Chapter IV Genetics

DNA and Protein Synthesis

Yalun Arifin
1

Basic definitions
DNA: The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner. RNA: A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.

DNA and RNA

Biochemistry of DNA
Double Helix Two DNA strands are antiparallel. Held together by base pairs: Hydrogen bonds between the nitrogen-containing bases A = T, and G = C

DNA Structure Reveals Key to Replication

Each of the two original strands serves as a template for construction of a new matching strand.

DNA and RNA

In RNA, thymine is replaced by uracil Nucleotides joined by covalent bonds between sugar and phosphate to make a chain Bases are laid out in specific and highly varied order, carrying code for protein synthesis

DNA Nucleotide O S P O S G S
A T PS PS S C G SP P GC S S P P AT PS T A S SP P S T P A G C T A A T S P PS S A C G P S G C

P
S O P P O S A T S O P

A T PS S AT P S P S P T A G C

SP

DNA: Central dogma

Central dogma in cells

In the absence of a nuclear membrane, DNA Transcription and RNA Translation are not physically separated.

DNA undergoes replication and transcription in the nucleus; proteins are made in the cytoplasm. RNA must therefore travel across the nuclear membrane before it is translated: transcription and translation are physically separated. The primary transcript, heterogeneous RNA (hnRNA), undergoes extensive posttranscriptional processing to make mRNA.

How do DNA keep the information?

The genetic information in DNA in kept in the sequences of bases in the nucleotides (A ,T, G, C). This code consists of 3 nucletiodes (e.g. ATG, AAA, TAA) that encodes a certain amino acid. Thus, 64 codes are possible to give the infinite number of genetic sequences.

DNA Replication
New helices are composed of half old (original) and half new nucleotides. Process catalyzed by enzymes: DNA polymerase catalyzes addition of matching bases, and proofreads. DNA ligase permanently attaches short sections to make one chromosome.

Protein Synthesis
How Proteins Are Made: Genetic Transcription, Translation, and Regulation

Proteins: Polypeptides
Strands of amino acids (20 different) joined by peptide bonds. Every protein has a unique amino acid sequence.

H H H3N C H C O O

O C

H3N

C
CH

CH2
CH3 isoleucine

glycine (gly)
ile H3N gly glu cys ala cys val ser

tyr

leu

asn

cys C asn

O O

val

gln

ser

cys

leu

gln

glu

tyr

 Protein Synthesis: Two Stages

Stage 1DNA contains information for protein but resides in the nucleus; proteins are made in the cytoplasm. Solution: Copy DNA into small strands of RNA (transcription). Stage 2Amino acids added in correct order by using the information on the RNA (translation).

OVERVIEW OF TRANSCRIPTION AND TRANSLATION

DNA TRANSCRIPTION (in nucleus) mRNA

ribosomes

tRNA mRNA TRANSLATION (in cytoplasm) protein

RNA nucleotide O O H C N H N H uracil (base) O ribose (sugar)

DNA nucleotide O O

H3C

C N H

H O

HO P O CH2 H O O Phosphate H group

OH OH

HO P O CH2 H O O Phosphate H group OH H

thymine (base)

deoxyribose (sugar)

RNA strand C U S
P S P S P sugar-phosphate handrail Bases:
cytosine (C) guanine (G) adenine (A) uracil (U)

DNA strand G A
P S P

C T
S

sugarphosphate handrail
Bases:
cytosine (C) guanine (G) adenine (A) thymine (T)

U U C

G T
S

C G C S
S P

A T A
P S

A T G C

Basic definitions
Intron: The DNA base sequences interrupting the protein- coding sequences of a gene; these sequences are transcribed into RNA but are cut out of the message before it is translated into protein.

Exons: the sequences in the DNA molecule that code for the amino acid sequences of corresponding proteins.
Messenger RNA: the template for protein synthesis; the form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell Transfer RNA: short-chain RNA molecules present in the cell (in at least 20 varieties, each variety capable of combining with a specific amino acid) that attach the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell (according to directions coded in the mRNA) Ribosomal RNA: RNA found in ribosome

 Three Types of RNA Transcribed

mRNA (messenger RNA) carries instructions for sequence of amino acids in a protein. rRNA (ribosomal RNA) important component of ribosomes. tRNA (transfer RNA) involved in matching correct amino acid to specific instructions in mRNA.

Table 14.2 Types of RNA Type of RNA Messenger RNA (mRNA) Functions in Function

Nucleus, migrates to ribosomes in cytoplasm

Cytoplasm

Carries DNA sequence information to ribosomes

Provides linkage between mRNA and amino acids; transfers amino acids to ribosomes

Transfer RNA (tRNA)

Ribosomal RNA (rRNA)

Cytoplasm

Structural component of ribosomes

 Transcription Uses Base Pairing

DNA used as a template to match complementary bases. C to G and A to U (not T). RNA polymerase catalyzes addition of new nucleotides into a single strand of RNA (called a transcript) from one strand of the double helix.

mRNA

CGUUCA GC A AGTAC C T GA

RNA nucleotides

DNA

mRNA

mRNA

 RNA Processing
mRNA is edited. Parts to be cut out are called introns. The remaining pieces (called exons) are joined together to make the finished product.

exon 1

INTRON

exon 2

INTRON

exon 3

enzyme enzymes cut into the introns edited mRNA transcript

 Making Sense of Junk DNA

Only 1.5% of our DNA codes for proteins (1 inch out of 6 feet). Rest is noncoding DNAhousekeeping (regulatory) sequences, tips of chromosomes, and junk:
Introns Repetitive Sequences

Selfish DNA Primates have 1 million Alu (280 base pairs long) repeats, 10% of DNA, congregate in gene-rich areas.

 Genetic Code: How DNA Codes for Amino Acid Sequence

Four bases in DNA, 20 amino acids in protein, not oneto-one code. Not two to one eitherThere are only 16 possible combinations of two bases of DNA (AA, AT, AC, AG, CA, etc.). Triplet codethree nucleotides (called a codon) signifying one amino acid.

THE TRIPLET CODE

DNA

G C

A TRANSCRIPTION

mRNA

C G U U C A U G G codon codon codon

A C U codon

TRANSCRIPTION

protein

arg

ser

trp

thr

 Codon Table
64 different possible combinations of the four nucleotidesmore than enough for the 20 different amino acids. Redundant = several different codons signify the same amino acid. Carries instruction codons for stopping (UGA, UAA, UAG) and starting (AUG) translation. Universal

Second Base U C phe leu UCU UCC UCA UCG ser UAU UAC UAA UAG A tyr stop stop his gln asn lys asp glu UGU UGC UGA UGG G cys stop trp arg U C A G

UUU UUC UUA UUG

First Base

CUU CUC CUA CUG

leu

CCU CCC CCA CCG

ACU ACC ACA ACG GCU GCC GCA GCG

pro

CAU CAC CAA CAG

AAU AAC AAA AAG GAU GAC GAA GAG

CGU CGC CGA CGG

AGU AGC AGA AGG GGU GGC GGA GGG

U C A G
U C A G U C A G

Third Base

AUU AUC ile AUA AUG met (start) GUU GUC GUA GUG val

thr

ser arg

ala

gly

 Translation Requires Translator

mRNA carries the instructions in the codons for each of the amino acids. tRNA molecules (transfer RNA) are translator molecule. tRNA can match the appropriate amino acid with the codon in the mRNA.

thr gly

mRNA

ribosome

 Structure of Transfer RNA

Part of the molecule binds an amino acid. The other end has three nucleotides (anticodon) that form a base pair with the codon in the mRNA.

amino acid

amino acid attached site

tRNA molecule

G CU anticodon CG A codon

mRNA attachment site

mRNA

 Ribosomes: The Location of Protein Synthesis

Large conglomerate of enzymes and ribosomal RNA (rRNA) in two subunits. A sitebinds tRNA-carrying amino acids. P sitebinds tRNA attached to growing chain of polypeptides.

mRNA

large subunit protein

small subunit

protein

large subunit

mRNA

P A site site

small subunit

 Steps of Translation

met

met

AUG

mRNA

start codon

leu leu

met

met

CUG A P site site

A P site site

met

leu

met

leu

A P site site

A P site site

thr
met

Polypeptide chain

leu

A P site site

 Genetic Regulation: Lac Operon

Operon = multipart genetic system. Bacteria (E. coli) synthesize certain enzymes only if substrate is present. Examplelactose, called an inducer Genes involved:
y (permease enzyme to help lactose enter the cell) z (-galactosidase enzyme to cut lactose into galactose and glucose) a gene i (codes for repressor protein)

lac operon regulator gene promotor operator

i gene
codes for repressor protein

z gene

y gene

a gene

DNA

binding site codes for of RNA -galactoseidase, polymerase which clips lactose molecules

codes for permease enzyme that transports lactose into cells

 Lac Operon: Regulatory DNA Sequences

Upstream promoter (acts as a binding site for RNA polymerase) Between promoter and first gene is operator. Repressor binds operator: prevents RNA polymerase from binding to the promoter. No transcription, so no enzymes made.

RNA polymerase i gene p o z gene repressor protein blocks binding of RNA polymerase y gene a gene DNA

no transcription

repressor protein

 Lac Operon: Lactose Inducer Present

Cell needs to make enyzmes only when lactose is present. Repressor binds lactose; it will not bind the operator, so transcription ensues.

2 RNA polymerase binds to promoter i gene repressor p o z gene y gene a gene

DNA

3 transcription proceeds

mRNA transcript
lactose

-galactosidase
1 lactose the (inducer) inactivates the repressor so that it cannot bind to the operator permease galactose glucose

lactose

 Magnitude of Metabolic Operations

Human cells have between 50,000 and 100,000 genes. But one cell usually makes only 5,000 to 20,000 specifically required proteins. Some are made continuously, and others are inducible.