Human

Anatomy and Physiology

Cell Functions
 Suggested Readings
McKinley
Chapter 2 – Atoms, ions, and molecules
• Section 2.7 – Biological Macromolecules (pages 51-67)
Chapter 3 – Energy, Reaction and Cell respiration
• Section 3.1 – 3.3 – energy and enzymes (pages 73-86)
• Section 3.4 – Metabolism (pages 87-103)
Chapter 4 – Biology of the Cell
• Section 4.7b – Chromosomes
• Section 4.8 – Transcription and translation (pages 137-
142)
 Suggested Readings
Tortora
Chapter 2 – Chemical organization
• Section 2.5-2.10 -Biological macromolecules (pages 43-59)
• Section 2.3 – Chemical reactions – 36-38
Chapter 25 – Metabolism (pages 954-991)
Chapter 3 – Biology of the Cell
• Section 3.5 – Chromosomes (pages 85-88)
• Section 3.6 – Transcription and translation (pages 88-91)
Energy Production
Formation of ATP in
the
Cytosol
• glycolysis
Mitochondria
• TCA cycle and ETC
 ATP (adenosine triphosphate)
Is the cell’s energy shuttle
Provides energy for cellular functions
Adenine NH2

N C
C N
O O O HC
CH
C
-O O O O CH2
O
N
N

O - O - O -
H H

Phosphate groups H H Ribose

Figure 8.8 OH OH
Energy is released from ATP when phosphate
bond is broken

P P P

Adenosine triphosphate (ATP)

H2O

P i
+ P P Energy

Figure 8.9 Inorganic phosphate Adenosine diphosphate (ADP)

 C6 H12 O6 + (6) O2 (6) CO2 + (6) H2O
(glucose + oxygen) (carbon dioxide + water)

(36) ADP + (36) Pi

36 ATP

re

ul

• Anabolism
• Transport
• Muscle contraction
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Possible Fuel Sources
Carbohydrates (CHO)
Monosaccarides – E.g. Glucose (C6H12O6), fructose
Dissaccarides (e.g. Lactose, Sucrose)
Polysaccarides (Starch)
Proteins
Made up of amino Acids
Fats
Glycerol and fatty acids
 Cellular Respiration
Breakdown of glucose or other fuels in the
presence of oxygen to yield ATP

Four stages of cellular respiration

1. Glycolysis
2. Preparatory step
3. Citric acid cycle
4. Electron transport system

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 Energy Energy

Energy Energy

Citric Electron
Glycolysis Preparatory acid transport
step cycle system

Mitochondrion

Cytoplasm
ATP ATP ATP

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Co-Enzymes
NAD+ becomes NADH (reduced)
FAD becomes FADH2

Act as H+ shuttles (recycled)

Move H+ and electrons to ETS
 ATP production
Electrons Electrons carried
carried via NADH and
via NADH FADH2

Oxidative
Citric phosphorylation:
Glycolsis
acid electron transport
Glucose Pyruvate cycle and
chemiosmosis

Cytosol
Mitochondrion

ATP ATP ATP

Substrate-level Oxidative
Substrate-level
phosphorylation phosphorylation
phosphorylation
Glycolysis
9 sequential reactions
breaks glucose into two pyruvate
Anaerobic (no oxygen needed)
Glycolysis
Two ATP in Glycolysis

1 Glucose

1 glucose in ATP
(6-carbon)

ADP
Energy
investment
ATP

4 ATP out ADP

Net of 2 ATP 2 Glyceraldehyde-3-phosphate (PGAL)

(3-carbon)

2 NAD+

2 NADH out 2 NADH + 2 H+

2 ADP

2 ATP
Shuttled to ETS Energy
yield

2 pyruvate 2 ADP

2 ATP

2 Pyruvate

Net is 2-2-2! (3-carbon)

 CH2OH 6
2 NAD+ Triose phosphate
Citric
HH H Glycolysis acid Oxidative dehydrogenase
HO H cycle phosphorylation
2 Pi
HO OH 2 NADH
H OH + 2 H+
Glucose 2
P O C O
ATP 1 CHOH

Hexokinase CH2 O P
ADP 1, 3-Bisphosphoglycerate
2 ADP
7
CH2OH P Phosphoglycerokinase
HH OH 2 ATP
OH H
HO
H OH 2 O–
Glucose-6-phosphate C
2 CHOH
Phosphoglucoisomerase CH2 O P
3-Phosphoglycerate
CH2O P
O CH2OH 8
H HO Phosphoglyceromutase
H HO
2 O–
HO H
Fructose-6-phosphate C O
3 H C O P
ATP
Phosphofructokinase CH2OH
2-Phosphoglycerate
9
ADP
2H O Enolase
2
P O CH2 O CH2 O P 2 O–
HO C O
H OH C O P
HO H
Fructose- CH2
1, 6-bisphosphate Phosphoenolpyruvate
4 2 ADP 10
Aldolase
Pyruvate kinase
2 ATP
5 H
P O CH2 Isomerase
C O 2 O–
C O
CHOH C O
CH2OH
CH2 O P C O
Dihydroxyacetone Glyceraldehyde- CH3
phosphate 3-phosphate
Figure 9.9 A Figure 9.8 B Pyruvate
Transfer into Mitochondria (Preparatory Step)
Loss of CO2
Irreversible
Pyruvate becomes Acetyl CoA
CYTOSOL MITOCHONDRION

NAD+ NADH + H+
O–
S CoA
2
C O
C O

C O
CH3
1 3
CH3
Acetyle CoA
Pyruvate CO2 Coenzyme A

Transport protein
TCA Cycle
Pyruvate Glycolysis Citric Oxidative
acid phosphorylatio
(from glycolysis, cycle
n

2 molecules per glucose)

Occurs in ATP ATP ATP

CO2

mitochondrial NADH
CoA

matrix + 3 H+ Acetyle CoA

CoA

CoA

Is the final Citric

acid
breakdown of FADH2
cycle
2 CO2

3 NAD+

the fuel FAD 3 NADH

+ 3 H+

molecule ATP
ADP + P i

Figure 9.11
 Citric

1 Acetyl CoA in Glycolysis Oxidative

acid phosphorylation
cycle

3 NADH out S
C
CoA
O
CH3

1 ATP out Acetyl CoA

CoA SH

C COO–
1 FADH2 out NAD+
NADH
+ H+
O
CH2
COO–
1 COO–
CH2
H2O
COO–
8 Oxaloacetate HO C COO– CH2
CO out
2 COO–
CH2
COO–
2
HO
HC COO–
CH
HO CH
Malate Citrate COO–
CH2
Isocitrate
COO–
Citric CO2
3
acid
For 1 glucose molecule H2O
7
COO–
cycle
NAD+

NADH
COO–
CH + H+
Fumarate
2 cycles HC
COO–
CoA SH CH2
CH2
C O
a-Ketoglutarate

6 4
COO– CoA SH COO– COO–

Net is 6-2-2! FADH2 CH2

CH2
5 CH2
CH2
NAD+
CO2
FAD COO– C O
Succinate Pi S CoA NADH
GTP GDP Succinyl + H+
CoA
Co-enzymes take electrons ADP

ATP
and H+ to ETS Figure 9.12
 Electron Transport Chain
2H + 1/ O2
Forms ATP (from food via
2

NADH) Controlled

Requires oxygen 2 H + + 2 e–
release of
energy for
synthesis
of
Transfers energy from

Free energy, G
ATP
ATP
ATP
NADH/FADH2 to ATP

ADP to form ATP

2
Uses ATP synthase e–
2 H+
1/
2 O2

enzyme H2O

Figure 9.5 B (b) Cellular respiration

 Oxidative Phosphorylation
Inner
Mitochondrial
Glycolysis
Oxidative
phosphorylation.
membrane
electron transport
and chemiosmosis

ATP ATP ATP

H+
H+

H+
H+
Cyt c
Protein complex
Intermembrane of electron
space carners
Q IV
I III
ATP
Inner II synthase
mitochondrial FADH2 H2O
membrane FAD+ 2 H+ + 1/2 O2
NADH+
NAD+ ADP + Pi ATP
(Carrying electrons
from, food) H+
Mitochondrial Chemiosmosis
Electron transport chain
matrix +
Electron transport and pumping of protons (H ), ATP synthesis powered by the flow
+
which create an H gradient across the membrane Of H back across the membrane
+

Figure 9.15 Oxidative phosphorylation

 ATP Synthase
INTERMEMBRANE SPACE A rotor within the
H+
membrane spins
H+ H+ clockwise when
Protein molecule H+ H+ H+ flows past
it down the H+
that makes ATP H+
H+
gradient.

A stator anchored
in the membrane
holds the knob
stationary.

H+ gradient A rod (for “stalk”)

extending into
Drives ATP the knob also
spins, activating
synthase H+
catalytic sites in
the knob.
Three catalytic
sites in the
ADP stationary knob
+ join inorganic
Pi ATP
Phosphate to ADP
to make ATP.
MITOCHONDRIAL MATRIX
Figure 9.14
Oxidative Phosphorylation
Each NADH can produce 3 ATP
Each FADH2 can produce 2 ATP

Outer membrane

Inner membrane
of mitochondrion

FADH2 FAD
NADH
NAD 1⁄ O
2 2 + 2H+ + 2e- H 2O ADP + Pi ATP

Electron transport system ATP Synthase

Flow of Energy
Glucose NADH/FADH2 ETC ATP

Electron shuttles MITOCHONDRION

CYTOSOL 2 NADH
span membrane
or
2 FADH2

2 NADH 2 NADH 6 NADH 2 FADH2

Glycolysis Oxidative
2 Citric phosphorylation:
2 Acetyl acid electron transport
Glucose Pyruvate CoA cycle and
chemiosmosis

+ 2 ATP + 2 ATP + about 32 or 34 ATP

by substrate-level by substrate-level by oxidative phosphorylation, depending
phosphorylation phosphorylation on which shuttle transports electrons
from NADH in cytosol

About
Maximum per glucose: 36 or 38 ATP

Figure 9.16
Glucose
1 Glucose molecule yields 38 ATP
Oxygen required for full aerobic process
• Anaerobic (glycolysis) – only yields 2 ATP

Uses about 40% of energy stored in glucose

Rest is lost as heat

First choice for fuels – quick to break down

Control of Cellular Respiration
Glucose

Glycolysis
AMP

Allosteric control Fructose-6-phosphate Stimulates

+
Phosphofructokinase
– –
Negative Fructose-1,6-bisphosphate
Inhibits Inhibits
feedback

phosphofructokinase Pyruvate

ATP Citrate
Acetyl CoA

Citric
acid
cycle

Oxidative
Figure 9.20 phosphorylation
Lactic Acid Formation
Reversible
If no O2 available – make ATP anaerobically
(low yield)
Lactic Acid Formation
If no O2 available – make
ATP anaerobically (low
yield) Glucose

(Glycolysis) (2) ATP

Lactic acid
Lactic acid
Causes “Muscle burn”
Pyruvate
buildup
Mitochondrial
metabolism
blocked without
oxygen

When O2 is available, Mitochondrion

converts back to
pyruvate
 Other Energy Sources
Glycogen (storage form of glucose)
Can quickly convert to glucose
1% of total energy reserves
Fats: 78% of total energy reserves
Triglycerides have twice the energy of
carbohydrates
Proteins: 21% of total energy reserves
Have the same amount of energy as
carbohydrates
• But require energy for processing
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Proteins as a Fuel
Amino acids converted to ketoacids
Low overall ATP yield
Last resort for energy
Eg. Starvation
Or high protein intake
 Fat as Fuel
Uses beta-oxidation to form acetyl CoA
Then enters TCA cycle
High energy yield
Most efficient storage
of energy

Beta oxidation is slow to

start – not used initially
 Fats Glycogen Protein

Glucose Amino acids

Figure 3.30

Carbon NH3 Urea (waste)

Fatty acids Glycerol Pyruvate
backbone

Acetyl Citric Electron

Preparatory acid
CoA transport
step cycle system

(2) many

ATP ATP

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High Protein – Low Carb Diets
Protein metabolism uses a lot of ATP
Less overall ATP yield
With low carbs – must turn to fat metabolism

High fat intake

Keeps you feeling fuller longer
• Releases leptin hormone = “fullness”
Metabolism and Exercise
Available energy sources for a muscle cell
include
Ready ATP
Creatine phosphate (“storage form” of ATP)
Blood plasma glucose
Glycogen in liver and muscle (storage)
Gluconeogenesis (liver)
Fatty acids (diet / storage)
 Overview of Muscle Metabolism
Intestine Blood Muscle tissue
Glucose
absorbed Contraction
Glycogen
1 Rest
Exercise ADP
Liver Liver glycogen Glucose + Myosin
Pi ATPase
Glucose Glycolysis
(anaerobic)
Ca-ATPase
Pyruvate
3
Lactate Lactate Pyruvate
ATP
Amino Lactate Relaxation
acids 4 +
Fatty Fatty Acetyl CoA creatine
acids acids
2

Contraction
Adipose Glycerol + fatty acids
Triglycerides
tissue

Rest
Oxidative
phosphorylation
Lipids stored in O2 and
adipose tissue citric acid
CO2
cycle Creatine ~P (PCr)
Lungs (aerobic) +
Gas exchange
at the lungs: O ADP
2
CO2

1 Glucose comes 2 Fatty acids can be 3 Lactate from anaerobic 4 Both aerobic and anaerobic
from liver glycogen used only in aerobic metabolism can be converted metabolism provide ATP for
or dietary intake. metabolism. to glucose by the liver. muscle contraction.

Figure 25-1
 Energy Systems
in Exercise

Mole of Time to
Energy Systems
ATP/min Fatigue
Immediate: Phosphagen 4 5 to 10 sec
(Creatine Phosphate and ATP)
Short Term: Glycolysis
2.5 1 - 2 min
(Glucose - Glycogen-Lactic Acid)
Long Term: Aerobic
2 min +
(Glucose, amino acids, 1
Unlimited time
Fatty acids – slowest to start)
 Energy Transfer Systems and
Exercise
100%
% Capacity of Energy System

Glycolysis

Aerobic

Phosphagen
(ATP-PCR)
10 sec 30 sec 2 min 5 min +
 DNA Replication
Needed for Mitosis and Meiosis
S phase
G C
A T
T A

DNA 1 nm

G C
3.4 nm

Double helix model A

C G
T
C G

T A

T A
A T

A T

G C
0.34 nm
A T
(a) Key features of DNA structure
DNA
Sugar-phosphate Nitrogenous
backbone bases

Polymer of nucleotides O–
O P O
5 end
5
CH2 H
CH3
O
O 1
O– 4 H
H N N
H
H H
3 2 O
H
Thymine (T)

Nucleotide has O
O
P O CH2
O
H
N
H
N
O– H H N H

a nitrogenous base H
H
H
N
H
N

Adenine (A)

a sugar O
O
P O CH2
O
H
H H
N H
O– H H N N

a phosphate group H
H
H
O
Cytosine (C)

O
5
O P O CH2 H N
O 1 O
O– 4 H H N
Phosphate H H
2 N H
3 N DNA nucleotide
OH H
N H
Sugar (deoxyribose) H
3 end
Guanine (G)
 5 end

O
OH
P Hydrogen bond

DNA has –O
O

O
3 end
OH

T A

two antiparallel O
O
O CH2
P

sugar-phosphate –O
O

H2C O
O
P
O–

O O
backbones O
G C

O CH2
O

3’ and 5’ ends
P
–O O
O–
O
P
O
H2C O O
C G

O O CH2
O
P O
–O O–
Nitrogenous O
H2C O
O
P
O
A T

bases are paired O CH2

in molecule’s
OH
3 end O
O–
P
O
O
interior Figure 16.7b
(b) Partial chemical structure
5 end
 H

N N H O CH3
Adenine always
binds with N N H N
Thymine Sugar N N

O Sugar
Adenine (A) Thymine (T)

O H N
Guanine always N

binds with cytosine

N
N H N
Sugar N
N

N H O Sugar
H
Figure 16.8 Guanine (G) Cytosine (C)
 DNA Replication
Each strand acts as a template for building a
new strand

Parent unwinds
Two daughters built; Base pairing rules
T
A T A T A A T A T A T
C G C G C G C G C G C G
T A T A T A T A T A T A
A T A T A T A T A T A T
G C G C G C C G C G C
G

(a) The parent molecule has two (b) The first step in replication is (c) Each parental strand now (d) The nucleotides are connected
complementary strands of DNA. separation of the two DNA serves as a template that to form the sugar-phosphate
Each base is paired by hydrogen strands. determines the order of backbones of the new strands.
bonding with its specific partner, nucleotides along a new, Each “daughter” DNA
A with T and G with C. complementary strand. molecule consists of one parental
strand and one new strand.

Figure 16.9 a–d

DNA Replication

Semi-conservative
Each daughter has 1 parent strand

Second
First replication
replication
Parent cell

Semiconservative
model. The two
strands of the
parental molecule
separate,
and each functions
as a template
for synthesis of
a new, comple-
mentary strand.
 DNA Replication
Begins at sites of origins
Eukaryotes have hundreds / thousands

Origin of replication Parental (template) strand

0.25 µm
Daughter (new) strand

1 Replication begins at specific sites

where the two parental strands
separate and form replication
bubbles. Bubble Replication fork

2 The bubbles expand laterally, as

DNA replication proceeds in both
directions.

3 Eventually, the replication

bubbles fuse, and synthesis of
the daughter strands is
complete. Two daughter DNA molecules

(a) In eukaryotes, DNA replication begins at many sites along the giant (b) In this micrograph, three replication
DNA molecule of each chromosome. bubbles are visible along the DNA of
Figure 16.12 a, b a cultured Chinese hamster cell (TEM).
 Overview
Overall direction of replication Lagging
Leading
1 Helicase unwinds the strand Origin of replication strand
parental double helix.
2 Molecules of single- 3 The leading strand is
strand binding protein synthesized continuously in the
stabilize the unwound 5→ 3 direction by DNA pol III. Lagging Leading
template strands.
strand OVERVIEW strand
DNA pol III

Leading
strand

5 Replication fork
DNA pol I DNA ligase
3
Primase 2
Parental DNA DNA pol III Lagging 1
Primer strand 3
4 Primase begins synthesis
3 5
of RNA primer for fifth 4
Okazaki fragment.

5 DNA pol III is completing synthesis of 6 DNA pol I removes the primer from the 5 end 7 DNA ligase bonds
the fourth fragment, when it reaches the of the second fragment, replacing it with DNA the 3 end of the
RNA primer on the third fragment, it will nucleotides that it adds one by one to the 3 end second fragment to
dissociate, move to the replication fork, of the third fragment. The replacement of the the 5 end of the first
and add DNA nucleotides to the 3 end last RNA nucleotide with DNA leaves the sugar- fragment.
of the fifth fragment primer. phosphate backbone with a free 3 end.
Figure 16.16
 Replication Sequence
First Steps:
Helicase unwinds helix
Binding proteins stabilize template strands
Topoisomerase stabilizes the “over-twist” ahead
of helicase

Primase “primes” strands

With RNA
DNA polymerase III
Elongates strand - Adds nucleotides to 3’ end only

Reads parent strand from 3’ to 5’

Builds the daughter from 5’ to 3’
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

A T A
P P OH
C Pyrophosphate 3 end C
OH
2 P
Figure 16.13 5 end 5 end
 DNA polymerase I replaces primer RNA
Ligase – “glues” together
Overall direction of replication Lagging
Leading
1 Helicase unwinds the strand Origin of replication strand
parental double helix.
2 Molecules of single- 3 The leading strand is
strand binding protein synthesized continuously in the
stabilize the unwound 5→ 3 direction by DNA pol III. Lagging Leading
template strands.
strand OVERVIEW strand
DNA pol III

Leading
strand

5 Replication fork
DNA pol I DNA ligase
3
Primase 2
Parental DNA DNA pol III Lagging 1
Primer strand 3
4 Primase begins synthesis
3 5
of RNA primer for fifth 4
Okazaki fragment.

5 DNA pol III is completing synthesis of 6 DNA pol I removes the primer from the 5 end 7 DNA ligase bonds
the fourth fragment, when it reaches the of the second fragment, replacing it with DNA the 3 end of the
RNA primer on the third fragment, it will nucleotides that it adds one by one to the 3 end second fragment to
dissociate, move to the replication fork, of the third fragment. The replacement of the the 5 end of the first
and add DNA nucleotides to the 3 end last RNA nucleotide with DNA leaves the sugar- fragment.
of the fifth fragment primer. phosphate backbone with a free 3 end.
Figure 16.16
Leading Strand
synthesize a complementary strand
continuously
moving toward the replication fork

Lagging Strand
synthesized as a series of segments
called Okazaki fragments
joined together by DNA ligase
Moves away from replication fork
Lagging Strand
Primase adds short primer sequence
DNA polymerase III adds nucleotides to 3’
end until it reaches next primer (Okazaki
segment)
DNA polymerase I replaces primer
nucleotides with DNA
Ligase bonds segments together
Leading Strand
Primase adds RNA primer once
DNA Poly III builds continuously toward
fork
Poly I replaces primer
Ligase binds it to other segment (initial
section)
 1 DNA pol Ill elongates
DNA strands only in the
5 3 direction. 3 2 One new strand, the leading strand,
Parental DNA 5 can elongate continuously 5 3
as the replication fork progresses.
5
3 Okazaki
3 The other new strand, the
fragments
lagging strand must grow in an overall
2 3 5 direction by addition of short
1 3
segments, Okazaki fragments, that grow
5 5 3 (numbered here in the order
DNA pol III they were made).

Template
strand

4 DNA ligase joins Okazaki

fragments by forming a bond between
Leading strand their free ends. This results in a
Lagging strand
3 continuous strand.
2 1

Template
strand DNA ligase
Figure 16.14 Overall direction of replication
Lagging Strand
3 5

5 3

Template
2 DNA pol III adds DNA nucleotides to the
strand primer, forming an Okazaki fragment.

3 RNA primer 3 5
1
5

3 After reaching the next

RNA primer (not shown),
DNA pol III falls off.
Okazaki 3
3 fragment
5
1
5
4 After the second fragment is
primed. DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off.
5 3
3 2
1
5

5 DNA pol 1 replaces the

RNA with DNA, adding to
the 3 end of fragment 2.
5 3
3
2 5
1

6 DNA ligase forms a bond 7 The lagging strand

between the newest DNA in this region is now
and the adjacent DNA of complete.
fragment 1.
5 3
3 2 5
1

Figure 16.15 Overall direction of replication

Primers
DNA polymerases cannot initiate synthesis of
polynucleotide
They can only add nucleotides to the 3 end

Initiated by RNA or DNA primer

Short nucleotide strand

Leading strand
Only 1 primer needed

Lagging strand
each Okazaki fragment must be primed
 A summary of DNA replication
Overall direction of replication Lagging
Leading
1 Helicase unwinds the strand Origin of replication strand
parental double helix.
2 Molecules of single- 3 The leading strand is
strand binding protein synthesized continuously in the
stabilize the unwound 5→ 3 direction by DNA pol III. Lagging Leading
template strands.
strand OVERVIEW strand
DNA pol III

Leading
strand

5 Replication fork
DNA pol I DNA ligase
3
Primase 2
Parental DNA DNA pol III Lagging 1
Primer strand 3
4 Primase begins synthesis
3 5
of RNA primer for fifth 4
Okazaki fragment.

5 DNA pol III is completing synthesis of 6 DNA pol I removes the primer from the 5 end 7 DNA ligase bonds
the fourth fragment, when it reaches the of the second fragment, replacing it with DNA the 3 end of the
RNA primer on the third fragment, it will nucleotides that it adds one by one to the 3 end second fragment to
dissociate, move to the replication fork, of the third fragment. The replacement of the the 5 end of the first
and add DNA nucleotides to the 3 end last RNA nucleotide with DNA leaves the sugar- fragment.
of the fifth fragment primer. phosphate backbone with a free 3 end.
Figure 16.16
Proof-reading/ Mismatch Repair

Enzymes cut out

and replace 2 A nuclease enzyme cuts
the damaged DNA strand

damaged stretches at two points and the

damaged section is
removed.
of DNA Nuclease

DNA 3 Repair synthesis by

polymerase a DNA polymerase
fills in the missing
Damage – eg. sun nucleotides.

DNA
ligase 4 DNA ligase seals the
Free end of the new DNA
To the old DNA, making the
strand complete.
Figure 16.17
Repeated Replications
Chromosome End of parental
DNA strands
5
Leading strand
Lagging strand
ends get shorter 3

with replication Last fragment Previous fragment

RNA primer
5
Lagging strand
nucleotide Primer removed but
3
Removal of primers and
sequences cannot be replaced
with DNA because
replacement with DNA
where a 3 end is available
no 3 end available
called telomeres for DNA polymerase 5

postpone the 3
Second round

erosion at ends 5
of replication

“junk DNA” New leading strand 3

New lagging strand 5
3
Further rounds
of replication
Shorter and shorter
Figure 16.18 daughter molecules
 Stem Cells

Eg. Blood stem cells,

Gametes

Telomerase
Catalyzes the
lengthening of telomeres
in germ cells
 Protein synthesis

Protein functions include

Transporters / Carriers
Channels / Pores
Antibodies
Storage and Structure
Hormones and Receptors
Contractile proteins
Enzymes
 Enzymes
Are a type of protein that acts as a catalyst,
speeding up chemical reactions

1 Active site is available for 2 Substrate binds to

a molecule of substrate, the enzyme.
Substrate
reactant on which the enzyme acts. (sucrose)

Glucose
Enzyme
OH (sucrase)
H2O
Fructose

H O

4 Products are released. 3 Substrate is converted

Figure 5.16 to products.
Polypeptides
Made up of amino acids
Folds and bends (secondary structure)

A protein
Consists of one or more polypeptides (quaternary)
 Transcription and Translation
DNA directs protein synthesis
One gene codes for 1 polypeptide

Ribosome
Cellular machinery for
translation
• Polypeptide synthesis
 DNA → RNA → protein

Transcription Nuclear
envelope
Synthesis of mRNA
(messenger RNA) under TRANSCRIPTION DNA

direction of DNA
Pre-mRNA
In nucleus RNA PROCESSING

mRNA

Translation Ribosome

Synthesis of polypeptide under TRANSLATION

Polypeptide
direction of RNA
On ribosome in cytosol
 DNA → RNA → protein

DNA Gene 2
molecule
Gene 1
Gene 3

DNA strand 3 5
(template) A C C A A A C C G A G T

TRANSCRIPTION

U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Figure 17.4 Amino acid
RNA Transcription

Catalyzed by RNA polymerase

pries the DNA strands apart

hooks together the RNA nucleotides

Follows base-pairing rules

• uracil substitutes for thymine
Synthesis of an RNA Transcript
Promoter
Transcription unit
5 3
3 5
DNA
3 stages RNA polymerase
Start point
1 Initiation. After RNA polymerase binds to
the promoter, the DNA strands unwind, and

Initiation the polymerase initiates RNA synthesis at the

start point on the template strand.
5 3

Elongation Unwound
3

RNA
Template strand of
DNA
5

DNA transcript
Termination 2 Elongation. The polymerase moves downstream, unwinding the
DNA and elongating the RNA transcript 5 → 3 . In the wake of
Rewound transcription, the DNA strands re-form a double helix.

RNA
5 3
3 3 5
5

RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.

5 3
3 5

5 3
Completed RNA
Figure 17.7 transcript
Initiation
Promoters signal
initiation of RNA TRANSCRIPTION

RNA PROCESSING

mRNA
DNA
Pre-mRNA
1 Eukaryotic promoters

TRANSLATION Ribosome

synthesis 5
Polypeptide

T A T A A AA
Promoter
3
AT A T T T T
3 5
TATA box Start point Template
DNA strand
2 Several transcription
factors
Transcription

Transcription factors 5
3
factors

3
5
3 Additional transcription
factors

Help RNA polymerase

to recognize promoter RNA polymerase II
Transcription factors

sequences 5
3 5
3
5
RNA transcript
Figure 17.8 Transcription initiation complex
Elongation
Elongation Non-template
strand of DNA
RNA nucleotides
RNA polymerase moves RNA
polymerase
along the DNA
T C C A A
A
3
3 end

Untwists the double helix U

5 A E G C A

exposes 10 to 20 DNA T A G G T T

bases at a time 5
Direction of transcription
Template
(“downstream”)
strand of DN
Base-pairs DNA template
with RNA nucleotides Newly made
RNA
 Termination
Polymerase transcribes polyadenylation
sequence (AAUAAA) in pre-mRNA and
beyond
Proteins cut mRNA free (10-35 nucleotides past poly-A)
Polymerase falls away from DNA (not understood)

A modified guanine nucleotide 50 to 250 adenine nucleotides

added to the 5 end added to the 3 end
TRANSCRIPTION DNA

RNA PROCESSING Pre-mRNA Protein-coding segment Polyadenylation signal

5 3
mRNA
G P P P AAUAAA AAA…AAA
Ribosome
TRANSLATION
Start codon Stop codon
5 Cap 5 UTR 3 UTR Poly-A tail
Polypeptide
 RNA Processing after
Transcription
Pre-mRNA
5 end receives a modified nucleotide cap
The 3 end gets a poly-A tail
• Helps to export mRNA to cytosol
• Protects mRNA from degradation
• Helps ribosomes attach in cytosol

A modified guanine nucleotide 50 to 250 adenine nucleotides

added to the 5 end added to the 3 end
TRANSCRIPTION DNA

RNA PROCESSING Pre-mRNA Protein-coding segment Polyadenylation signal

5 3
mRNA
G P P P AAUAAA AAA…AAA
Ribosome
TRANSLATION
Start codon Stop codon
5 Cap 5 UTR 3 UTR Poly-A tail
Polypeptide
 RNA splicing
Removes introns and joins exons
• Introns – non-coding (no genes)
• Exons – expressed (has genes)

5 Exon Intron Exon Intron Exon 3

TRANSCRIPTION DNA Pre-mRNA 5 Cap Poly-A tail
1 30 31 104 105 146
RNA PROCESSING Pre-mRNA

mRNA Coding Introns cut out and

segment exons spliced together
Ribosome
TRANSLATION

Polypeptide
mRNA 5 Cap Poly-A tail
1 146
3 UTR 3 UTR
 RNA Splicing - spliceosomes
RNA transcript (pre-mRNA)
5
Intron
snRNP – small
Exon 1 Exon 2

Protein
1
nuclear snRNA Other proteins

snRNPs
ribonucleoproteins Spliceosome

Recognize splice
2 5
sites

Spliceosome
components
Cut-out
intron
3 mRNA
5
Exon 1 Exon 2
Proteins
modular structure
Each exon codes for different domain

Gene
DNA
Exon 1 Intron Exon 2 Intron Exon 3
Transcription
RNA processing
Translation

Domain 3

Domain 2
Domain 1

Polypeptide
Translation TRANSCRIPTION DNA

mRNA
Ribosome
TRANSLATION
Polypeptide

Formation of
Amino
protein using Polypeptide acids

mRNA tRNA with

template amino acid

Ribosome attached

Gly

tRNA

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

5 Codons 3
mRNA
messenger RNA
TRANSCRIPTION DNA

mRNA

mRNA carries TRANSLATION

Ribosome

Polypeptide

message as a Amino
series of codons Polypeptide acids

tRNA with
amino acid
Ribosome attached

Gly

tRNA

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

5 Codons 3
mRNA
Codons
Gene determines sequence of bases along
mRNA molecule

sequence of base triplets, or codons

Codon in mRNA
either translated into an amino acid or serves
as stop signal
 Genetic Universal Code
Bacteria to Humans
Second mRNA base
U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UAC
U UUC UCC
Ser
UGC C
UUA UCA UAA Stop UGA Stop A
Leu UAG Stop UGG Trp G
UUG UCG

Third mRNA base (3 end)

First mRNA base (5 end)

CUU CCU CAU CGU U

His
CUC CCC CAC CGC C
C Leu Pro Arg
CUA CCA CAA CGA A
Gln
CUG CCG CAG CGG G
AUU ACU AAU AGU U
Asn
A
AUC lle ACC AAC AGC Ser C
Thr
AUA ACA AAA AGA A
Met or Lys Arg
AUG start ACG AAG AGG G
GUU GCU GAU GGU U
G GUC GCC GAC Asp GGC C
Val Ala Gly
GUA GCA GAA GGA A
Figure 17.5 GUG GCG GAG Glu GGG G
 Transfer RNA
Translation uses transfer RNA (tRNA’s) to shuttle
amino acids to building polypeptide
3
Amino acid A
C
Each tRNA is specific attachment site C
A 5
C G
for an amino acid G C
C G
U G
U A
A U
U C A U
* C A C AG UA A G *
G * C U C
*
C G U G U * C G A G G
* * U C * A G G
* G AG C
(a) Two-dimensional structure. The four base-paired regions and three G C Hydrogen
loops are characteristic of all tRNAs, as is the base sequence of the U A bonds
amino acid attachment site at the 3 end. The anticodon triplet is * G
A
unique to each tRNA type. (The asterisks mark bases that have been A* C
chemically modified, a characteristic of tRNA.) * U
A G
A

Figure 17.14a Anticodon

 tRNA
Anti-codon – binds to mRNA codon
RNA strand (~80 nucleotides)
~ L-shaped 5 Amino acid
attachment site
3 3
Amino acid A
C
attachment site C Hydrogen
A 5 bonds
C G
G C
C G
U G
U A
A U
U C A U
* C A C AG UA A G *
G * CUC *
C G U GU * C G A G G
* * U C * A G G
* G AG C A AG
G C Hydrogen
U A bonds
* G 3 5
A Anticodon
A* C Anticodon
* U (c) Symbol used
A
A G (b) Three-dimensional structure in this book
Anticodon
Aminoacyl-tRNA synthetase
Amino acid Aminoacyl-tRNA
synthetase (enzyme)
Joins each amino P P P Adenosine

acid to the ATP

correct tRNA Pyrophosphate P Pi

P Adenosine

Pi
Pi
Phosphates
tRNA

Binding site P Adenosine

specific to amino AMP

acid Aminoacyl tRNA

(an “activated
Figure 17.15 amino acid”)
Ribosomes
Facilitate coupling of tRNA anticodons with
mRNA codons during protein synthesis

made of proteins and TRANSCRIPTION DNA

ribosomal RNA or TRANSLATION

mRNA
Ribosome

rRNA Polypeptide

Growing
Exit tunnel

polypeptide
tRNA
molecules
Large
subunit
E
P A

Small
subunit

5
mRNA 3

(a) Computer model of functioning ribosome. This is a model of a bacterial

ribosome, showing its overall shape. The eukaryotic ribosome is roughly
similar. A ribosomal subunit is an aggregate of ribosomal RNA molecules
and proteins.
 Ribosome
has three binding sites for tRNA
The A site P site (Peptidyl-tRNA
• “add” binding site)
A site (Aminoacyl-
tRNA binding site)
The P site E site
(Exit site)
• “peptide” Large
subunit
The E site E P A

• “exit”
mRNA
binding site Small
subunit

(b) Schematic model showing binding sites. A ribosome has an mRNA

binding site and three tRNA binding sites, known as the A, P, and E sites.
Figure 17.16b This schematic ribosome will appear in later diagrams.
We can divide translation into three stages
Initiation
Elongation
Termination Amino end Growing polypeptide

Next amino acid

to be added to
polypeptide chain

tRNA

mRNA 3

Codons
5
 Initiation
Brings mRNA, initiator tRNA (with first
amino acid- Met) and two subunits of a
ribosome together
Start codon Large
ribosomal
P site subunit
3 U A C 5
5 A U G 3

Initiator tRNA
GTP GDP
E A
mRNA
5 3 5 3
Start codon

mRNA binding site Small Translation initiation complex

ribosomal
subunit
1 A small ribosomal subunit binds to a molecule of 2 The arrival of a large ribosomal subunit completes
mRNA. In a prokaryotic cell, the mRNA binding site the initiation complex. Proteins called initiation
on this subunit recognizes a specific nucleotide factors (not shown) are required to bring all the
sequence on the mRNA just upstream of the start translation components together. GTP provides
codon. An initiator tRNA, with the anticodon UAC, the energy for the assembly. The initiator tRNA is
base-pairs with the start codon, AUG. This tRNA in the P site; the A site is available to the tRNA
carries the amino acid methionine (Met). bearing the next amino acid.
Figure 17.17
 Elongation
Amino acids are added one by one to
polypeptide
TRANSCRIPTION DNA
Amino end Codon recognition
mRNA
of polypeptide
Ribosome
TRANSLATION
Polypeptide

E
mRNA 3
Ribosome ready for P A
5 site site
next aminoacyl tRNA
2 GTP
2 GDP

E E

P A P A

GDP
GTP

Translocation E Peptide bond formation

P A

Figure 17.18
 Termination
ribosome reaches a stop codon in the
mRNA
Release
factor
Free
polypeptide

5
3 3
3
5 5
Stop codon
(UAG, UAA, or UGA)

Site accepts release protein Hydrolysis and release

Polyribosome
Completed
Growing polypeptide
polypeptides
Many ribosomes Incoming
ribosomal
can translate 1 subunits
Start of End of
mRNA
mRNA at once (5 end)
mRNA
(3 end)
(a) An mRNA molecule is generally translated simultaneously
by several ribosomes in clusters called polyribosomes.

Ribosomes
mRNA

0.1 µm
(b) This micrograph shows a large polyribosome in a prokaryotic
Figure 17.20a, b cell (TEM).
After Translation
Possible changes:

Enzyme may be cleaved (eg. Insulin)

Sugars or lipids may be attached
Removal of lead amino acids
Ribosomes
Free in cytosol or bound to ER

Synthesis of all proteins starts on free

ribosomes

Export proteins signalled to ER by signal

recognition particle (srp)
 Signal mechanism for targeting proteins to
the ER
1 Polypeptide 2 An SRP binds 3 The SRP binds to a 4 The SRP leaves, and 5 The signal- 6 The rest of
synthesis begins to the signal receptor protein in the ER the polypeptide resumes cleaving the completed
on a free peptide, halting membrane. This receptor growing, meanwhile enzyme polypeptide leaves
ribosome in synthesis is part of a protein complex translocating across the cuts off the the ribosome and
the cytosol. momentarily. (a translocation complex) membrane. (The signal signal peptide. folds into its final
that has a membrane pore peptide stays attached conformation.
and a signal-cleaving enzyme. to the membrane.)

Ribosome

mRNA
Signal
peptide ER
membrane
Signal
Signal-
peptide
recognition Protein
removed
particle
(SRP) SRP
receptor
CYTOSOL protein

Translocation
ERLUMEN
complex

Figure 17.21
Mutations
One wrong nucleotide – one wrong amino
acid – dysfunctional protein
Wild-type hemoglobin DNA Mutant hemoglobin DNA In the DNA, the
3 5 3 5 mutant template
C T T C A T strand has an A where
the wild-type template
has a T.

mRNA mRNA
The mutant mRNA has
G A A G U A a U instead of an A in
one codon.
5 3 5 3

Normal hemoglobin Sickle-cell hemoglobin

The mutant (sickle-cell)
Glu Val hemoglobin has a valine
(Val) instead of a glutamic
acid (Glu).
 Substitutions, insertions or deletions
Produce nonsense or mutation

Wild type Wild type

mRNA
A U G A A G U U U GG C U A A A U GA A GU U U GG C U A A
5 3 mRNA 5 3
Protein Met Lys Phe Gly Protein Met Lys Phe Gly Stop
Stop
Amino end Amino end Carboxyl end
Carboxyl end
Base-pair substitution Base-pair insertion or deletion
No effect on amino acid sequence Frameshift causing immediate nonsense
U instead of C Extra U
A U G A A G U U U G G U U A A AU GU A AG U U U G GC U A

Met Lys Phe Gly Met Stop

Stop
Frameshift causing
Missense A instead of G extensive missense U Missing
A U G A A GU U G G C U A A
A U G A A G U U U A G U U A A
Met Lys Leu Ala
Met Lys Phe Ser Stop Insertion or deletion of 3 nucleotides:
Nonsense no frameshift but extra or missing amino acid
U instead of A A A G Missing
A U G U A G U U U G G C U A A
A U G U U U G G C U A A
Met Stop
Met Phe Gly
Stop
Summary
TRANSCRIPTION DNA
1 RNA is transcribed
from a DNA template.
3

5 RNA RNA
transcript polymerase
RNA PROCESSING Exon
2 In eukaryotes, the
RNA transcript
RNA transcript (pre-
(pre-mRNA)
mRNA) is spliced and
Intron
modified to produce
mRNA, which moves Aminoacyl-tRNA
from the nucleus to the synthetase
cytoplasm. NUCLEUS

Amino
FORMATION OF
acid
INITIATION COMPLEX AMINO ACID ACTIVATION
CYTOPLASM 3 After leaving the tRNA
4 Each amino acid
nucleus, mRNA attaches attaches to its proper tRNA
to the ribosome. with the help of a specific
enzyme and ATP.
mRNA Growing
polypeptide
Activated
amino acid

Ribosomal
subunits

5
TRANSLATION
5 A succession of tRNAs
E A add their amino acids to
the polypeptide chain
AAA Anticodon
as the mRNA is moved
UG G U U U A U G through the ribosome
one codon at a time.
Codon (When completed, the
polypeptide is released
Ribosome from the ribosome.)
Epigenetics
Chemical mechanisms that
control the expression of
genes

Methylation - repressors
Histones – control longer
sections