structural region

16

Structural genes

-genes that are necessary for expression

17

What is the preferred carbon source for E. coli?

Glucose

18

When does E. coli use other sources?

ONLY if...
1. glucose is absent
2. another sugar is present(lactose)

19

Why does E. coli prefer not to use other sources besides glucose?

-to use other sources, it must use more enzymes, which requires more energy

20

Is the Lac Operon on or off when glucose only is present?

OFF

21

repressor protein when glucose only is present?

-encoded by the laclgene, always present and bound to the operator, blocks RNA polymerase
-cannot transcribe gene

22

adneylyl cyclase when glucose only is present

-glucose inhibits adenylyl cyclase
-no cAMP
-cannot form CAP/cAMP complex
-cannot initiate transcription

23

Is the lac operon on or off when lactose only is present?

ON

24

adenylyl cyclase when lactose only is present

-able to make cAMP
-CAP/cAMP complex forms and binds to binding site
-RNA polymerase CAN EFFICIENTLY INITIATE TRANSCRIPTION

25

allolactose

-isomer of lactose
-when lactose is present, this is produced and binds to the repressor to prevent it from binding to the operator

26

is Lac operon on of off when glucose AND lactose are present?

OFF
-glucose inhibits adenylyl cyclase so no CAP complex to initiate transcription
-lactose produces allolactose, which binds to the repressor, but if there is no CAP complex, it does not matter
-no transcription

27

is the transcriptional control from prokaryotes and eukaryotes the same?

-nah bro
-the DNA structure is different, so they both do it, but its different

28

Eukaryote transcriptional control

-controlled by the regulatory sequences of DNA
-usually embedded in the noncoding regions of the genome

29

Cis-acting

-influence expression of genes only on the same chromosome
-only control genes downstream from it
-does not influence neighboring genes
-regulatory seguence of DNA that control transcription of eukaryotes

30

trans-acting

-transcription factors
-proteins
-interact with cis-acting regulatory sequences of DNA
-no trans-acting=no transcription

31

Binding of trans-acting regulators to DNA is achieved by one of the following...

-zinc fingers
-leucine zipper
-helix-turn-helix in the protein

32

Enhancers

-DNA sequences that increase the rate of initiation of transcription
-only recognize certain transcription factors

33

Where are enhancers normally located?

-typically on the SAME chromosome
-gene and enhancer are on same chromosome
-can be close to each other of thousands of base pairs away
-can be upstream OR downstream or in intron regions
-can act in tissue specific manner if the DNA binding proteins are only present in certain tissues

34

how are enhancers brought closer to the basal promoter?

-by bending the DNA molecule

35

Transcription factors

-trans-acting molecules
-DNA binding domain

36

Transcription factor activation domain

-bind to other transcription factors
-interact with RNA polymerase II to stabilize formation of the initiation complex and recruit chromatin modifying proteins

37

PEPCK gene expression is induced by...

-cortisol

38

PEPCK transcriptional control

-cortisol diffuses into hepatocyte and binds to intracellular receptor
-cortisol-receptor complex binds to glucocorticoid response element(in nucleus) to induce transcription of PEPCK

39

cortisol

-steroid hormone
-fat soluble

40

post-transcriptional control types

-alternative splicing
-mRNA editing
-mRNA stability

41

alternative splicing

-tissue specific isoforms of proteins can be made from the same pre-mRNA
-make different isoforms

42

how many genes in humans undergo alternative splicing?

60% of the 25000 genes

43

tropomyosin

-actin filament-binding protein
-contraction of muscles, in cytoskeleton
-undergoes alternative splicing

44

mRNA editing

-additional posttranscriptional modification in which base in mRNA is altered

45

Apo B mRNA in intestine

-the C residue in the CAA codon for glutamine is deaminated to U
-changes codon to a stop codon
-results in a shorter protein

46

which Apo B mRNA is in intestine and which is in liver?

-Apo B 48 in intestine
-Apo B 100 in liver

47

What does Apo B 48 mean?

48% of the message was coded

48

RNA interference (RNAi) types

-mechanism of reducing gene expression by...
-repressing translation
-increasing the degradation of specific mRNA

49

Which type of RNA interference is more common?

-increasing the degradation of specific mRNA

50

fundamental role of RNA interference

-cell proliferation, differentiation, apoptosis

51

RNA interference and AMD

-Neovascular AMD is triggered by over production of VEGF, leading to excess blood vessels behind retina
-RNA interference in trials is trying to degrade VEGF and prevent the making of new blood vessels

52

microRNA

-miRNA
-very short RNA(20 base pairs)
-mediates RNAi
-acts as a guide strand to traget specific mRNA that contain the complementary sequence

53

RNAi mechanism

-protein complex(RNA-induced silencing complex) works with miRNA
-expression of gene is reduced by cleaving RNA or blocking translation

54

siRNA

-double stranded short interfering RNA
-induced into a cell from an outside source can trigger RNAi
-if you know the target, you know what to introduce to fix it

55

translational control: elF-2 inhibition and promotion

- promoted by dephosphorylation
-inhibited by phosphorylation

56

phosphorylation of elF-2

-inhibits elF-2 function by inhibiting GDP-GTP exchange
-inhibits translation at the initiation step
-catalyzed by KINASES that are activated in response to environmental conditions

57

what environmental conditions activate kinases for phosphorylation of elF-2?

-amino acid starvation
-double stranded RNA
-misfolded proteins in rough ER

58

Post-translational control: modification of polypeptide chain

-after the chain is formed
involves...
-trimming
-covalent attachments
-protein folding
-protein degradation

59

triming

-post-translational control
-they are initially synthesized as large precursors then cleaved to become functionally active
-digestive proteins

60

covalent attachments

-post-translational control
-phosphorylation
-glycosylation
-hydroxylation
-many others

61

protein folding

-directed by chaperones

62

protein degradation

-post-translational control
-by ubiquitination
-proteins target molecules to degrade them

63

euchromatin

-loosely packed DNA
-less dense
-accessible for transcription

64

heterochromatin

-tightly packed DNA
-not easily accessible for transcription
-more dense

65

epigenetic regulation is modification in...

-histones
-DNA

66

CpG islands

-regions in NDA rich in CG that are prone to modification for epigenetics

67

mechanisms of epigenetic reglation

-acetylation and methylation

68

acetylation of histones

-results in loose packing of DNA
-transcription factors can bind and transcription can go

69

methylation of DNA and histones

-makes nucleosomes pack tightly together
-less exposed, less accessible for transcription

70

what can cause epigenetic changes>

-development
-diet
-chemicals
-drugs
-aging

71

epigenetic changes can result in...

-cancer
-autoimune disease
-mental disorders
-diabetes

72

transposons(Tns)

-mobile segments of DNA that move in a random manner from one site to another on the same OR different chromosome

73

movement of Tns is mediated by...

-transponase
-enzyme encoded by Tn

74

Direct movement of Tns

-transponase cuts out and then inserts the Tn at a new site
-cut and paste

75

replicative movement of Tns

-Tn is copied and the copy is inserted elsewhere and original remains in place

76

diseases associated with transpostion

-hemophilia A
-duchenne muscular dystrophy
-can cause antibiotic resistance