midterm - quiz 2 - lectures 7,8,9 Flashcards
T OR F: each gene has information for one protein
TRUE - one gene one protein hypothesis
what is gene expression
cellular process in which the info held in the DNA sequence of a gene is used for making final product (polypeptide chain)
rRNA tRNA and other RNA genes encode…
info for making RNA molecules that are not translated into proteins
what is a gene (parts)
protein encoding gene
promoter
transcription unit 5’ -> 3’ , UTR, coding region
terminator
what is a promoter
transcription start site
what is a transcription unit
sequence for mRNA
what is UTR
untranslated region
protection - regulation
what is termination sequence
transcription stop site
Gene expression occurs in 2 steps, name and brief description
1 - transcription: synthesis of mRNA using template DNA strand
2 - translation: synthesis of proteins using mRNA as template
in prokaryotes transcription…
and translation are couples and occur together in cytoplasm
in eukaryotes transcription…
occurs first in nucleus and translation occurs second in cytoplasm after mRNA export (through nuclear pores)
in prokaryotes describe chromatin, genes, promoters, transcription and translation, mRNA
chromatin - none
genes - operons, promoter - multiple genes
promoters - no TATA box
t&t - simultaneous
mRNA - polycistronic, multiple coding regions per mRNA, no splicing (no introns), no processing
in eukaryotes describe chromatin, genes, promoters, transcription and translation, mRNA
chromatin - euchromatin vs heterochromatin
genes - one promoter per gene
promoters - TATA box present, TBP TATA binding protein
t&t - separate (nucleus/cytoplasm)
mRNA - monocistronic, 1 mRNA = 1 coding region, splicing removal of introns, processing
name components of transcription
RNA polymerase and general transcription factors
DNA template strand
ribonucleotides (NTPs)
mRNA (product of transcription)
name 3 main steps of transcription
initiation
elongation
termination
where does promoter lie in transcription
upstream of start site and coding region of gene
describe transcription initiation
RNA polymerase binding to promoter
in eukaryotes - TATA box TBP is key to recognition of promoter and recruitment and binding of RNA polymerase II (transcribes protein coding genes)
describe transcription elongation
mRNA synthesis 5’->3’
mRNA sequence is complementary and antiparallel to that of template strand
describe transcription termination
release of mRNA and RNA polymerase
in eukaryotes - a polyadenylation signal and site are involved
similarities between transcription and DNA replication
energy requited NTP/dNTP
formation of bubble (unidirectional vs bidirectional movement)
synthesis is always 5’->3’
differences of RNA polymerase (transcription) vs DNA polymerase (DNA rep) (6)
Initiation at promoter
no primer needed - RNA polymerase has helicase activity
bubble does not grow
one template used -> hybrid parent strands reanneal and RNA is realease
no proof reading
stops at terminator
name components of translation
mRNA: holds codons
ribosomal subunits (small and large)
rRNA
charged tRNA
pool of amino acids
describe rRNA
scaffold of ribsosomal subunits and peptidyl transferase catalytic activity (ribozyme)
describe charged tRNA (gen / 4)
clover, L shaped
anticodon - second loop
amino acid attachment site 3’ end
brings amino acid into position of growing polypeptide chain
name 3 steps of translation
initiation
elongation
termination
describe translation initiation (5 steps)
1 - binding of small subunit and translation initiation factors to 5’ UTR, in eukaryotes requires 5’ CAP
2 - scanning for start AUG codon
3 - pairing of anticodon of initiatior tRNA with start codon
4 - GTP hydrolysis
5 - binding of large subunit
describe translation elongation
synthesis of protein amino to carboxy terminus
describe translation termination
occurs when ribosome reaches stop codon
release factor recognizes codons and causes dissociation of the polypeptide chain from last tRNA molecule
small and large subunits dissociate from mRNA
name 4 steps of translation elongation
1 - charge tRNA binds to A site
2 - peptide bond formation, rRNA catalyst
3 - translocation, ribosome moves along mRNA
4 - exit of uncharged tRNA
what is A site
pockets in large ribosomal subunits
amino acyl
binding of incoming charged tRNA
what is P site
peptidyl
binding site for tRNA holding nascent - growing polypeptide chain
what is E site
exit for uncharged tRNA
why is energy needed during elongation
peptide bond formation (by rRNA)
translocation of ribosome relative to mRNA
describe difference between charged tRNA and uncharged tRNA
charged tRNA = bound with aa, amino acyl + tRNA but doesnt have neg or pos charge
uncharged tRNA = tRNA with no aa
describe mRNA codons
universal - all organisms use same genetic code
redundant - amino acid can be specified by more than one codon
not all mutations are expressed and produce defective protein
but not ambiguous - one codon never specifies more than one aa
what does accuracy of translation depend on
specific pairing between anticodon (tRNA) and codon (mRNA)
specific attachement of an aa to a corresponding tRNA by amino acyl tRNA synthase
T OR F transcription and translation dont require energy
F - ARE energy requiring
describe mRNA processing and splicing (gen)
post-transcriptional modifications
nucleus
pre-mRNA
Sn-RNA - spliceosome (ribonucleoprotein complex)
ONLY IN EUKARYOTES
describe processing
addition of 5’ CAP (modified guanine) and 3’ poly A tail
serve to protect mRNA from degradation and required for export and efficient translation initiation
describe splicing
removal of introns and rejoining of exons, spliceosome
describe spliceosome
protein + SnRNA
ribonucleoprotein complex made of protein SNRNPS (proteins + SnRNA (catalyzes splicing = ribozyme))
describe introns
presence of introns provides an additional regulatory step in overall control of gene expression
introns allow for alternative splicing (more proteins per gene)
describe mutations
changes in nucleotide sequence of DNA and/or mRNA of a gene
name types of mutations
substitution
silent
missense
nonsense
insertion/deletion in exons (frameshift)
describe substitution mutations
can be silent, missense or nonsense
describe silent
change of last redundant nucleotide of a codon - doesn’t change aa sequence
describe missense
change in sequence of a single or multiple codon - changes aa of protein
extensive = causes frameshift and causes loss of function or altered function
describe nonsense
change in sequence of codon to stop codon = premature termination of translation - truncated non functional protein
describe insertion/deletion in exons (frameshift)
extensive missense with frameshift = within an exon - elongated and non functional protein
immediate nonsense with frameshift = stop codon - truncated and non functional protein
what happens if there is a mutation in intron or silent mutation
no effect on amino acid sequence of corresponding protein
what are exons and introns
eukaryotic coding sequences - exons
introns - non coding regions of DNA
describe signal peptide
20 amino acids at N terminus of nascent polypeptide chain is recognized by SRP and brought to translocation complex, where translation resumes and polypeptide is gradually translocated into ER lumen
signal peptide is cleaved once protein has been completely synthesized and translocated into ER lumen
are secreted proteins the predicted size
NO - 20 amino acids shorter than predicted by gene sequence
what is endomembrane system
RER
golgi
vesicle
plasma membrane
what are constitutive genes
always expressed
encode house keeping genes (ribosomal, general t&t genes, basal metabolic genes, sustain basal activity of cell)
what are structural proteins needed for
maintaining cell shape
actin and microtubules
why are RNA molecules essential
for translation
rRNA tRNA
what are regulated genes
induced (turned on) or repressed (turned off)
when change in internal or external cellular environment happens
describe response to environment
Homeostasis
growth and development of body plan and organs
cell specific genes: expressed only in specific cells and tissues
where does regulation of gene expression occur
at level of transcription initiation
what is positive control
gene expression is induced
increase rate of transcription initiation (binding of RNA polymerase to promoter)
greater levels mRNA = greater levels of corresponding protein
what is negative control
gene expression is repressed
blocking transcription (repressor bound to DNA control element)
lower levels mRNA = lower levels of corresponding protein
describe repressible genes in prokaryotic regulation of gene expresion
on -> turned off (repressible operons)
code for enzymes of anabolic pathways synthesizing essential products (aa, nt)
exL trp: tryptophan aa synthesis
describe inducible genes in prokaryotic regulation of gene expression
off -> turned on (inducible operons)
codes for enzymes of catabolic pathways breaking down non essential carbon sources for energy
ex: lac: lactose breakdown
describe regulation at the level of transcription initiation in prokaryotic regulation of gene expression
negative control - active repressor that binds to operator and stops transcription
lac or trp operon
positive control - catabolite activator protein CAP binds to promoter and increases transcription
lac or any operon involved in utilization of non essential carbon sources
describe operons
only in bacteria
group of genes of the same function under control of same and single promoter
describe polycistronic mRNA
single mRNA with multiple coding regions for multiple proteins
describe repressible operons
any synthesis operon
repressible genes - on get turned off
ex: trp operon encodes enzymes involved in synthesis of amino acid tryptophan
describe inducible operons
any catabolism of alternative sugars operon
inducible genes - off but get turned on
ex: lac operon encodes enzyme involved in uptake and breakdown of lactose to glucose and galactose
state essential carbon sources
glucose
state alternative sugars
lactose
sucrose
arabinose
maltose
describe tryptophan synthesis
anabolic pathway
default on
repressed by high levels tryptophan
rapid regulation of enzyme activity - feedback inhibition
slow but longer lasting regulation of enzyme production (level of transcription initiation, repressor protein, co repressor tryptophan)
describe trp operon default state
default on
low levels tryptophan
repressor inactive
describe trp operon repressed
operon off
Tryptophan levels high
Tryptophan co repressor binds to allosteric site of repressor
repressor is active and binds to operator blocking RNA polymerase from binding to promoter
Transcription is blocked
no protein products
describe default state lac operon
default off
lactose absent
repressor active
binds to operator and blocks RNA polymerase from binding to promoter
no transcription
describe induced state lac operon
low/moderate levels
lactose present
glucose high
allolactose binds to allosteric site of repressor
repressor inactive
transcription occurs but CAP inactive
low levels of transcription
describe overexpression lac operon
lactose is present
glucose absent
repressor is inactive
CAP active
MAX transcription
describe CAP
catabolite activator protein
universal activator protein in bacteria, induces expression of many operons involved in breakdown of carbon sources
what happens when CAP is active
cAMP levels are high when glucose is scarce or absent
cAMP binds to CAP to activate it
what happens when CAP inactive
cAMP levels are low when glucose is present
describe lac genes (3)
lac I = not part of lac operon, codes for an active repressor
lac Z = codes for B galactosidase, enzymes cleave lactose disaccharide
lac Y = codes for permease, transporter for lactose
control of chromatin is…
pretranscriptional control
describe euchromatin
loose DNA with nucleosomes
genes can be expressed or induced
DNA demethylation - removal of CH3 from nitrogenous base of C
histone tail acetylation = acetyl groups -COOH3 are added to lysine of histone protein tails
histone proteins = wrapped with DNA in nucleosomes
describe acetylation of histone tails (associations)
euchromatin loose DNA
promoters accessible (rna pol binds to
promoter)
transcription occurs
gene induction
describe heterochromatin
compact DNA - looped domains - metaphase chromosome
genes are auto repressed
DNA methylation - addition of methyl
may be linked with increased histone deacetylation
describe deacetylation of histone tails (associations)
heterochromatin (compact DNA)
promotes hidden (rna pol doesn’t bind)
no transcription
gene repression
describe control of transcription initiation - binding of RNA polymerase to promoter
promoters are more complex
subtle fine tune adjustments in gene expression
what does basal minimal promoter consist of (control of transcription initiation)
TATA box (25nt from transcription initiation site)
DNA sequence for binding RNA polymerase and general transcription factors
what are control elements (control of transcription initiation)
regulatory elements (RE) or switched
upstream of minimal promoter
enhancers and silencers
NON CODING
activators are…
specific transcription factors - proteins that bind to - enhancer control elements
repressors are…
specific transcription factors - proteins that bind to - silencer control elements
regulatory elements and their…
respective DNA binding proteins control assembly of an active RNA polymerase and associated general transcription factors to the promoter
describe modes of action of activators and repressors
activators = proteins that bind to enhancers
promote binding of RNA pol and DNA control elements to promoter VIA recruitment of mediator proteins
activate general transcription factors and RNA pol
repressors = proteins that bind to silencers
block action of activators by binding on or near enhancers
describe coexpression of genes with similar functions in eukaryotes
genes have identical control elements upstream of their promoters respond to same activators and repressors
subject to similar regulation
ex = steroid responsive genes and heat shock genes
describe cell type specific expression in eukaryotes
all cells in organism have same set of genes
specific combos of transcription factors are present (active) in different cell types, only subsets of genes are on or off
ex = liver cell expressed albumin gene and lens cell expressed crystalline gene
describe cell communication
asses environments and maintain homeostasis
important during growth and development to activate right sequence of genes
describe local and long distance signaling
direct contact (gap junctions/planodesmata, cell-cell recognition)
local signalling =
paracrine signalling
synaptic signalling
long distance signalling (endocrine and hormonal)
name 3 steps of communication
reception
signal transduction
cellular response
describe reception gen
binding of signalling molecule usually hormone to receptor protein of the target cell
signalling molecule acts as ligand bc it interacts with specific site of receptor
describe signal transduction gen
transmission of signal by activation of cascade of events involving relay molecules and proteins
initial signal transformer to another
describe cellular response gen
target cell responds by changing cytoskeleton or by activating metabolic enzyme -cytoplasmic or by activating expression of specific genes in response to signal - n
name 2 types of receptors
embedded in plasma membrane
intracellular
describe receptors embedded in pm
contain site for binding of signalling molecule on surface of cell
ex: G protein coupled receptor, tyrosine kinase receptors)
describe intracellular receptors
require signalling molecule enters cytoplasm by crossing membrane first
once bound with signaling molecule receptors translocate to nucleus where they act as transcription factors in activation of specific genes
ex= steroid receptors
how many steps does signal transduction have
6
describe a in signal transduction
activation of a series of steps involving relay molecules and proteins
called a cascade or domino effect
describe b in signal transduction
transformation of initial signal into a different form
involves activator by phosphorylation of relay molecules
describe c in signal transduction
rapid transmission bc relay molecules are already in place just need to be activated
describe d in signal transduction
amplification bc one signaling molecule can lead to activation of millions of target proteins
describe e in signal transduction
fine tuning bc several steps are involved that can be regulated
signal transduction pathway can be used in different cell types to provide specific outcome
describe f in signal transduction
termination bc steps can be inhibited
involves de phosphorylation of relay molecules by protein phosphatases
name 3 ex of signal transduction pathways
phosphorylation/ de phosphorylation cascades involving protein kinases and protein phophatases
second messengers = non proteins, small molecules or ions (cAMP ca2+ or IP3)
combo of both are observed
describe epinephrine stimulation
leads to breakdown of glycogen to glucose by glycogen phosphorylase
1 - reception = binding of epinephrine to a G protein coupled receptor
2 - signal transduction = activation of adenylyl cyclase (formation of cAMP, activation of PKA and phosphorylation cascade)
3 - cellular response = phosphorylation of glycogen phosphrylase (hydrolysis of glycogen to glucose)
4 - termination (de phosphorylation with PP, phosphodiestherase, GDP - G protein inactive, detached hormone epinephrine)
describe cellular response
varied depending on signaling molecule and type of target cell receiving signal
- nuclear response = activation of specific genes
- cytoplasmic response - activation of specific enzymes or proteins or change in cellular shape
describe steroid communication (cellular response)
activated cellular receptors act as transcription factors that bind to specific enhancers (slower but longer lasting response)
- reception = intracellular receptor for steroid hormone
- transduction = translocation of hormone receptor complex from cytoplasm to nucleus
- cellular response = nuclear, activation of transcription settled responsive genes (binds to RE enhancer)
describe insulin
leads to import of glucose in target cells such as liver and muscle
activated bc insulin causes the glucose transporters to be expressed at pm
promotes storage of glucose as glycogen by leading to activation of glycogen synthase
describe growth factor stimulation of cell cycle
tyrosine receptor
Ras-G protein proto-oncogene - protein kinase cascade
nuclear response = activation of cell cycle
hyperactive Ras - oncoprotein
describe UV induced DNA damage and inhibition of cell cycle
no receptor per se (DNA damage)
protein kinase cascade
activation of p53 transcription factor - tumour suppressor protein
nuclear response - expression of cell cycle inhibitor p21
inactive p53 - inactive tumour suppressor protein
