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Organic Molecules
Chapter 3
2-
Carbon: The Central Atom


Carbon is the central
atom in all organic
molecules.
Carbon has unique
bonding properties.
–
–
3-
Can combine with other
carbon atoms in long
chains
Can form ring structures
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Carbon: The Central Atom

Carbon atoms
participate in four
covalent bonds.
–
–
–
3-
Has four electrons in the
outer energy level
Can double bond with
oxygen
Can triple bond with
other carbon atoms
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Organic Molecules

Organic Molecules
–
–
–

Some Inorganic molecules are incorporated
as well
–
3-
Composed of Carbon and Hydrogen
Elements Nitrogen, Oxygen, Phosphate, Sulfur
also included in small amounts as trace elements
These six elements compose 98.5% of body
weight (Saladin, 5th ed.)
The Heme group in Hemoglobin contains Fe, for
example
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Biochemistry

The study of the chemistry of living things

4 Classes of Biological Molecules
1. Carbohydrates
2. Nucleic Acids
3. Proteins
4. Lipids

3-
The Classes are determined by the
proportions of C, H, O in the molecule
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Organic Molecules
Organic molecules are composed of:
1. A Central Carbon or Carbon Chain
2. Functional Groups
3-
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The Carbon Skeleton

All organic molecules have a carbon skeleton.
–

This determines the overall shape of the molecule.
Organic molecules differ in these ways:
–
–
–
The length and arrangement of the carbon skeleton
The kinds and location of atoms attached to it
How the attached atoms are combined together


3-
These combinations are called functional groups.
Functional groups determine the chemical nature of the
molecule.
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Organic Molecules

The carbon chain backbone of a molecule or
Carbon Skeleton:
–CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3

3-
Recall: Carbon makes 4 covalent bonds
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Functional Groups
3-

Functional Groups are specific combinations
of bonded atoms attached to a Carbon
Skeleton

The Functional Groups determine the
chemistry of the molecule

Functional groups behave in chemically
predictable ways
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Functional Groups
3-
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Isomers

Several factors determine the properties of an
organic molecule.
–
–

The types of atoms in the molecule
The 3-D arrangement of atoms within the molecule
Organic molecules can have the same number and
composition of atoms, but can have different
arrangements.
–
These are called isomers.

3-
Molecules with the same empirical formula but different
structural formulas
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Isomers
Pentose
C5H10O5
empirical formula
Hexose
C6H12O6
empirical formula
67
Hexose Isomers
3-
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Macromolecules of Life


Macromolecules are very large organic
molecules.
Most important organic compounds found in
living things are large macromolecules
–
–
–
–
3-
Carbohydrates
Proteins
Nucleic acids
Lipids
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Macromolecules


Biological molecules are typically
Marcomolecules
Very large molecules with high molecular
weights
–

Macromolecules are Polymers assembled
from smaller Monomers
–
–
3-
DNA over a meter long
Monomers - small, identical or similar subunits
Polymers - covalently bonded monomers
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Polymers
• Proteins - amino acid monomers polymerize to
form proteins
• Nucleic acids - nucleotide monomers polymerize
to form DNA and RNA Macromolecules
• Carbohydrates:
•Simple sugar monomers polymerize to form complex sugars
•Monosaccharides polymerize to form disaccharides,
polysaccharides
3-
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Polymerization




3-
The joining monomers to form a polymer
Dehydration Synthesis - the chemical
reaction for how living cells form polymers
A bond is formed between monomers and
water is produced as a product of the
reaction
As the name implies, water is lost during the
reaction
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Dehydration Synthesis
3-

A hydroxyl (-OH) group is removed from one
monomer, and a hydrogen (H+) from another

A new covalent bond is formed between the
monomers

Water is released as a by-product
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Dehydration Synthesis
3-
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Hydrolysis

The reaction for the separation of joined
monomers
–

Opposite of dehydration synthesis
–
–
–
3-
“Splitting with water”
a water molecule ionizes into –OH and H+
the covalent bond linking one monomer to the
other is broken
the –OH is returned to one monomer, the H+ is
returned to the other
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Hydrolysis
3-
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 1.
Carbohydrates
 Sugars
3-
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Carbohydrates





Organic molecules composed of carbon, hydrogen
and oxygen
All follow the general formula CH2O
Names end in –ose
Serve as the primary energy source for most living
things
Also serve as structural support
–

Important components of nucleic acids
–
3-
Plant cell walls
DNA and RNA
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Carbohydrates

Sugars, Starches, Fibers

Names of carbohydrates often built from:
–
–
–

3-
word root ‘sacchar-’
the suffix ’-ose’
both mean ‘sugar’ or ‘sweet’
Monosaccharide or Glucose
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Carbohydrates

Carbohydrates are composed of carbon
backbones with Hydroxyl Groups and a
Carboxyl Group
–
–
3-
R-OH
R-COOH

The carbon backbone may be a in straight
line or a closed ring of carbon atoms

Polar and therefore Hydrophilic Molecules
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Carbohydrates
60
Carbohydrates

The Proportions of C, H, and O for
Carbohydrates follow the General Formula:
–
–


3-
CnH2nOn
n = number of carbon atoms
For glucose, n = 6, so formula is C6H12O6
2:1 ratio of hydrogen to oxygen
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Simple Sugars

Simple sugars are described by the number
of carbons in the molecule.
–
–
–

Common names of simple sugars:
–
–
–
3-
Triose-3 carbons
Pentose-5 carbons
Hexose-6 carbons
Glucose
Fructose
Galactose
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Simple Sugars

Numbering the C’s
–

For Example:
–

3-
Carbohydrates are classified by the number of
Carbon atoms they contain
Ribose is a pentose sugar because it contains 5
carbon atoms. Glucose is a hexose sugar
because it contains 6 carbon atoms
Many Carbohydrates have informal names
that do not provide information about the
molecule
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Simple Sugars

Numbering the Carbons
–

The Carbons of Carbohydrates are
numbered

For Example:
–
–
3-
Numbering System allows the molecules to be
described efficiently
Describing locations of covalent bonds
Ribose vs 2’ Deoxy-ribose
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Carbohydrate Structure
Numbering the Carbons
Ribose vs. 2 Deoxyribose
• Ribose
• 2’ Deoxyribose
7
Simple Sugars
32
Simple Sugars

There are over 200 different monosaccharides

Monosaccharides differ in the number of
carbon atoms they contain in the C-C
backbone (Ex. hexose vs. pentose)

Monosaccharides also differ in their 3-D shape
–
3-
Isomers
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Isomers of Monosaccharides
Pentose
C5H10O5
empirical formula
Hexose
C6H12O6
empirical formula
67
Functions of Monosaccharides

Energy Source
–
–
–

efficiently oxidized for energy
the C-H bonds are high in energy
the C-H bonds are oxidized
Most Important example:
–
Glucose in Cellular Respiration
C6H12O6 + 6O2
 Glucose Oxygen

3-
6H2O + 6CO2 +Energy
Water Carbon Dioxide
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Complex Carbohydrates

When two or more simple sugars are
combined, they form complex carbohydrates.
–

Formed via dehydration synthesis
Disaccharides
–
Two simple sugars



3-
Sucrose
Lactose
Maltose
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Polysaccharides

Structure
–

Functions
–
–
–
3-
Multiple Monosaccharides linked together
1. Structural Molecules
2. Signaling Molecules
3. Energy Storage
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Polysaccharides


Contain many simple sugars
Examples of polysaccharides:
–
Starch and glycogen

–
Used for energy storage in plants (starch) and animals
(glycogen)
Cellulose


Important component of plant cell walls
Humans cannot digest cellulose; it is the fiber in our diet.
–
Helps facilitate movement of food through the digestive
tract
–
3-
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Complex Carbohydrates
3-
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Glycogen
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CH2OH
O
O
O
O
CH2OH
O
CH2OH
O
CH2
O
(a)
CH2OH
O
O
CH2OH
O
O
O
O
O
(b)
Figure 2.18
2-73
Glycogen
Stryer's Biochemistry Fig. 23-2
82
Complex Carbohydrates

Starch: energy storage polysaccharide in
plants

Cellulose: structural molecule of plant cell
walls
–
3-
fiber in our diet
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Complex Carbohydrates

Conjugated carbohydrates – covalently
bound to lipid or protein
–
glycolipids

–
glycoproteins


3-
external surface of cell membrane
external surface of cell membrane
mucus of respiratory and digestive tracts
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Viral Bioinformatics Resource Center
athena.bioc.uvic.ca/.../copy9_of_sample/surface
24
 2.
Amino Acids
 Proteins
3-
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Amino Acids

Protein - a polymer of amino acids
–
3-
Amino acids - the monomers of proteins

20 Amino acids are used to construct
proteins

Peptide Bonds are the covalent bonds
between adjacent amino acids
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Protein Functions

Structure
–
–

Communication
–
–
3-
keratin – tough structural protein gives strength to
hair, nails, and skin surface
collagen – durable protein contained in deeper
layers of skin, bones, cartilage, and teeth
some hormones and other cell-to-cell signals
receptors to which signal molecules bind
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Protein Functions

Membrane Transport
–


3-
channels in cell membranes
carrier proteins – transports solute particles
to other side of membrane
turn nerve and muscle activity on and off
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Protein Functions

Catalysis
–

Recognition and Protection
–
–
–
3-
enzymes
immune recognition
antibodies
clotting proteins
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Protein Functions

Movement
–




3-
motor proteins - molecules with the ability to
change shape repeatedly
Cell adhesion
proteins bind cells together
immune cells to bind to cancer cells
keeps tissues from falling apart
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Amino Acid Structure

A Central carbon with 4 attachments:
1. amino group (NH2)
2. carboxyl group (COOH)
3. radical group (R group)
4. hydrogen

3-
Properties of amino acid determined by the
-R group
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Amino Acid Structure
3-
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Amino Acid Structure
3-

By definition, all amino acids have the amine
and carboxyl functional groups in common

Amino differ in the side chains

Different side chains (-R Groups) give amino
acids different chemical properties (for
example, some amino acids are hydrophobic,
some are hydrophilic)
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Representative Amino Acids
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Some nonpolar amino acids
Some polar amino acids
Methionine
H
Cysteine
H
H
N
N
C
H
CH2
CH2
S
C
H
CH3
O
OH
O
Tyrosine
H
SH
H
H
C
OH
Arginine
N
H
N
CH2
OH
H
C
O
CH2
C
C
H
H
C
NH2+
(CH2)3
O
C
NH2
C
OH
NH
Figure 2.23a
OH
(a)
• Note: they differ only in the R group
2-86
Amino Acid Structure

The structure of the R group dictates the
chemical properties of the amino acid.

Amino acids can be classified as:
–
–
–
–
–
3-
1. nonpolar
2. polar
3. charged
4. aromatic
5. special functions (acidic, basic)
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Fig. 3.20
Peptides

Peptide – any molecule composed of two or
more amino acids joined by peptide bonds
–
–

Peptides
–
–
–
3-
Peptide Bond – joins the amino group of one
amino acid to the carboxyl group of the next
formed by dehydration synthesis
–
dipeptides have 2
oligopeptides have fewer than 10 to 15
polypeptides have more than 15
proteins have more than 50
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Peptide Bonds
3-

Amino acids are joined together into
polypeptide chains through a
DEHYDRATION REACTION

Similarly, Polypeptide chains are cleaved
apart through a HYDROLYSIS REACTION
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Amino Acid Polymerization
59
Amino Acid Polymerization
3-
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The Formation of a Peptide Bond
Dehydration Reaction:
The loss of water
Hydrolysis Reaction
Hydrolysis Reaction:
The Bond is Cleaved with
water
H2O
Find the Peptide Bond
Peptide Bond
Terminal Animo Group
Side Chain
Carboxyl Group
Peptide
Bond
Amino Group
Side Chain
Protein Structure and Shape

Protein properties and functions depend on
Protein Conformation
–


3-
Conformation – unique three dimensional shape
of protein crucial to function
Because of unique conformations, proteins
are very specific to their functions
Protein conformation depends on the
environment
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Protein Structure and Shape

Four Level of Protein Structure
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
3-
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1. Primary Structure



3-
The sequence of amino acids in a polypeptide
constitutes the primary structure of the protein.
This sequence is dictated by information in genes
(DNA).
All levels of protein structure depend on the primary
sequence.
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2. Secondary Structure

Polypeptides twist and fold into
their secondary structure.
–
Some sequences of amino
acids twist into a helix.

–
Some sequences of amino
acids remain straight and fold
back on themselves.


3-
This is called an alpha helix.
This is called a beta-pleated
sheet.
Held in place by bonds between Rgroups within the polypeptide chain
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Fig. 3.21a
Fig. 3.22-2
Fig. 3.22-3
3. Tertiary Structure



3-
3-D shape of protein
The various alpha
helices and beta
pleated sheets interact
to form a globular
structure.
This globular structure
is unique for each
polypeptide.
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Fig. 3.22-4
4. Quaternary Structure


Some proteins contain more
than one polypeptide chain.
Each of these polypeptides
has its own unique tertiary
structure.
–

3-
These polypeptides interact
to form a more complex
globular structure.
Quaternary structure can be
stabilized by disulfide bonds.
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Fig. 3.22
Form and Function



The protein’s overall shape
determines its job.
If a protein is not shaped
properly, it likely will not work
properly.
Example:
–
–
–

Denaturation:
–
3-
Sickle cell anemia
A mutation in the gene causes
the protein to have a different
shape.
This shape change results in a
change in function.
When heat or other
environmental conditions break
the bonds that stabilize tertiary
structure.
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Types of Proteins

Structural proteins
–
–

Regulatory proteins
–
–

Determine what activities will occur in a protein
Enzymes and hormones
Carrier proteins
–
3-
Important in maintaining the shape of cells and
organisms
Collagen
–
Transport molecules from one place to another
Lipoproteins
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Enzymes

Enzymes - special class of proteins that
functions as biological catalysts
–

facilitate chemical reactions
The Rules to be an Enzyme
1. It is a protein molecule that speeds up a chemical
reaction
2. Enzymes are not changed during the reaction
3. Enzymes can be re-used many times
3-
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 3.
Nucleic Acids
 DNA
3-
and RNA
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Nucleic Acids




The largest biological
molecules
Store and transfer
information within a cell
Include DNA and RNA
Are made of
nucleotides
–
–
–
3-
5-carbon sugar
Phosphate group
Nitrogenous group
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Nucleotides
3-
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Nucleic Acids

DNA = Deoxyribonucleic Acid
–

RNA = Ribonucleic Acid
–
–
3-
Function to store, transport, and control hereditary
information
carries out genetic instruction for synthesizing
proteins
assembles amino acids in the right order to
produce proteins
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Nucleic Acids
3-

Nucleic Acids are composed of Carbon,
Hydrogen, Oxygen, Nitrogen and
Phosphorous atoms

Nucleotides are the building blocks of
nucleic acids (DNA and RNA) and ATP
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Nucleotides

3 components of nucleotides
1. Nitrogenous base
2. Ribose Sugar (monosaccharide)
3. Phosphate groups
3-
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Nucleotides
3-
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Nucleotides - Nitrogenous Base

3-
There are 5 different Nitrogenous Bases to
choose from when building Nucleic Acids:
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Nucleotides - Nitrogenous
Base
87
Nucleotides - Nitrogenous Base
3-
• DNA is composed
• RNA is composed of
of the Nitrogenous
Bases: Thymine,
Cytosine, Adenine,
and Guanine
the Nitrogenous Bases:
Uracil, Cytosine,
Adenine, and Guanine
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Nucleotides - Ribose Sugar

The Nucleotides of DNA
–
–
3-
The name,
Deoxyribonucleic Acid,
tells us the structure of
the ribose sugar in the
Nucleotides of DNA
It lacks a hydroxyl group
at C2
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Nucleotides - Ribose Sugar

The Nucleotides of RNA
–
3-
The name, Ribonucleic
acid, tells us the
structure of the ribose
sugar in the RNA
Nucleotides
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Nucleotides - Phosphate Group
3-

Both The Phosphate Group and the
Nitrogenous Base attach to the central
Ribose Sugar

The Phosphate Group is important in forming
the “Backbone” of the Nucleic Acid Molecule
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The Phosphate Group of Nucleotides
158
Polymerization of Nucleotides to
Make Nucleic Acids



3-
Nucleotides are covalently bound together
into long strands through a Dehydration
Reaction
The Phosphate of one Nucleotide is bound to
the Ribose Sugar of an adjacent nucleotide
These Phosphate-Ribose bonds form the
backbones of the Nucleic Acid Molecules
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The Backbone is formed by multiple C3C5 phospho-ribose linkages
160
The Backbone is formed by multiple C3C5 phospho-ribose linkages
161
DNA Molecular Structure


Two DNA strands are united by
hydrogen bonds to form the doublehelix
DNA base pairing
–
–

Law of Complementary Base Pairing
–
3-
A – T with 2 hydrogen bonds
C – G with 3 hydrogen bonds
One strand serves as the template for the
complementary strand
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The Structure of DNA
3-
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Complementary Base Pairing
164
Fig. 3.16-1
Nucleic Acids
100
DNA

DNA stores the genetic code for constructing
proteins
–

Genes
–
3-
the code is stored in the order of nitrogenous bases
along a single stand
Each segment of DNA that codes for a protein is known
as a gene.
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DNA and Chromosomes
3-

Each DNA strand has many genes.

Each DNA strand (molecule) is called a
chromosome.

Human cells have 46 chromosomes in each
cell
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The Functions of DNA

DNA is able to:
–
–
–
–
3-
Replicate itself
Store information and transmit it to offspring
Direct synthesis of proteins
Mutate (change chemically)
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RNA


RNA is a single-stranded molecule.
Base pairs with itself and DNA
–
–

RNA is found in three different forms:
–
–
–

3-
A-U
G-C
mRNA (messenger RNA)
rRNA (ribosomal RNA)
tRNA (transfer RNA)
RNA functions in the decoding of DNA and the
construction of proteins
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The Functions of DNA
3-
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DNA vs. RNA
3-
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Other Nucleotide Molecules

ATP: Adenosine triphosphate
–

NAD+ and FAD
–
3-
primary energy currency of the cell
electron carriers for many cellular reactions
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 4.
Lipids
 Fats
3-
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Lipids


Commonly called fats
Large and nonpolar
–
–

Composed of C, H, O
–

Do not dissolve in water
Dissolve in other nonpolar molecules like acetone
Contain fewer oxygen atoms than carbohydrates
There are three main types of lipids:
1. True fats (Triglycerides)
2. Phospholipids
3. Steroids
3-
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1. True Fats (Triglycerides)

Function:
– energy source

Structure:
1. A glycerol molecule
2. Three fatty acids
3-
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1. True Fats (Triglycerides)

Composed of 2 Parts:
1. Glycerol Molecule
2. Three Fatty Acids (tri)

3 fatty acids covalently bonded to a
glycerol molecule
–
–
3-
each bond formed by dehydration synthesis
broken down by hydrolysis
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1. True Fats (Triglycerides)

Glycerol is a 3 carbon molecule with 3
hydroxyl groups
–
3-
One, two, or three fatty acids can bind at the
locations of the Hydroxyl Groups to form a lipid
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1. True Fats (Triglycerides)

Fatty Acids are chains of 4 to 24 carbon
atoms
–
There is a carboxyl group on one end of the chain

–
There is a methyl group on the other end of the
chain

–
3-
-COOH
-CH3
Hydrogen atoms bonded along the side
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Fatty Acids
• Chain of 4 to 24 carbon atoms
– carboxyl group on one end, methyl group on the
other and hydrogen bonded along the side
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
H
HO
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Figure 2.19
2-77
Triglyceride Synthesis
Glycerol + 3 Fatty Acids
A Triglyceride + 3H2O
A Dehydration Rxn.
96
Fatty Acids

Classes of Fatty Acids
1. Saturated - carbon chains are saturated with
hydrogen
2. Unsaturated - carbon chains contain C=C bonds
3. Polyunsaturated – contains many C=C bonds
3-
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Saturated and Unsaturated
Fatty Acids
3-
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Saturated and Unsaturated
Fatty Acids
87
Saturated and Unsaturated
Fatty Acids




3-
The Saturation or Unsaturation of the Fatty Acids affects the
properties of the lipid
Unsaturations put “kinks” in the fatty acids
Kinks in the fatty acids prevent them from stacking together,
making them less stable solids
Unsaturated Fats are usually liquids at room temperature –
plant fats Copyright
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Saturated and Unsaturated
Fatty Acids



3-
Saturated fats are not kinked
They stack together making the lipid more
stable solids
Saturated Fats are usually solid at room
temperature – animal fats and waxes
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Saturation
• Saturated Fatty Acids
• Unsaturated Fatty Acids
94
2. Phospholipids

3-
Similar to triglycerides
except that one fatty
acid is replaced by a
phosphate group on
the glycerol
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3. Phospholipids
• Phospholipids are Amphiphilic molecules
– fatty acid “tails” are hydrophobic
– phosphate “head” is hydrophilic
Polar Head Group
Nonpolar Hydrocarbon Tail
101
2. Phospholipids




3-
Phospholipids form droplets or
lipid bilayers in water
The hydrophobic tail regions of
the phospholipid move toward the
inside of the droplets
The hydrophilic head regions are
exposed to the water environment
Phospholipids form cell
membranes
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Phospholipid droplet in
water
125
Phospholipid bilayer in
water
126
4. Steroids


Composed of 4 carbon rings
Steroids are important components of cell
membranes.
–

Steroids often serve as hormones and serve in
regulation of body processes.
–
3-
Cholesterol
Testosterone, estrogen
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Overview
3-
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