Gene Expression & Regulation

Front 1

what is gene expression?

Back 1

-process by which infor. from a gene is used in the synthesis of a functional gene product.

ex: DNA > RNA> protein > trait

Front 2

gene product includes what?

Back 2

-protein coding genes: produce proteins

-non-protein coding genes:

-rRNA genes & tRNA genes: functional RNA

Front 3

what is univeral?

Back 3

process of gene expression is used by all known life, eukaryotes, prokar,viruses

Front 4

gene expression dtermines organism behavior depending on what?

Back 4

-nature of gene expressed

-extent of expression

-not depends on size of genome

(environmental conditions affecting gene expression)

Front 5

based on how the genes are regulated, genes fall into what two categories?

Back 5

1.) housekeeping genes

2.) high regulated genes

Front 6

what is house keeping genes?

Back 6

-necessary for basic function of any cell

-under minimal regulatory control

-genes are expressed at any time at the same level

ex: actin, GADPH, ubiquitin

Front 7

what is highly regulated genes?

Back 7

-expressed under high regulatory control

-allows for cellular adaptation, variation, differentiation, & development

-provide max. growth rate under certain environ. stimuli

Front 8

Highly regulated genes include what?

Back 8

1.) constuttive gene: a gene that is transcribed continually

2.) facultative gene: gene which only transcribed when needed

3.) inducible gene: whose expression is either responsive to environ. change or dependent on the position in the cell cycle.

Front 9

what is activators?

Back 9

DNA binding protein, positive regulation, increases gene transcription or up regulate

Front 10

what is repressors?

Back 10

DNA binding protein, negative regulatin, decrease or eliminates gene transcription or down regulate

Front 11

what is operon?

Back 11

several genes w/related functions that are regulated together

Front 12

what is operator?

Back 12

DNA site where repressor binds

Front 13

Prokaroytic genome?

Back 13

-polycistornic (operons) (mRNA coding for more than 1 polypeptide)

-proteins belonging to same regulatory pathway are grouped on the same part of chrome.

-have no repetitive sequences except for some rRNA and tRNA genes

-NO INTR0N (extremely efficient)

Front 14

Eukaryotic genomes?

Back 14

-monocistronic

-pretiens beloging to same regulatory pathway are rarely grouped on the same part of the chrome.

-many DNA segments are repeated, hundreds, thoussands of tmes

-introns in their genes (lots of non-coding sequence)

Front 15

in prokaryotic what is polycistronic?

Back 15

mRNA coding for more than one polypeptide

Front 16

what is operons?

Back 16

several genes w/related functions that are regulated together.

-one piece of mRNA codes for several related proteins.

Front 17

And operon consists of what?

Back 17

-structrual genes

-regulatory genes

-individual promotor for structural genes and regulatory genes

Front 18

what is structural genes?

Back 18

code for the enzymes/proteins of interest

Front 19

what are regulatory genes?

Back 19

control the expression of structural genes by expressing regulatory proteins

Front 20

where is the operator located?

Back 20

btw the promotor & the first structural gene and involved in transcription of structural gene in prokaryotes

Front 21

features of transcription regulation in prokaryotes include?

Back 21

-bacterial genes controlled by extracellular signal (molecules in growth medium as signals are communicated to genes by regulatory protein)

-regulatory proteins are DNA-binding proteins that recognize specific sites at or near the genes they control

Front 22

name the types of transcriptional regulation in prokaryotes?

Back 22

1.) positive regulators or activators

2.) negative regulators or repressors

3.) combinatin regulators

4.) feedback inhibit regulators

Front 23

which two types of transcriptional regulation in prokarotyes are most involved?

Back 23

positve and negtiave regulators

Front 24

what is positive regulation?

Back 24

-aka up regulation

-protein binds to regulatory region of gene to turn on expression

-utilizes activators to increase the level of transcription

-someitmes, activators must associate w/a signal molecule to function

Front 25

what i negative regulation?

Back 25

aka down regulation

-protein binds to regulatory region of gene to turn off expression

-utilizes represssors, only functions if it complexes w/ a signal molecule

-somtimes, an inducer is needed to stimulate transcription

Front 26

what is combination regulation?

Back 26

-uses both pos. and neg. regulatin for the same operon

-allows increase sensitivity

-frequently the same proteins can act as repressor or inducer (depends on conditions w/in the cell)

Front 27

what is feedback inhibition regulation?

Back 27

-product of the pathway inhibits enzyme activity

-can occur at level of transcription or translation (enzyme produced inhibits transcription/translation, enzyme present can be inactivated)

-small allosteric effector molecules can also be used to activate or inhibit enzyme activity

Front 28

what is lac operon?

Back 28

-1st operon discovered

-contains 3 structural genes coding e. coli proteins that permit the bacteria to use the sugar lactose

Front 29

ware are the 3 structural gens and functions?

Back 29

1.) lacZ : galactoside premises which transports galactose into the cells

2.) lacY: beta-galactosidase cuts the lactose into galactose and glucose

3.) lac A: thiogalactoside rids the cell of toxic thiogalactosides

Front 30

all genes are grouped how?

Back 30

lacZ, lacY, lacA (ZYA)

Front 31

all 3 genes are transcribed together producing what?

Back 31

1 mRNA, polycistronic message that starts from a single promotor

-each gene has its own ribosome binding site

-each gene can be transcribed by separate ribosomes that bind independtly of each other

Front 32

look at the image

Back 32

Front 33

what is the regulatory element of Lac operon?

Back 33

lac1 gene

Front 34

what happens in the regulatory element of Lac operon - lac1 gene?

Back 34

- has its own prmotor gene

-produced constitutively repressor protein

Front 35

-when lactose absent, what happens?

Back 35

repressor proteins binds to the operator and inhibit transcription or turns it off.​

-SAmpLe of neg. control

Front 36

when lactose is present what happens?

Back 36

lactose binds to repressor

-operon is depressed

-transcription turned on, genes express and enzymes produced

SAMPLE OF substrate induction

Front 37

in Lac operon the protein and allosteric regulation include?

Back 37

-repressor and inducer

Front 38

what happens in the repressor in allosteric protein?

Back 38

binding of one molecule to the protein changes shape o a remote site on that protein and alters its interaction w/a second molecule

Front 39

what is an inducer (one molecule lactose) of lac operon do?

Back 39

binds the repressor causing the repressor to change conformation that favors release from the operator

-second molecule - allosteric regulation

Front 40

what happens in the lac operon positive regulation?

Back 40

-when glucose is scarce, CAP is activated by binding w/ cyclic AMP.

-activated CAP attachees to the promotor of lac operon and increases infinity of RNA poly, = accelerating transcription

Front 41

image of lac operon

Back 41

Front 42

in lac operon, if there is glucose and there is lactose what happens?

Back 42

-glucose = yes

-lactose = yes

-transcription = low

-cAMP = low

Front 43

in lac operon, if there is glucose and there is NO lactose what happens?

Back 43

-glucose = yes

-lactose = no

-transcription = none

-cAmp = low

Front 44

in lac operon, if there is NO glucose and there is lactose what happens?

Back 44

-glucose = no

-lactose = yes

-transcrpition = yes (high)

-cAMP = high

Front 45

what is trp operon?

Back 45

-contains all the enzymes needed to synthesize tryptophan

-example of end product repression (feedback inhibition)

Front 46

in the absence of tryptophan what happens?

Back 46

repressor stays in inactive form, trp operon = open

Front 47

what opens when there is tryptophan?

Back 47

either from synthesis or from environment, trtptophan will bind to the repressor and the active repressor.

-active form of repressor will bind to the operator, turn off gene expression and stop manufacturing the amino acid tryptophan

Front 48

trp operon image

Back 48

Front 49

araBAD operon consists of 3 genes which are?

Back 49

araB, araA, araD ( BAD) that coded for three digestive enzymes involved in breakdown of arabinose are clustered together

Front 50

the three proteins in araBAD are dependent on?

Back 50

initiation of trancspriton from a single promotor

(PBAD)

Front 51

imaga araBAD

Back 51

Front 52

araBAD operon is only turned on when what?

Back 52

substrate arabionose inducer is present

Front 53

what happens in araBAD operon when there is NO arabinose?

Back 53

AraC acts as a repressor, which binds to operator/promoter region to inhibit the binding of RNA polymerase

Front 54

what happens in araBAD operon when there is arabinose?

Back 54

AraC acts as activator, AraC-arbainose complex undergoes conformational change and performs as activator

-binds to operator/promotor region to stimulate RNA poly. activity

Front 55

image of ARA BAD operon 2

Back 55

Front 56

eukaryotic genomes is?

Back 56

-monocistronic

-proteins belong on same regulatory pathway

-many dNA segments are repeated

-introns (lots of non-coding seqence)

-most cells are genetically identical

-differential gene expression leads diff. cell types

-errors in gene expression = diseases

Front 57

list the 7 possible points of control (points in gene expression regulation) in eukarytoes?

Back 57

1.) chromatin modification

2.) transcrption

3.) RNA processiong (splicing)

4.) mRNA transport

5.) mRNA degradation and storage

6.) translation

7.) post-translation modifications/modulation of protein activity

Front 58

chromatin structure, genes w/in highly packed heterochromatic are usually not what?

Back 58

expressed

Front 59

histones modifiaction and DNA methylation influcence both what?

Back 59

chromatin structure & gene expression

Front 60

what is histone modification?

Back 60

histone acetylation, acetyl groups are attached to pos. charged lysines in histone tails

-this process loosens chromatin structure, = initiation of transcrptions

Front 61

image of histone modification

Back 61

Front 62

what is DNA methylation?

Back 62

-addiation of methyl groups to certain bases in DNA, associated w/reduced transcrption

-DNA methylation can causes long term inactivation of genes in cellular differentiation such as FMR1 gene in fragile X syndrome

Front 63

differential mentation can occur in ...

Back 63

single genes or entire chrome. regions

Front 64

site of methylation is important because?

Back 64

-methylation is a promotor region will turn off transcrpition, if the coding region is highly methylated, there is no effect on gene activity

-prevents binding of transcrpition factors & thus blocks RNA polymerase 2.

Front 65

chromatin-modifying enzymes provide what?

Back 65

initial control of gene expression by making a region of DNA either more or less able to bind to transcript machineary

Front 66

most eukar. genes are regulated by some what?

Back 66

non-coding DNA sequence and certain binding proteins

Front 67

what factors involved in regulation of transcriptin in ekukarotyes?

Back 67

-regulated by several basal transcription factors and specific transcription factors such as enhancers and activators.

Front 68

what is several basal transcription factors?

Back 68

forms complex w/ the RNA polymerase to recognize a promotor and initiate transcription

Front 69

what is an enhancer?

Back 69

short region of DNA that can be bound w/ proteins to enhance transcription levels of genes

-enhancers can be located very far away from gene or close to promotor.

Front 70

whtw is an activator?

Back 70

-a protein that binds to an enhancer and stimulates transcription of a gene.

-Bound activators cause mediator proteins to interact w/ proteins at the promotor.

Front 71

image organization of eukaryotic gene

Back 71

Front 72

enhancers do not act on the promoter region itself but...

Back 72

are bound by activator proteins

Front 73

some activators and repressors act indirectly by influencing what?

Back 73

chromatin structure to promote or silence transcription

Front 74

unlike genes of proakarytoic operon, each of the coordinately controlled eukary. has what?

Back 74

a promotor and control elements

-these genes can be scattered over diff. chromosomes, but each has the same combo of control elements

Front 75

what are the 3 levels of alternative splicing mRNA in eukaryotes?

Back 75

1.) splicing (occur in trans btw 2 diff. transcriptions) the 2 exon carried on 2 diff. RNA molecules can be spliced together

2.) a single gene can generate two diff. mRNA and thus diff. protein products (most occur w/in a single transcript)

3.) single gene can generate hundreds of mRNA

Front 76

list the MRNA modificaaions before transport?

Back 76

-5' capping

-poly A Tail

Front 77

what is 5" capping in eukaryotes?

Back 77

5' cap regulate mRNA export from nuclear to cytopplasm

-5' cap prevent degradation of mRNA

Front 78

what is Poly A tail in eukaryotes?

Back 78

-regulati mRNA export of MRNA

-protect mRNA from degradation

-regulation translation

Front 79

once processed (capped, intron-free & polyadenlyated) mRNA is packaged and exported from where?

Back 79

from the nucleus to the cytoplasm for translation

Front 80

the life span of mRNA molecules in the cytoplasm is a key to determining what?

Back 80

protein synthesis

Front 81

Eukaryotic mRNA is more what?

Back 81

long lived than prokaryotic mRNA

Front 82

The mRNA life span is determined in part by what?

Back 82

sequences in the lead and trailer regions

-5' cap and poly A tail prevent degradation of mRNA by exonucleases

Front 83

regulation of translation in eukaryotes?

Back 83

-translation can be regulated simultaneously

-eukaryotic cell can decrease overall rate of translation based on the presence of any given substance

Front 84

post translation modifications is...

Back 84

modifications of amino acid side chains, these modifications include phosphorylation, acetylation, methylation and glycosylation

Front 85

what is protein phophorlyation?

Back 85

-post translational modification which is the most prominent modification

-can either increase or decrease activity of the target protein

Front 86

after translation, various types of protein processing includes what?

Back 86

-cleavage

-addition chemical grps

Front 87

what are proteasomes?

Back 87

giant protein complexes inside all eukearty and located in nucleus & cytoplasm.

-function: degrade unneded or damaged proteins