Lecture 26 (Transcription & Translation)
- The A site of the ribosome is the ______ site for an aminoacyl tRNA. - The P site is where a _____ bond forms that adds an amino acid to the growing polypeptide chain. - The E site is where tRNAs no longer bound to an amino acid ___ the ribosome.
- acceptor -peptide -exit
The -# box is found 10 bases upstream (in the opposite direction of RNA polymerase movement during transcription) from the transcription start site (the +1 site) and consists of the sequence TATAAT
-10
All bacterial promoters have a -(#) box and a -(#) box, the remainder of the promoter sequence varies.
-10; -35
Transcription occurs in three stages
1. Initiation 2. Elongation 3. Termination
The CCA sequence at the _' end of each tRNA is the binding site for amino acids.
3'
Many of the eukaryotic promoters include a unique sequence called the TATA box, centered about __ base pairs upstream of the transcription start site.
30
The -35 box, consisting of the sequence TTGACA, is (#) bases upstream from the +1 site.
35
Bacterial promoters are comprised of __-__ base pairs and have two key regions
40-50
-The _____ serves as a recognition signal for the translation machinery.
5' cap
There are __ different codons but only about 40 tRNAs in most cells
61
- Over __% of all genes are structural
90%
1. An aminoacyl tRNA carrying the correct anticodon for the mRNA codon enters the _ site
A
Characteristics of Transfer RNA: -___ is required to attach tRNA to an amino acid.
ATP
The initiation phase of translation begins at the ___ start codon
AUG
(bacteria/eukaryotes) have one RNA polymerase while (bacteria/eukaryotes) have three distinct types, RNA polymerase I, II, and III.
Bacteria; eukaryotes
tRNA: • Common features of tRNA's -______ structure with three stem-loops -Anticodon on (2nd/ 1st) stem-loop -Acceptor stem for AA binding on '3 end
Cloverleaf 2nd
Transcription - A ___ sequence is copied into an ___ sequence
DNA;RNA
_____ are removed by splicing
Introns
At the start of the elongation phase, the initiator tRNA is in the _ site, and the _ and _ sites are empty.
P;E;A
__________ bond is formed by RNA polymerase after base pairing occurs.
Phosphodiester
_____: Site for RNA polymerase binding signals the beginning of transcription.
Promoter
Prokaryotic RNA polymerase is a holoenzyme made up of the core enzyme, which has the ability to synthesize ___, and a sigma subunit
RNA
In bacteria the transcription termination signal codes for RNA forming a hairpin structure, which causes the ___ _______ to separate from the RNA transcript, ending transcription
RNA polymerase
Most bacteria have several types of sigma proteins. -Each type allows ___ ______ to bind to a different type of promoter and therefore a different kind of gene
RNA polymerase
Initiation is the first phase of transcription. - However, ___ ______ cannot initiate transcription on its own. -_____, a protein subunit, must first bind to the polymerase
RNA polymerase;sigma
The transcription of eukaryotic genes by RNA polymerase generates a primary ___ ______ that contains exons and introns
RNA transcript
____: Site for binding of regulatory proteins. The role is to influence the rate of transcription. Can be found in a variety of locations.
Regulatory Sequence
______ catalyze translation of the mRNA sequence into protein
Ribosomes
____, and not RNA polymerase, makes the initial contact with DNA that starts transcription, supporting the hypothesis that sigma is a regulatory protein
Sigma
Initiation Phase: (6 steps) - _____ joins to RNA polymerase - Then sigma joins to the promoter region (downstream/upstream) of the transcription site
Sigma upstream
Transcription ends with a _______ phase. In this phase, RNA polymerase encounters a transcription termination signal in the DNA template.
Termination
_____: Contains the information that specifies an amino acid sequence.
Transcribed region
2. Francis Crick proposed that an ______ _____ holds amino acids in place while interacting directly and specifically with a codon in mRNA
adapter molecule
Characteristics of Transfer RNA: -Enzymes called aminoacyl tRNA synthetases "charge" the tRNA by catalyzing the addition of _____ ___ to tRNAs.
amino acids
Peptide bonds form between _____ ____ on the tRNAs in the P and A sites.
amino acids
2. The initiator ______ tRNA bearing N-formylmethionine (f-met) binds to the start codon.
aminoacyl
Characteristics of Transfer RNA: - A tRNA covalently linked to its corresponding amino acid is called an ______ tRNA
aminoacyl
All of the tRNAs in a cell have the same structure, shaped like an upside-down L. They vary at the ______ and attached amino acid
anticodon
The triplet on the loop at the opposite end is the ______ that base pairs with the mRNA codon.
anticodon
An aminoacyl tRNA binds to the codon in the A site via complementary base pairing between ____ and _____
anticodon and codon
All three tRNAs are bound at their ______ to the corresponding mRNA codon
anticodons
In (bacteria/eukaryotes), the information in DNA is converted to mRNA directly. In (bacteria/eukaryotes), however, the product of transcription is an immature primary transcript, or pre-mRNA.
bacteria;eukaryotes
In eukaryotes, a group of proteins called ____ transcription factors bind to the DNA promoter, thus initiating transcription
basal
• An incoming ribonucleoside triphosphate (NTP) pairs with a complementary ____ on the DNA template strand, and RNA polymerization begins.
base
Primary RNA transcripts are also processed by the addition of a 5′ ___ and a poly(A) tail
cap
The other DNA strand is called the non-template, or _____ strand, which matches the sequence of the mRNA, except that RNA has uracil (U) in place of thymine (T).
coding
Thus, one tRNA is able to base pair with more than one type of _____.
codon
Characteristics of Transfer RNA: -For each of the 20 amino acids, there is (the same/ a different) aminoacyl tRNA synthetase and one or more tRNAs
different
There were two hypotheses regarding the specification of amino acid sequence by a sequence of nucleotide bases: 1. mRNA codons and amino acids interact (in-/directly)
directly
As with bacteria, the RNA polymerase (does/does not) bind directly to the promoter.
does not
Sigma opens the DNA ____ ____ and the template strand is threaded through the RNA polymerase active site.
double helix
- Sigma opens up the ____ ____ - The newly exposed template strands is threaded into the ____ _____ of RNA polymerase
double helix active site
During the _______ phase of transcription, RNA polymerase moves along the DNA template and synthesizes RNA in the 5' -> 3' direction
elongation
A ___ is an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product
gene
A cell builds the proteins it needs from instructions encoded in its ______ according to the central dogma of molecular biology.
genome
Basal transcription factors perform a similar function to bacterial sigma proteins. - However, basal transcription factors include many proteins, and they are not part of a ______.
holoenzyme
Sigma polymerase together form a _____, an enzyme made up of a core enzyme and other required proteins and RNA
holoenzyme
1. RNA polymerase and sigma form a ______ 2. Sigma recognizes and binds to a _______
holoenzyme promoter
• Sigma dissociates from the core enzyme once the _______ phase of transcription is completed.
initiation
Translation has three phases: ?
initiation, elongation, and termination
The intervening noncoding sequences are called _____, and are not in the final mRNA.
introns
3. The (small/large) ribosomal subunit binds, completing the complex
large
- The poly(A) tail extends the ___ of an mRNA by protecting it from degradation
life
Eukaryotic genes are much larger than their corresponding mature ____.
mRNA
Multiple ribosomes attached to an _____ form a polyribosome.
mRNA
The interaction between the small subunit and the _____ is mediated by initiation factors
mRNA
Translation initiation is a three-step process in bacteria: 1. The ____ binds to a small ribosomal subunit.
mRNA
In bacteria, transcription and translation can occur simultaneously. Bacterial ribosomes begin translating an ____ before __ _____ has finished transcribing it
mRNA; RNA polymerase
Eukaryotes have a much (less/more) diverse and complex series of promoters than do prokaryotes
more
The protein-coding regions of eukaryotic genes are interrupted by _______ regions. - To make a functional mRNA, these _____ regions must be removed.
noncoding;noncoding
To resolve this deficit, Francis Crick proposed the wobble hypothesis. This hypothesis proposes that the anticodon of tRNAs can still bind successfully to a codon whose third position requires a __________ pairing.
nonstandard base
In eukaryotes, transcription and translation are separated. mRNAs are synthesized and processed in the ____ and then transported to the ______ for translation by ribosomes.
nucleus; cytoplasm
RNA polymerase performs this synthesis by transcribing (only one strand/many strands) of DNA, called the template strand
only one strand
2. A _____ bond forms between the amino acid on the aminoacyl tRNA in the A site and the growing polypeptide on the tRNA in the P site
peptide
Like the DNA polymerases, an RNA polymerase performs a template-directed synthesis in the 5′ to 3′ direction. But unlike DNA polymerases, RNA polymerases do not require a _____ to begin transcription
primer
Sigma acts as a regulatory factor, guiding RNA polymerase to specific_____ sequences on the DNA template strand
promotor
Ribosomes contain _____ and ribosomal RNA (rRNA)
protein
The active site of the ribosome is entirely _____ RNA
ribosomal
During translation, three distinct tRNAs line up within the ______.
ribosome
In bacteria, the start codon is preceded by a ______ binding site (also called the Shine-Dalgarno sequence) that is complementary to a section of one rRNA in the small ribosomal subunit.
ribosome
The _____ is a molecular machine that synthesizes proteins in a three-step sequence
ribosome
Translocation occurs when elongation factors move the mRNA down the _______ three nucleotides at a time, and the tRNA attached to the growing protein moves into the _ site
ribosome;P
Thus, ribosomal RNA catalyzes peptide bond formation and the ribosome is a _______
ribozyme
tRNA: Cells make many different tRNA molecules encoded by different genes • tRNA named by the AA they carry -tRNAser carries _____ - _______ code means more than one type of tRNA may be produced for each AA
serine Degenerate
Transcription begins when ____, as part of the holoenzyme complex, binds to the -35 and -10 boxes.
sigma
Ribosomes can be separated into two subunits: - The____ subunit, which holds the mRNA in place during translation. - The ____ subunit, where peptide bonds form
small;large
Small nuclear ribonucleoproteins (snRNPs) form a complex called a ________. This ______ catalyzes the splicing reaction.
spliceosome;spliceosome
- RNA strand is _______ - Sigma lets go of ___ _____ once initiation has begun....
synthesized RNA polymerase
After peptide bond formation, the polypeptide on the tRNA in the P site is transferred to the _____ in the A site.
tRNA
The secondary structure of tRNA folds over to produce an Lshaped (tertiary/secondary) structure.
teritiary
3. The ribosome moves ahead _____ bases and all _____ tRNAs move down one position; the tRNA in the E site exits.
three;three
With the addition of cap and tail and completion of splicing, processing of the primary RNA _____ is complete. The product is a mature mRNA.
transcript
The first step in converting genetic information into proteins is _______, the synthesis of an mRNA version of the instructions stored in DNA
transcription
The adapter molecule was later found to be a small RNA called ____ RNA (tRNA)
transfer
• Other genes code for the RNA itself - ______ ____ - translates mRNA into amino acids - Ribosomal RNA (rRNA) - part of _______
transfer RNA ribosomes
In _____, the sequence of bases in the mRNA is converted to an amino acid sequence in a protein
translation
Exons are the coding regions of eukaryotic genes that (will not/will) be part of the final mRNA product.
will
A gene is composed of specific sequences organized in a way that allows the DNA to be transcribed into RNA (4)
- Promoter - Regulatory sequence - Transcribed region - Terminator
Signals end of transcription.
Terminator
Where are the other 3?
They are the stop codons