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Chapter IV Genetics
DNA and Protein Synthesis
Yalun Arifin
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
P
S
P
S
P
S
G
T
A
A
C
T
S
P
S
P
S
P
DNA
G C
Nucleotide A T SP
SPSPSS
PP
SP
SPSPSS
PP
SP
SPSPSS
PP
SP
SPSPSS
PP
A T
C GO
O
OO
O
OG C
T A
A T
G C
T A
A T
A
C G
A T
A T
T A
G C
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 post-transcriptional 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 ReplicationNew 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.
• Proteins: Polypeptides – Strands of amino acids (20 different) joined by peptide
bonds.
– Every protein has a unique amino acid sequence.
Protein SynthesisHow Proteins Are Made: Genetic Transcription, Translation, and Regulation
gly
ile
val
glu
gln
cys
cys asn
cys
tyr
asn
glu
ala
ser
val
cys
ser
leu
tyr
gln
leu
H
C
H
H3N CO
O–
glycine (gly)
C
H
H3N CO
O–CH
CH2
CH3
isoleucine
H3N CO
O–
• Protein Synthesis: Two Stages– Stage 1—DNA 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 2—Amino acids added in correct order by using the information on the RNA (translation).
OVERVIEW OF TRANSCRIPTION AND TRANSLATION
DNA
mRNA
TRANSCRIPTION(in nucleus)
ribosomes
mRNA
protein
TRANSLATION(in cytoplasm)
tRNA
RNA strand DNA strand
C
UG C
A T
C
G
AU
UC
C
C
G
G
A
A
T
T
A T
CG
SP
PS
SP
PS
S
SP
PS
SP
PS
S
RNA nucleotide DNA nucleotide
sugar-phosphatehandrail
Bases: cytosine (C) guanine (G) adenine (A) uracil (U)
Bases: cytosine (C) guanine (G) adenine (A) thymine (T)
sugar-phosphatehandrail
SP
PS
SP
PS
S
O O
H H3C C
N
N
HOH
C
N
NH
O
O
H
HH
OH
H
O
O
H
HH
OH
ribose(sugar)
uracil(base)
CH2OPHO
O
O–
CH2OPHO
O
O–
Phosphate group
Phosphate group
thymine(base)
deoxyribose(sugar)
Basic definitionsIntron: 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 14.2Types of RNA
Type of RNA Functions in Function
Messenger RNA(mRNA)
Nucleus, migratesto ribosomesin cytoplasm
Carries DNA sequenceinformation to ribosomes
Transfer RNA(tRNA)
Cytoplasm Provides linkage between mRNAand amino acids;transfers aminoacids to ribosomes
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.
mRNAC G UU AC
G C A A G T A CC T G A
mRNA
mRNA
DNA
RNA nucleotides
UG G
A C U
• 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 DNA—housekeeping (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 one-
to-one code.
– Not two to one either—There are only 16 possible combinations of two bases of DNA (AA, AT, AC, AG, CA, etc.).
– Triplet code—three nucleotides (called a codon) signifying one amino acid.
THE TRIPLET CODE
DNA
mRNA
protein arg ser trp thr
codon codon codon codonC G U U C A U G G A C U
G C A A G T A C C T G A
TRANSCRIPTION
TRANSCRIPTION
• Codon Table– 64 different possible combinations of the four
nucleotides—more 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
U C A G
U
C
A
G
GACU
GACU
GACU
GACU
UUUUUCUUAUUG
CUUCUCCUACUG
AUUAUCAUAAUG
GUUGUCGUAGUG
phe
leu
leu
ile
met (start)
val
UCUUCCUCAUCG
CCUCCCCCACCG
ACUACCACAACG
GCUGCCGCAGCG
ser
pro
thr
ala
UAUUACUAAUAG
CAUCACCAACAG
AAUAAC
AAGAAA
GAUGACGAAGAG
tyr
stopstop
his
gln
asn
lys
asp
glu
UGUUGCUGAUGG
CGUCGCCGACGG
AGUAGCAGAAGG
GGUGGCGGAGGG
cys
stoptrp
arg
ser
arg
gly
Firs
t B
ase
Third
Base
Second Base
• 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.
mRNA
ribosome
glythrgluleuser
phe
asp
tyr
• 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
C AG
mRNA attachment site
codonmRNA
• Ribosomes: The Location of Protein Synthesis– Large conglomerate of enzymes and ribosomal RNA
(rRNA) in two subunits.
– A site—binds tRNA-carrying amino acids.
– P site—binds tRNA attached to growing chain of polypeptides.
mRNA
protein
large subunit
small subunit
protein
mRNA
large subunit
small subunit
P A
Psite
Asite
• Steps of Translation
met met
metmet
leu
mRNA
start codon
AUG
CUG
Psite
Asite
Psite
Asite
GAC
leu
UCA
met leu
met
metleu
leu
Psite
Asite
thr
Psite
Asite
Psite
Asite
Polypeptide chain
• Genetic Regulation: Lac Operon– Operon = multipart genetic system.
– Bacteria (E. coli) synthesize certain enzymes only if substrate is present.
– Example—lactose, 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)
codes for repressor protein
regulator gene
i gene p o z gene y gene a gene DNA
lac operon
promotoroperator
binding siteof RNApolymerase
codes for permease enzymethat transportslactose into cells
codes for-galactoseidase,which clipslactose molecules
• 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.
i gene p o z gene y gene a gene DNA
repressorprotein
repressor protein blocks binding of RNA polymerase
RNA polymerase
no transcription
• 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.
i gene p o z gene y gene a gene DNA
repressor
lactose
galactose glucose
-galactosidase
mRNA transcript
transcription proceeds3
cell membrane
lactose
RNA polymerasebinds to promoter
2
lactose the (inducer)inactivates the repressorso that it cannot bind to the operator
1
permease
• 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.