Biochemistry
Chemical Building Blocks of Life
Carbon Compounds and Life
Aside from water, living organisms
consist mostly of carbon-based
compounds
 Carbon is unparalleled in its ability to
form large, complex, and diverse
molecules
 A compound containing carbon is said to
be an organic compound
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Carbon Bonding

All compounds can be classified into 2 broad
categories
Organic Compounds:
 Inorganic
are made primarily of
Compounds: do not
carbon atoms
contain carbon atoms
 Most matter in living
(with a few
organisms that is not
exceptions)
water is made of
organic compounds
Carbon is so interesting…it could have a whole
branch of chemistry by itself (2 Reasons)
1.


They have 4 valence electrons
each e- can join with an e- from
another atom to form a strong
covalent compound
Can bond with many elements
including H, O, P, S, & N
Carbon is so interesting…it could have a whole
branch of chemistry by itself (2 Reasons)
2. They can bond to another carbon atom
 A. Gives the ability to form straight
chains, branched chains, or rings
 B. These carbon-carbon bonds can be
single, double, or triple covalent bonds
 C. Can share 2 or 3 e
No other element even comes close to
matching carbon’s versatility
Hydrocarbons
Hydrocarbons are organic molecules
consisting of only carbon and hydrogen
 Many organic molecules, such as fats,
have hydrocarbon components
 Hydrocarbons can undergo reactions
that release a large amount of energy
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Hydrocarbons

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Hydrocarbons: made of only C & Hstore a lot of energy (energy rich)
Makes good fuels
Hydrocarbons are nonpolar

Propane gas is a hydrocarbon w/ 3 carbon
atoms
HHH
H-C-C-C-H
HHH
Gasoline is rich in
hydrocarbon
The Chemical Groups Most Important to
Life
Functional groups are the
components of organic molecules that
are most commonly involved in chemical
reactions
 The number and arrangement of
functional groups give each molecule its
unique properties
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Functional Groups


Ex: -OH can make molecules it is attached
to polar. –OH is important to all living
things
Molecules can be thought of as a C-H
core
Examples of functional group

A Hydrogen atom
bonded with an
Oxygen atom (-OH)
called hydroxyl
group


A Carboxyl group
(COOH) is alcohol with
a hydroxyl group
attached to one of its
carbon atoms.
The –OH makes alcohol
a polar molecule
7 Functional groups that are
important in the Chemistry of life
1.
2.
3.
4.
5.
6.
7.
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group
The Primary
Functional Chemical
Groups
These groups tend to
act as units during
reactions.
Amino Acid Groups
make molecules more
basic
Carboxyl Groups make
molecules more acidic
Carbohydrates
alcohols
Formaldehyde
Amino Acids,
Vinegar
Ammonia
Amino acids
Proteins
rubber
Phospholipids
ATP, nucleic
acids
Macromolecules


Many of the molecules in living cells are
so large they are known as
macromolecules which means “giant
molecules”.
They are made from thousands of
smaller molecules
Macromolecules

They are formed by a process known as
polymerization where large compounds
are built by joining smaller ones
together
Macromolecules


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Made of small building blocks of molecules
called monomers
Monomers combine to form polymers
A polymer consist of repeated units of
monomers
The units may be identical or structurally
related to each other
Large polymers are called macromolecules
Polymer is a long molecule build by linking together when
many smaller molecules bond together {similar chemical
subunits}
Example: complex carbohydrates like starch are polymers
Building Macromolecules

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Monomers link to form polymers by a
chemical reaction known as condensation
reaction. (also called dehydration synthesis)
In condensation, the small molecules that are
bonded together to make a polymer have an
–H & -OH group that can be removed to form
H-O-H.
The subunits become bonded by a covalent
bond
Dehydration Synthesis
/ Condensation Reaction
Breaking down polymers


In addition to building polymers by
condensation reaction, living organisms
have to break them down
The breakdown of some complex
molecules happens through hydrolysis
reaction, Water is used to break down
a polymer
Hydrolysis


Hydrolysis is the reverse of a
condensation reaction/dehydration
synthesis
The addition of water to some complex
molecules (including polymers) under
certain conditions can break the bonds
that hold them together
Dehydration Synthesis
Hydrolysis
http://video.lonestar.edu/media/nhscienc
e/dehydrat/dehydrat.html
How are macromolecules
formed?


HO
Answer: Dehydration Synthesis
It forms polymers by combining
monomers by “removing water”
H
HO
H
H2O
HO
H
How are macromolecules
separated or digested?


Answer: Hydrolysis
Separates monomers by adding water
HO
H
H2O
HO
H
HO
H
4 Major Categories of Biological
Macromolecules
1.
2.
3.
4.
Carbohydrates
Proteins
Lipids
Nucleic Acids
Sometimes these organic compounds are
referred to as biomolecules
These macromolecules are all polymers
1. CARBOHYDRATES
Carbohydrates

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Organic compounds made of C, H, & O
in a ratio of 1C : 2H : 1O
They serve as a source of energy
Others used as structural material
Monomers of monosaccharides (simple
sugars)
3 Classes of Carbohydrates

Small sugar molecule  to Large sugar
molecule



Monosaccharides
Disaccharides
Polysaccharides
Monosaccharides



A monomer of carbohydrate
One sugar unit of C, H, & O
General Formula (CH2O)n where n is
any whole number from 3 to 8
Monosaccharides

Most common:
1. Glucose (C6H12O6) made by plants
during photosynthesis
2. Fructose (C6H12O6) found in fruits &
is the sweetest
3. Galactose (C6H12O6) found in milk
glucose
Isomers


Glucose, fructose, and galactose have
the same molecular formula but
different structures
Isomers are molecules that have the
same molecular formula but different
structures

The different structures determine the
different properties
Disaccharides “Double Sugars”

Two Sugar Units

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Sucrose=Glucose + Fructose (Table Sugar) (found
in sugarcane and sugar beets)
Maltose=Glucose + Glucose (Malt sugar)
Lactose=Glucose + Galactose
(milk sugar)(breast milk)
glucose
glucose
Disaccharide Formula
C6H12O6 + C6H12O6=C12H24O12
Dehydration Synthesis
-
H2O
---------------------------------------------------
C12H22O11
Are Disaccharides isomers?
Polysaccharides “Many
Sugars”

Many sugar units (3 or more)

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Starch: storage from of sugar in plant
Glycogen: animals store glucose in the form of
glycogen
-much of the glucose that comes from food is
stored in your liver & muscle cells used as quick
energy
Cellulose: makes up plant cell walls
-Chitin: form of cellulose; makes up the
exoskeleton of insects & arthropods; fungi cell
walls
glucose
glucose
glucose
glucose
cellulose
glucose
glucose
glucose
glucose
PROTEINS
Proteins include a diversity of structures,
resulting in a wide range of functions

Proteins account for more than 50% of
the dry mass of most cells
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Protein functions include defense, storage,
transport, cellular communication,
movement, and structural support
Proteins perform the
chemistry of the cell

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Made mostly of C, H, O, & N
Formed from the linking of monomers
called amino acids
The proteins within living organisms are
immensely diverse in structure &
function


Hair, horns, skin, muscles and many
catalysts are mostly proteins
There are 7 functions of proteins
7 Functions of Proteins
1. Enzyme catalysis: facilitate chemical
reactions by stressing particular bonds
2. Defense: cell surface receptors that
recognize foreign microbes Example:
antibodies
3. Transport molecules & ions: Examplehemoglobin carries oxygen
4. Support: make up hair, nails, skin, ligaments,
tendons, bones
7 Functions of Proteins
5. Motion: muscles contract through the
sliding motion of 2 kinds of protein
filaments Ex. Actin & myosin of muscles
6. Regulation: small proteins called hormones
serve as intercellular messengers in
animals.
7. Storage: calcium & iron are stored by
binding into ions to specific storage proteins
Amino Acids: Monomers of
Proteins


There are only 20 amino acids, & all
share a basic structure
What makes one protein different from
another? The order and arrangement of
amino acids!
Amino Acid Structure

An amino acid molecule contains:
an amino group (-NH2)
a carboxyl group (-COOH)
a single Hydrogen Atom
R-group (side chain)-what makes them different

The remainder group is what makes one
amino acid different from another.
The main difference among
Amino acids is their R group
R-group can be simple or
complex
R-group gives different
shapes
Carboxyl (COOH)
Amino (NH2)
Hydrogen (H)
R-Group
*All bonded to carbon
The Peptide Bond

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A peptide bond is a covalent bond that
links two amino acids to form a
dipeptide
Forms when the amino end of one
amino acid joins the carboxyl end of
another
polypeptide

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Polypeptides are long chains of amino
acids
The amino acid sequence of the protein
determines how each protein bends and
folds on itself and how the protein
intertwines.
Condensation
reaction
The Shape of a protein is very
important because it determines
the protein’s function.
Proteins consist of long amino
acid chains folded into complex
shapes.
Levels of Protein Structure
1. Primary Structure: Order of amino
acids (encoded in our genes)


EX. Proline-glutamine-alanine
If you put these in a different order you
have a different protein
Amino Acids (aa)
aa1
aa2
aa3
Peptide Bonds
aa4
aa5
aa6
Levels of Protein Structure
2. Secondary Structure: Hydrogen bonds
form between amino acids arranged
into spirals (coils) or pleated sheets
Alpha Helix
Beta Pleated Sheet
Hydrogen Bonds
Levels of Protein Structure
3. Tertiary Structure: The spiral or pleated
sheets fold on themselves making a 3-D
shape
Alpha Helix
Beta Pleated Sheet
Levels of Protein Structure

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Quaternary Structure: clustering of many proteins (2
or more polypeptide chains join to form a functional
protein)
Globular in shape
Ex:
Forms in aquatic environments
hemoglobin
subunits
What Determines Protein Structure?


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In addition to primary structure, physical and
chemical conditions can affect structure
Alterations in pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
This loss of a protein’s native structure is
called denaturation
Denaturation

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Protein shape can be influenced by conditions like
temperature & solvents a protein is dissolved
Ex: cooking an egg changes the shape of the
proteins in the egg white
Ex: Salt-curing & Pickling denatures the enzymes of
microorganisms and keeps them from growing on
food
LIPIDS
Lipids
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Lipids are large, nonpolar organic molecules
They do not dissolve in water
Include: triglycerides, phospholipids, steroids,
waxes, fats, oils, hormones and pigments
Stores the most energy
Phospholipids make up cell membrane
structure
Functions of Lipids

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Protects against water loss
Long term energy storage
Chemical messengers
(hormones/steroids)
Chemical defenses
Protects against heat loss (insulation)
Protects against physical shock
Fats
Fats are constructed from two types of
smaller molecules: glycerol and fatty
acids
 Glycerol is a three-carbon alcohol with a
hydroxyl group attached to each carbon
 A fatty acid consists of a carboxyl
group attached to a long carbon
skeleton
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Fatty Acids

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Fatty Acids are unbranched
carbon chains that make up
most lipids
Contain long C chain with a
carboxyl group attached at
one end
COOH-Polar
Carbon Chain-Non-polar
Plasma Membrane
Found in the cell
Hydrophilic head
Hydrophobic tail
Saturated & Unsaturated fatty
acids


Saturated Fatty Acids: each C-atom is
covalently bonded to 4 atoms, each full
or saturated
Unsaturated Fatty Acids: has C-atoms
that are not bonded to the maximum
number of atoms they can bond with;
instead they form double bonds within
the carbon chain
Good fats
Corn oil, olive oil
Bad fats
Butter, Animal fat

Fats made from saturated fatty acids
are called saturated fats and are solid at
room temperature


Most animal fats are saturated
Fats made from unsaturated fatty acids,
called unsaturated fats or oils, are liquid
at room temperature

Plant fats and fish fats are usually
unsaturated
The major function of fats is energy storage
 Fat is a compact way for animals to carry
their energy stores with them

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3 Classes of Lipids

3 classes of lipids; important to living
things contain fatty acids
1. Triglycerides (fats)
2. Phospholipids
3. Waxes
1. Triglycerides

Triglycerides have 3 fatty acids joined
to one glycerol


Saturated triglycerides: have high melting
points & tend to be hard at room
temperature (butter & fats in red meat)
Unsaturated triglycerides: usually soft or
liquid at room temperature (plant seeds
where they serve as energy & C-source for
germinating plants)
(b) Fat molecule (triacylglycerol)
2. Phospholipids

Phospholipids have 2 fatty acids and a
phosphate group attached to a
molecule of glycerol

The cell membrane is made of 2 layers of
phospholipids called the lipid bilayer that
forms a barrier between the inside and
outside of the cell
Phospholipids
The two fatty acid tails are hydrophobic,
but the phosphate group and its
attachments form a hydrophilic head
 Phospholipids are major constituents of
cell membranes

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Hydrophobic tails
Hydrophilic head
Figure 3.14ab
Choline
Phosphate
Glycerol
Fatty acids
(a) Structural formula
(b) Space-filling model
3. Waxes

Waxes consist of a long fatty-acid chain
joined to a long alcohol chain

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Are waterproof
Form a protective coating on the outer
surface of plants
Form protective layers in animals (earwax)
NUCLEIC ACIDS
Nucleic acids store, transmit, and help
express hereditary information
The amino acid sequence of a
polypeptide is programmed by a unit of
inheritance called a gene
 Genes are made of DNA, a nucleic
acid made of monomers called
nucleotides
 Nucleic Acids store and transfer genetic
information in the cell

The Roles of Nucleic Acids

There are two types of nucleic acids


Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA provides directions for its own
replication
 DNA directs synthesis of messenger
RNA (mRNA) and, through mRNA,
controls protein synthesis

The Components of Nucleic Acids

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Nucleic acids are polymers called
polynucleotides
Each polynucleotide is made of monomers
called nucleotides
Each nucleotide consists of a nitrogenous
base, a pentose (5-carbon) sugar, and one or
more phosphate groups
The portion of a nucleotide without the
phosphate group is called a nucleoside
3 Parts of a DNA nucleotide:
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5-Carbon Sugar (Deoxyribose)
A Phosphate Group
A nitrogen base (adenine, guanine,
thymine or cytosine)
A-T; T-A
G-C; C-G
3 Parts of a RNA nucleotide:


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5 Carbon sugar (ribose)
A phosphate group
A Nitrogen base (adenine, uracil,
guanine, cytosine)
A-U; G-C
The DNA Code

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The sequence of A,T,C,G (genes)
(genes are on chromosomes)
Code for amino acids which make up
proteins for structures and enzymes
Shape: double helix (twisted ladder)
H bond holds nitrogen bases together
Base pair rule: A-T, G-C
4 Main Difference between
DNA & RNA

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DNA double stranded
RNA single stranded
DNA has deoxyribose sugar
RNA has ribose sugar
DNA has thymine
RNA has uracil
DNA remains in the nucleus
RNA carries the DNA code to a ribosome