Unit 4 Flashcards
Ways that gene expression/protein activity can be regulated:
-transcriptional regulation
-histone modifications
-phosphorylation of a protein - activate/deactivate
-protein-protein interactions - activate/deactivate
-ubiquitination - degrade protein
The human genome has ______ base pairs from each parent and ____ base pairs total
3 billion, 6 billion
The human genome has _____ protein coding genes
22,000
The human genome has ___ genes per million bp
7
Humans get their complexity from _____
regulation
The human genome has lots of ____ in between genes
space
The central dogma states that….
we hold our genetic information in our DNA
DNA replication is where you replicate the entire ____
chromosome
Template strand is read…
3’ to 5’
RNA polymerase is responsible for…
synthesizing RNA from DNA during transcription
RNA polymerase does not read the ____ strand
coding
Only ___ size fragments will be copied, not the entire chromosome
gene
Transcription is very _____; only transcribe ____ needed in a given ___ ___
regulated, genes, cell type
RNA is made __ to __ and is _____ to the template strand
5’ to 3’, complementary
The central dogma links ____ and ____
Genotype and phenotype
____ _____ determines ___ ____ which can determine ___ and thus can determine ____
DNA sequence, Protein sequence, function, phenotype
An individual inherits one blue allele and one brown allele for an eye color gene. The individual has brown eyes how?
I. The protein made from the brown allele is more stable.
II. The mRNA from the brown allele is more highly expressed.
III. The mRNA from the brown allele is more stable.
IV. The version of the protein produced by the brown allele functions more strongly/efficiently than the protein from the blue allele.
A. One of these is possible.
B. Two of these is possible.
C. Three of these is possible.
D. All of these are possible.
D. All of these are possible.
Any step of gene expression can be regulated.
The TATA box will be transcribed.
False
The enhancer sequence must be directly upstream of the gene it regulates.
False
Activator proteins bind the enhancer (switch) sequences at all times.
False
Only ___ or ____ genes are expresses in a given cell type during translation/transcription
Half or fewer
Some genes expressed ____ while others ___
A lot, not at all
RNA is ____ stranded which make it much less ____
Single, stable
RNA is ________ _____ not deoxyribonucleic acid bc there is an ___ group on the __ ______ not an ___
Ribonucleic acid, -OH, 2’ carbon, -H
RNA uses ____ to pair with ____ instead of thymine
Uracil, adenine
RNA is about ___ long which is _____ than a chromosome
2 kb (2000 bp), smaller
RNA can ___ on itself making it more ____
Fold, stable
within a single strand, ____ ____ ____ b/t different regions can give rise to _____ ____
Complementary base pairing, complex shapes
____, _____, and ____ RNAs fold on themselves the most
tRNAs, rRNAs, splicing
Promoter
Specific sequence at the beginning of the gene that is important in starting trasncription
Enhancer/switch
DNA sequence that can be upstream or downstream of the gene and is important for starting transcription
The DNA of the promoter is recognized by specific ____ ____
Transcription factors
Transcription factors bring ___ ____ to the promoter
RNA polymerase
RNA polymerases is ______ and it can’t go.
Dephosphorylated
Activators bind to
Enhancers/switches
When the activator binds, the DNA physically ____ to interact with the ____ region
Bends, promoter
Sometimes another protein called a _____ is needed to get the activator to bind to the promoter region
Mediator
mRNA
Messenger RNA codes for proteins
Lots of RNA polymerases can transcribe ____ of RNA pretty ___
Lots, fast
TBP (TATA binding protein) scans along the DNA until it finds the sequence called the ____ ____
TATA box
The TATA box is called that bc
It has a lot of T’s and A’s in it
The TATA box is located at
-30 (30 nucleotides upstream of the txn start site)
Transcription starts at the ___ site
+1T
TBP is apart of
TFIID (txn factor 2 D)
-35 and -30 are considered the
Core promoter
When TBP binds it ____ the ___ to allow other factors to bind
Distorts, helix
_____ transcription factors bind to ____ promoters
General, many
Examples of general TF’s include:
TFIID, TFII…, TFIIH
Mediator proteins
Bridge between general txn factors and regulatory factors
RNA polymerase has a ____ ____
Long tail
_____-_____ ____ and ____-_____ _____ are ____ _____ that will ride along w/ RNA polymerase
Chromatin-remodeling complex, histone-modifying enzyme, elongation factors
Transcription regulators or activators
Only bound to DNA switches after a signal from environment
Some activators are close to the ____
Promoter
Some switches are ____ ___ from the ____ but the DNA loops to allow activators to bind to mediator
Far away, promoter
TFIIH _____ RNA polymerase tail in order to start _____
Phosphorylates, transcription
TFIIH ____ open the ____
Pries, helix
___ proteins must be moved ___
Histone, out of the way
____ transcription factors can remodel ______ to allow other factors
Pioneer, chromatin
Pioneer transcriptions factors can bind ____ even when it is wrapped around ____
DNA, histones
Once the histones are moved out of the way, _____ transcription factors can bind
General
____ factors are proteins that are _____ to RNA polymerase tail and can use energy from ___
Remodeling, hooked, ATP
Remodeling factors will use the energy from ATP to do a few things:
Shift nucleosome, swap in histone variants, remove histones
Remodeling factors actions allow RNA polymerase to…
Keep moving through
RNA polymerase ____ at ____ locations after txn of a sequence required for ___ ____ addition
Stops, random, polyA tail
Tail gets ____ and falls off
Dephosphorylated
All genes ____ transcribed in the same direction. Different ____ can be used as templates
Are not, strands
Which of the following are present in your liver cells?
A. Switches (enhancers) associated with genes transcribed in the kidney
B. Switches associated with genes transcribed in the liver.
C. Active activators for genes transcribed in the liver.
D. Active activators for genes transcribed in the kidney
E. Answers B and C are correct
F. Answers A, B, and C are correct
G. Answers A, B, C, and D are correct
F. Answers A, B, and C are correct
Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5’-TTTTTTTTTTTTTTTT-3’ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant?
A. DNA
B. tRNA
C. rRNA
D. mRNA
E. All of the RNAs would be equally abundant
D. mRNA (bc it stick to the poly A tail of the mRNA)
Transcription is similar to DNA replication in that
A. An RNA transcript is synthesized discontinuously and the pieces are then joined together.
B. It uses the same enzyme as that used to synthesize RNA primers during DNA replication.
C. The newly synthesized RNA remains paired to the template DNA.
D. nucleotide polymerization occurs only in the 5’ to 3’ direction
D. Nucleotide polymerization occurs only in the 5’ to 3’ direction
Introns are removed by
Splicing
A _ ___ and a __ ___ ___ are added to the primary transcript
5’ cap, 3’ polyA tail
RNA processing takes place in the
Nucleus
RNA processing includes
The addition of a 5’ cap and 3’ polyA tail and splicing of introns
Why does RNA processing occur?
To add stability and enhance translation
Introns are ____ but not ____
Transcribed, translated
Introns are ____ and exons are spliced ______ by the _____
Removed, together, spliceosome
The spliceosome is a
Complex of SnRNPs (RNA and protein)
Splicing is ____ bc base pairing b/t specific sequences @ intron/exon boundary + RNA component of SnRNPS
Specific
Why do eukaryotes have introns if they are just removed from the transcript?
Alternative splicing allow for more than one protein to be created
Proteins bind to the ___ and ___
Cap and tail
Improperly processed RNAs are ____
Degraded
mRNA exits through the ___ ____ into the ____
Nuclear pore, cytoplasm
How long do mRNAs last before they are degraded?
Minutes to hours
Proteins that bind to the cap and tail can _____ with each other to make a ___ of ___ that is ready for _____
Interact, loop, mRNA, translation
All _____ use the genetic code
Organisms
The genetic code is:
-non-overlapping
-redundant (many a.a. encoded by more than one codon)
-universal (all organisms on earth use)
-all codons encode something
-an a.a.
-stop translation
What would be the consequence(s) if each amino acid was only encoded by one codon?
A. There would be fewer problems with accurate translation
B. Errors in DNA or RNA sequence would have worse consequences
C. Errors in DNA or RNA sequence would have better outcomes
D. There would be more problems with accurate translation
B. Errors in DNA or RNA sequence would have worse consequences
Why aren’t codons two nucleotides?
A. They would encode too few amino acids
B. Errors in DNA or RNA sequence would have worse consequences
C. There could be more amino acids, thus more protein variation
A. They would encode too few amino acids
Amino-acyl tRNA synthetases are the proteins that actually _____. It reads both the ____ language and ____ language.
Translate, nucleotides, amino acids
There are ___ amino-acyl tRNA synthetases for 20 ___ ___
20, amino acids
Amino-acyl tRNA synthetases ____ the correct ___ ____ to the ____
Attach, amino acid, tRNA
Synthetases have to recognize the _____ in the _____
Anticodon, tRNA
Synthetases also have to recognize the specific ____ ___
Amino acid
Synthetase will attach the correct ___ ___ to ___
Amino acid, tRNA
The ____ assembles on the mRNA, scans to find the ___ codon, “reads” ____ codon at a time and synthesize ___ bond formation of the amino acids brought in by the ____.
Ribosome, stop, one, peptide, tRNA
____ subunit of a ribosome binds then ___ subunit binds.
Small, large
______ factors help bring in the initiator ____
Initiation, tRNA
Ribosome will scan down the ____ until first ____ is found
RNA, AUG
There is only one AUG codon in an mRNA
False
(There is more than one AUG, just encodes methionine when its later)
mRNA: U U A G A C U A A U G U U C A A C G G U G U G U A
What is the amino acid sequence encoded by this stretch of RNA? The U on the left side is the 5’ end of the RNA.
Met, Phe, Asn, Gly, Val
The ribosome is a large ___-____ _____
RNA-protein complex
Ribosomes are made up of ___ and ____
rRNAs and proteins
Ribozyme RNAs ____ the reaction
Catalyze
A site is where the tRNAs ____
Enter
The p site is where the ____ with the growing ___ ____ ___ is gonna be
tRNA, amino acid chain
E site is where the tRNA will ___
Exit
The anticodon is on the ___
tRNA
“Charged” tRNA has an ___ ___ attached
Amino acid
Peptide bond formation is catalyzed by ____ in the ____
rRNAs, ribosome
Can “_____” in the ___ base pair
Wobble, third
The large subunit _____. ___ is now open. Growing chain attached to tRNA in the ____
Translocates, A site, P site
Small subunit then ____ after the large subunit translocates. The ____ is ejected through the ____. New ___ can enter.
Translocates, tRNA, E site, tRNA
____ factor recognizes the ___ codon and the ______ disassociates.
Release, stop, ribosome
Where in the cell are ribosomes found?
-Free ribosomes in the cytoplasm
-attached to rough ER
Are mRNAs translated more than once?
Yes, about 40 times
Many ____ target bacterial _____ and ____ machinery
Antibiotics, transcription, translation
The bacterial transcription/translation is ______ enough from ours that drugs can target bacterial machinery without affecting ______
Different, eukaryotes
Tetracycline
Blocks binding of tRNA to bacterial ribosomes
Streptomycin
Inhibits elongation phase in bacterial ribosomes
Gene expression can be regulated at ___ ___
Every step
Which of the following statements about the genetic code is FALSE?
A. The “stop” codon specifies an amino acid.
B. “Start” codons do not specify amino acids.
C. Some triplet codons do not encode an amino acid.
D. Both A and B are false
E. A, B, and C are false
D. Both A and B are false
You have sequenced the Abd gene from a cancer and identified a mutation that introduces a premature “stop” codon where there was previously a lysine. Which statement describes the likely effect of this mutation on Abd transcription?
A. The mutant Abd mRNA will be shorter than normal.
B. The mutant Abd mRNA will be transcribed as usual by RNA polymerase.
C. The mutant Abd mRNA will not be transcribed.
D. The mutant Abd mRNA will not be polyadenylated.
E. The mutant Abd mRNA will not be capped at its 5’ end.
B. The mutant Abd mRNA will be transcribed as usual by RNA polymerase.
(Stop codons stop translation not TRANSCRIPTION)
A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infections. This is because
A. All of the proteins found in a neuron are completely different from the proteins found in a white blood cell.
B. The neuron and the white blood cell within an individual have the same genome.
C. The neuron expresses some mRNAs that the white blood cell does not.
D. Neurons and white blood cells are differentiated cells and thus no longer need to transcribe and translate genes.
C. The neuron expresses some mRNAs that the white blood cell does not
Which of the following might decrease the transcription os only one specific gene in a eukaryotic cell?
A. A decrease in the amount of RNA polymerase
B. A mutation that introduces a premature stop codon into the gene coding sequence
C. A mutation in the gene’s promoter that significantly affects the binding of a transcription factor
D. A decrease in the activity of histone modifying enzyme
C. A mutation in the gene’s promoter that significantly affects the binding of a transcription factor
A is more global
B DOES NOT AFFECT TRANSCRIPTION
C is more global
____ genes are constitutively expressed in all cell types
Housekeeping
Housekeeping genes are
Necessary for cellular fxn
How many genes are expressed in a cells?
About 10-50% of genes are actually expressed in a given cell
Genes expressed in ____ are different than genes expressed in ____
Kidney, neurons
______ regulation is the most common mechanism of regulation
Transcriptional
______/_____ changes are an example of transcriptional regulation
Histone/chromatin
_____ transcription factors rearrange ____
Pioneer, chromatin
_____ transcription factors ______ the opening of ____ to allow txn factors to bind
Pioneer, regulate, DNA
Pioneer TF bind to ____
Double stranded DNA
Acetylation
More gene expression
_____ are highly decorated with ____
Histones, PTMs (post-translational modifications)
Methylation
Can recruit other proteins to remodel chromatin to make it more or less accessible
Phosphorylation
Can recruit transcription factors
-cross-talk b/t other modifications
Histone proteins are ____ charged
Positively
DNA is ____ charged
Negatively
Histones and DNA are ___ compacted
Tightly
When you add an ____ group to a positively charged lysine, it _____ the charge, and ____ the histone/DNA interaction
Acetyl, neutralizes, loosens
What enzymes add and remove acetyl groups?
-Histone acetyltransferases add acetyl groups
-Histone deacetylases remove acetyl groups and close chromatin
There are ___ common histones
4
H3 can only be incorporated in __ phase
S
H3 histone variant, H3.3, can be incorporated _____ the cell cycle
Throughout
H3.3 is involved in specific ____ cancers
Brain
You can regulate _____ by regulating ______ factors and ____
Transcription, transcription, activators
Repressors can repress ______ by
Transcription;
1.) modifying chromatin
2.) repress or proteins can bind to enhancers to prevent activator from binding
Combinatorial control
Complex interaction of histone modification/chromatin remodeling/transcriptional activators and repressors can regulate txn
Splicing regulation is controlled by
Binding of proteins/RNAs in spliceosome to exon-introns boundaries
Example of splicing regulation is
Antibody production
One antibody is in a _____ ____ form while another is in _____ form but they are both encoded by the same ____
Membrane bound, secreted, gene
Sequences in ___ and ___ ___ can bind proteins that regulate how fast the mRNA is ____
5’, 3’ UTR, degraded
microRNAs inhibit ____/ enhance ______ of _____ ____
Translation, destruction, target RNAs
Which of the following methods is not used by cells to regulate the amount of a protein in the cell?
A. Genes can be transcribed into mRNA with different efficiencies
B. Many ribosomes can bind to a single mRNA molecule.
C. Proteins can be tagged with ubiquities, marking them for degradation
D. Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.
D. Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.
Does the mechanism of regulating translation occur on a one-on-one basis or more globally?
Global response to stress
eIF2 is a
Protein involved in translation initiation
During translational regulation eIF2 is ____ in response to ____ ____ and stops ____
Phosphorylated, cellular stress, translation
Post-translational regulation examples
- Phosphorylation
- Ubiquitination
- Other modifications
Phosphorylation can change the _____ of a protein which can ____ or ____ it
Conformation, activate, inhibit
Ubiquitination marks protein for ______ by _____
Destruction, proteosome
____ ____ in cancer cells is very different than normal cells
Gene expression
