Cell Bio Chapter 11 The Central Dogma: From DNA to Protein

Gene

Stores information to make polypeptides.

Gene expression

A procedure to produce a functional protein using the information stored in the correlated gene.

Central Dogma

A DNA-based gene encoding an RNA based message that is then translated into a protein

Transcription

process by which an RNA is synthesized from a DNA template in the nucleus

Translation

process by which proteins are synthesized from an mRNA template in the cytoplasm

Messenger RNA (mRNA)

An intermediate between a gene (DNA) and a polypeptide (Protein).

Function of mRNA

Allows the cell to separate information storage from information utilization and greatly amplify its synthetic output

RNA polymerase

Enzyme synthesizing RNA from DNA template.

Promoter

DNA region where RNA polymerase binds.

Promoter function

Determines which of the two DNA strands will be used as the template and where transcription will begin and Facilitates initiation of transcription.

Transcription factors

A group of proteins that control the rate of transcription of genetic information from DNA to messenger RNA, by binding to promoter region

primary transcript (pre-mRNA)

Initial RNA product, precursor to mature mRNA.

Ribonucleoside triphosphates substrates (NTPs)

are cleaved to nucleoside monophosphates as they are polymerized into RNA chain

Direction of RNA chain

5' to 3' direction antiparallel to the DNA template

DNA-RNA Hybrid

Temporary structure during transcription, about 9 base pairs.

Transcription bubble

Region where DNA unwinds during transcription.

Processive

RNA polymerase remains attached to DNA during synthesis.

Number of RNA polymerases in prokaryotes

one

Core Enzyme

Five subunits forming prokaryotic RNA polymerase.

Sigma Factor

Protein aiding RNA polymerase binding to specific promoter sites.

Transcription unit

DNA segment corresponding to a primary transcript.

mRNA

Messenger RNA coding for specific polypeptides.

Eukaryotic mRNA

Contains specific modifications at both ends.

5' cap of eukaryotic mRNA

Methylated guanosine cap on mRNA's.

Function of the 5'-cap of eukaryotic mRNA

Prevents the 5’-end of mRNA from being digested by enzymes, Aids in transport of the mRNA out of the nucleus and plays an important role in the initiation of translation.

3' cap of eukaryotic mRNA

poly(A) tail, composed of 50-250 adenosine residues

Function of 3' cap of eukaryotic mRNA

Protect the mRNA from premature degradation by enzymes

RNA polymerase II

makes all eukaryotic mRNA precursors in nucleus

General Transcription Factors (GTFs)

Proteins forming preinitiation complex( PIC) with RNA polymerase II.

Preinitiation Complex (PIC)

Assembly of GTFs at promoter for transcription initiation.

TATA Box

Consensus sequence critical for eukaryotic transcription initiation.

TFIIH

Complex with kinase and helicase activities for transcription.

Protein kinase

The enzyme that transfers phosphate groups from ATP to protein. (phosphorylate RNA polymerase II)

Helicase

The enzyme that unwinds DNA double helix to generate the transcription bubble

Exon

Parts that contribute to the mature RNA, including coding sequence

Intron

Noncoding sequence removed from pre-mRNA.

RNA Splicing

Process of removing introns and joining exons to produce the mRNA.

Alternative Splicing

A regulated process during gene expression that results in a single gene coding for multiple proteins

Transcription in prokaryotes

Single RNA polymerase binds randomly to DNA.

Cotranscriptional Processing

Simultaneous processing of RNA during transcription.

Cytoplasm

Location where mRNA is translated into proteins.

Template Strand

DNA strand used for RNA synthesis during transcription.

Codons

Information stored in a gene is present as a genetic code.

Properties of Codons

Triplets of nucleotides, Non-overlapping, and Degenerate

The first two codon bases for a particular amino acid are _________, whereas the third base may vary.

invariant(never changing)

Synonymous Mutation

Mutation that does not change the amino acid sequence.

Non-synonymous Mutation

Mutation that results in an amino acid change.

Nonsense Mutation

Mutation creating a premature termination codon.

Frameshift Mutation

Insertion or deletion altering the reading frame of mRNA.

tRNA

Translate a sequence of mRNA codons into a sequence of amino acid residues: decoding

tRNA transfer appropriate amino acid to specific __________.

Codons

tRNA structure

73 to 93 nucleotides with cloverleaf shape.

Anticodon

A stretch of three sequential nucleotides resides in tRNA, which decodes codon information by forming complementary base pairs between codons on the mRNA transcript.

Wobble hypothesis

tRNA can recognize variable third codon bases.

3rd position of U

with A or G (codon)

3rd position of G

with U or C (codon)

3rd position of I

with U, C, or A (codon)

Aminoacyl-tRNA synthetases

Enzymes linking amino acids to tRNAs.

Ribosomes

Cellular structures where translation occurs. (Complex translating mRNA into proteins.)

Ribosome complex

Consist of protein subunits(large or small), Ribosomal RNAs, and Transfer RNAs

Eukaryotic ribosome protein subunits

Small (40S) and large (60S) subunits.

Ribosomal RNAs

Act as structural support for ribosome complex and catalyze the chemical reaction in which amino acids are covalently linked to one another.

Transfer RNAs

Required to translate the information in the mRNA nucleotide code into the amino acid

tRNA binding sites

A(aminoacyl), P(peptidyl), and E(exit) sites in ribosome.

Translation process is _________ between prokaryotes and eukaryotes

similar

Components required for translation

Various tRNAs with their attached AA, Ribosomes, A messenger RNA, Numerous proteins with different functions, GTP, Cations, and rRNA

3 steps of translation

initiation, elongation, termination

what is required for initiation of protein synthesis?

Initiation factors (eIFs)

Initiation codon

AUG (methionine)

Step 1 (Initiation) of Translation

43S complex binds to the 5' end of mRNA complex and scan for the AUG start codon

Step 2 (Initiation) of Translation

Large subunit (60S) joins the complex after 43S complex reaches the appropriate AUG codon

Components of 43S complex

Ribosomal 40S subunit, Initiator tRNA linked to a methionine (AUG), eIFs: eIF2-GTP

Components of mRNA complex

mRNA, eIF4E, eIF4A, and eIF4G

eIF4E function

binds to 5'-cap

eIF4A function

remove double stranded structure

eIF4G function

links 5' and 3' end

Kozak sequence

Defines the AUG start codon.

Elongation Cycle of Protein Synthesis

process of adding each subsequent amino acid to the growing polypeptide chain.

Elongation factors (eEFs)

Proteins required during the elongation phase (also 2 GTP).

Major Steps in Elongation of Translation

Aminoacyl-tRNA selection, Peptide bond formation, Translocation and Releasing the deacylated tRNA

With the charged amino acid in the P site, the next aminoacyl-tRNA binds to the vacant _________ is the first step for elongation.

A-site

Any aminoacyl-tRNA can enter the A site, but ONLY the one with a ______________________ can trigger the ribosome's conformational change.

complementary anticodon

peptidyl transferase

Enzyme responsible for catalyzing peptide bond formation

_____________ of the amino acid bound to the A site tRNA links to ____________ of the amino acid bound to the P site tRNA to form a peptide bond.

Amine nitrogen, carboxyl carbon

Translocation

procedure by which the ribosome moves three nucleotides (one codon) in the 5’ to 3’ direction on the mRNA molecule

Releasing the deacylated tRNA

The deacylated tRNA leaves the ribosome and empty the E site of the ribosome

Stop codons

UAA, UAG, or UGA signal termination.

Release factors

Proteins that recognize stop codons.

eRF1

Release factor for Eukaryotic cells, which recognize all the stop codons

Polyribosome (polysome)

A complex of multiple ribosomes on mRNA, allowing simultaneous translation.

polyribosomes function

increase the rate of protein synthesis