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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
S
P
S
P
S
P
S
S
P
P
S
P
S
P
S
P
S
S
P
P
S
P
S
P
S
P
S
S
P
P
S
P
S
P
S
P
S
S
P
P
A T
C G
O
O
O
O
O
O
G 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 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.


Proteins: Polypeptides
Strands of amino acids (20 different) joined by peptide
bonds.
Every protein has a unique amino acid sequence.
Protein Synthesis
How 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
H
3
N C
O
O

glycine (gly)
C
H
H
3
N C
O
O

CH
CH
2

CH
3

isoleucine
H
3
N
C
O
O

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
mRNA
TRANSCRIPTION
(in nucleus)
ribosomes
mRNA
protein
TRANSLATION
(in cytoplasm)
tRNA
RNA strand DNA strand
C
U
G C
A T
C
G
A
U
U
C
C
C
G
G
A
A
T
T
A T
C G
S
P
P
S
S
P
P
S
S
S
P
P
S
S
P
P
S
S
RNA nucleotide DNA nucleotide
sugar-phosphate
handrail
Bases:
cytosine (C)
guanine (G)
adenine (A)
uracil (U)
Bases:
cytosine (C)
guanine (G)
adenine (A)
thymine (T)
sugar-
phosphate
handrail
S
P
P
S
S
P
P
S
S
O O
H H
3
C
C
N
N
H OH
C
N
N
H
O
O
H
H H
OH
H
O
O
H
H H
OH
ribose
(sugar)
uracil
(base)
CH
2
O P HO
O
O

CH
2
O P HO
O
O

Phosphate
group
Phosphate
group
thymine
(base)
deoxyribose
(sugar)
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 Functions in Function
Messenger RNA
(mRNA)
Nucleus,
migrates
to ribosomes
in cytoplasm
Carries DNA
sequence
information to
ribosomes
Transfer RNA
(tRNA)
Cytoplasm
Provides linkage
between mRNA
and amino acids;
transfers amino
acids 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.

mRNA
C G U U A C
G C A A G T A C C T G A
mRNA
mRNA
DNA
RNA nucleotides
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 one-
to-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
mRNA
protein arg ser trp thr
codon codon codon codon
C 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
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
U C A G
U
C
A
G
G
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
AUU
AUC
AUA
AUG
GUU
GUC
GUA
GUG
phe
leu
leu
ile
met (start)
val
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
ser
pro
thr
ala
UAU
UAC
UAA
UAG
CAU
CAC
CAA
CAG
AAU
AAC
AAG
AAA
GAU
GAC
GAA
GAG
tyr
stop
stop
his
gln
asn
lys
asp
glu
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
cys
stop
trp
arg
ser
arg
gly
F
i
r
s
t

B
a
s
e

T
h
i
r
d

B
a
s
e

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
gly thr
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
C
U
anticodon
C A G
mRNA attachment site
codon
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
protein
large subunit
small subunit
protein
mRNA
large subunit
small subunit
P
site
A
site
Steps of Translation
met met
met
met
leu
mRNA
start codon
AUG
CUG
P
site
A
site
P
site
A
site
leu
met
leu
met
met
leu
leu
P
site
A
site
thr
P
site
A
site
P
site
A
site
Polypeptide
chain
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)
codes for
repressor
protein
regulator gene
i gene p o z gene y gene a gene DNA


lac operon
promotor
operator
binding site
of RNA
polymerase
codes for
permease enzyme
that transports
lactose into cells
codes for
-galactoseidase,
which clips
lactose 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
repressor
protein
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 proceeds 3
lactose
RNA polymerase
binds to promoter
2
lactose the (inducer)
inactivates the repressor
so 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.