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chapter 17
Dr. Radhika Reddy
122
Biology
Undergraduate 2
11/06/2013

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Term
What is the The Central Dogma?
Definition
A cell builds the proteins it needs from instructions encoded in its genome
Term
The first step in converting genetic information into proteins is?
Definition
transcription
Term
What is transcription?
Definition
Synthesis of an mRNA version of the instructions stored in DNA
Term
What performs this mrna synthesis by transcribing only one strand of DNA?
Definition
RNA polymerase
Term
When RNA polymerase synthesizes mrna from a single strand of DNA. That dna strand is called the?
Definition
Template strand
Term
The other DNA strand not being transcribed is called what?
Definition
non-template, or coding strand
Term
Like the DNA polymerases an RNA polymerase performs a template-directed synthesis in what direction?
Definition
5prime to 3prime
Term
Unlike DNA polymerases
RNA polymerases do not require?
Definition
a primer to begin transcription
Term
Bacteria have how many RNA polymerase?
Definition
1
Term
Eukaryotes have how many distinct types of RNA polymerase?
Definition
3
Term
What are the three distinct types of rna polymerase in uekaryotes?
Definition
RNA polymerase I, II, and III
Term
What is the is the first phase of transcription?
Definition
Initiation
Term
What is Sigma?
Definition
a protein subunit that must first bind to the polymerase
Term
Sigma and RNA polymerase together to form a?
Definition
holoenzyme
Term
What is a holoenzyme?
Definition
An enzyme made up of a core enzyme and other required proteins
Term
Prokaryotic RNA polymerase is a holoenzyme made up of?
Definition
the core enzyme and a sigma subunit
Has the ability to synthesize RNA
Term
Sigma acts as a regulatory factor
Guiding RNA polymerase to ?
Definition
specific promoter sequences
On the DNA template strand
Term
Bacterial promoters are comprised of how many base pairs?
Definition
40-50
Term
Bacterial promoters have two key regions what are they?
Definition
-10 and -35 box
Term
The –10 box is found where?
Definition
10 bases upstream from the transcription start site
Term
The –35 box is located where?
Definition
Is 35 bases upstream from the +1 site
Term
Transcription begins when?
Definition
When sigma, as part of the holoenzyme complex binds to the –35 and –10 boxes
Term
What makes the initial contact with DNA that starts transcription?
Definition
Sigma
Term
Why do most bacteria have several types of sigma proteins?
Definition
Each type allows RNA polymerase to bind to a different type of promoter, therefore a different kind of gene
Term
what opens the DNA double helix?
Definition
sigma
Term
The template strand is threaded through the what?
Definition
RNA polymerase active site
Term
An incoming ribonucleoside triphosphate (NTP) pairs with what?
Definition
a complementary base on the DNA template strand
Term
Once RNA polymerization begins what does sigma do?
Definition
dissociates from the core enzyme
Term
What happens during the elongation phase of transcription ?
Definition
RNA polymerase moves along the DNA template
Synthesizes RNA in the 5prime to 3prime direction
Term
Transcription ends with what phase?
Definition
termination phase
Term
describe termination phase.
Definition
RNA polymerase transcribes a transcription termination signal in the DNA template into RNA
Term
In bacteria the transcription termination signal codes for RNA that forms what type of structure?
Definition
hairpin
Term
What is the significance of the hairpin structure in termination signal of bacteria?
Definition
Causes the RNA polymerase to separate from the RNA transcript
Ending transcription
Term
Eukaryotes or prokaryotes have more diverse and complex series of promoters ?
Definition
Eukaryotes
Term
Many of the eukaryotic promoters include
A unique sequence called the ?
Definition
TATA box
Term
where is the TATA box located?
Definition
Centered about 30 base pairs upstream of the 1
Term
As with bacteria, the RNA polymerase does not bind directly to the?
Definition
promoter
Term
In eukaryotes, a group of proteins called ? bind directly to the promoter
Definition
basal transcription factors
Term
In eukaryotes, basal transcription factors do what?
Definition
Initiate transcription
Term
basal transcription factors are not part of a? (grouping)
Definition
holoenzyme
Term
In eukaryotes the product of transcription is ?
Definition
an immature primary transcript
Or pre-mRNA
Term
What are the two steps that have to take place with the pre-mrna?
Definition
Splicing
Adding Caps and Tails to RNA Transcripts
Term
The protein-coding regions of eukaryotic genes are interrupted by ?
Definition
noncoding regions
Term
To make a functional mRNA these noncoding regions must?
Definition
be removed
Term
What are exons?
Definition
Are the coding regions of eukaryotic genes that will be part of the final mRNA product
Term
what are introns?
Definition
The intervening noncoding sequences not in the final mRNA
Term
Eukaryotic genes are what relative size compared to their corresponding mature mRNA?
Definition
much larger than
Term
The transcription of eukaryotic genes by RNA polymerase generates a
Definition
primary RNA transcript
Term
A primary RNA transcript contains?
Definition
exons and introns
Term
Introns are removed by
Definition
splicing
Term
Small nuclear ribonucleoproteins (snRNPs) form a complex called a ?
Definition
spliceosome
Term
What does the Spliceosome do?
Definition
Spliceosome catalyzes the splicing reaction
Term
RNA processing is complete upon what 3 events?
Definition
Completion of splicing
Addition of the cap
Addition of the poly(A) tail
Term
Primary RNA transcripts are also processed by the addition of a ?
Definition
5prime cap and poly(A) tail
Term
once the 5prime cap and poly(A) tail are added what is the product?
Definition
The product is a mature mRNA
Term
The 5prime cap serves as a ?
Definition
recognition signal for the translation machinery
Term
The poly(A) tail does what?
Definition
extends the life of an mRNA by protecting it from degradation
Term
what is translation
Definition
The sequence of bases in the mRNA is converted to an amino acid sequence in a protein
Term
What do Ribosomes do?
Definition
Catalyze translation of the mRNA sequence into protein
Term
true or false: In bacteria, transcription and translation can occur simultaneously
Definition
true
Term
when do bacterial ribosomes begin translating an mRNA ?
Definition
Before RNA polymerase has finished transcribing it
Term
Multiple ribosomes attached to an mRNA form a ?
Definition
polyribosome
Term
true or false:In eukaryotes, transcription and translation are done simultaneously?
Definition
false. In eukaryotes, transcription and translation are separated
Term
mRNAs are synthesized and processed where?
Definition
nucleus
Term
mRNAs are synthesized and processed
in the nucleus then transported to the ? for what?
Definition
cytoplasm for translation by ribosomes
Term
What was Crick's hypotheses regarding the specification of amino acid sequence by a sequence of nucleotide bases.
Definition
Francis Crick proposed that an adapter molecule holds amino acids in place while interacting directly and specifically with a codon in mRNA.
Term
What was the competing hypothesis to Cricks hypothesis?
Definition
mRNA codons and amino acids interact directly
Term
The adapter molecule was later found to be a small RNA called?
Definition
tRNA
Term
amino acids are transferred from the RNA ?
Definition
the growing end of a new polypeptide
Term
The experiment also confirmed
Aminoacyl tRNAs act as the what?
Definition
interpreter in the translation process
Term
What is required to attach tRNA to an amino acid?
Definition
ATP
Term
Enzymes called ? “charge” the tRNA
Definition
aminoacyl tRNA synthetases
Term
aminoacyl tRNA synthetases “charge” the tRNA by ?
Definition
Catalyzing the addition of amino acids to tRNAs
Term
What is an aminoacyl tRNA
Definition
A tRNA covalently linked to its corresponding amino acid is called an
Term
Where is the binding site for amino acids
Definition
CCA sequence at the 3prime end of each tRNA
Term
Where are the anticodon that base-pairs with the mRNA codon
Definition
The triplet on the loop at the opposite end
Term
The secondary structure of tRNA folds over to produce a ? shaped tertiary structure.
Definition
L-shaped
Term
True or False: All of the tRNAs in a cell have a different structure
Definition
false All of the tRNAs in a cell have the same structure
Term
All of the tRNAs vary at what two places?
Definition
The anticodon
The attached amino acid
Term
How many different codons are there?
Definition
61
Term
How many tRNA codons are in most cells?
Definition
40
Term
To resolve this deficit, Francis Crick proposed what hypothesis?
Definition
wobble hypothesis
Term
Wobble hypothesis proposes?
Definition
The anticodon of tRNAs can still bind successfully to a codon whose third position requires a nonstandard base pairing
Term
One tRNA is able to base-pair with how many types of codon?
Definition
more than one type
Term
Ribosomes contain what two things?
Definition
Protein
Ribosomal RNA (rRNA)
Term
What are they?
Definition
small subunit and large subunit
Term
what does the small subunit do?
Definition
The small subunit holds the mRNA in place during translation
Term
What does the large subunit do?
Definition
The large subunit is where peptide bonds form
Term
During translation how many distinct tRNAs line up within the ribosome
Definition
three
Term
The active site of the ribosome is entirely made of what?
Definition
ribosomal RNA
Term
Ribosomal RNA catalyzes formation of what?
Definition
peptide bonds
Term
What is a ribozyme?
Definition
An RNA with catalytic activity
Term
All three tRNAs are bound at their anticodons to ?
Definition
the corresponding mRNA codon
Term
The A site of the ribosome is the ? site for aminoacyl tRNA.
Definition
acceptor site
Term
The A site of the ribosome is the ? site for aminoacyl tRNA.
Definition
acceptor site
Term
where is a peptide bond formed that adds an amino acid to the growing polypeptide chain?
Definition
P site
Term
? is where tRNAs no longer bound to an amino acid exit the ribosome
Definition
E site
Term
The ribosome is a molecular machine that
does what?
Definition
Synthesizes proteins in a three-step sequence
Term
An aminoacyl tRNA carrying the correct anticodon for the mRNA codon enters what site?
Definition
A site
Term
A peptide bond forms between ?
Definition
The amino acid on the aminoacyl tRNA in the A site
And the growing polypeptide on the tRNA in the P site
Term
The ribosome moves where?
Definition
ahead 3 bases
Term
Translation has three phases what are they
Definition
Initiation
Elongation
Termination
Term
The initiation phase of translation begins where?
Definition
At the AUG start codon
Term
In bacteria the start codon is preceded by ?
Definition
ribosome binding site
Term
Interaction between the small subunit and the mRNA is mediated by
Definition
initiation factors
Term
Translation initiation is a three-step process in bacteria. Describe the three processes.
Definition
The mRNA binds to a small ribosomal subunit
The initiator aminoacyl tRNA bearing N-formylmethionine (f-met) binds to the start codon
The large ribosomal subunit binds, completing the complex
Term
Elongation has three steps, describe them.
Definition
Arrival of the aminoacyl tRNA
Peptide bond formation
Translocation
Term
At the start of the elongation phase
The initiator tRNA is located where?
Definition
is in the P site
Term
At the start of the elongation phase what is located at the E and A sites?
Definition
nothing.
Term
At the start of the elongation phase
An aminoacyl tRNA binds to ?
Definition
the codon in the A site
Term
peptide bonds form between amino acids on the ?
Definition
tRNAs in the P and A sites
Term
After peptide bond formation, the polypeptide on the tRNA in the P site
does what?
Definition
Is transferred to the tRNA in the A site
Term
Translocation occurs when ?
Definition
Elongation factors move the mRNA down the ribosome three nucleotides at a time and the tRNA attached to the growing protein moves into the P site
Term
The termination phase starts when?
Definition
the A site encounters a stop codon
Term
When the A site encounters a stop codon
This causes a protein to do what?
Definition
enter the A site
Term
This protein that enters the A site is called a?
Definition
release factor
Term
Release factors resemble tRNAs in size and shape but what is different about them?
Definition
do not carry an amino acid
Term
These factors catalyze?
Definition
hydrolysis of the bond
Term
What speeds folding of the protein
Definition
Molecular chaperones
Term
What determines a protein’s shape and therefore its function?
Definition
Folding
Term
Before they are ready to go to work in a cell Most proteins go through an extensive series of processing steps
Called ?
Definition
post-translational modification
Term
Many proteins are altered by enzymes that do what? Why?
Definition
add or remove a phosphate group
These changes often switch the protein from an inactive state to an active state or vice versa
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