The Nucleus: Information Central

• The nucleus contains most of the cell’s genes and is usually

the most conspicuous organelle
• The nuclear envelope encloses the nucleus, separating it
from the cytoplasm
• Pores regulate the entry and exit of molecules from the
nucleus
• The shape of the nucleus is maintained by the nuclear
lamina, which is composed of proteins
• The nuclear membrane is a double membrane; each
membrane consists of a lipid bilayer
• In the nucleus, DNA and proteins form genetic material
called chromatin
• Chromatin condenses to form discrete chromosomes
• The nucleolus is located within the nucleus and is the site of
ribosomal RNA (rRNA) synthesis
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 Nucleus
1 µm Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane

Nuclear pore

Pore
complex

Rough ER
Surface of
nuclear envelope
Ribosome 1 µm

0.25 µm

Close-up of nuclear
envelope

Pore complexes (TEM) Nuclear lamina (TEM)

Concept: A chromosome consists of a DNA molecule
packed together with proteins
• The bacterial chromosome is a double-stranded, circular
DNA molecule associated with a small amount of protein
• In a bacterium, the DNA is “supercoiled” and found in a
region of the cell called the nucleoid
• Eukaryotic chromosomes have linear DNA molecules
associated with a large amount of protein
• Chromatin is a complex of DNA and protein, and is found
in the nucleus of eukaryotic cells
• Histones are proteins that are responsible for the first level
of DNA packing in chromatin

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 Structure of a chromatin

Nucleosome
(10 nm in diameter)
DNA
double helix
(2 nm in diameter)
H1
Histones
Histone tail

DNA, the double helix Histones Nucleosomes, or “beads

on a string” (10-nm fiber)
 Structure of a chromosome

Chromatid
(700 nm)

30-nm fiber

Loops Scaffold

300-nm fiber

Replicated
chromosom
e (1,400 nm)
30-nm fiber Looped Metaphase
domains (300- chromosome
nm fiber)
 Structure of chromatin
• Chromatin is organized into fibers
• 10-nm fiber
– DNA winds around histones to form nucleosome “beads”
– Nucleosomes are strung together like beads on a string
by linker DNA
• 30-nm fiber
– Interactions between nucleosomes cause the thin fiber to
coil or fold into this thicker fiber
• 300-nm fiber
– The 30-nm fiber forms looped domains that attach to
proteins
• Metaphase chromosome
– The looped domains coil further
– The width of a chromatid is 700 nm

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 Structure of a chromatin

• Most chromatin is loosely packed in the nucleus during

interphase and condenses prior to mitosis
• Loosely packed chromatin is called euchromatin
• During interphase a few regions of chromatin (centromeres
and telomeres) are highly condensed into heterochromatin
• Dense packing of the heterochromatin makes it difficult for the
cell to express genetic information coded in these regions
• Histones can undergo chemical modifications that result in
changes in chromatin organization
– For example, phosphorylation of a specific amino acid on
a histone tail affects chromosomal behavior during
meiosis

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Concept: Nucleic acids store and transmit hereditary
information
• The amino acid sequence of a polypeptide is programmed
by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid
• There are two types of nucleic acids:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA) and,
through mRNA, controls protein synthesis
• Protein synthesis occurs in ribosomes

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 DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm Ribosome
via nuclear pore

3 Synthesis
of protein

Amino
Polypeptide acids
 The Structure of Nucleic Acids

• Nucleic acids are polymers

called polynucleotides
• Each polynucleotide is made
of monomers called
nucleotides
• Each nucleotide consists of a
nitrogenous base, a pentose
sugar, and a phosphate group
• The portion of a nucleotide
without the phosphate group
is called a nucleoside
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 5' end

5'C
Polynucleotide, or nucleic acid

3'C

Nucleoside

Nitrogenous
base

5'C

Phosphate 3'C
group Sugar
5'C (pentose)

3'C (b) Nucleotide

3' end
 Nitrogenous bases
Pyrimidines

Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Purines

Adenine (A) Guanine (G)

 Nucleotide Monomers

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases:
– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
– Purines (adenine and guanine) have a six-
membered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the
sugar is ribose
• Nucleotide = nucleoside + phosphate group
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 Sugar–phosphate Nitrogenou
Nucleotide Polymers backbone
s
bases

5 end
• Nucleotide polymers are linked
to build a polynucleotide
Thymine
• Adjacent nucleotides are joined (T)

by covalent bonds that form

between the –OH group on the
3 carbon (of the sugar) of one
nucleotide and the phosphate on Adenine
(A)
the 5 carbon on the next
• These links create a backbone of
sugar-phosphate units with Cytosine (C)
nitrogenous bases as
appendages
• The sequence of bases along a
Phosphate DNA nucleo
DNA or mRNA polymer is unique
Sugar
for each gene (deoxyribose)
Guanine (G)
3 end
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 The DNA Double Helix

• A DNA molecule has two

polynucleotides in a spiral, forming
a double helix
• In the DNA double helix, the two
backbones run in opposite 5 → 3
directions from each other,
referred to as antiparallel
• One DNA molecule includes many
genes
• The nitrogenous bases in DNA pair
up and form hydrogen bonds:
adenine (A) always with thymine
(T), and guanine (G) always with
cytosine (C)
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Key features of DNA structure
 Structure of DNA continued
• The width suggested that the DNA
molecule was made up of two
strands, forming a double helix
• Watson and Crick reasoned that the
base pairing was dictated by the
base structures
Hydrogen Bonds
• They determined that adenine (A)
paired only with thymine (T), and
guanine (G) paired only with cytosine
(C)
• The Watson-Crick model explains
Chargaff’s rules: in any organism the
amount of A = T, and the amount of
G=C
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 Base Pairing to a Template Strand
• Since the two strands of DNA are complementary, each
strand acts as a template for building a new strand in
replication
• In DNA replication, the parent molecule unwinds, and two
new daughter strands are built based on base-pairing rules

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 Fig. 16-10
Replication Models First Second
Parent cell replication replication

(a) Conservative
• Watson and Crick’s model
semiconservative model of
replication predicts that when
a double helix replicates, each
daughter molecule will have (b) Semiconservative
model
one old strand (derived or
“conserved” from the parent
molecule) and one newly
made strand
(c) Dispersive model
• Competing models were the
conservative model (the two
parent strands rejoin) and the
dispersive model (each strand
is a mix of old and new)
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 DNA Replication: A Closer Look

• The copying of DNA is remarkable in its speed and

accuracy
• More than a dozen enzymes and other proteins participate
in DNA replication
• Replication begins at special sites called origins of
replication, where the two DNA strands are separated,
opening up a replication “bubble”
• A eukaryotic chromosome may have hundreds or even
thousands of origins of replication
• Replication proceeds in both directions from each origin,
until the entire molecule is copied

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 DNA Replication: Prokaryotes
Origin of
replication Parental (template) strand

Daughter (new) strand

Double- Replication fork

stranded Replication
DNA molecule bubble
0.5 µm
Two
daughter
DNA
molecules

(a) Origins of replication in E. coli

 DNA Replication: Eukaryotes
Origin of replication Double-stranded DNA molecule

Parental (template) strand

Daughter (new) strand

0.25 µm
Bubble Replication fork

Two daughter DNA molecules

(b) Origins of replication in eukaryotes

 DNA Replication: Proteins involved
• At the end of each replication bubble is a replication fork, a Y-
shaped region where new DNA strands are elongating
• Helicases are enzymes that untwist the double helix at the
replication forks
• Single-strand binding protein binds to and stabilizes single-
stranded DNA until it can be used as a template
• Topoisomerase corrects “over-winding” ahead of replication
forks by breaking, swiveling, and rejoining DNA strands
• DNA polymerases cannot initiate synthesis of a polynucleotide;
they can only add nucleotides to the 3 end
• The initial nucleotide strand is a short RNA primer
• An enzyme called primase can start an RNA chain from scratch
and adds RNA nucleotides one at a time using the parental DNA
as a template
• The primer is short (5–10 nucleotides long), and the 3 end
serves as the starting point for the new DNA strand
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 DNA Replication: Proteins involved

Single-strand binding Primase

proteins

Topoisomerase 3
5 RNA 3
primer

5
5
3
Helicase
 Synthesizing a New DNA Strand
• Enzymes called DNA polymerases catalyze the elongation of
new DNA at a replication fork
• Most DNA polymerases require a primer and a DNA template
strand
• The rate of elongation is about 500 nucleotides per second in
bacteria and 50 per second in human cells
• Each nucleotide that is added to a growing DNA strand is a
nucleoside triphosphate
• dATP supplies adenine to DNA and is similar to the ATP of
energy metabolism
• The difference is in their sugars: dATP has deoxyribose while
ATP has ribose
• As each monomer of dATP joins the DNA strand, it loses two
phosphate groups as a molecule of pyrophosphate
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 DNA Replication: Adding nucleotides
New strand Template strand
5 end 3 end 5 end 3 end

Sugar A T A T
Phosphate Base

C G C G

G C G C

DNA polymerase
3 end A T A
T

C Pyrophosphate 3 end C

Nucleoside
triphosphate 5 end 5 end
The replication bubble with two forks
Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork
Overview
Origin of replication
Leading strand Lagging strand

Primer

Lagging strand Leading strand

Overall directions
of replication
 Origin of replication
The Leading strand
3
5
5 RNA primer
“Sliding clamp”
3
5 DNA pol III
Parental DNA

3
5

5
3

5
 Overview
Origin of replication
Leading strand Lagging strand

Lagging strand
2
1
Leading strand
Overall directions
of replication

To elongate the other new strand, called the lagging strand,

DNA polymerase must work in the direction away from the
replication fork
The lagging strand is synthesized as a series of segments called
Okazaki fragments, which are joined together by DNA ligase
 Overview
Origin of replication
Leading strand Lagging strand

Leading strand
Lagging strand
Single-strand Overall directions
binding protein of replication
Helicase
Leading strand

5 DNA pol III

3
3
Primer Primase
5
Parental DNA 3
DNA pol III Lagging strand
5
4
DNA pol I DNA ligase
3 5
3 2 1
3
5

The Lagging strand

Table 16-1
Proofreading and Repairing DNA
• DNA polymerases proofread
newly made DNA, replacing any
incorrect nucleotides
Nuclease
• In mismatch repair of DNA,
repair enzymes correct errors in
base pairing DNA
• DNA can be damaged by polymerase
chemicals, radioactive
emissions, X-rays, UV light, and
certain molecules (in cigarette
smoke for example)
• In nucleotide excision repair, DNA
ligase
a nuclease cuts out and
replaces damaged stretches of
DNA
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Replicating the Ends of DNA Molecules

• Limitations of DNA polymerase create problems for the linear

DNA of eukaryotic chromosomes
• The usual replication machinery provides no way to complete
the 5 ends, so repeated rounds of replication produce
shorter DNA molecules
• Eukaryotic chromosomal DNA molecules have at their ends
nucleotide sequences called telomeres
• Telomeres do not prevent the shortening of DNA molecules,
but they do postpone the erosion of genes near the ends of
DNA molecules
• It has been proposed that the shortening of telomeres is
connected to aging

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 Telomeres

• If chromosomes of germ cells

became shorter in every cell
cycle, essential genes would
eventually be missing from
the gametes they produce
• An enzyme called
telomerase catalyzes the
lengthening of telomeres in
germ cells
• The shortening of telomeres might protect cells from cancerous
growth by limiting the number of cell divisions
• There is evidence of telomerase activity in cancer cells, which
may allow cancer cells to persist
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