Section 2
Biochemical Building Blocks
Chapter 5
Amino Acids, Peptides, &
Proteins
Section 5.1: Amino Acids
Figure 5.1 Protein
Diversity
Proteins are molecular tools
They are a diverse and complex group of
macromolecules
Section 5.1: Amino Acids
Proteins can be distinguished by the number,
composition, and sequence of amino acid residues
Amino acid polymers of 50 or less are peptides;
polymers greater than 50 are proteins or
polypeptides
There are 20 standard amino acids
Section 5.1: Amino Acids
Figure 5.3 General
Structure of the aAmino Acids
19 have the same general structure:
central (a) carbon, an amino group,
carboxylate group, hydrogen atom, and
an R group (proline is the exception)
At pH 7, the carboxyl group is in its
conjugate base form (-COO-) while the
amino group is its conjugate acid form (NH3+); therefore, it is amphoteric
Molecules that have both positive and
negative charges on different atoms are
zwitterions and have no net charge at
pH 7
The R group is what gives the amino
acid its unique properties
Section 5.1: Amino Acids
Figure 5.2 The
Standard Amino
Acids
Amino Acid Classes
Classified by their ability to interact with water
Nonpolar amino acids contain hydrocarbon groups
with no charge
Section 5.1: Amino Acids
Figure 5.2 The Standard Amino Acids
Amino Acid Classes Continued
Polar amino acids have functional groups that can
easily interact with water through hydrogen bonding
Contain a hydroxyl group (serine, threonine, and
tyrosine) or amide group (asparagine)
Section 5.1: Amino Acids
Figure 5.2 The
Standard Amino
Acids
Amino Acid Classes Continued
Acidic amino acids have side chains with a
carboxylate group that ionizes at physiological pH
Basic amino acids bear a positive charge at
physiological pH
At physiological pH, lysine is its conjugate acid
(-NH3+), arginine is permanently protonated, and
histidine is a weak base, because it is only partly
ionized
Section 5.1: Amino Acids
Section 5.1: Amino Acids
Biologically Active Amino Acids
Amino acids can have other biological
roles
1. Some amino acids or derivatives
can act as chemical messengers
Neurotransmitters (tryptophanderivative serotonin) and
hormones (tyrosine-derivative
thyroxine)
Figure 5.5 Some Derivatives of Amino Acids
Section 5.1: Amino Acids
2. Act as precursors for other
molecules (nucleotides and
heme)
3. Metabolic intermediates
(arginine, ornithine, and
citrulline in the urea cycle)
Figure 5.6 Citruline
and Ornithine
Section 5.1: Amino Acids
Figure 5.7 Modified
Amino Acid Residues
Found in Polypeptides
Modified Amino Acids in Proteins
Some proteins have amino acids that are modified
after synthesis
Serine, threonine, and tyrosine can be phosphorylated
g-Carboxyglutamate (prothtrombin), 4-hydroxyproline
(collagen), and 5-hydroxylysine (collagen)
Section 5.1: Amino Acids
Amino Acid Stereoisomers
Because the a-carbon (chiral carbon) is attached to
four different groups, they can exist as stereoisomers
Except glycine, which is the only nonchiral standard
amino acid
The molecules are mirror images
of one another, or enantiomers
They cannot be superimposed
over one another and rotate
plane, polarized light in opposite
directions (optical isomers)
Figure 5.8 Two Enantiomers
Section 5.1: Amino Acids
Figure 5.9 D- and L-Glyceraldehyde
Molecules are designated as D or L (glyceraldehyde is
the reference compound for optical isomers)
D or L is used to indicate the similarity of the
arrangement of atoms around the molecule’s
asymmetric carbon to the asymmetric carbon of the
glyceraldehyde isomers
Chirality has a profound effect on the structure and
function of proteins
Section 5.1: Amino Acids
Titration of Amino Acids
Free amino acids contain ionizable groups
The ionic form depends on the pH
When amino acids have no net charge due to
ionization of both groups, this is known as the
isoelectric point (pI) and can be calculated using:
pK1 + pK2
pI =
2
This formula only works if there is no pKR. If there is a pKR,
then you will need to determine which pK values are on either
side of zero net charge!
Section 5.1: Amino Acids
Section 5.1: Amino Acids
Alanine is a simple amino
acid with two ionizable
groups
Alanine loses two protons in
a stepwise fashion upon
titration with NaOH
Isoelectric point is reached
with deprotonation of the
carboxyl group
Figure 5.10 Titration of Two
Amino Acids: Alanine
Section 5.1: Amino Acids
pK1+pKR
2
Amino acids with ionizable side
chains have more complex titration
curves
= pKI
-2
-1
+1
0
Figure 5.10 Titration of Two
Amino Acids: Glutamic Acid
Glutamic acid is a good example,
because it has a carboxyl side chain
group
Glutamic acid has a +1 charge at
low pH
Glutamic acid’s isoelectric point
as base is added and the acarboxyl group loses a proton
As more base is added, it loses
protons to a final net charge of -2
Section 5.1: Amino Acids
Amino Acid Reactions
Amino acids, with their
carboxyl, amino, and various R
groups, can undergo many
chemical reactions
 Peptide bond and disulfide
bridge are of special interest
because of the effect they have
on structure
Figure 5.11 Formation of
a Dipeptide
Section 5.1: Amino Acids
Peptide Bond Formation:
polypeptides are linear
polymers of amino acids linked
by peptide bonds
Peptide bonds are amide
linkages formed by nucleophilic
acyl substitution
Dehydration reaction
Linkage of two amino acids is
a dipeptide
Figure 5.11 Formation of
a Dipeptide
Section 5.1: Amino Acids
Linus Pauling was the first to
characterize the peptide bond as
rigid and flat
Found that C-N bonds between
two amino acids are shorter than
other C-N bonds
Gives them partial doublebond characteristics (they are
resonance hybrids)
Because of the rigidity, one-third
of the bonds in a polypeptide
backbone cannot rotate freely
Limits the number of
conformational possibilities
Figure 5.12 The Peptide Bond
Section 5.1: Amino Acids
Cysteine oxidation leads to a
reversible disulfide bond
A disulfide bridge forms when
two cysteine residues form this
bond
Helps stabilize polypeptides
and proteins
Figure 5.13 Oxidation of
Two Cysteine Molecules
to Form Cystine
Section 5.2: Peptides
Less structurally complex than larger proteins,
peptides still have biologically important functions
Glutathione is a tripeptide found in most all
organisms and is involved in protein and DNA
synthesis, toxic substance metabolism, and amino
acid transport
Vasopressin is an antidiuretic hormone that
regulates water balance, appetite, and body
temperature
Oxytocin is a peptide that aids in uterine
contraction and lactation
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Section 5.3: Proteins
Of all the molecules in a living organism, proteins
have the most diverse set of functions:
Catalysis (enzymes)
Structure (cell and organismal)
Movement (amoeboid movement)
Defense (antibodies)
Regulation (insulin is a peptide hormone)
Transport (membrane transporters)
Storage (ovalbumin in bird eggs)
Stress Response (heat shock proteins)
Section 5.3: Proteins
Due to recent research, numerous multifunction
proteins have been identified
Proteins are categorized into families based on
sequence and three-dimensional shape
Superfamilies are more distantly related proteins
(e.g., hemoglobin and myoglobin to neuroglobin)
Proteins are also classified by shape: globular and
fibrous
Proteins can be classified by composition: simple
(contain only amino acids) or conjugated
Conjugated proteins have a protein and nonprotein
component (i.e., lipoprotein or glycoprotein)
Section 5.3: Proteins
Protein Structure
Proteins are extraordinarily
complex; therefore, simpler images
highlighting specific features are
useful
Space-filling and ribbon models
Levels of protein structure are
primary, secondary, tertiary, and
quaternary
Figure 5.15 The Enzyme
Adenylate Kinase
Section 5.3: Proteins
Figure 5.16 Segments of b-chain in HbA and HbS
Primary Structure is the specific amino acid
sequence of a protein
Homologous proteins share a similar sequence and
arose from the same ancestor gene
When comparing amino acid sequences of a protein
between species, those that are identical are invariant
and presumed to be essential for function
Section 5.3: Proteins
Secondary Structure: Polypeptide
secondary structure has a variety of
repeating structures
Figure 5.18 The a-Helix
Most common include the a-helix and bpleated sheet
Both structures are stabilized by hydrogen
bonding between the carbonyl and the N-H
groups of the polypeptide’s backbone
The a-helix is a rigid, rod-like structure
formed by a right-handed helical turn
a-Helix is stabilized by N-H hydrogen
bonding with a carbonyl four amino acids
away
Glycine and proline do not foster
a-helical formation
Section 5.3: Proteins
Figure 5.19 b-Pleated
Sheet
The b-pleated sheets form when two or more
polypeptide chain segments line up, side by side
Section 5.3: Proteins
Each b strand is fully
extended and stabilized by
hydrogen bonding between
N-H and carbonyl groups of
adjacent strands
Parallel sheets are much
less stable than
antiparallel sheets
Figure 5.19 b-Pleated Sheet
Section 5.3: Proteins
Figure 5.20 Selected Supersecondary Structures
Many proteins form supersecondary structures
(motifs) with patterns of a-helix and b-sheet structures
(a) bab unit
(b) b-meander
(c) aa unit
(d) b-barrel
(e) Greek key
Section 5.3: Proteins
Tertiary Structure refers to unique threedimensional structures formed by globular proteins
Also prosthetic groups
Protein folding is the process by which a nascent
molecule acquires a highly organized structure
Information for folding is contained within the
amino acid sequence
Interactions of the side chains are stabilized by
electrostatic forces
Tertiary structure has several important features
1. Many polypeptides fold in a way to bring distant amino
acids into close proximity
2. Globular proteins are compact because of efficient packing
Section 5.3: Proteins
Tertiary structure has several important features
1. Many polypeptides fold in a way to bring distant amino acids
into close proximity
2. Globular proteins are compact because of efficient packing
3. Large globular proteins (200+ amino acids) often contain
several domains
Domains are structurally independent segments that have
specific functions
Core structural element of a domain is called a fold
4. A number of proteins called mosaic or modular proteins consist
of repeated domains
Fibronectin has three repeated domains (F1, F2, and F3)
Domain modules are coded for by genetic sequences
created by gene duplications
Section 5.3: Proteins
Figure 5.21 Selected Domains Found in Large Numbers of Proteins
Section 5.3: Proteins
Figure 5.23 Interactions
That Maintain Tertiary
Structure
Interactions that stabilize tertiary structure are
hydrophobic interactions, electrostatic interactions
(salt bridges), hydrogen bonds, covalent bonds, and
hydration
Section 5.3: Proteins
Figure 5.25 Structure of
Immunoglobulin G
Quaternary structure: a protein that is composed of
several polypeptide chains (subunits)
Multisubunit proteins may be composed, at least in
part, of identical subunits and are referred to as
oligomers (composed of protomers)
Section 5.3: Proteins
Reasons for common occurrence of
multisubunit proteins:
1. Synthesis of subunits may be
more efficient
2. In supramolecular complexes
replacement of worn-out
components can be handled
more effectively
3. Biological function may be
regulated by complex
interactions of multiple
subunits
Figure 5.25 Structure of
Immunoglobulin G
Section 5.3: Proteins
Polypeptide subunits held together
with noncovalent interactions
Covalent interactions like
disulfide bridges
(immunoglobulins) are less
common
Other covalent interactions
include desmosine and
lysinonorleucine linkages
Figure 5.26 Desmosine
and Lysinonorleucine
linkages
Section 5.3: Proteins
Interactions between subunits are often affected by
ligand binding
An example of this is allostery, which controls protein
function by ligand binding
Can change protein conformation and function
(allosteric transition)
Ligands triggering these transitions are effectors
and modulators
Section 5.3: Proteins
Figure 5.27 Disordered
Protein Binding
Unstructured proteins: Some proteins are partially
or completely unstructured
Unstructured proteins referred to as intrinsically
unstructured proteins (IUPs) or natively unfolded
proteins
Often these proteins are involved in searching out
binding partners (i.e., KID domain of CREB)
Section 5.3: Proteins
Figure 5.28 The Anfinsen
Experiment
Loss of Protein Structure: Because of small differences
between the free energy of folded and unfolded proteins,
they are susceptible to changes in environmental factors
Disruption of protein structure is denaturation (reverse is
renaturation)
Denaturation does not disrupt primary protein structure
Section 5.3: Proteins
The Folding Problem
The direct relationship between a protein’s primary
sequence and its final three-dimensional conformation
is among the most important assumptions in
biochemistry
Painstaking work has been done to be able to predict
structure by understanding the physical and chemical
properties of amino acids
X-ray crystallography, NMR spectroscopy, and sitedirected mutagenesis
Section 5.3: Proteins
Important advances have
been made by biochemists in
protein-folding research
This research led to the
understanding that it is
not a single pathway
A funnel shape best
describes how an unfolded
protein negotiates its way to a
low-energy, folded state
Numerous routes and
intermediates
Figure 5.29 The Energy Landscape
for Protein Folding
Section 5.3: Proteins
Small polypeptides (<100
amino acids) often form
with no intermediates
Larger polypeptides often
require several
intermediates (molten
globules)
Many proteins use
molecular chaperones to
help with folding and
targeting
Figure 5.30 Protein Folding
Section 5.3: Proteins
Molecular chaperones assist
protein folding in two ways:
Preventing inappropriate
protein-protein interactions
Helping folding occur rapidly
and precisely
Two major classes: Hsp70s and
Hsp60s (chaperonins)
Figure 5.31 Space-Filling
Model of the E. Coli
Chaperonin, called the
GroES-GroEL Complex
Section 5.3: Proteins
Hsp70s are a family of
chaperones that bind and
stabilize proteins during the
early stages of folding
Hsp60s (chaperonins) mediate
protein folding after the protein
is released by Hsp70
Increases speed and
efficiency of the folding
process
Both use ATP hydrolysis
Both are also involved in
refolding proteins
If refolding is not possible,
molecular chaperones promote
protein degradation
Figure 5.32 The Molecular Chaperones
Section 5.3: Proteins
Fibrous Proteins
Typically contain high
proportions of a-helices
and b-pleated sheets
Often have structural
rather than dynamic
roles and are water
insoluble
Keratin (a-helices) and
silk fibroin (b-sheets)
Figure 5.33 a-Keratin
Section 5.3: Proteins
Globular Proteins
Biological functions often include
precise binding of ligands
Myoglobin and hemoglobin
Both have a specialized heme
prosthetic group used for
reversible oxygen binding
Figure 5.36 Heme
Section 5.3: Proteins
Myoglobin: found in high
concentrations in cardiac
and skeletal muscle
The protein component
of myoglobin, globin, is a
single protein with eight
a-helices
Encloses a heme [Fe2+]
that has a high affinity
for O2
Figure 5.37 Myoglobin
Section 5.3: Proteins
Hemoglobin is a roughly spherical
protein found in red blood cells
Figure 5.38 The OxygenBinding Site of Heme
Created by a Folded
Globin Chain
Primary function is to transport
oxygen from the lungs to tissues
HbA molecule is composed of 2
a-chains and 2 b-chains (a2b2)
2% of hemoglobin contains dchains instead of b-chains (HbA2)
Embryonic and fetal hemoglobin
have e- and g-chains that have a
higher affinity for O2
Section 5.3: Proteins
Figure 5.39 Hemoglobin
Comparison of myoglobin and hemoglobin identified
several invariant residues, most having to do with
oxygen binding
Four chains of hemoglobin arranged as two identical
ab dimers
Section 5.3: Proteins
Figure 5.41 Equilibrium
Curves Measure the
Affinity of Hemoglobin and
Myoglobin for Oxygen
Hemoglobin shows a sigmoidal oxygen dissociation
curve due to cooperative binding
Binding of first O2 changes hemoglobin’s
conformation making binding of additional O2 easier
Myoglobin dissociation curve is a hyperbolic simpler
binding pattern
Section 5.3: Proteins
Binding of ligands other than oxygen affects
hemoglobin’s oxygen-binding properties
pH decrease enhances oxygen release from
hemoglobin (Bohr effect)
The waste product CO2 also enhances oxygen
release by increasing H+ concentration
Binding of H+ to several ionizable groups on
hemoglobin shifts it to its T state
Section 5.3: Proteins
Figure 5.42 The Effect of 2,3Bisphosphoglycerate (BPG) on
the Affinity Between Oxygen
and Hemoglobin
2,3-Bisphosphoglycerate (BPG) is also an important
regulator of hemoglobin function
Red blood cells have a high concentration of BPG,
which lowers hemoglobin’s affinity for O2
In the lungs, these processes reverse
Section 5.4: Molecular Machines
Molecular Machines
Purposeful movement is a hallmark of living things
This behavior takes a myriad of forms
Biological machines are responsible for these
behaviors
Usually ATP or GTP driven
Motor proteins fall into the following categories:
1. Classical motors (myosins, dyneins, and
kinesin)
2. Timing devices (EF-Tu in translation)
3. Microprocessing switching devices (G proteins)
4. Assembly and disassembly factors (cytoskeleton
assembly and disassembly)
Chapter 7
Carbohydrates
Chapter 7: Overview
Carbohydrates are the most abundant biomolecule
in nature
Have a wide variety of cellular functions: energy,
structure, communication, and precursors for other
biomolecules
They are a direct link between solar energy and
chemical bond energy
Section 7.1: Monosaccharides
Figure 7.1 General Formulas
for the Aldose and Ketose
Forms of Monosaccharides
Monosaccharides, or simple sugars, are polyhydroxy
aldehydes or ketones
Sugars with an aldehyde functional group are
aldoses
Sugars with an ketone functional group are ketoses
Section 7.1: Monosaccharides
Monosaccharide Stereoisomers
An increase in the number of
chiral carbons increases the
number of possible optical
isomers
2n where n is the number of chiral
carbons
Almost all naturally occurring
monosaccharides are the D form
All can be considered to be
derived from D-glyceraldehyde
or nonchiral dihydroxyacetone
Figure 7.3 The D Family of Aldoses
Section 7.1: Monosaccharides
Figure 7.5 Formation of
Hemiacetals and Hemiketals
Cyclic Structure of Monosaccharides
Sugars with four or more carbons exist primarily in
cyclic forms
Ring formation occurs because aldehyde and ketone
groups react reversibly with hydroxyl groups in an
aqueous solution to form hemiacetals and hemiketals
Section 7.1: Monosaccharides
Figure 7.6 Monosaccharide
Structure
The two possible diastereomers that form because of
cyclization are called anomers
Hydroxyl group on hemiacetal occurs on carbon 1 and
can be in the up position (above ring) or down position
(below ring)
In the D-sugar form, because the anomeric carbon is
chiral, two stereoisomers of the aldose can form the aanomer or b-anomer
Section 7.1: Monosaccharides
Figure 7.7 Haworth Structures
of the Anomers of D-Glucose
Haworth Structures—these structures more
accurately depict bond angle and length in ring
structures than the original Fischer structures
In the D-sugar form, when the anomer hydroxyl is up
it gives a b-anomeric form (left in Fischer projection)
while down gives the a-anomeric form (right)
Section 7.1: Monosaccharides
Figure 7.8 Furan and Pyran
Five-membered rings are called furanoses and sixmembered rings are pyranoses
Cyclic form of fructose is fructofuranose, while
glucose in the pyranose form is glucopyranose
Figure 7.9 Fischer and Haworth Representations of D-Fructose
Section 7.1: Monosaccharides
Reaction of Monosaccharides
The carbonyl and hydroxyl groups can undergo
several chemical reactions
Most important include oxidation, reduction,
isomerization, esterification, glycoside formation, and
glycosylation reactions
Section 7.1: Monosaccharides
Figure 7.17 Formation
of Acetals and Ketals
Glycoside Formation—hemiacetals and hemiketals
react with alcohols to form the corresponding acetal
and ketal
When the cyclic hemiacetal or hemiketal form of the
monosaccharide reacts with an alcohol, the new linkage
is a glycosidic linkage and the compound a glycoside
Section 7.1: Monosaccharides
Figure 7.18 Methyl Glucoside Formation
Naming of glycosides specifies the sugar component
Acetals of glucose and fructose are glucoside and
fructoside
Section 7.1: Monosaccharides
If an acetal linkage is formed between the hemiacetal
hydroxyl of one monosaccharide and the hydroxyl of
another, this forms a disaccharide
In polysaccharides, large numbers of monosaccharides
are linked together through acetal linkages
Section 7.1: Monosaccharides
Glycosylation Reactions attach sugars or glycans
(sugar polymers) to proteins or lipids
Catalyzed by glycosyl transferases, glycosidic
bonds are formed between anomeric carbons in
certain glycans and oxygen or nitrogen of other
types of molecules, resulting in N- or O-glycosidic
bonds
Section 7.1: Monosaccharides
Glycation is the reaction of reducing sugars with
nucleophilic nitrogen atoms in a nonenzymatic reaction
Most researched example of the glycation reaction is
the nonenzymatic glycation of protein (Maillard
reaction)
The Schiff base that forms rearranges to a stable
ketoamine, called the Amadori product
Can further react to form advanced glycation end
products (AGEs)
Promote inflammatory processes and involved in
age-related diseases
Section 7.1: Monosaccharides
Figure 7.20 The Maillard
Reaction
Section 7.1: Monosaccharides
Figure 7.21 a-D-glucopyranose
Important Monosaccharides
Glucose (D-Glucose) —originally called dextrose, it is
found in large quantities throughout the natural
world
The primary fuel for living cells
Preferred energy source for brain cells and cells
without mitochondria (erythrocytes)
Section 7.1: Monosaccharides
Figure 7.22 b-D-fructofuranose
Fructose (D-Fructose) is often referred to as fruit
sugar, because of its high content in fruit
On a per-gram basis, it is twice as sweet as sucrose;
therefore, it is often used as a sweetening agent in
processed food
Section 7.1: Monosaccharides
Figure 7.23 a-D-galactopyranose
Galactose is necessary to synthesize a variety of
important biomolecules
Important biomolecules include lactose, glycolipids,
phospholipids, proetoglycan, and glycoproteins
Galactosemia is a genetic disorder resulting from a
missing enzyme in galactose metabolism
Section 7.2: Disaccharides
Figure 7.27 Glycosidic Bonds
Disaccharides
Two monosaccharides linked by a glycosidic bond
Linkages are named by a- or b-conformation and by
which carbons are connected (e.g., a(1,4) or b(1,4))
Section 7.2: Disaccharides
Disaccharides Continued
Lactose (milk sugar) is the
disaccharide found in milk
One molecule of galactose linked to
one molecule of glucose (b(1,4)
linkage)
It is common to have a deficiency in
the enzyme that breaks down
lactose (lactase)
Lactose is a reducing sugar
Figure 7.28 a- and b-lactose
Section 7.2: Disaccharides
Disaccharides Continued
Sucrose is common table sugar
(cane or beet sugar) produced in
the leaves and stems of plants
One molecule of glucose linked to
one molecule of fructose, linked by
an a,b(1,2) glycosidic bond
Glycosidic bond occurs
between both anomeric carbons
Sucrose is a nonreducing sugar
Figure 7.31 Sucrose
Section 7.3: Polysaccharides
Polysaccharides (glycans) are composed of large
numbers of monosaccharides connected by glycosidic
linkages
Smaller glycans made of 10 to 15 monomers called
oligosaccharides, most often attached to polypeptides
as glycoproteins
Two broad classes: N- and O-linked oligosaccharides
Section 7.3: Polysaccharides
N-linked
oligosaccharides
are attached to
polypeptides by
an N-glycosidic
bond with the
side chain amide
nitrogen from the
amino acid
asparagine
Three major
types of
asparagine-linked
oligosaccharides:
high mannose,
hybrid, and
complex
O-Glycosidic
linkages
attach glycans
to the side
chain hydroxyl
of serine or
threonine
residues or the
hydroxyl
oxygens of
membrane
lipids
Figure 7.32 Oligosaccharides
Linked to Polypeptides
Section 7.3: Polysaccharides
Homoglycans
Have one type of monosaccharide and are found in
starch, glycogen, cellulose, and chitin (glucose
monomer)
Starch and glycogen are energy storage molecules
while chitin and cellulose are structural
Chitin is part of the cell wall of fungi and arthropod
exoskeleton
Cellulose is the primary component of plant cell
walls
No fixed molecular weight, because the size is a
reflection of the metabolic state of the cell producing
them
Section 7.3: Polysaccharides
Figure 7.33 Amylose
Starch—the energy reservoir of plant cells and a
significant source of carbohydrate in the human diet
Two polysaccharides occur together in starch:
amylose and amylopectin
Amylose is composed of long, unbranched chains of Dglucose with a(1,4) linkages between them
Section 7.3: Polysaccharides
Figure 7.33 Amylose
Amylose typically contains thousands of glucose
monomers and a molecular weight from 150,000 to
600,000 Da
The other form is amylopectin, which is a branched
polymer containing both a(1,6) and a(1,4) linkages
Branch points occur every 20 to 25 residues
Section 7.3: Polysaccharides
Glycogen is the carbohydrate storage molecule in
vertebrates found in greatest abundance in the liver
and muscle cells
Up to 8–10% of the wet weight of liver cells and 2–3%
in muscle cells
Similar in structure to amylopectin, with more branch
points
More compact and easily mobilized than other
polysaccharides
Section 7.3: Polysaccharides
Figure 7.34 (a) Amylopectin
and (b) Glycogen
Section 7.3: Polysaccharides
Figure 7.35 The
Disaccharide Repeating
Unit of Cellulose
Cellulose is a polymer of D-glucopyranosides linked
by b(1,4) glycosidic bonds
It is the most important structural polysaccharide of
plants (most abundant organic substance on earth)
Section 7.3: Polysaccharides
Figure 7.36 Cellulose
Microfibrils
Pairs of unbranched cellulose molecules (12,000
glucose units each) are held together by hydrogen
bonding to form sheetlike strips, or microfibrils
Each microfibril bundle is tough and inflexible with a
tensile strength comparable to that of steel wire
Important for dietary fiber, wood, paper, and textiles
Section 7.3: Polysaccharides
Heteroglycans
High-molecular-weight carbohydrate polymers that
contain more than one type of monosaccharide
Major types: N- and O-linked glycosaminoglycans
(glycans), glycosaminoglycans, glycan components of
glycolipids, and GPI (glycosylphosphatidylinositol)
anchors
GPI anchors and glycolipids will be discussed in
Chapter 11
Section 7.3: Polysaccharides
Heteroglycans Continued
N- and O-Glycans—many proteins have N- and Olinked oligosacchaarides
N-linked (N-glycans) are linked via a b-glycosidic bond
O-linked (O-glycans) have a disaccharide core of
galactosyl-b-(1,3)-N-acetylgalactosamine linked via an
a-glycosidic bond to the hydroxyl of serine or threonine
residues
Glycosaminoglycans (GAGs) are linear polymers with
disaccharide repeating units
Five classes: hyaluronic acid, chondroitin sulfate,
dermatan sulfate, heparin and heparin sulfate, and
keratin sulfate
Varying uses based on repeating unit
Section 7.4: Glycoconjugates
Glycoconjugates result from
carbohydrates being linked
to proteins and lipids
Proteoglycans
Distinguished from other
glycoproteins by their high
carbohydrate content (about
95%)
Occur on cell surfaces or
are secreted to the
extracellular matrix
Figure 7.38 Proteoglycan Aggregate
From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press
Section 7.4: Glycoconjugates
Glycoproteins
Commonly defined as proteins that are covalently
linked to carbohydrates through N- and O-linkages
Several addition reactions in the lumen of the
endoplasmic reticulum and Golgi complex are
responsible for final N-linked oligosaccharide structure
O-glycan synthesis occurs later, probably initiating in
the Golgi complex
Carbohydrate could be 1%–85% of total weight
Glycoprotein Functions occur in cells as soluble and
membrane-bound forms and are nearly ubiquitous in
living organisms
Vertebrate animals are particularly rich in
glycoproteins
Section 7.4: Glycoconjugates
Figure 7.39 The Glycocalyx
Section 7.5: The Sugar Code
Living organisms require large coding capacities
for information transfer
Profound complexity of functioning systems
To succeed as a coding mechanism, a class of
molecules must have a large capacity for variation
Glycosylation is the most important
posttranslational modification in terms of coding
capacity
More possibilities with hexasaccharides than
hexapeptides
Section 7.5: The Sugar Code
In addition to their immense combinatorial
possibilities they are also relatively inflexible, which
makes them perfect for precise ligand binding
Lectins
Lectins, or carbohydrate-binding proteins, are
involved in translating the sugar code
Bind specifically to carbohydrates via hydrogen
bonding, van der Waals forces, and hydrophobic
interactions
Section 7.5: The Sugar Code
Lectins Continued
Biological processes
include binding to
microorganisms,
binding to toxins, and
involved in leukocyte
rolling
Figure 7.40 Role of Oligosaccharides in
Biological Recognition
Section 7.5: The Sugar Code
The Glycome
Total set of sugars and glycans in a cell or organism
is the glycome
Constantly in flux depending on the cell’s response
to environment
There is no template for glycan biosynthesis; it is
done in a stepwise process
Glycoforms can result based upon slight variations
in glycan composition of each glycoprotein
Chapter 11
Lipids and Membranes
Section 11.1: Lipid Classes
Figure 11.1 Fatty
Acid Structure
Fatty Acids
Monocarboxylic acids that typically contain
hydrocarbon chains of variable lengths (12 to 20 or
more carbons)
Numbered from the carboxylate end, and the acarbon is adjacent to the carboxylate group
Terminal methyl carbon is denoted the omega (w)
carbon
Important in triacylglycerols and phospholipids
Section 11.1: Lipid Classes
Section 11.1: Lipid Classes
Most naturally occurring fatty acids
have an even number of carbons in an
unbranched chain
Fatty acids that contain only single
carbon-carbon bonds are saturated
Fatty acids that contain one or more
double bonds are unsaturated
Figure 11.2 Isomeric
Forms of Unsaturated
Molecules
Can occur in two isomeric forms: cis
(like groups on the same side) and trans
(like groups are on opposite sides)
Section 11.1: Lipid Classes
Figure 11.3 Space-Filling and
Conformational Models
The double bonds in most naturally occurring fatty
acids are cis and cause a kink in the fatty acid chain
Unsaturated fatty acids are liquid at room
temperature; saturated fatty acids are usually solid
Monounsaturated fatty acids have one double bond
while polyunsaturated fats have two or more
Section 11.1: Lipid Classes
Plants and bacteria can synthesize all fatty acids
they require from acetyl-CoA
Animals acquire most of theirs from dietary sources
Nonessential fatty acids can be synthesized while
essential fatty acids must be acquired from the diet
Omega-3 fatty acids (i.e., a-linolenic acid and its
derivatives) may promote cardiovascular health
Certain fatty acids attach to proteins called acylated
proteins; the groups (acyl groups) help facilitate
interactions with the environment
Myristoylation and palmitoylation
Section 11.1: Lipid Classes
Eicosanoids
Figure 11.4a Eicosanoids
A diverse group of powerful, hormone-like (generally
autocrine) molecules produced in most mammalian
tissues
Include prostaglandins, thromboxanes, and
leukotrienes
Mediate a wide variety of physiological processes:
smooth muscle contraction, inflammation, pain
perception, and blood flow regulation
Section 11.1: Lipid Classes
Figure 11.4a Eicosanoids
Eicosonoids are often derived from arachidonic acid
or eicosapentaenoic acid (EPA)
Prostaglandins contain a cyclopentane ring and
hydroxyl groups at C-11 and C-15
Prostaglandins are involved in inflammation,
digestion, and reproduction
Section 11.1: Lipid Classes
Figure 11.4b Eicosanoids
Thromboxanes differ structurally from other
eicosanoids in that they have a cyclic ether
Synthesized by polymorphonuclear lymphocytes
Involved in platelet aggregation and vasoconstriction
following tissue injury
Section 11.1: Lipid Classes
Figure 11.4c Eicosanoids
Leukotrienes were named from their discovery in
white blood cells and triene group in their structure
LTC4, LTD4, and LTE4 have been identified as
components of slow-reacting substance of anaphylaxis
Other effects of leukotrienes: blood vessel fluid
leakage, white blood cell chemoattractant,
vasoconstriction, edema, and bronchoconstriction
Section 11.1: Lipid Classes
Figure 11.5 Triacylglycerol
Triacylglycerols
Triacylglycerols are esters of glycerol with three fatty
acids
Neutral fats because they have no charge
Contain fatty acids of varying lengths and can be a
mixture of saturated and unsaturated
Section 11.1: Lipid Classes
Depending on fatty acid
composition, can be termed
fats or oils
Figure 11.6 Space-Filling and
Conformational Models of a
Triacylglycerol
Fats are solid at room
temperature and have a high
saturated fatty acid
composition
Oils are liquid at room
temperature and have a high
unsaturated fatty acid
composition
Section 11.1: Lipid Classes
Figure 11.5 Triacylglycerol
Roles in animals: energy storage (also in plants),
insulation at low temperatures, and water repellent
for some animals’ feathers and fur
Better storage form of energy for two reasons:
1. Hydrophobic and coalesce into droplets; store an
equivalent amount of energy in about one-eighth the
space
2. More reduced and thus can release more electrons
per molecule when oxidized
Section 11.1: Lipid Classes
Figure 11.8 The Wax Ester
Melissyl Cerotate
Wax Esters
Waxes are complex mixtures of nonpolar lipids
Protective coatings on the leaves, stems, and fruits
of plants and on the skin and fur of animals
Wax esters composed of long-chain fatty acids and
long-chain alcohols are prominent constituents of
most waxes
Examples include carnuba (melissyl cerotate) and
beeswax
Section 11.1: Lipid Classes
Figure 11.9 Phospholipid
Molecules in Aqueous
Solution
Phospholipids
Amphipathic with a polar head group (phosphate and
other polar or charged groups) and hydrophobic fatty
acids
Act in membrane formation, emulsification, and as a
surfactant
Spontaneously rearrange into ordered structures when
suspended in water
Section 11.1: Lipid Classes
Two types of phospholipids: phosphoglycerides and
sphingomyelins
Sphingomyelins contain sphingosine instead of
glycerol (also classified as sphingolipids)
Phosphoglycerides contain a glycerol, fatty acids,
phosphate, and an alcohol
Simplest phosphoglyceride is phosphatidic acid
composed of glycerol-3-phosphate and two fatty
acids
Phosphatidylcholine (lecithin) is an example of
alcohol esterified to the phosphate group as choline
Section 11.1: Lipid Classes
Section 11.1: Lipid Classes
Another phosphoglyceride,
phosphatidylinositol, is an
important structural
component of glycosyl
phosphatidylinositol (GPI)
anchors
GPI anchors attach
certain proteins to the
membrane surface
Proteins are attached
via an amide linkage
Figure 11.10 GPI Anchor
Section 11.1: Lipid Classes
Figure 11.11 Phospholipases
Phospholipases
Hydrolyze ester bonds in glycerophospholipid
molecules
Three major functions: membrane remodeling, signal
transduction, and digestion
Membrane remodeling—removal of fatty acids to
adjust the ratio of saturated to unsaturated or
repair a damaged fatty acid
Section 11.1: Lipid Classes
Phospholipases Continued
Signal Transduction—phospholipid hydrolysis
initiates the signal transduction by numerous
hormones
 Digestion—pancreatic phospholipases degrade
dietary phospholipids in the small intestine
Toxic Phospholipases—various organisms use
membrane-degrading phospholipases as a means of
inflicting damage
Bacterial a-toxin and necrosis from snake
venom (PLA2)
Section 11.1: Lipid Classes
Figure 11.12 Sphingolipid Components
Sphingolipids
Important components of animal and plant
membranes
Sphingosine (long-chain amino alcohol) and ceramide
in animal cells
Section 11.1: Lipid Classes
Sphingomyelin is found in
most cell membranes, but is
most abundant in the myelin
sheath of nerve cells
Figure 11.13 Space-Filling and
Conformational Models of
Sphingolmyelin
Section 11.1: Lipid Classes
Figure 11.14a Selected
Glycolipids
The ceramides are also precursors of glycolipids
A monosaccharide, disacchaaride, or oligosaccharide
attached to a ceramide through an O-glycosidic bond
Most important classes are cerebrosides, sulfatides,
and gangliosides (may bind bacteria and their toxins)
Section 11.1: Lipid Classes
Figure 11.14b Selected Glycolipids
Cerebrosides have a monosaccharide for their head
group
Galactocerebroside is found in brain cell
membranes
Sulfatides are negatively charged at physiological pH
Gangliosides possess oligosaccharide groups; occur in
most animal tissues and GM2 is involved in Tay-Sachs
disease
Section 11.1: Lipid Classes
Figure 11.15
Isoprene
Isoprenoids
Vast array of biomolecules containing repeating fivecarbon structural units, or isoprene units
Isoprenoids consist of terpenes and steroids
Terpenes are classified by the number of isoprene
units they have
Monoterpenes (used in perfumes), sesquiterpines (e.g.,
citronella), tetraterpenes (e.g., carotenoids)
Section 11.1: Lipid Classes
Figure 11.16 Vitamin K, a
Mixed Terpenoid
Carotenoids are the orange pigments found in plants
Mixed terpenoids consist of a nonterpene group
attached to the isoprenoid group (prenyl groups)
Include vitamin K and vitamin E
Section 11.1: Lipid Classes
Figure 11.17 Prenylated
Proteins
A variety of proteins are covalently attached to prenyl
groups (prenylation): farnesyl and geranylgeranyl
groups
Unknown function, but may be involved in cell
growth
Section 11.1: Lipid Classes
Figure 11.18 Structure
of Cholesterol
Steroids are derivatives of triterpenes with four fused
rings (e.g., cholesterol)
Found in all eukaryotes and some bacteria
Differentiated by double-bond placement and various
substituents
Section 11.1: Lipid Classes
Cholesterol is an important molecule in animal cells
that is classified as a sterol, because C-3 is oxidized to a
hydroxyl group
Essential in animal membranes; a precursor of all
steroid hormones, vitamin D, and bile salts
Usually stored in cells as a fatty acid ester
The term steroid is commonly used to describe all
derivatives of the steroid ring structure
Section 11.1: Lipid Classes
Figure 11.19 Animal Steroids
Section 11.1: Lipid Classes
Lipoproteins
Figure 11.21 Plasma
Lipoproteins
Term most often applied to a
group of molecular complexes
found in the blood plasma of
mammals
Transport lipid molecules
through the bloodstream from
organ to organ
Protein components
(apolipoproteins) for lipoproteins
are synthesized in the liver or
intestine
Section 11.1: Lipid Classes
Lipoproteins are classified according to their density:
Chylomicrons are large lipoproteins of extremely low
density that transport triacylglycerol and cholesteryl
esters (synthesized in the intestines)
Very low density lipoproteins (VLDL) are synthesized
in the liver and transport lipids to the tissues
Low density lipoproteins (LDL) are principle
transporters of cholesterol and cholesteryl esters to
tissues
High density lipoprotein (HDL) is a protein-rich
particle produced in the liver and intestine that seems
to be a scavenger of excess cholesterol from membranes
Section 11.2: Membranes
A membrane is a noncovalent heteropolymer of lipid
bilayer and associated proteins (fluid mosaic model)
Membrane Structure
Proportions of lipid, protein, and carbohydrate vary
considerably among cell types and organelles
Section 11.2: Membranes
Figure 11.25 Lateral
Diffusion in Biological
Membranes
Membrane lipids: phospholipids form bimolecular
layers at relatively low concentrations; this is the
basis of membrane structure
Membrane lipids are largely responsible for many
membrane properties
Membrane fluidity refers to the viscosity of the lipid
bilayer
Rapid lateral movement is apparently responsible for
normal membrane function
Section 11.2: Membranes
The movement of molecules
from one side of a membrane
to the other requires a
flipase
Membrane fluidity largely
depends on the percentage of
unsaturated fatty acids and
cholesterol
Cholesterol contributes
to stability with its rigid
ring system and fluidity
with its flexible
hydrocarbon tail
Figure 11.24 Diagrammatic View of
a Lipid Bilayer
Section 11.2: Membranes
Selective permeability is provided by the hydrophobic
chains of the lipid bilayer, which is impermeable to
most all molecules (except small nonpolar molecules)
Membrane proteins help regulate the movement of
ionic and polar substances
Small nonpolar substances may diffuse down their
concentration gradient
Self-sealing is a result of the lateral flow of lipid
molecules after a small disruption
Asymmetry of biological membranes is necessary for
their function
The lipid composition on each side of the membrane
is different
Section 11.2: Membranes
Figure 11.26 Integral and
Peripheral Membrane Proteins
Membrane Proteins—most functions associated with
the membrane require membrane proteins
Classified by their relationship with the membrane:
peripheral or integral
Section 11.2: Membranes
Figure 11.27 Red Blood Cell
Integral Membrane Proteins
Integral proteins embed in
or pass through the
membrane
Red blood cell anion
exchanger
Peripheral proteins are
bound to the membrane
primarily through
noncovalent interactions
Can be linked covalently
through myristic, palmitic, or
prenyl groups
GPI anchors link a wide
variety of proteins to the
membrane
Section 11.2: Membranes
Figure 11.28 Lipid Rafts
Membrane Microdomains—lipids and proteins in
membranes are not uniformly distributed
Specialized microdomains like “lipid rafts” can be
found in the external leaflet of the plasma membrane
Section 11.2: Membranes
Figure 11.29 The Lipid
Raft Environment
Lipid rafts often include cholesterol, sphingolipids, and
certain proteins
Lipid molecules are more ordered (less fluid) than nonraft regions
Lipid rafts have been implicated in a number of
processes: exocytosis, endocytosis, and signal
transduction
Section 11.2: Membranes
Figure 11.30 Transport
across Membranes
Membrane Function
There are a vast array of membrane functions,
including transport of polar and charged substances
and the relay of signals
Section 11.2: Membranes
Membrane Transport—the mechanisms are vital to
living organisms
Ions and molecules constantly move across the
plasma membrane and membranes of organelles
Important for nutrient intake, waste excretion,
and the regulation of ion concentration
Biological transport mechanisms are classified according
to whether they require energy
Section 11.2: Membranes
Figure 11.30 Transport
across Membranes
In passive transport, there is no energy input, while
in active transport, energy is required
Passive is exemplified by simple diffusion and
facilitated diffusion (with the concentration gradient)
Active transport uses energy to transport molecules
against a concentration gradient
Section 11.2: Membranes
Simple diffusion involves the propulsion of each solute
by random molecular motion from an area of high
concentration to an area of low concentration
Diffusion of gases O2 and CO2 across membranes is
proportional to their concentration gradients
Does not require a protein channel
Facilitated diffusion uses channel proteins to move
large or charged molecules down their concentration
gradient
Examples include chemically gated Na+ channel
and voltage-gated K+ channel
Section 11.2: Membranes
Figure 11.31 The Na+-K+ ATPase
and Glucose Transport
Active transport has two forms: primary and secondary
In primary active transport, transmembrane ATPhydrolyzing enzymes provide the energy to drive the
transport of ions or molecules
Na+-K+ ATPase
Section 11.2: Membranes
Figure 11.31 The Na+-K+ ATPase
and Glucose Transport
In secondary active transport, concentration
gradients formed by primary active transport are
used to move other substances across the membrane
Na+-K+ ATPase pump in the kidney drives the
movement of D-glucose against its concentration
gradient
Section 11.2: Membranes
Membrane Receptors provide mechanisms by
which cells monitor and respond to changes in their
environment
Chemical signals bind to membrane receptors in
multicellular organisms for intracellular
communication
Other receptors are involved in cell-cell recognition
Binding of ligand to membrane receptor causes a
conformational change and programmed response
Chapter 17
Nucleic Acids
Section 17.1: DNA
Figure 17.2 Two Models of
DNA Structure
Scientists have studied how organisms organize and
process genetic information, revealing the following
principles:
1. DNA directs the function of living cells and is
transmitted to offspring
DNA is composed of two polydeoxynucleotide strands
forming a double helix
Section 17.1: DNA
Figure 17.2 Two Models of
DNA Structure
A gene is a DNA sequence that contains the base
sequence information to code for a gene product,
protein, or RNA
The complete DNA base sequence of an organism is its
genome
DNA synthesis, referred to as replication, involves
complementary base pairing between the parental and
newly synthesized strand
Section 17.1: DNA
2. The synthesis of RNA
begins the process of decoding
genetic information
Figure 17.3a An Overview of
Genetic Information Flow
RNA synthesis is called
transcription and involves
complementary base pairing
of ribonucleotides to DNA
bases
Each new RNA is a
transcript
The total RNA transcripts
for an organism comprise its
transcriptome
Section 17.1: DNA
3. Several RNA molecules
participate directly in the
synthesis of protein, or
translation
Figure 17.3b An Overview of
Genetic Information Flow
Messenger RNA (mRNA)
specifies the primary
protein sequence
Transfer RNA (tRNA)
delivers the specific amino
acid
Ribosomal RNA (rRNA)
molecules are components
of ribosomes
Section 17.1: DNA
The proteome is the entire
set of proteins synthesized
4. Gene expression is the
process by which cells
control the timing of gene
product synthesis in
response to environmental
or developmental cues
Figure 17.3b An Overview of
Genetic Information Flow
Metabolome refers to the
sum total of low molecular
weight metabolites
produced by the cell
Section 17.1: DNA
The Central dogma schematically summarizes the
previous information
Includes replication, transcription, and
translation
The central dogma is generally how the flow of
information works in all organisms, except some
viruses have RNA genomes and use reverse
transcriptase to make DNA (e.g., HIV)
DNA
RNA
Protein
Section 17.1: DNA
DNA consists of two
polydeoxynucleotide strands
that wind around each other to
form a right-handed double
helix
Each DNA nucleotide
monomer is composed of a
nitrogenous base, a deoxyribose
sugar, and phosphate
Figure 17.4 DNA Strand Structure
Section 17.1: DNA
Nucleotides are linked by 3′,5′phosphodiester bonds
These join the 3′-hydroxyl of
one nucleotide to the 5′phosphate of another
Figure 17.4 DNA Strand Structure
Section 17.1: DNA
Figure 17.5 DNA Structure
The antiparallel nature of the two strands allows
hydrogen bonds to form between the nitrogenous bases
Two types of base pair (bp) in DNA: (1) adenine
(purine) pairs with thymine (pyrimidine) and (2) the
purine guanine pairs with the pyrimidine cytosine
Section 17.1: DNA
Figure 17.6 DNA Structure:
GC Base Pair Dimensions
The dimensions of
crystalline B-DNA have
been precisely measured:
1. One turn of the double
helix spans 3.32 nm and
consists of 10.3 base pairs
Section 17.1: DNA
Figure 17.6 DNA Structure:
AT Base Pair Dimensions
2. Diameter of the double
helix is 2.37 nm, only
suitable for base pairing a
purine with a pyrimidine
3. The distance between
adjacent base pairs is
0.29-0.30 nm
Section 17.1: DNA
DNA is a relatively stable molecule with several noncovalent
interactions adding to its stability
1. Hydrophobic interactions—internal base clustering
2. Hydrogen bonds—formation of preferred bonds: three
between CG base pairs and two between AT base pairs
3. Base stacking—bases are nearly planar and stacked,
allowing for weak van der Waals forces between the rings
4. Hydration—water interacts with the structure of DNA
to stabilize structure
5. Electrostatic interactions—destabilization by
negatively charged phosphates of sugar-phosphate
backbone are minimized by the shielding effect of water
on Mg2+
Section 17.1: DNA
Mutation types—The most common are small single
base changes, also called point mutations
This results in transition or transversion
mutations
Transition mutations, caused by deamination, lead to
purine for purine or pyrimidine for pyrimidine
substitutions
Transversion mutations, caused by alkylating agents
or ionizing radiation, occur when a purine is
substituted for a pyrimidine or vice versa
Section 17.1: DNA
Point mutations that occur in a population with any
frequency are referred to as single nucleotide
polymorphisms (SNPs)
Point mutations that occur within the coding portion
of a gene can be classified according to their impact on
structure and/or function:
Silent mutations have no discernable effect
Missense mutations have an observable effect
Nonsense mutations changes a codon for an amino
acid to that of a premature stop codon
Section 17.1: DNA
Insertions and deletions, or indels, occur from one to
thousands of bases
Indels that occur within the coding region that are
not divisible by three cause a frameshift mutation
Genome rearrangements can cause disruptions in
gene structure or regulation.
Occur as a result of double strand breaks and can
lead to inversions, translocations, or duplications
Section 17.1: DNA
DNA Structure: The Genetic Material
In the early decades of the twentieth century, life
scientists believed that of the two chromosome
components (DNA and protein) that protein was most
likely responsible for transmission of inherited traits
The work of several scientists would lead to another
conclusion
Section 17.1: DNA
DNA Structure: Variations on a
Theme
Figure 17.12 A-DNA, B-DNA,
and Z-DNA
Watson and Crick’s discovery is
referred to as B-DNA (sodium
salt)
Another form is the A-DNA,
which forms when RNA/DNA
duplexes form
Z-DNA (zigzag conformation) is
left-handed DNA that can form
as a result of torsion during
transcription
Section 17.1: DNA
DNA can form other structures, including
cruciforms, which are cross-like structures, probably
a result of palindromes (inverted repeats)
Packaging large DNA molecules to fit inside a cell or
nucleus requires a process termed supercoiling
Section 17.1: DNA
DNA Supercoiling
Facilitates several
biological processes:
packaging of DNA,
replication, and
transcription
Linear and circular DNA
can be in a relaxed or
supercoiled shape
Figure 17.13 Linear and Circular DNA
and DNA Winding
Section 17.1: DNA
Chromosomes and Chromatin
Figure 17.17 The E. coli
Chromosome Removed
from a Cell
DNA is packaged into
chromosomes
Prokaryotic and eukaryotic
chromosomes differ significantly
Prokaryotes—the E. coli
chromosome is a circular DNA
molecule that is extensively
looped and coiled
Supercoiled DNA complexed
with a protein core
Section 17.1: DNA
Eukaryotes have extraordinarily
large genomes when compared to
prokaryotes
Figure 17.18 Electron
Micrograph of Chromatin
Chromosome number and length
can vary by species
Each eukaryotic chromosome
consists of a single, linear DNA
molecule complexed with histone
proteins to form nucleohistone
Chromatin is the term used to
describe this complex
Section 17.1: DNA
Figure 17.18 Electron
Micrograph of Chromatin
Nucleosomes are formed by the
binding of DNA and histone proteins
Nucleosomes have a beaded
appearance when viewed by
electron micrograph
Histone proteins have five major
classes: H1, H2A, H2B, H3, and H4
A nucleosome is positively coiled
DNA wrapped around a histone core
(two copies each of H2A, H2B, H3,
and H4)
Section 17.1: DNA
Prokaryotic Genomes—Investigation of E. coli has
revealed the following prokaryotic features:
1. Genome size—usually considerably less DNA and
fewer genes (E. coli 4.6 megabases) than eukaryotic
genomes
2. Coding capacity—compact and continuous genes
3. Gene expression—genes organized into operons
Prokaryotes often contain plasmids, which are usually
small and circular DNA with additional genes (e.g.,
antibiotic resistance)
Section 17.1: DNA
Eukaryotic Genomes—Investigation has revealed the
organization to be very complex
The following are unique eukaryotic genome features:
1. Genome size—eukaryotic genome size does not
necessarily indicate complexity
2. Coding capacity—enormous protein coding capacity,
but the majority of DNA sequences do not have coding
functions
3. Coding continuity—genes are interrupted by
noncoding introns, which can be removed by splicing
from the primary RNA transcript
Section 17.1: DNA
Existence of introns and exons allows eukaryotes to
produce more than one polypeptide from each proteincoding gene
Alternative splicing allows for various combinations of
exons to be joined to form different mRNAs
Intergenic sequences are those sequences that do not
code for polypeptide primary sequence or RNAs
Section 17.1: DNA
Of the 3,200 Mb of the human genome, only 38%
comprise genes and related sequence
Only 4% codes for gene products
Humans have about 23,000 protein coding
genesand several ncRNA genes
Section 17.1: DNA
Figure 17.24 Human
Protein-Coding Genes
25% of known proteincoding genes are related to
DNA synthesis and repair
21% signal transduction
17% general biochemical
functions
38% other activities
Over 60% of the human
genome is intergenic sequences
Section 17.1: DNA
Two classes: tandem repeats and interspersed genomewide repeats
Tandem repeats (satellite DNA) are DNA sequences
in which multiple copies are arranged next to each
other
Certain tandem repeats play structural roles
like centromeres and telomeres
Some are small, like microsatellites (1-4 bp) and
minisatellites (10-100 bp)
Used as markers in genetic disease, forensic
investigations, and kinship
Section 17.1: DNA
Interspersed genome-wide repeats are repetitive
sequences scattered around the genome
Often involve mobile genetic elements that can
duplicate and move around the genome
Transposons and retrotransposones
LINEs (long interspersed nuclear elements) and
SINEs (short interspersed nuclear elements) are
two types of transposons
Section 17.2: RNA
RNA is a versatile molecule, not
only involved in protein
synthesis, but plays structural
and enzymatic roles as well
Differences between DNA and
RNA primary structure:
Figure 17.25 Secondary
Structure of RNA
1. Ribose sugar instead of
deoxyribose
2. Uracil nucleotide instead of
thymine
Section 17.2: RNA
3. RNA exists as a single strand
that can form complex threedimensional structures by base
pairing with itself
4. Some RNA molecules have
catalytic properties, or ribozymes
(e.g., self-cleavages or cleave other
RNA)
Figure 17.25 Secondary
Structure of RNA
Section 17.2: RNA
Transfer RNA
Transfer RNA (tRNA) molecules
transport amino acids to ribosomes
for assembly (15% of cellular RNA)
Average length: 75 bases
Figure 17.26a Transfer RNA
At least one tRNA for each amino
acid
Structurally look like a warped
cloverleaf due to extensive
intrachain base pairing
Section 17.2: RNA
Amino acids are attached via
specific aminoacyl-tRNA
synthetases to the end
opposite the three nucleotide
anticodon
Figure 17.26b Transfer RNA
Anticodon allows the tRNA
to recognize the correct
mRNA codon and properly
align its amino acid for
protein synthesis
The tRNA loops help
facilitate interactions with
the correct aminoacyl-tRNA
synthetases
Section 17.2: RNA
Ribosomal RNA
Ribosomal RNA (rRNA) is the most abundant RNA
in living cells with a complex secondary structure
Components of ribosomes (eukaryotes and
prokaryotes)
Similar in shape and function, both have a small and
large subunit, but differ in size and chemical
composition
Eukaryotic are larger (80S) with a 60S and 40S
subunit, while prokaryotic are smaller (70S) with 50S
and 30S subunits
Section 17.2: RNA
Figure 17.27 rRNA Structure
rRNA plays a role in scaffolding as well as enzymatic
functions
Ribosomes also have proteins that interact with rRNA
for structure and function
Section 17.2: RNA
Messenger RNA
Messenger RNA (mRNA) is the carrier of genetic
information from DNA to protein synthesis
(approximately 5% of total RNA)
mRNA varies considerably in size
Prokaryotic and eukaryotic mRNA differ in several
respects
Prokaryotes are polycistronic while eukaryotes are
usually monocistronic
mRNAs are processed differently; eukaryotic mRNA
requires 5′ capping, 3′ tailing, and splicing
Section 17.2: RNA
Noncoding RNA
RNAs that do not directly code for polypeptides are
called noncoding RNAs (ncRNAs)
Micro RNAs and small interfering RNAs are among
the shortest and involved in the RNA-induced
silencing complex
Small Nucleolar RNAs (snoRNAs) facilitate chemical
modifications to rRNA in the nucleolus
Section 17.2: RNA
Noncoding RNA
Small interfering RNAs (siRNAs) are 21-23 nt
dsRNAs that play a crucial role in RNA interference
(RNAi)
Small nuclear RNAs (snRNAs) combine with proteins
to form small nuclear ribonucleoproteins (snRNPs)
and are involved in splicing
Section 17.3: Viruses
Viruses lack the properties that distinguish life
from nonlife (e.g., no metabolism)
Once a virus has infected a cell, its nucleic acid can
hijack the host’s nucleic acid and proteinsynthesizing machinery
The virus can then make copies of itself until it
ruptures the host cell or integrates into the host cell’s
chromosome
Section 17.3: Viruses
A viral infection can provide biochemical insight,
because it subverts the host cell’s function
Viruses can cause numerous different diseases, but
have also been invaluable in the development of
recombinant DNA technology
Human papillomavirus can cause cervical cancer