exam 4 Flashcards
Central Dogma of Molecular Biology
DNA is transcribed to RNA which is translated to protein
gene expression in prokaryotes vs eukaryotes
BACTERIAL: in cytoplasm; no mRNA processing (no introns)
EUKARYOTIC: transcription in nucleus, translation in cytoplasm; mRNA processing (introns spliced out, leaving only exons from pre-mRNA)
the triplet code
3 bases of RNA (codons) that code for a specific amino acid; what allows 4 nucleotides to code for 20 naturally occurring amino acids
codon
three-nucleotide sequence on messenger RNA that codes for a single amino acid; multiple codons for one amino acid; no two amino acids have the same code; almost universal
redundancy (codons)
multiple codons exist for one amino acid
unambiguous code (codons)
no two amino acids share a codon
transcription promoter (prokaryote)
DNA sequence to which RNA polymerase binds
RNA polymerase (prokaryote)
enzyme the initiates and drives RNA synthesis
start point (prokaryote)
where the transcription starts
transcription unit (prokaryote)
gene to be transcribed (codes for RNA) + termination sequence
initiation of prokaryotic transcription
-Sigma factor recognizes a DNA sequence at -10 and -35 region, RNA pol subunits bind to sigma (2alpha, beta, beta’)
-(sigma stays) RNA pol pulls DNA apart W/O A PRIMER and catalyzes joining of RNA nucleotides using DNA template strand (makes complementary mRNA to DNA template)
initiation of eukaryotic transcription
-several GENERAL transcription factors bind to promoter sequence
-activators bind to enhancer sequences (can be far away)
-RNA pol binds to transcription factors
-coactivators bring everything together and make the transcription complex
activators
bind to enhancer sequences and activate transcription
co-activators
Bridge activators and RNA polymerase but do not bind DNA directly (bring everyone together)
transcription factors
proteins that mediate the binding of RNA polymerase and the initiation of transcription; bind to promoter sequence
Elongation of RNA transcript (prokaryotes)
-RNA pol untwists double helix
-new bases add to 3’ end (U instead T)
*gene can be transcribed simultaneously by several RNA pol (makes multiple copies of mRNA from the same template)
Termination of prokaryotic transcription
-RNA pol stops at the end of the terminator (“falls off”)
*RNA translated without any processing
RNA processing
*only in eukaryotes
splicing out of introns in pre-mRNA, yielding mRNA
product of RNA processing
(pre-mRNA)-introns+5’ cap+Poly-A tail
5’ cap
modified guanine nucleotide added to 5’ end of pre-mRNA to protect it
Poly-A tail
50-250 adenine nucleotides added onto the 3’ end of a pre-mRNA
spliceosome
A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.
ribozyme
a type of RNA that can act as an enzyme (contained in spliceosome)
alternative RNA splicing
different splicing methods result in different combinations of exons
*increases variability without increasing the number of genes (24k)
*introns are great places for chiasmata
*rearrangement of exons can allow rapid evolution
mRNA
(messenger RNA)
has genetic code (64 codons)
tRNA
(transfer RNA)
80 nucleotides long
has anticodon that brings in specific aa
amino acyl tRNA synthetase
enzyme that puts the proper amino acid on the proper tRNA (using ATP)
*recognizes physical and chemical properties of amino acids, tRNA anticodon
tRNA structure
-anticodon base pairs in an antiparallel manner with codons on mRNA
-attachment site is 3’ end (amino acid adds here)
ribosome structure
-large subunit
-small subunit
*sequences highly conserved between closely related species.
*mitochondria/chloroplasts have their own ribosomes
large ribosomal subunit
joins amino acids to form a polypeptide chain (catalyst)
A site
Aminoacyl-tRNA binding site (tRNA binds to mRNA)
P site
Peptidyl-tRNA-binding site (amino acid binds to tRNA)
E site
Exit site
ribosome-level initiation of translation
-small ribosomal subunit binds to mRNA, as does initiator tRNA (Met attached)
-large ribosomal subunit joins and completes initiation complex
ribosome-level elongation of translation
-anticodon on tRNA recognizes codon on mRNA
-very first tRNA is on P site, next enters A site (with GTP addn)
-peptide bond forms between amino acids on both tRNAs
-tRNA on P site translocates (with GTP add’n) to E site, leaves; tRNA on A site translocates to P site, is ready for next aminoacyl tRNA
ribosome-level termination of translation
-Release factor enters A site as ribosome reaches stop codon on mRNA
-this promotes hydrolysis (breaking of peptide bond between tRNA and polypeptide
-ribosomal subunits and other components dissociate
small ribosomal unit
decodes mRNA sequence
Energy of translation (eukaryotes)
-charging tRNA with aa = 1ATP
-ribosome assembly (small + large subunit) = 1GTP
-singular aa addition = 2GTP
-termination = 1GTP
signal recognition particle (SRP)
-SRP binds to signal peptide & stops polypeptide synthesis
-SRP binds to receptor protein on ER (basically transports translation to the ER)
-SRP detaches and translation continues
mutation
change in genetic material
point mutation
chemical changes in just one base pair of a gene
EX. sickle cell anemia
reading genetic code direction
5’-3’
viruses
-100x smaller than bacteria
-obligate intracellular parasites (require a host)
-non-cellular infectious particles
-composition: nucleic acid, protein, sometimes membrane
how viruses are grouped
how their genomes are organized
coronavirus class
ssRNA (single stranded RNA)
ex. of coronavirus that causes human diseases?
SARS
how bacteriophage infect bacteria
-bind to surface of bacteria and inject genome into bacteria cell
-reproduce inside cell, assemble new virus
-eventually cell undergoes lysis and releases all that viral genetic material
lytic cycle
cell bursts open
lysis
cell bursting open
lysogenic cycle
cell divides before lysis
viruses un eukaryotes
-viruses enter cells using receptors or by fusion of membranes
-DNA or RNA genomes enter (transcribed in nucleus, translated/virus assembles in cytoplasm)
*some viruses can incorporate genome into host’s genome
Influenza (flu)
-surface proteins (HA, NA proteins change often) facilitate viral entry
-replicates
-eukaryotic cell forms little vesicles (viral shedding)
HIV virus
uses reverse transcription to incorporate itself into genome
reverse transcription
-viral RNA uses reverse transcriptase to form DNA
-DNA codes for RNA
-RNA codes for protein
examples of pandemics
Spanish flu (18-100mill deaths); HIV (36mill+ deaths); Ebola; Swine flu; SARS CoV1 & MERS; SARS CoV2/COVID
applications of viruses
- virotherapy: can target cells with certain receptors (ex. target cancerous cells)
- gene therapy: deliver genetic information to cells (theoretical atm)
- vaccines: deliver genetic information for proteins to be attacked by immune system (boosts immune system)
vaccines
introduce something resembling a virus, immune system responds, immune system develops ‘memory’ to fight virus
attenuated virus vaccine
uses less virulent/less harmful version of a virus
inactivated/dead virus vaccine
heat or chemically killed virus
protein/subunit vaccine
viral surface protein is used to generate immunity
mRNA vaccine
uses mRNA to encode viral protein (Pfizer, Moderna!)
CRISPR
Clustered Regularly Interspaced Short Palindromic Repeats
-way for bacteria to recognize and destroy viral genomes
CRISPR process
-viral DNA inserted into bacterium
-viral DNA incorporated at CRISPR locus
-GAH
prion
small misfiled proteins that can induce misfolding in other proteins–> lead to large protein clumps
prion disease
-brain, neurodegenerative
-Creutzfeldt-Jakob disease (CJD), mad cow disease…
operon
a group of genes that operate together
-consists of single promoter that controls multiple gene transcripts
why do bacteria have operons?
-need to respond quickly to changes in environment/cellular needs
-bacteria live in competitive world
**Maximizes efficiency
polycistronic
when single transcript has multiple translation start sites for multiple genes
operon structure
promoter
operator
enhancer/silencer
transcription unit
promoter (operon)
RNA polymerase binding site (-10, 35, alpha factor, etc)
operator (operon)
where repressor binds to prevent transcription
enhancer/silencer (operon)
upstream/downstream DNA sequences that increase or decrease transcription
transcription unit (operon)
5’UTR, 3’UTR, open reading frame/protein coding region
trp operon
-when tryptophan is present, binds to trpR (repressor of top operon) –> no transcription of operon
-when tryptophan is absent, trpR is inactive and does not bind to repressor–> no transcription of operon, no synthesis of proteins
lac operon
-when lactose is present, binds to lac repressor and inactivates it; operon is transcribed and makes things that metabolize lactose
-high levels of cAMP mean low glucose; CAP/CRP can bind to cAMP and promote RNA pol binding to lac promoter
low glucose, lactose available
lac operon activated
high glucose, lactose available
lac operon activated and yields low amounts of pdt
low glucose, lactose unavailable
repressor bound, no lactose metabolism
high glucose, lactose unavailable
lac genes not expressed
permease
transports lactose into the cell
inducer
A specific small molecule that inactivates the repressor in an operon.
feedback inhibition
presence of a product inhibits factors that contribute to its production (ex. tryptophan)
positive regulation
presence of a product spurs production of factors that work with it
riboswitch
RNA that base pairs with itself to form 3D shape. shape can help with its translation or prevent it
*this regulation helped by a small molecule
methods of transcription initiation regulation
-acetylation/deacetylation of histone tails
-methylation/demethylation of DNA
(de)acetylation of histone tails
adding acetyl group to histone tail makes positive histone tail negative, which repels DNA backbone
*resulting DNA is more spread out, transcription factors can reach base pairs better
histone code
the hypothesis that specific combinations of chemical modifications of histone proteins contain information that influences chromatin condensation and gene expression
(de)methylation of DNA
added methyl groups pose steric challenge to transcription agents
epigenetic inheritance
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.
gene silencing
A gene that is not expressed owing to epigenetic regulation.
-chronic trauma can make this last generations
control elements
segments of noncoding DNA in eukaryotic genes that help regulate transcription by binding to certain proteins.
Activators/specific transcription factors
-bind to enhancer DNA sequences
-tissue specific (ensures transcription occurs at the correct time in the correct place)
enhancer
A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes.
-its control elements can bind to 1 or 2 activator proteins
combinatorial control
combination of many factors determines the expression of any given gene; provides variety
coordinated control
outside signal may result in transcription of multiple genes via single (or set of) activator(s)
-genes spread out but have common enhancers/activators
-compensates for eukaryotes’ lack of operons
differential gene expression
the process by which genes are “turned on” or expressed in different cell types
miRNA
micro RNA
-small, single-stranded, bind to complementary mRNA sequences
-regulates the amount of protein produced by a eukaryotic gene (by degrading mRNA or blocking translation)
frameshift mutation
insertion or deletions not divisible by 3; messes up code after such insertions or deletions
white flower specific mutation
base pair change in intron 6 (between exons 6 and 7) in transcription factor bHLH
what sequence does spliceosome look for?
GGTA. cuts between 2 As
molecular basis of complete dominance
transcription factor turns on pathway (ex. transcription factor turns on pathway that makes purple pigment to color pea flowers)
*Need very little transcription factor to turn on genes
molecular basis of incomplete dominance
turning on gene IN a pathway ** more transcription factor more red????*
transcription factor gradient
what it sounds like. determines directionality/parts of developing cell
bicoid gradient
-high concentration–> head
-low concentration –> tail
dorsal gradient
-high concentration–> belly
-low concentration–> back
MyoD
“master regulatory gene” that produces proteins that commit the cell to becoming skeletal muscle; transcription factor that binds to enhancers of various target genes
-also indirectly tuns off cell cycle
determination
The point during development at which a cell becomes committed to a particular fate due to cytoplasmic effects or to induction by neighboring cells.
differentiation
process in which cells become specialized in structure and function
hox genes
Class of homeotic genes. Changes in these genes can have a profound impact on morphology.
-determine identity of body segments
Hardy-Weinberg null hypothesis
frequencies of alleles and genotypes in a population remain constant from generation to generation
uses of HW principle
- to detect evolution (if we reject the null)
- to find the frequency of heterozygotes (if we fail to reject the null)
Hardy-Weinberg equation
p^2 + 2pq + q^2 = 1
phylogenetic tree
diagram showing evolutionary relationships of organisms with a common ancestor; resembles a tree
cladogram
A diagram that is based on patterns of shared, derived traits and that shows the evolutionary relationships between groups of organisms
phylogram
Branch length is proportional to the amount of character change
uses of phylogenetic trees
-forensic evidence
-mapping influenza/virus evolution (Robert g Webster)
How many viruses cause the common cold?
~200
Beta coronaviruses
include MERS, SARS, SARS-CoV-2
does the flu or coronavirus evolve faster?
flu
parsimony
simplest phylogenetic tree; least number of steps
basic principle of cancer
uncontrolled cell proliferation
-checkpoints that keep cell cycle under control are gone, we have unrestricted mitosis
Henrietta Lacks
Cancer cells taken without her knowledge, became HeLa cell line.
HeLa cell uses
infectious disease research, space research, make other cell lines, science policy, etc
meaning of all cancer being genetic
all cancer stems from mutations in DNA during mitosis. not necessarily inherited
Mary Claire King
discovered BRCA1/BRCA2: increase risk of breast and cervical cancer
3 levels of protection against cancer
- genes that regulate proteins that stimulate the cell cycle
- transcription factors that induce transcription of mRNA, translation of proteins which can stop cell cycle (ex. p53)
- programmed cell death genes (apoptosis)
genes that regulate cell cycle + cancer
genes regulate proteins that stimulate cell cycle
*if defective, these proteins can be unregulated and always on –> unregulated mitosis
transcription factors that lead to translation of cell-cycle-inhibiting proteins + cancer
these transcription factors (ex p53) eventually lead to the translation of proteins that can inhibit the cell cycle/fix DNA
*if defective, nothings is stopping cell cycle or fixing DNA–> unregulated mitosis of cells with defective genes
cell death genes + cancer
if the damaged DNA is too far gone, the cell can die, destroying the mutation before it can proliferate
*if defective, mutation allowed to proliferate unchecked
oncogene
cancer causing gene
proto-oncogene
a gene that regulates normal cell division (NORMAL); point mutation within this can make an oncogene which can cause hyperactive or degradation-resistant protein
defective Ras (KRAS) protein
oncogene can result in defective Ras that is always on (doesn’t require activated TRK to work); this can result in the over expression of protein from the transcription factor in the nucleus and result in unchecked cell proliferation
defective p53 (TP53) transcription factor
p53 defective and can’t respond to the signal to make a protein that stops the cell cycle, results again in unchecked cell proliferation
full-blown cancer
malignant cancer goes metastatic
why are many mutations needed to cause cancer?
many redundant backup mechanisms for stopping cell division
as of 2017, how many mutations result in cancer?
4-10 (half of driver substitutions in yet to be discovered genes)
fraction of cancerous mutations due to environment?
1/3
*DNA replication errors main cause
3 breast cancer oncogenes
- Estrogen receptor (ER)
- Progesterone receptor (PR)
- HER2 receptor
2 breast cancer tumor suppressors
- BRCA1
- BRCA2
*unrelated proteins also involved in DNA repair
treatments for ER/PR overexpression
hormone repressors
treatments for HER2 overexpression
“Herceptin”- prevents dimerization of HER2
Triple negative breast cancer
no expression of ER, PR, or HER2, very hard to treat
what kind of cancer did Dr. Jackman have
colorectaL
