Exam 4 Flashcards
transcription
- process where RNA polymerase synthesizes one strand of RNA from a DNA template
- begins when DNA in a chromosome unwinds near gene to be transcribed
ribonucleotides
- assemble along the unwound DNA strand in a complementary sequence
- only one strand in a gene is transcribed
- but dif genes may be transcribed from dif strands
both eukaryotic and prokaryotic genes contain…
- transcriptional units made up of:
- promoter
- RNA-coding sequence(s)
- terminator region
promoter
- DNA sequence that the transcription apparatus recognizes and binds to
- located in the 5’UTR (upstream)
bacterial transcription
- many genes transcribed at once
- genes and proteins are almost always colinear
- 3 steps:
- initiation
- elongation
- termination
initiation of transcription
- first step in bacterial transcription
- RNApol binds to DNA at the gene’s promoter
- DNA helix unwinds
- RNA synthesis begins
elongation of transcription
- second step in bacterial transcription
- DNA threaded thru RNApol at transcription bubble
- RNA strand growing 5’ -> 3’
- A in DNA [paired with U in RNA
- 30-50 nucleotides per second
termination of transcription
- 3rd step in bacterial transcription
- RNApol reaches “bumps” in terminator region and falls off
polycistronic RNA
- in bacterial cells many genes can be transcribed at once
- RNA that codes form multiple proteins
genes and proteins are almost always ______ in bacteria
-colinear
eukaryotic transcription
- additional step to transcription after initiation, elongation, and termination
- final step= RNA processing
- step modifies newly synthesized RNA (heterogeneous nuclear RNA)
complex internal organization of eukaryotic genes
- promoter region
- introns (noncoding nucleotides that are transcribed but not translated into amino acid sequence of protein)
- exons (intervene between coding sequences)
RNA processiong
- final step of transcription of eukaryotic cells
- modifies heterogeneous nuclear RNA:
- caps added for initiation of translation and stability
- poly adenine tail (30-100 A’s long) added
- slicing removes introns
why transcription is a highly regulated process
- initiation of transcription (ex lac operon)
- splicing (alternative splicing yields dif proteins from same gene)
- nuclear export (mature mPNA hidden in nucleus and released w signals like first responders)
mutations to splice sights
- cause genetic disorders
- ex. beta-thalassemia inherited blood disorders
- improper splicing results in defective form of hemoglobin and anemia
translation of mRNA
- mRNA is translated from language of nucleic acids to amino acids (protein)
- enzymes and RNA translate mRNA
- euk: mature mRNA exported out of nucleus into cytoplasm to be translated by ribosomes
ribosomal RNA (rRNA)
-major component of ribosomes/ organelles that construct proteins
transfer RNA (tRNA)
- interpreters that read mRNA code and insert amino acids into growing protein
- cloverleaf structure
- amino acid attachment site at 3’ end (always CCA)
- each has unique anticodon which pairs to codon on mRNA during translation
- hydrogen bonds bwtn bases
flow of genetic info
- DNA is transcribed into RNA (genetic info is copied into mRNA)
- RNA is translated into protein (amino acids are polymerized into polypeptides which are then folded into proteins)
one gene, one-polypeptide hypothesis
-some proteins are composed of multiple polypeptides
proteins have variety of functions
- fibroin (spider’s web)
- luciferin (generates bioluminescence, firefly ex.)
- ricin (natural poison in castor beans)
3 characteristic groups of all (20) amino acid
- amino group (-NH2)
- carboxyl group (-COOH/ -COO)
- unique side chain (-R)
peptide bonds
-join amino acids to form polypeptide chains
polypeptides
- polar
- read from N-terminus to C-terminus
- after formation it folds into 3D shape (determined by a.a. sequence)
- once folded, polypeptide makes a protein
how is a proteins 3D shape determined
-protein’s amino acid sequence determines 3D structure and function
4 levels of protein structure
- primary
- secondary
- tertiary
- quaternary
primary level
- linear amino acid sequence in polypeptide chain
- most important level
secondary level
- hydrogen bonding btwn peptide bonds (backbone)
- causes amino acid to fold in pattern on itself
- forms 3D alpha helix fig, pleated flat sheet (or beta sheet), and randomized coil structures
- interactions btwn NH and CO groups
tertiary level
- folding of secondary structure back on itself again (side chain interactions)
- forms 3D folded polypeptide chain pattern
quaternary level
-interactions between two or more polypeptide chains
the genetic code
- info to encode a single a.a. is carried in sequence of 3 nucleotides
- code is degenerate (several code words have same meaning)
- multiple stop codons
- one start codon (AUG)
codon
-sequence of 3 nucleotides/ each triplet
how many combos of nucleotides encode the 20 a.a.
-3 nucleotides gives 4^3 dif combos
nucleic acid code in mature mRNA is _______ into amino acids to synthesize polypeptides
-translated
3 sites in the ribosome
- aminoacyl (A) site: site for the next aminoacyl tRNA, closest to 3’ end of mRNA
- peptidyl (P ) site: site of growing polypeptide chain
- exit (E) site: site where spent tRNA is expelled
structure of tRNA
- amino acid attaches to 3’ end (sticks out)
- anticodon loop: anticodons on this cul-de-sac attach and decode the mRNA
4 stages of protein synthesis
- tRNA charging
- initiation
- elongation/ translocation
- termination
tRNA charging
-requires amino acid, tRNA and energy (ATP)
initiation of protein synthesis
-requires initiation factor proteins (IF’s) to assemble the small and large ribosomal subunits onto mRNA template
elongation/ translocation of protein synthesis
- building blocks occupy A site, P site, and E site
- tRNA with amino acid attaches to mRNA
- repeat these steps xMANY
- everytime peptide blond forms, elongation is repeated
termination of protein synthesis
-elongation ceases once a stop codon is reached (UAA, UAG or UGA)
-release factors bind the ribosome and complex falls off
[later: mRNA and tRNA then used again to make new polypeptide]
the central dogma
-DNA is transcribed into RNA which is translated into a protein
Alzheimer’s disease or genetic disorders cause
-mutations can cause protein misfolding which results in genetic disorders like Alzheimers
cystic fibrosis (CF)
- results from defective folding of CF transmembrane conductance regulator (CFTR) protein
- delta 508 = misfolded protein that is identified as destructive, then destroyed before the protein can even leave the ER
prion diseases
-protein refolding diseases
prions
-proteins refolded into infectious conformation that then causes several disorders (ex. mad cow)
Creutzfeldt- Jakob disease (vCJD)
- human variant of mad cow disease (BSE)
- prions cause normal proteins in body to refold into new, infectious 3D shapes
- new infectious shapes kill cells in brain and nervous system
- brain matter becomes sponge like with holes/ voids in brain (unable to communicate btwn brain and body)
gene expression
-genes (in nucleus of eukaryotes) that are turned on and off in response to external stimuli
gene regulation
-encompasses the mechanisms and systems that control the expression of genes
central dogma fails to explain _____
- the way the flow of information is regulated
- does connect genotype to phenotype tho
e.coli biochemical flexibility
- e.coli is able to have biochem flexibility (converts nourishment into what it needs) because of gene regulation
- this optimizes energy efficiency bc it would be too hard for the e.coli to constantly produce all the enzymes for every Dif environment
gene
- any DNA sequence that is transcribed into an RNA molecule (which may or may not encode protein)
- include DNA sequences for proteins, rRNA, tRNA, snRNA, and other types of RNA
- may be expressed all the time or intermittently
structural genes
-encode proteins used in metabolism, biosynthesis, or that play structural role in the cell
regulatory genes
-encode proteins or RNAs that interact with other sequences affecting transcription or translation
constitutive genes
-expressed all the time
regulatory elements
- DNA sequences that are not transcribed, but still play role in regulating other nucleotide sequences
- ex. promoter, operator, etc.
many levels of gene regulation/ control
- alteration of structure
- transcription
- mRNA processing
- RNA stability
- translation
- post-translational modification
positive control gene expression
- stimulate gene expression
- activator (regulatory protein that binds to DNA) involved
negative control gene expression
- inhibit gene expression
- repressor involved
operon
- group of bacterial structural genes that are transcribed together (into a polycistronic mRNA)
- controlled by single promotor
where does the operon regulate the expression of structural genes
- transcriptional level
- most important level in bacteria
inducer
- a substance that stimulates transcription in an inducible system of gene expression
- usually a small molecule that binds to a repressor so that it cannot bind to the DNA sequence so that transcription can occur
repressor
-regulatory protein that binds to DNA sequence (on operator) to stop transcription
inducible operon
- transcription is normally off, can be turned on by inducer
- inducer binds to activator on mRNA
- activator attaches to mRNA at CAP site before RNA pol binding site
repressible operon
- transcription is normally on, can be turned off by repressor
- corepressor can bind to repressor
- binds to operator behind RNA pol
negative inducible operon
- transcription is off when active protein binded, but when inducer binds to protein transcription occurs
- ex. lac operon
negative repressible operon
-transcription is on but when corepressor binds to inactive repressor protein it binds to mRNA and stops transcription
allosteric
- shape change in repressor protein caused by corespressor
- enables repressor to bind with operator
repressible operons usually control ____ that carry out _________ of molecules (amino acids)
- control proteins
- carry out biosynthesis
gene regulation in eukaryotic cells
- genes not organized into operons so can’t transcribe in polycistronic mRNA (groups)
- chromatin structure affects expression of genes
- gene regulation can happen at RNA processing level
- nuclear export of mRNAs regulates
- RNA degradation regulates
how does chromatin structure affect gene expression (eukaryotic)
- DNA must partially unwind from histone proteins before transcription
- HATs; DNA wraps around histones, but histone will loosen grip when acetyl group is transferred
how does gene regulation happen at RNA processing (eukaryotic)
- alternative splicing allows pre-mRNA to be spliced in many dif ways
- may generate dif proteins in dif tissues or at dif times in development
RNA degradation
- form of gene regulation (eukaryotic)
- greater time lag transcription and translation allows mRNA stability to be manipulated in eukaryotes
lac operon
- ex. of initiation of transcription
- ex. of negative inducable set of genes
- without lactose: repressor protein binds to lacO operator not allowing transcription
- lactose present:allolactose (present if lactose present) binds to repressor protein which does not allow it to bind to mRNA, this allows transcription to happen; transcription then produces more enzymes needed to break down glucose so it can transcribe more.
allolactose
- isomer of lactose (present if lactose is present)
- acts as an inducer of transcription
- if allolactose is bound to inducer then inducer does not bind, so RNApol can bind to transcribe
