-------------------------------BIOCHEM 8-28-

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Releasing factor binds to stop codon

Spliceosomes primarily which snRNA?
Lac operons consist of: promoter, initiator, proteins
Definition of some word: I forget

I. Immediate and delayed response to environment (transcription)

a. Transcriptional regulation of genes
b. mRNA stability
c. alternate splicing/ alternate transcripts
II. Long term responses
a. Gene rearrangement
b. Gene amplification
c. Mutations/recombination
III. Definitions
a. Gene is expressed: transcribed
b. Levels of expression = amount of mRNA
c. Constitutive expression: always transcribed
d. Regulated expression: modulated transcription (up or down)
IV. Regulattion of gene transcription
a. Major mechanisom for regulating
b. Lac operon: coordinated unit of gene expression
i. Regulator genes
ii. Operator sitex
iii. Structural genes
1. CHART
2. Organization: promoter region, operator, z,y a gene
3. Proteins: z: Beta galactosidase, Y: permease A:
transacetylase
4. Function: lactose -> glucose + galactose _> atp
c. E.Coli can use glucose or lactors
i. Prefers to use glucose as a source of carbon and energy
ii. Can use lactose due to ability to synthesize B galactidase from
the lac operon
iii. Converts lactose to glucose and galactose
d. Absence of lactose
i. Repressor bound to operator site prevents transcription of z,y,a
1. 4x106 as strong as to random sites on DNA
e. Lactose present
i. Repressor-inducer complex doesn’t bind DNA
ii. B galactiosidase, permease, and transacetylase transcribed
f. Inducer
i. When glucose is absent and lactose present, some lactose
converts to 1,6 allolactose (inducer)
ii. Inducer binds to the repressor and inactivates repressor
iii. Induder = alpha-1,6 linked galactose + glucose
iv. Allows RNA polymerase to bind to the promoter
g. Catabolite repression: if both galactorse and glucose present
i. Levels of glucose are important
1. Alter cAMP levels
2. Repressor and inducer bind in the absence of glucose to
RNA polymerase to transcribe Z, Y, A
h. Carbolite Repression
i. Absence of glucose leads to increase in cAMP
ii. cAMP binds catabolite activator protein (CAP; cAMP response
protein = CRP)
iii. Polymerase stabilized; transcription stimulated x50
iv. Lactose and glucose present
1. cAMP levels low since glucose present
2. CAP doesn’t bind to polymerase
3. Very little or no transcription of lac operon genes
v. Lactose but no glucose
1. Inducer binds repressor preventing binding to promoter
2. cAMP levels high since no glucose
3. Cap binds to & stabilizes polyhmerase
4. Transcription of lac genes occurs
i. Tryptophan operon
i. Post transcriptional regulation
ii. Transcription/translation tightly coupled in bacteria, thus
translation occurs as soon as Shine-Delgarno sequence
transcribed
iii. Encodes 5 enzymes that convert chorismate into tryptophan
iv. Trp mRNA contains short open reading frame
1. Contains 14 aa peptide + untranslaged attenuator
sequence
v. Tryptophan never use in transcription, practically
1. Procedes attenuator region: can have 2 confirmations
vi. High [Trp}
1. If high levels available, the ribosome passed quickly and
the termination turn forms
2. Don’t remember region; remember 2 different
conformations
vii. Low [Trp]
1. When trp levels low, ribosomes stall at trp codons,
allowing the alternative turn to fomr, preventing the
formation of the termination turn
j. Post transcriptional regulation
i. Other attenuated operons include: threonine, phenylalanine, and
histidine
ii. Can’t exist in euk: transcription/translation separated
k. SUMMARY;
i. Several types of mechanisms can regulate gene expression
ii. In absence of lactose, repressor binds to lac operon
iii. Inducer
iv. Catabolite
v. Attenuation
------------------------------------------EUKARYOTIC GENE
EXPRESSION-------------------------------------------

I. Eukaryotic gene expression

a. Larger genomes require greater complexity of regulation
b. Different cell types requires increased levels of regulation
c. Genes are NOT organized in operons
d. Transcription and translation are NOT coupled (mRNA modificiation
ETC)
e. Tissue specific Gene expression
i. Negative or positive regulation by reg. molecule can alter
gene exp.
ii. Most euk. Genes not express are unless “turned on”
iii. Program in ind. Cells to control. Exp. Of specific genes
iv. Development requires program of gene exp;.
1. Genes inovled in dev. Are ofthen transcription factors
2. Cells can signal each other and modify gen exp.
Depending on position (positional information)
v. Most occurs at level of transcription
f. Structure of euk. Gene and products
i. Upstream enhancers (can be downstream)
1. Proteins combine with it and loop around to interact
with polymerase
ii. Promoter
iii. TATA box
iv. 5’ UTR to 3’ UTR ->
1. Initial transcript still in nucleaus: 5’ cap and 3’ poly-A
tail ->
a. Introns removed ->
i. Final mRNA in cytoplasm
g. Regulation of gene expression
i. Mostly at the transcriptional level
1. DNA ->
a. Transcriptional control
2. Primary RNA transcript ->
a. RNA processing control
3. mRNA travels through nuclear pore
a. Translation control
4. Protein
a. Protein activity control
h. Althering Genes available for transcription
i. Chromatin remodeling
ii. Methylation of DNA
1. Form 5 methylcytosine located in GC islands (GC-rich
region)
2. Globin gene highly methylated in non-erythroid cells
3. Important in fetal development
iii. Gene rearrangement
 1. Ig genes
iv. Gene amplification
1. Not normally physiological mechanism
2. Occurs in response to stimuli
a. DHFR amplification in response to methyl
substiture