From DNA to Protein

Chapter 9

Biology Concepts and Applications, Eight Edition, by Starr, Evers, Starr. Brooks/Cole, Cengage Learning 2011.

9.1 Ricin and Your Ribosomes

Ricin• Naturally occurring protein that is highly toxic

•A dose smaller then a few grains of salt can kill an adult (die of low blood pressure and respiratory failure)

• One of Ricin’s two polypeptide chains is an enzyme that inactivated ribosomes•The second polypeptide chain binds to the plasma

membrane allowing the cell to take up Ricin by endocytosis

Ribosomes• Assembly amino acids into proteins

• Proteins are critical to all life processes

Proteins

All proteins consist of polypeptide chains• A linear sequence of amino acids

Each chain corresponds to the nucleotide base sequence of a gene

The Path From Genes to Proteins

1. Transcription• Enzymes use the base sequence of a gene in the

DNA as a template to make a strand of RNA

2. Translation• Information in the RNA strand is decoded

(translated) into a sequence of amino acids

Prokaryotes and Eukaryotes

In prokaryotic cells (no nucleus)• Transcription and translation occur in cytoplasm

In eukaryotic cells• Genes are transcribed in the nucleus

• Resulting mRNA is translated in the cytoplasm

Key Concepts: INTRODUCTION

Life depends on enzymes and other proteins

All proteins consist of polypeptide chains

Chains are sequences of amino acids that correspond to sequences of nucleotide bases in DNA called genes

The path leading from genes to proteins has two steps: transcription and translation

9.2 The Nature of Genetic Information

Genetic information consists of the nucleotide base sequence of DNA

The linear order, or sequence, of the four bases in the strand is the genetic information

Genetic information occurs in subsets called genes•Genes part of the DNA sequence that

specifies an RNA or protein production

Transcription: DNA to RNA

Two DNA strands unwind in a specific region

RNA polymerase assembles a strand of RNA• Covalently bonds RNA nucleotides (adenine,

guanine, cytosine, uracil) according to the nucleotide sequence of the exposed gene

Three Types of RNA

Messenger RNA (mRNA)• Carries protein-building codes from DNA to

ribosomes

Ribosomal RNA (rRNA)• Forms ribosomes (where polypeptide chains are

assembled)

Transfer RNA (tRNA)• Delivers amino acids to ribosomes

RNA and DNA Compared

RNA Base Pairing

Fig. 13.2, p.198

phosphategroup

base(uracil)

sugar (ribose)

Gene Transcription

Definition: The process by which the information in a gene becomes converted to an RNA or protein product

RNA polymerase enzyme that carries out transcription

Promoter in DNA, a sequence to which RNA polymerase binds

Fig. 13.3, p.198

Fig. 13.3, p.198

Fig. 13.3, p.198

gene region

RNA polymerase, the enzymethat catalyzes transcription

DNA templateunwinding

newly formingRNA transcript

DNA templatewinding up

Fig. 13.3, p.198

Fig. 13.3, p.198

RNA Modification: Alternative Splicing

Before mRNA leaves the nucleus:• Introns are removed during RNA processing

• Some exons are removed along with introns; remaining exons are spliced together in different combinations•Most are not removed during RNA processing•Alternative splicing

•RNA processing event in which some exons are removed or joined in various combinations

• Poly-A tail is added to 3’ end of new mRNA

The Poly-A Tail

The longer its poly-A tail, the more time an mRNA transcript (and its protein-building message) will remain intact in the cytoplasm

Post-Translational RNA Modification

Fig. 13.4, p.199

unit of transcription in DNA strand

mature mRNA transcript

exon exon exonintronintron

transcription into pre-mRNA

cap poly-A tail

snipped out snipped out

5' 3'

Key Concepts: TRANSCRIPTION

During transcription, the two strands of the DNA double helix are unwound in a gene region

Exposed bases of one strand become the template for assembling a single strand of RNA (a transcript)

Messenger RNA is the only type of RNA that carries DNA’s protein-building instructions

RNA and the Genetic Code

Messenger RNA (mRNA) carries DNA’s protein-building information to ribosomes for translation

mRNA’s genetic message is written in codons• Sets of three nucleotides along mRNA strand

•The genetic code •The concept that a set of three nucleotides

specifies a particular amino acid

Codons

Codons specify different amino acids• A few codon signals stop during translation

Sixty-four possible codons constitute a highly conserved genetic code

Genetic Code: RNA Triplets

From DNA to Polypeptide

Fig. 13.5, p.200

aminoacids

DNA

mRNA

mRNAcodons

threonine proline glutamate glutamate lysine

Variation in Genetic Code

Variant codons occur among prokaryotes, prokaryote-derived organelles (such as mitochondria), and some ancient lineages of single-celled eukaryotes

Key Concepts: CODE WORDS IN THE TRANSCRIPTS

The nucleotide sequence in RNA is read three bases at a time

Sixty-four base triplets that correspond to specific amino acids represent the genetic code, which has been highly conserved over time

tRNA and rRNA Function in Translation

Transfer RNA (tRNA) • Anticodon binds to mRNA codon

• Also binds amino acid specified by codon

Different tRNAs carry different amino acids• tRNAs deliver free amino acids to ribosomes

during protein synthesis

tRNA

rRNA Ribosomal RNA (rRNA) and proteins make up

the two subunits of ribosomes

Three Stages of Translation

mRNA-transcript information directs synthesis of a polypeptide chain during translation

Translation proceeds in three stages• Initiation

• Elongation

• Termination

Initiation

One initiator tRNA, two ribosomal subunits, and one mRNA come together as an initiation complex

Methionine (M) • tRNA carries M M is the first amino acid of the

new polypeptide chain

Initiation

Elongation

tRNAs deliver amino acids to the ribosome in the order specified by mRNA codons

Ribosomal rRNA catalyzes the formation of a peptide bond between amino acids

Elongation

Peptide Bond Forms between Met and Valine

Elongation

Elongation

Termination

Translation ends when RNA polymerase encounters a STOP codon in mRNA• New polypeptide chain and mRNA are released

• Ribosome subunits separate from each other

Termination

Fig. 13.8, p.202

mRNA

initiatortRNA

smallribosomalsubunit

largeribosomalsubunit

Initiation

A mature mRNAleaves the nucleusand enters cytoplasm,which has many freeamino acids, tRNAs,and ribosome subunits.An initiator tRNA bindsto a small ribosomalsubunit and the mRNA.

A large ribosomalsubunit joins, and thecluster is now calledan initiation complex.

Fig. 13.8, p.202

A peptide bondforms between thesecond and thirdamino acids (here,valine and leucine).

A peptide bondforms between thefirst two amino acids(here, methionineand valine).

An initiator tRNAcarries the amino acidmethionine, so the firstamino acid of the newpolypeptide chain will be methionine. A second tRNA binds the second codon of the mRNA (here, thatcodon is GUG, so thetRNA that binds carriesthe amino acid valine).

Elongation

The first tRNAis released and theribosome moves tothe next codon in themRNA. A third tRNAbinds to the thirdcodon of the mRNA(here, that codon isUUA, so the tRNAcarries the aminoacid leucine).

Fig. 13.8, p.202

A peptide bondforms between thethird and fourthamino acids(here, leucineand glycine)

The second RNAis released and theribosome moves to the next codon. A fourth tRNA binds the fourth mRNA codon (here, that codon is GGG, sothe tRNA carries the amino acid glycine).

Steps d and e are repeated over and over until the ribosome encounters a STOP codon in the mRNA. The mRNA transcript and the new polypeptide chain are released from the ribosome. The two ribosomal subunits separate from each other. Translation isnow complete. Either the chain will join the pool of proteins in the cytoplasm or it will enter rough ER of the endomembrane system (Section 4.8).

Termination

Key Concepts: TRANSLATION

During translation, amino acids become bonded together into a polypeptide chain in a sequence specified by base triplets in messenger RNA

Transfer RNAs deliver amino acids one at a time to ribosomes

Ribosomal RNA catalyzes the formation of peptide bonds between the amino acids

Transcription-Translation Concepts

Many ribosomes may simultaneously translate the same mRNA, this is called polysomes

Transcription and translation both occur in the cytoplasm

Compared to DNA, RNA is not very stable• An mRNA may last only a few minutes before it

gets disassembled by enzymes in the cytoplasm

Translation is Energy intensive (use ATP)

Mutated Genes and Their Protein Products

Mutations are permanent, small-scale changes in the base sequence of a gene

Common mutations include • Insertions

•one or more base pairs are inserted into the DNA

• Deletions •one or more base pairs are lost

• Base-pair substitutions•A single base-pair is changed

Common Gene Mutations

Transposable Elements

Segments of DNA that can insert themselves anywhere in a chromosome

Some Causes of Mutations

Natural and synthetic chemicals• Cigarette smoke

Environmental agents• Ionizing radiation• Nonionizing radiation

Key Concepts: MUTATIONS IN THE CODE WORDS

Mutations in genes may result in changes in protein structure, protein function, or both

The changes may lead to variation in traits among individuals

SUMMARY: Protein Synthesis

Fig. 13.11, p.206

mRNA

Final protein

cytoplasmicpools ofamino acids,ribosomalsubunits,and tRNAs

Convergenceof RNAs

Transcription Assembly of RNA on unwound regions of DNA molecule

At an intactribosome,synthesis ofa polypeptidechain at thebinding sitesfor mRNAand tRNAs

Translation

mRNAprocessing

maturetRNA

ribosomalsubunits

mature mRNAtranscripts

proteins

tRNArRNA

Animation: Base-pair substitution

Animation: Frameshift mutation

Animation: Gene transcription details

Animation: Genetic code

Animation: Pre-mRNA transcript processing

Animation: Protein synthesis summary

Animation: Structure of a ribosome

Animation: Structure of a tRNA

Animation: Translation

Animation: Uracil-thymine comparison