1. Chapter 12
Molecular Biology
Of the Gene

2. One gene differs from another only by the sequence of the nucleotide bases in DNA
How does base sequence determine the uniqueness of a species or of individual traits between members of a species?
DNA specifies proteins which make unique structures that make up all the characteristics of an organism
DNA’s sequence of nucleotides  sequence of amino acids  specific enzymes  structures

3. In 1900’s, scientists knew the genetic material:
Must store information about development, structure, and metabolic activities of a cell
Must be stable, so it could be replicated in cell division and passed on
Must be able to undergo rare changes called mutations to provide variability required for evolution
In the1920’s, Frederick Griffith was working on a vaccine against Streptococcus pneumoniae
Notices some colonies were shiny and smooth
Other colonies had a rough appearance

4. Smooth colony individuals had a capsule, but those of the rough colony did not
S strain caused death when injected into mice
R strain did not
Heat-killed S strain mixed with living R strain caused death in mice when injected and when they were isolated from the mice had capsules

5. Fig. 12.1
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6. Oswald Avery worked on whether genetic material was protein or DNA
Subjected materials to proteinases and a capsule was still produced
Subjected materials to DNase and it was not
DNA was shown to be the genetic material
DNA structure:
Contains four nitrogenous bases
-Two purines- adenine (A) and guanine (G) that were double ringed
-Two pyrimidines- thymine (T) and cytosine (C) that were single ringed

7. Percentage of each type of nucleotide differs from species to species
Within a species, DNA has a constancy of bases
% of A always equals % of T and % of G always equally % of C. These relationships are called Chargaff’s rules

8. Fig. 12.3 NH2 C CH3 adenine (A) C thymine (T) HN C N C N CH
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
NH2 C
CH3
adenine
(A) C
thymine
(T) HN C N C N CH
nitrogen-containing
base O C CH HC C N N N O O HO P O 5
CH2 O HO P O 5
CH2 O O C 4 H H C O C H H C 1 4 1
sugar = deoxyribose H C C H H C C H
NH2 3 2 O 3 2 OH H OH H C
guanine
(G) C
cytosine
(C) C N N CH HN CH C O C CH
H2N C N N O N O
phosphate HO P O 5
CH2 O 5 HO P O
CH2 O O C H H C O C 4 1 H H C 4 1 H C C H H C H C2 3 2 3
a. Purine nucleotides OH H
b. Pyrimidine nucleotides OH H
DNA Composition in Various Species (%)
Species A T G C
Homo sapiens (human)
31.0
31.5
19.1
18.4
Drosophila melanogaster (fruit fly)
27.3
27.6
22.5
22.5
Zea mays (corn)
25.6
25.3
24.5
24.6
Neurospora crassa (fungus)
23.0
23.3
27.1
26.6
Escherichia coli (bacterium)
24.6
24.3
25.5
25.6
Bacillus subtilis (bacterium)
28.4
29.0
21.0
21.6
c. Chargaff’s data

9. Each human chromosome usually contains about 140 million base pairs
Because any of the four nucleotides can be present at each position, the total possible nucleotide sequences is 4 to the 140th x 10 to the 6th or 4 to the 140,000,000th
Rosalind Franklin’s work with x-ray diffraction determined that DNA was a double helix

10. Fig. 12.4 Rosalind Franklin diffraction pattern diffracted X-rays a.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Rosalind Franklin
diffraction pattern
diffracted
X-rays a.
X-ray beam
Crystalline
DNA b. c.
© Photo Researchers, Inc.; 12.4c: © Science Source/Photo Researchers, Inc.

11. Watson and Crick constructed a model of DNA and received the 1962 Nobel prize
Polymers of nucleotides in a double helix form
Sugar-phosphate back bones on outside and paired bases inside
Two DNA strands are antiparallel, meaning that the sugar-phosphate groups of each strand are oriented in opposite directions
5’ end of one strand is paired to the 3’ end of the other strand
Complementary base pairing means a purine always bonds to a pyrimidine

12. They have an antiparallel arrangement to insure that bases are oriented properly so can interact
This is the only model having molecular width revealed by Franklin’s x-ray diffraction pattern

13. Fig. 12.5
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
3.4 nm
0.34 nm
2 nm b. d. d. C a.
sugar-phosphate
backbone G T
3 end P
5 end 5 G C 2 3 A 4 S 1 P 1 S 4 A 3 2 5 T P P c. G C P
Complementary
base pairing C G P
a: © Kenneth Eward/Photo Researchers, Inc.; d: © A. Barrington Brown/Photo Researchers, Inc.

14. Term DNA replication refers to process of copying a DNA molecule
A template is a mold used to produce a shape complementary to itself
During DNA replication, each DNA strand serves as a template for a new strand in a daughter molecule
DNA replication is semiconservative replication because each daughter DNA double helix contains an old strand from parential DNA double helix and a new strand

15. daughter DNA double helix
Fig. 12.6
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. G C G C G A T A
region of parental
DNA double helix T A C G A T A G C G C G A
region of
replication:
new nucleotides
are pairing
with those of
parental strands C G C G A T A T T A T A G C T C A T A G A T A A A T G A G T G T
region of
completed
replication A C C C A G C G
new
strand
old
strand A
daughter DNA double helix
old
strand
new
strand
daughter DNA double helix

16. Steps in replication:
1) Unwinding of parental DNA is caused by the breaking of weak hydrogen bonds between paired bases
Enzyme called helicase necessary to unwind the molecule
2) Complementary base pairing occurs when new complementary nucleotides, always in the nucleus, are paired
3) Joining finishes replication by joining the complementary nucleotides to form new strands
Each new daughter DNA molecule contains an old strand and a new strand

17. Steps 2 and 3 are done with the enzyme complex called DNA polymerase
DNA replication must occur before a cell can divide
Cancer is characterized by rapid cell division
Sometimes treated with chemotherapeutic drugs that are analogs to one of four nucleotides
Analogs have similar but not identical structure
They cause replication to stop and cells to die
Bacteria have a single circular loop of DNA that must be replicated before the cell divides
Process begins at origin of replication site

18. The strands are separated, unwound, and DNA polymerase binds to each side and begins copying
The two DNA polymerases meet at a termination region, then the chromosomes separate
Bacteria cells require about 40 minutes to replicate, but bacterial cells can divide every 20 minutes
So replication can begin even before previous round is complete
In eukaryotes, DNA replication begins at numerous origins of replication along the length of the chromosome

19. Replication fork is the V shape of strands formed when replication bubbles spread bidirectionly until they meet
Chromosomes are long and linear and replicate at about 500-5,000 base pairs per minute
Because there are many individual origins of replication, the diploid DNA in humans of over 6 billion base pairs takes some hours
In linear chromosomes, DNA polymerase cannot replicate to the ends
Ends of chromosomes composed of telomeres which are short DNA sequences that are repeated over and over

20. Telomeres are added back by the enzyme telomerase
Eventually telomeres are lost and the cell cannot replicate
In stem cells, this process preserves the ends of chromosomes and prevents the loss of DNA after successive rounds of replication
DNA polymerase is very accurate and makes a mistake approximately once per 100,000 base pairs, but has proof reading capability so overall error rate is one in 100 million base pairs

21. Fig. 12.7 origin replication is complete replication is occurring in
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
origin
replication is
complete
replication is
occurring in
two directions
a. Replication in prokaryotes
replication fork
replication bubble
parental strand
new DNA
duplexes
daughter strand
b. Replication in eukaryotes

22. RNA is a polymer composed of nucleotides
Contains sugar ribose and bases adenine (A) cytosine, (C), guanine (G),and uracil (U) which replaces the thymine in DNA
Single stranded and does not form a helix
RNA comes in three major classes:
Messenger RNA (mRNA) takes message from DNA in nucleus to ribosomes in cytoplasm
Transfer RNA (tRNA) transfers amino acids to the ribosomes
Ribosomal RNA (rRNA) along with ribosomal proteins, make up the ribosomes where polypeptides are synthesized

23. Two major steps in synthesizing a protein from information in the DNA
Transcription where one of the DNA strands acts as a template to make messenger RNA
Translation where the messenger RNA directs the sequence of amino acids into a polypeptide
Sequence of nucleotides in DNA to mRNA specify the order of amino acids in polypeptide
Genetic code:
Codon is a triplet code where three nucleotides code for one of the twenty amino acids
Code is degenerate meaning most amino acids have more than one codon

24. Code is unambiguous meaning each triplet codon has only one meaning
Code has one start signal (AUG) and three stop signals (UAA) (UGA) and (UAG)
Code is universal

25. Fig. 12.10 First Base Second Base Third Base U C A G UUU phenylalanine
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
First
Base
Second Base
Third
Base U C A G
UUU
phenylalanine
UCU
serine
UAU
tyrosine
UGU
cysteine U
UUC
phenylalanine
UCC
serine
UAC
tyrosine
UGU
cysteine C U
UUA
leucine
UCA
serine
UAA
stop
UGA
stop A
UUG
leucine
UCG
serine
UAG
stop
UGG
tryptophan G
CUU
leucine
CCU
proline
CAU
histidine
CGU
arginine U
CUC
leucine
CCC
proline
CAC
histidine
CGC
arginine C C
CUA
leucine
CCA
proline
CAA
glutamine
CGA
arginine A
CUG
leucine
CCG
proline
CAG
glutamine
CGG
arginine G
AUU
isoleucine
ACU
threonine
AAU
asparagine
AGU
serine U
AUC
isoleucine
ACC
threonine
AAC
asparagine
AGC
serine C A
AUA
isoleucine
ACA
threonine
AAA
lysine
AGA
arginine A
AUG (start)
methionine
ACG
threonine
AAG
lysine
AGG
arginine G
GUU
valine
GCU
alanine
GAU
aspartate
GGU
glycine U
GUC
valine
GCC
alanine
GAC
aspartate
GGC
glycine C G
GUA
valine
GCA
alanine
GAA
glutamate
GGA
glycine A
GUG
valine
GCG
alanine
GAG
glutamate
GGG
glycine G

26. Messenger RNA has a sequence of bases complementary to a portion of one DNA strand
When a gene is transcribed, a segment of DNA helix unwinds and unzips
Rna nucleotides pair with complementary DNA nucleotides; this is known as the template strand
RNA polymerase joins the nucleotides together in the 5’  3’ direction or adds a nucleotide to the 3’ end of polymer under construction
Transcription begins when RNA polymerase attaches to promoter in DNA

27. Promoter defines the start of transcription, the direction of transcription, and the strand to be transcribed
Initiation of transcription is the binding of RNA polymerase to promoter
Elongation of mRNA continues until RNA polymerase comes to DNA stop codon sequence
Causes release of mRNA now called mRNA transcript
RNA transcript is called pre-mRNA and is modified before leaving the nucleus
Receives a cap at 5’ end and a tail at 3’ end

28. Cap is modified guanine (G) nucleotide which tells ribosome where to attach when translation begins
Tail consists of adenine (A) nucleotides
This poly-A tail helps transport of mRNA out of nucleus and inhibits degration of mRNA by hydrolytic enzymes
Pre-mRNA is composed of exons and introns
Exons are segments that will be expressed
Introns are segments in between exons that will not be expressed
During pre-mRNA splicing, introns are removed

29. In prokaryotes, introns splice themselves out
In eukaryotes, DNA splicing is done by spliceosomes which contain small nuclear RNA (snRNA)
Spliceosomes use ribozymes whose catalytic activity works like enzymes that are made of protein
Presence of introns allows a cell to pick and chose which exons will go into a particular mRNA
What is an exon in one mRNA could be an intron in another mRNA
Called alternate mRNA splicing

30. Some introns give rise to micro RNA (miRNA) which are involved in regulating the translation of mRNA
Introns may also encourage crossing-over during meiosis, and permit exon shuffling which can play a role in evolution of new genes

31. Fig
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exon
exon
exon
DNA
intron
intron
transcription
exon
exon
exon
pre-mRNA 5
intron
intron 3
exon
exon
exon 5 3
cap
intron
intron
poly-A tail
spliceosome
exon
exon
exon 5 3
cap
poly-A tail
pre-mRNA
splicing
intron RNA
mRNA 5 3
cap
poly-A tail
nuclear pore
in nuclear envelope
nucleus
cytoplasm

32. Translation takes place in the cytoplasm of eukaryotic cells
Transfer RNA (tRNA) molecules transfer amino acids to the ribosomes
tRNA is a single stranded nucleic acid that doubles back on itself to create regions where complementary bases hydrogen bond to one another
There is at least one tRNA molecule for each of the 20 amino acids
Amino acids bind to 3’ end of tRNA
The opposite end contains an anticodon that is complementary to a specific mRNA codon

33. Fig. 12.14 amino acid leucine 3 5 Hydrogen bonding amino acid end
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
amino
acid
leucine 3 5
Hydrogen
bonding
amino acid end
anticodon G A A
anticodon end C A G U C C U U C C U C
mRN A 5 3
codon a. b.

34. In eukaryotes, ribosomal RNA (rRNA) is produced from a DNA template in the nucleolus of a nucleus
Packaged with proteins into two ribosomal subunits one larger than the other
They move into the cytoplasm where they combine when translation begins
May remain in cytoplasm or attach to endoplasmic reticulum
Ribosomes have a binding site for mRNA and three binding sites for tRNA
When ribosome moves down a mRNA molecule, the polypeptide increases by one AA at a time

35. Several ribosomes are often attached to and translating the same mRNA
The entire complex is called a polyribosome

36. Courtesy Alexander Rich
Fig
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
large subunit 5 3
mRNA
tRNA binding
sites
small subunit
a. Structure of a ribosome
b. Binding sites of ribosome
outgoing
tRNA
polypeptide
incoming
tRNA
mRNA
c. Function of ribosomes
d. Polyribosome
Courtesy Alexander Rich

37. Translation requires three steps:
1) Initiation brings all the translation components together
Initiation factors (proteins) assemble small ribosome subunit, mRNA, initiator tRNA, and large ribosomal subunit
2) Elongation where polypeptide increases in length one amino acid at a time
Requires elongation factors (proteins) for binding tRNA anticodons to mRNA codons
3) Termination of polypeptide occurs at a stop codon

38. Requires protein called release factor which binds to stop codon and cleaves the polypeptide from the last tRNA

39. Fig
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Met
Met
asp
Met
Met
Thr
peptide
bond
tRNA
Ser
Ser
Ser
Ser
Ala
Ala
Ala C U G
Ala
Trp
peptide
Trp U G
Trp
anticodon
Trp
Val
bond G
Val
Val
Val
Asp
Asp
Asp A U C C A U C A U C U G C A U C U G C U G G U A G A C G U A G A C G U A G A C G U A G A C A C C 3 3 5 5 5 3 5 3 1
A tRNA–amino acid
approaches the
ribosome and binds
at the A site. 2
Two tRNAs can be at a
ribosome at one time;
the anticodons are
paired to the codons. 3
Peptide bond formation
attaches the peptide
chain to the newly
arrived amino acid. 4
The ribosome moves forward; the
“empty” tRNA exits from the E site;
the next amino acid–tRNA complex
is approaching the ribosome.
Elongation

40. Fig. 12.18 release factor stop codon Termination 3
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release factor
Asp
Ala T rp V al U U A A
Glu U G A
stop codon 3
The ribosome comes to a stop
codon on the mRNA. A release
factor binds to the site. U U C G A A A U G 3 5
The release factor hydrolyzes the bond
between the last tRNA at the P site and
the polypeptide, releasing them. The
ribosomal subunits dissociate.
Termination

41. Gene has been expressed once its product is made and is operating in the cell
Eukaryotic chromosome contains a single double helix DNA molecule, but is composed of more than 50% protein
Histones are the large majority and play a primary structural role
A human cell contains at least 2 meters of DNA