Chapter 9 From DNA to Protein

Albia Dugger • Miami Dade College

Chapter 9From DNA to Protein

9.1 The Aptly Acronymed RIPs

• A tiny amount of ricin, a natural protein found in castor-oil seeds, can kill an adult human – there is no antidote

• Ricin is a ribosome-inactivating protein (RIP) – it inactivates the organelles which assemble amino acids into proteins

• Other RIPs include shiga toxin, made by Shigella dysenteriae bacteria, and enterotoxins made by E. coli bacteria, including the strain O157:H7

Some RIPs

9.2 DNA, RNA, and Gene Expression

• Transcription converts information in a gene to RNA

DNA → transcription → mRNA

• Translation converts information in an mRNA to protein

mRNA → translation → protein

The Nature of Genetic Information

• Each DNA strand consists of a chain of four kinds of nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C)

• The sequence of the bases in the strand is the genetic code

• All of a cell’s RNA and protein products are encoded by DNA sequences called genes

Converting a Gene to an RNA

• Transcription• Enzymes use the nucleotide sequence of a gene to

synthesize a complementary strand of RNA

• DNA is transcribed to RNA• Most RNA is single stranded• RNA uses uracil in place of thymine• RNA uses ribose in place of deoxyribose

A DNA Nucleotide

base (guanine)

3 phosphate groups

A DNA nucleotide: guanine (G), or deoxyguanosine triphosphate

sugar (deoxyribose)

An RNA Nucleotide

base (guanine)

3 phosphate groups

An RNA nucleotide: guanine (G), or guanosine triphosphate

sugar (ribose)

ANIMATED FIGURE: Gene transcription details

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Figure 9-3 p151

DNA deoxyribonucleic acid

RNA ribonucleic acidadenine A adenine A

sugar– phosphate backboneguanine G guanine G

cytosine C cytosine C

thymine T uracil U

DNA has one function: It permanently stores a cell’s genetic information, which is passed to offspring.

RNAs have various functions. Some serve as disposable copies of DNA’s genetic message; others are catalytic. Still others have roles in gene control.

Nucleotide bases of DNA

nucleotide base

base pair

Nucleotide bases of DNA

RNA in Protein Synthesis

• Messenger RNA (mRNA)• Contains information transcribed from DNA

• Ribosomal RNA (rRNA)• Main component of ribosomes, where polypeptide chains

are built

• Transfer RNA (tRNA)• Delivers amino acids to ribosomes

Converting mRNA to Protein

• Translation• The information carried by mRNA is decoded into a

sequence of amino acids, resulting in a polypeptide chain that folds into a protein

• mRNA is translated to protein• rRNA and tRNA translate the sequence of base triplets in

mRNA into a sequence of amino acids

Gene Expression

• A cell’s DNA sequence (genes) contains all the information needed to make the molecules of life

• Gene expression• A multistep process including transcription and translation,

by which genetic information encoded by a gene is converted into a structural or functional part of a cell or body

Take-Home Message: What is the nature of genetic information carried by DNA?

• Genetic information occurs in DNA sequences (genes) that encode instructions for building RNA or protein products

• A cell transcribes the nucleotide sequence of a gene into RNA

• Although RNA is structurally similar to a single strand of DNA, the two types of molecules differ functionally

• A messenger RNA (mRNA) carries a protein-building code in its nucleotide sequence; rRNAs and tRNAs interact to translate the sequence into a protein

9.3 Transcription: DNA to RNA

• RNA polymerase assembles RNA by linking RNA nucleotides into a chain, in the order dictated by the base sequence of a gene

• A new RNA strand is complementary in sequence to the DNA strand from which it was transcribed

DNA Replication and Transcription

• DNA replication and transcription both synthesize new molecules by base-pairing

• In transcription, a strand of mRNA is assembled on a DNA template using RNA nucleotides• Uracil (U) nucleotides pair with A nucleotides• RNA polymerase adds nucleotides to the transcript

The Process of Transcription

• RNA polymerase and regulatory proteins attach to a promoter (a specific binding site in DNA close to the start of a gene)

• RNA polymerase moves over the gene in a 5' to 3' direction, unwinds the DNA helix, reads the base sequence, and joins free RNA nucleotides into a complementary strand of mRNA

RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. In most cases, the base sequence of the gene occurs on only one of the two DNA strands. Only the DNA strand complementary to the gene sequence will be translated into RNA.

promoter sequence in DNA

gene regionRNA polymerase

1

Stepped Art

2 The polymerase begins to move along the DNA and unwind it. As it does, it links RNA nucleotides into a strand of RNA in the order specified by the base sequence of the DNA. The DNA winds up again after the polymerase passes. The structure of the “opened” DNA at the transcription site is called a transcription bubble, after its appearance.

DNA unwindingDNA winding up

RNA

3 Zooming in on the gene region, we can see that RNA polymerase covalently bonds successive nucleotides into an RNA strand. The base sequence of the new RNA strand is complementary to the base sequence of its DNA template strand, so it is an RNA copy of the gene.

direction of transcription

Figure 9-4 p152

Figure 9-5 p153

RNA transcripts DNA molecule

Post-Transcriptional Modifications

• In eukaryotes, RNA is modified before it leaves the nucleus as a mature mRNA

• Introns• Nucleotide sequences that are removed from a new RNA

• Exons• Sequences that stay in the RNA

Alternative Splicing

• Alternative splicing• Allows one gene to encode different proteins• Some exons are removed from RNA and others are

spliced together in various combinations

• After splicing, transcripts are finished with a modified guanine “cap” at the 5' end and a poly-A tail at the 3' end

Figure 9-6 p153

promoter exon intron exon intron exon

gene

DNA

transcription

new transcriptexon intron exon intron exon

RNA processing

finished RNA

exon exon exon

cap poly-A tail

5′ 3′

ANIMATED FIGURE: Pre-mRNA transcript processing



Take-Home Message:

How is RNA assembled?

• In transcription, RNA polymerase uses the nucleotide sequence of a gene region in a chromosome as a template to assemble a strand of RNA

• The new strand of RNA is a copy of the gene from which it was transcribed

9.4 RNA and the Genetic Code

• Base triplets in an mRNA encode a protein-building message

• Ribosomal RNA (rRNA) and transfer RNA (tRNA) translate that message into a polypeptide chain

mRNA – The Messenger

• mRNA carries protein-building information to ribosomes and tRNA for translation

• Codon• A sequence of three mRNA nucleotides that codes for a

specific amino acid• The order of codons in mRNA determines the order of

amino acids in a polypeptide chain

Genetic Code

• Genetic code• Consists of 64 mRNA codons (triplets)• Twenty kinds of amino acids are found in proteins• Some amino acids can be coded by more than one codon

• Some codons signal the start or end of a gene • AUG (methionine) is a start codon• UAA, UAG, and UGA are stop codons

Figure 9-7a p154

Figure 9-7b p154

From DNA to RNA to Amino Acids

a gene region in DNA

transcription

codon codon codon

mRNA

translation

methionine (met)

tyrosine (tyr)

serine (ser)

amino acid sequence

rRNA and tRNA – The Translators

• tRNAs deliver amino acids to ribosomes • tRNA has an anticodon complementary to an mRNA

codon, and a binding site for the amino acid specified by that codon

• Ribosomes, which link amino acids into polypeptide chains, consist of two subunits of rRNA and proteins

tRNA Structure

anticodon

amino acid attachment site

anticodon

Translation: Ribosome and tRNA

Take-Home Message: What roles do mRNA, tRNA, and rRNA play during translation?

• mRNA carries protein-building information; the bases in mRNA are “read” in sets of three during protein synthesis; most base triplets (codons) code for amino acids; the genetic code consists of all sixty-four codons

• Ribosomes, which consist of two subunits of rRNA and proteins, assemble amino acids into polypeptide chains

• A tRNA has an anticodon complementary to an mRNA codon, and it has a binding site for the amino acid specified by that codon; transfer RNAs deliver amino acids to ribosomes

ANIMATED FIGURE: Structure of a ribosome



9.5 Translation: RNA to Protein

• Translation converts genetic information carried by an mRNA into a new polypeptide chain

• The order of the codons in the mRNA determines the order of the amino acids in the polypeptide chain

Translation

• Translation occurs in the cytoplasm of cells

• Translation occurs in three stages:• Initiation• Elongation• Termination

Initiation

• An initiation complex is formed• A small ribosomal subunit binds to mRNA• The anticodon of initiator tRNA base-pairs with the start

codon (AUG) of mRNA• A large ribosomal subunit joins the small ribosomal subunit

Elongation

• The ribosome assembles a polypeptide chain as it moves along the mRNA• Initiator tRNA carries methionine, the first amino acid of

the chain• The ribosome joins each amino acid to the polypeptide

chain with a peptide bond

Termination

• When the ribosome encounters a stop codon, polypeptide synthesis ends• Release factors bind to the ribosome• Enzymes detach the mRNA and polypeptide chain from

the ribosome

1 Ribosome subunits and an initiator tRNA converge on an mRNA. A second tRNA binds to the second codon.

first amino acid of polypeptide

start codon (AUG)

initiator tRNA

Stepped Art

A peptide bond forms between the first two amino acids.

peptide bond

2

The first tRNA is released and the ribosome moves to the next codon. A third tRNA binds to the third codon.

3 A peptide bond forms between the second and third amino acids.

4

The second tRNA is released and the ribosomemoves to the next codon. A fourth tRNA binds the fourth codon.

5 A peptide bond forms between the third and fourth amino acids.

The process repeats until the ribosome encounters a stop codon in the mRNA.

6

Figure 9-11 p156

Figure 9-12a p157

Transcription polysomes

ribosome subunits

tRNA

Convergence of RNAs

mRNA

Translationpolypeptide

ANIMATED FIGURE: Translation



Polysomes

• Many ribosomes may simultaneously translate the same mRNA, forming polysomes

mRNA polysomes newly forming polypeptide

Take-Home Message:How is mRNA translated into protein?

• Translation converts protein-building information carried by mRNA into a polypeptide

• During initiation, an mRNA, an initiator tRNA, and two ribosome subunits join

• During elongation, amino acids are delivered to the complex by tRNAs in the order dictated by successive mRNA codons; the ribosome joins each to the end of the polypeptide chain

• Termination occurs when the ribosome reaches a stop codon in the mRNA; the mRNA and the polypeptide are released, and the ribosome disassembles

9.6 Mutated Genes and Their Protein Products

• If the nucleotide sequence of a gene changes, it may result in an altered gene product, with harmful effects

• Mutations• Small-scale changes in the nucleotide sequence of a cell’s

DNA that alter the genetic code

Mutations and Proteins

• A mutation that changes a UCU codon to UCC is “silent” – it has no effect on the gene’s product because both codons specify the same amino acid

• Other mutations may change an amino acid in a protein, or result in a premature stop codon that shortens it – both can have severe consequences for the organism

Common Mutations

• Base-pair-substitution• May result in a premature stop codon or a different amino

acid in a protein product• Example: sickle-cell anemia

• Deletion or insertion• Can cause the reading frame of mRNA codons to shift,

changing the genetic message• Example: thalassemia

Hemoglobin and Anemia

• Hemoglobin is a protein that binds oxygen in the lungs and carries it to cells throughout the body

• The hemoglobin molecule consists of four polypeptides (globins) folded around iron-containing hemes – oxygen molecules bind to the iron atoms

• Defects in polypeptide chains can cause anemia, in which a person’s blood is deficient in red blood cells or in hemoglobin

Mutations in the Beta Globin Gene

Figure 9-13a p158

Figure 9-13b p158

Figure 9-13c p158

Figure 9-13d p158

Figure 9-13e p158

Sickle-Cell Anemia

• Sickle-cell anemia is caused by a base-pair substitution which produces a beta globin molecule in which the sixth amino acid is valine instead of glutamic acid (sickle hemoglobin, HbS)

• HbS molecules stick together and form clumps – red blood cells become distorted into a sickle shape, and clog blood vessels, disrupting blood circulation throughout the body

• Over time, sickling damages organs and causes death

Figure 9-14 p159

sickled cell

glutamic acid valine

normal cell

ANIMATED FIGURE: Sickle-cell anemia



Thalassemia and Frameshifts

• Another type of anemia, beta thalassemia, is caused by the deletion of the twentieth base pair in the beta globin gene

• Deletions cause a frameshift, in which the reading frame of the mRNA codons shifts

• Frameshifts garble the genetic message, just as incorrectly grouping a series of letters garbles the meaning of a sentence

Thalassemia and Transposable Elements

• Beta thalassemia can also be caused by insertion mutations, which also cause frameshifts

• Insertion mutations are often caused by the activity of transposable elements, which are segments of DNA that can insert themselves anywhere in a chromosome

Take-Home Message: What happens after a gene becomes mutated?

• Mutations that result in an altered protein can have drastic consequences

• A base-pair substitution may change an amino acid in a protein, or shorten it by introducing a premature stop codon

• Frameshifts that occur after an insertion or deletion change an mRNA’s codon reading frame, so they garble its protein-building instructions

ANIMATED FIGURE: Base-pair substitution



ANIMATION: Frameshift mutation



Chapter 9 From DNA to Protein

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