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Extracting information from DNA is called
Gene expression
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Transcription
- Reading the DNA and making some type of RNA
- The first half of gene expression
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How long is the amino acid code made by the rRNA
20
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If uracil is found in DNA what happens
Enzymes remove them quickly
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What is one treatment for cancer related to Thymine and Uracil
A drug replaces the Thymine with Uracil and therefore is marked to die
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How is RNA different from DNA
- It is smaller
- Contains ribose instead of deoxyribose
- Contains uracil instead of thymine
- Most RNAs are single stranded
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What is another class of RNA's that functions in splicing
Small nuclear RNA's called snRNA
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What does RNA Polymerase I do
It makes pre rRNA in the Nucleolus
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What does RNA polymerase II do
It makes mRNA precursur in the nucleoplasm, and snRNA
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What does RNA Polymerase III do
It makes tRNA, rRNA, as well as snRNA. But is only active in about 10% of the cells
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What inhibits the Pol I, II, and III
Alpha amanitin (very small amounts needed)
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What is the most important component of the ribosomes
rRNA
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RNA in ribosomes of Eukaryotes consists of
- 28S (large subunit)
- 18S (small subunit)
- 5.8S (large subunit)
- 5S (large subunit)
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The major human rRNA species are synthesized by cleavage from a common 13 kb transcription unit which is part of a 40 kb tandemly repeated unit that occurs 80 times on each of which chromosomes tips
13,14,15, 21 and 22
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Transcription Unit 13kb is clipped down by
RNases to smaller units
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How are most of the rRNA's synthesized in the cell
The larger rRNAs are synthesized as a unit by RNA pol I and then processed
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What poisons have terrorists used to kill people
Ricin (Residue from castor oil)
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What does Ricin do to the ribosome
It removes one adenine from the 28S rRNA
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How does Ricin alter ribosomes
The Ricin A is an enzyme that binds and depurinates a specific adenine of the 28S rRNA
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Ricin interferes with the ability of the eukaryotic ribosome to interact with eEF1 and eEF2. How does it do this?
By depurinating an adenine in the 28S rRNA thereby inactivating the large 60s ribosomal subunit.
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What are the smallest of the 3 major RNA's
tRNA
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Every tRNA has what attached to the 3' end
CCA, The A (adenosine) is where amino acids are attached
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How many codons are there
64 (61 code for amino acids)
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RNA's contain Thymine, How is it possible if RNA polymerase do not incorporate thymine when making RNA
The U or C that is incorporated by RNA pol is post-transcriptionally changed to a T
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What are some of the modifications that occur in the tRNA pre-transcriptionally
- Some of the nucleotides are removed
- Some of the nucleotides are modified
- CCA is added to the 3' end of all tRNA's
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What would happen to the dihydrouridine if it were available during the transcription of tRNA genes
It would be ignored because you only incorporate A, C, G, and U when making a tRNA, all others will be ignored
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MIDD is a mutation in what mitochondrial DNA- encoded gene having what effect
- tRNA(leu,uur)
- Damages Complex 1 in Ox Phos therefore making less ATP
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What RNA group causes Maternally Inherited Diabetes and Deafness (MIDD)
- tRNA
- The disease causes hearing loss, Diabetes, and Cardiomyopathy.
- This is caused by the change in just one base, often it happens in the mitochondria
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What is MELAS and how is it caused
- Mitochondrial Encephalopathy, Lactic Acidosis, Stroke-Like Episodes
- This is caused by the change in just one tRNA base, often it happens in the mitochondria
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DNA in the mitochondria doesn't do what as readily as that in the nucleus
Get repaired
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A mutated tRNAleu reduces the amount of what made in the mitochondria
Complex I which affects the amount of ATP made
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Topoisomerase is used for both
DNA replication and RNA transcription
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The base sequence of the strand of DNA used as the template for transcription has the base sequence GATCTAC. What is the base sequence of the RNA product? (All sequences are written according to standard convention.)
GUAGAUC
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Unlike DNA polymerases, RNA polymerases
Can initiate synthesis of their polynucleotide product
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The growth of RNA proceeds
5'-3'
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A coding strand is written
5'-3' the coding strand contains the coding genes
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What is the coding strand
This is the strand that is above the template strand that contains the exact nucleotides as end product of the transcription differing only by the T's being replaced by U's
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Nucleotides are always added to what end
The 3' prime end
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What are the Eukaryotic promoters
CAAT box and TATA (Hogness) box
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Promoters most of the time will be where
Usually up stream
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What is a promoter
A gene where the proteins bind to direct the RNA polymerase II to start making RNA
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What is an Enhancer
They bind to activators that stimulate the transcription factors to make the RNA polymerase more active. They are a sequence of DNA that binds to the portein.
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Genes that are considered housekeeping genes that are consistently being made are considered
Constitutive (essential)
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Genes that are needed at lower levels are limited how
Their promoters are usually weak
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What are regulated genes
They are genes expressed at different levels under specific conditions
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What is LCR (Locus control region)
Opens up the chromatin to be coded whereas without it they cannot. Used often to regulate periods in life for a gene to be expressed
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Enhancers, and many silencers, can be found
- They can be found 5’ of a coding region, 3’ of a coding region, and in the introns of a gene
- The point is that they are recognized easily no matter their orientation
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What keeps the globin genes off in non-erythrocytes
They lack (LCR's) Locus control regions that are only expressed in erythrocytes
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Exons vs Entrons
Exons code for proteins, Entrons don't
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The pre-mRNA is processed in what 3 ways
- 5' cap is added
- Splicing out of Introns
- The addition of a poly A tail
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C terminal domain (CTD)
Required to modify mRNA, It coordinates the processing events of capping, splicing and polyadenylation (poly A tail)
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The N terminus is located where on the protein when it is being made
On the beginning of the protein, the C terminus is on the end
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Whats the significance of the 5' cap
Are unique in eukaryotic mRNA
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What coordinates transcription with pre-mRNA processing
The C-terminal domain of RNA pol II
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The 5' end of an Intron you have a --, in the middle an -, and at the 3' an --
- (5' to 3') GU, A, AG
- If any are mutated the gene won't be spliced out
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Splicing of Eukaryotes is carried out by
A combination of snRNA's and proteins called spliceosomes
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The splicing of introns in mRNA precursors is carried out by
Spliceosomes
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What is the function of th 5' cap
Essential unit for the ribosome to bind to the 5’ end of the mRNA.
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A geneticist introduces the genes for a super-spliceosome into the human germline that is able to remove every intron without fail. In which way would people with this genetic innovation differ from the rest of the species?
They would produce fewer unique proteins
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The 5' cap and the 3' poly-A tail are added in the production of mature eukaryotic mRNA. The 5' cap and the 3' poly-A tail have which respective functions?
Translation initiation and transcript stability
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Gene expression involves what two processes
- Transcription – reading the DNA to make RNA
- Translation – reading the mRNA to make protein
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A specific codon ALWAYS codes for the
Same amino acid
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The four Characteristics of the Genetic Code are
- Specificity- Always codes for one amino acid
- Universality- Every organism uses the genetic code
- Redundancy- An amino acid may have more then one code for it
- Nonoverlapping and commaless- the code is read from a fixed starting point, taken three at a time. Nothing tells the ribosome where a codon starts or stops.
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No signal exists in the genetic code to
Indicate the end of one codon and the beginning of another
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A mutation that changes one of the nucleotides in a gene’s coding region are one of three senerios
- 1. Not change the amino acid for which the codon is coding (silent mutations)
- 2. Change the amino acid for which the codon is coding (missense mutations).
- 3. Change the codon to a stop codon (nonsense mutations)
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Frame-shift mutations can happen by
The addition or subtraction of any nucleotides, and will create a protein that is usually “nonsensical” or “nonsensical and truncated”.
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Frame-shift mutations have what end effect
The amino acid sequence beyond the frame shift is always altered
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Aminoacyl-tRNA synthetases is
Needed to attach amino acids to tRNAs and are very accurate in hooking the correct amino acid to the correct tRNA
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ATP and GTP roles in translation
ATP is needed to hook up tRNAs and amino acids; GTP is needed to translate the mRNA
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How many high energy phosphate-bond equivalents are needed for activating amino acids for protein synthesis
2, ATP and GTP
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The anticodon base pairs in what fashion on the tRNA
Complementary fashion with the codon in the mRNA during translation
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The ribosomes of the prokaryotes and eukaryotes are different how
- Eukaryotic ribosomes
- –Are 80S in size
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Some of the tRNAs can recognize more than one codon how, what is this called
- Non-traditional base pairing between the 1st codon on the tRNA and 3rd on the mRNA
- Wobble position
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eIF4 initiation factors bind to what having what effect
5’ cap (cap binding proteins – CBPs) also known as an translation initiator factor
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Alternative splicing is the reason we can
- Make so many proteins with so few genes, 74% of the genes do this
- This is selective splicing essentially
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Polyadenylation is
The addition of a poly(A) tail to an RNA molecule
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Transcription is terminated in Eukaryotes by
Rat1 Race, this follows the transcription and once it catches up it, it terminates transcription
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With what mRNA codon would the tRNA 5' UAC 3' be able to form a codon-anticodon base pairing interaction?
5' GUA 3'
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Which base, when it occurs in the wobble position in tRNA, can bind to three different bases (A, U and C)?
Inosine
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Formation of the peptide bond during protein synthesis does not require
ATP or GTP
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Peptide bond formation is catalyzed by
The large subunit rRNA
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Cycloheximide inhibits the peptidyl transferase reaction in eukaryotes. It does so by binding to
The 60S ribosomal subunit
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Most mRNA are translated by more than one ribosome at a time and are called
Polysomes
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Translation is terminated by a release factor (RF) and what stop codons
UGA, UAG, or UAA codons
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Ferritin is
A cytosolic iron binding protein expressed when iron is abundant in the cell. Transferrin is its receptor
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Interferon in response to pathogens being in the system allow
communication between cells to trigger the protective defenses of the immune system that eradicate pathogens or tumors.
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What is the target of the polio protease
eIF-4G
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Which post-translational modification is most frequently used to rapidly alter protein function
Phosphorylation
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Diphtheria toxin is produced by the gram positive bacilli effects what in translation
eEF2 making it so tRNA cannot move to the P site
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Ribonuclease (Rnase)
is a type of nuclease that catalyzes the degradation of RNA into smaller components
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Poly A Binding Proteins (PBP)
Activate translation
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