Bio Lecture #21

genome

A cell builds the proteins it needs from instructions encoded in its _________ according to the central dogma of molecular biology.

wobble hypothesis

Ability of the tRNAs to recognize more than one codon; the codons differ in their third nucleotide. Hypothesis proposes that the anticodon of tRNAs can still bind successfully to a codon whose 3rd position requires a nonstandard base pairing.

-10; -35

All bacterial promoters have a ________ box and a ________ box, the remainder of the promoter sequence varies.

upside-down L

All of the tRNA in a cell have the same structure, shaped like an _______________ ____. They vary at the anticodon and attached amino acid.

NTP (ribonucleoside triphosphate)

An incoming _______ pairs w/ a complementary base on the DNA template strand, and RNA polymerization begins.

RNA polymerase

As w/ bacteria, the _____ ____________ does not bind directly to the promoter.

elongation

At the start of the ___________ phase, the initiator tRNA is in the P site, and the E and A site are empty.

elongation phase

During this phase of transcription, RNA polymerase moves along the DNA template and synthesizes RNA in the 5'--->3' direction.

RNA processing

During this process, both ends of the primary transcript are usually altered; the regions coded by introns are removed, and the ends of the RNA receive a cap and tail.

three

During translation, ________ distinct tRNAs line up within the ribosome. Each are bound at their anticodons to the corresponding mRNA codon.

transfer RNA

Each _________ ______ carries an amino acid corresponding to the tRNAs 3-base-long anticodon.

aminoacyl tRNA synthetase

Enzymes called ___________ ________ ____________ "charge" the tRNA by catalyzing the addition of amino acids to tRNAs.

exons; introns

Eukaryotic genes are composed of ________, the regions of DNA expressed, and ______, the intervening regions of DNA that do not encode protein.

larger

Eukaryotic genes are much _______ than their corresponding mature mRNA.

transfer RNA (tRNA)

Francis Crick proposed that an adapter molecule holds amino acids in place while interacting directly and specifically w/ a codon in mRNA. The adapter molecule was later found to be a small RNA called:

bacteria

In _________, transcription and translation can occur simultaneously.

eukaryotes

In ____________, transcription and translation are separated.

hairpin

In bacteria the transcription terminal signal codes for RNA forming a ________ structure, which causes the RNA polymerase to separate from the RNA transcript, ending transcription.

DNA

In bacteria, the info in _______ is converted to mRNA directly.

Ribosome binding site

In bacteria, the start codon is preceded by a _________ ___________ ___________ that is complementary to a section of 1 tRNA in the small ribosomal subunit.

basal transcription factors

In eukaryotes, a group of proteins called _______ ______________ __________ bind to the DNA promoter, thus initiating transcription. These factors perform a similar function to bacterial sigma proteins.

immature primary transcript (pre-mRNA)

In eukaryotes, the product of transcription is an ___________ ___________ _______________. Before primary transcripts can be translated, they have to be processed in a complex series of steps.

anticodon

In the ribosome, the tRNA ___________ binds to a 3-base-long mRNA condo, causing the amino acid carried by the transfer RNA to be added to the growing protein.

translation

In this, the sequence of bases in the mRNA is converted to an amino acid sequence in a protein.

splicing

Introns are removed by this.

initiation, elongation, termination

List the 3 phases in Translation:

TATA box

Many of the eukaryotic promoters include a unique sequence called the ______ ______, centered about 30 base pairs upstream of the transcription start site.

phosphate group

Many proteins are altered by enzymes that add or remove a ____________ ________.

sigma proteins

Most bacteria have several types of _______ ___________. Each type allows RNA polymerase to bind to a different type of promoter and therefore a different kind of gene.

post-translation modification

Most proteins go through an extensive series of processing steps, collectively called ______________________ ________________, before they are ready to go to work in a cell.

core enzyme

Prokaryotic RNA polymerase is a holoenzyme made up of the _____ ____________, which has the ability to synthesize RNA, and a sigma subunit.

template strand

RNA polymerase performs this synthesis by transcribing only one strand of DNA, called the ____________ _________.

small; large

Ribosomes can be separated into 2 subunits: 1.) the _____ subunit, which holds the mRNA in place during translation. 2.) the _____ subunit, where peptide bonds form.

intermediate molecules

Ribosomes translate mRNAs into proteins w/ the help of __________ ____________ called transfer RNA (tRNA)

Promoter

Sigma acts as a regulatory factor, guiding RNA polymerase to specific _____________ sequences on the DNA template strand.

core enzyme (Sigma)

Sigma dissociates from the ______ __________ once the initiation phase of transcription is completed.

double helix

Sigma opens up the DNA _______ _________ and the template strand is threaded through the RNA polymerase active site.

holoenzyme

Signma and RNA polymerase together form a ________________, an enzyme make up of a core enzyme and other required proteins.

translocation

This occurs when elongation factors move the mRNA down the ribosome 3 nucleotides at a time, and the tRNA attached to the growing protein moves into the P site.

Initiation (d)

This phase of translation begins at the AUG start codon.

termination

This phase starts when the A site encounters a stop codon. This causes a release factor to enter the site.

5' cap

This serves as a recognition signal for the translation machinery.

E site

This site is where tRNAs, no longer bound to an amino acid, exit the ribosome. Holds a tRNA that will exit.

P site

This site of the ribosome is where a peptide bond forms that adds an amino acid to the growing polypeptide chain. Holds the tRNA w/ growing polypeptide attached.

removed

To make a functional mRNA, these noncoding regions must be __________.

35; 10

Transcription begins when sigma, as part of the holoenzyme complex, bind to the -______ and -______ boxes.

termination phase

Transcription ends with a _____________ ____________. In this phase, RNA polymerase encounters a transcription terminal signal in the DNA template.

sigma (not RNA)

What makes the initial contact w/ DNA that starts transcription, supporting the hypothesis that _______ is a regulatory protein.

exons

________ are the coding regions of eukaryotic genes that will be part of the final mRNA product.

ATP

________ is required to attach tRNA to an amino acid.

bacterial promoters

__________ ____________ are comprised of 40-50 base pairs and have 2 key regions.

Bacteria

___________ have only one RNA polymerase while eukaryotes have 3 distinct types (RNA polymerase I, II, and III).

sigma

___________, a protein subunit, must first bind to the polymerase in order for RNA polymerase to initiate transcription.

translation initiation

____________ ____________ is a 3-step process in bacteria: 1.) The mRNA binds to a small ribosomal subunit. 2.) The initiator aminoacyl tRNA bearing N-formylmethionine (f-met) binds to the start codon. 3.) The large ribosomal subunit binds, completing the complex.

eukaryotes; prokaryotes

______________ have a much more diverse and complex series of promoters than do _____________.

aminoacyl tRNA

a tRNA covalently lined to its corresponding amino acid is called an __________ _________.

poly(A) tail

this extends the life of an mRNA by protecting it from degradation.

Initiation

this is the first phase of transcription.

A site

The __ _____ of the ribosome is the acceptor site for an aminoacyl tRNA. Holds an aminoacyl tRNA.

ribosome

The ____________ is a molecular machine that synthesizes proteins in a 3-step sequence. 1.) An aminoacyl tRNA carrying the correct anticodon for the mRNA codon enter the A site. 2.) A peptide bond forms b/w the amino acid on the aminoacyl tRNA in the A site and the growing polypeptide on the tRNA in the P site. 3.) The ribosome moves ahead 3 bases and all 3 tRNAs move down one position; the tRNA in the E sites exits.

Ribosomal RNA

The active site of the ribosome is entirely __________ ______.

transcription

The first step in converting genetic info into proteins is __________________, the synthesis of an mRNA version of the instructions stored in DNA.

initiation factors

The interaction b/w the small subunit & the mRNA is mediated by _________ ___________.

Introns

The intervening noncoding sequences are called ___________, and are not in the final mRNA. These must be removed from eukaryotic RNA

non-template (coding strand)

The other DNA strand is called ____________________, which matches the sequence of the mRNA, except that RNA has uracil (U) in place of thymine (T).

noncoding regions

The protein-coding regions of eukaryotic genes are interpreted by ____________ _______.

primary RNA transcript

The transcription of eukaryotic genes by RNA polymerase generates a ___________ ______ _____________ that contains exons and introns.

61

There are _____ different codons, but only about 40 tRNAs in most cells.

tRNAs

These are Crick's adapter molecules.

peptide bonds

These bonds form b/w amino acids on the tRNA in the P and A sites.

ribosomes

These catalyze translation of the mRNA sequence into protein.

RNA polymerases

These do not require a primer to begin transcription.

snRNPs (small nuclear ribonucleoproteins)

These form a complex called a splicesome. The splicesome catalyzes the splicing reaction.

Release factors

These resemble tRNAs in size and shape but do NOT carry an amino acid.

Molecular chaperones

These speed folding of the protein!

folding

This determines a protein's shape and therefore its function.

polyribosome

This is formed when multiple ribosomes are attached to an mRNA.