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