Biomolecules
Overview
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Energy and matter
Atoms, molecules, and chemical bonds
Importance of organic and inorganic
nutrients and metabolites
Structure and function of carbohydrates,
lipids, proteins, and nucleic acids
Enzymes and ATP help run the metabolic
reactions of the body
Energy
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The capacity to do work (put matter into
motion)
Types of energy
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Kinetic – energy in action
Potential – energy of position; stored (inactive)
energy
Energy is easily converted from one form to
another
During conversion, some energy is “lost” as
heat
Why is chemistry important to
anatomy and physiology?
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Chemistry is the science that deals
with matter
Matter is anything that takes up space
and has mass
Smallest stable units of mass are
atoms
Elements vs. Molecules
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Elements are atoms of one particular
type (from the periodic table)
Molecules are groups of atoms that
contain more than one element
Elements found in the body
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13 principal elements
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Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)
Calcium (Ca), phosphorus (P), potassium (K),
sulfur (S), sodium (Na), chlorine (Cl),
magnesium (Mg), iodine (I), and iron (Fe)
13 trace elements
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(e.g. zinc, manganese)
Elements with unfilled electron
shells are reactive
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To become stable they form chemical
bonds.
Three main types of chemical bonds
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Intramolecular:
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Ionic bonds (charged atoms resulting from
the gain or loss of electrons)
Covalent bonds (electrons are shared)
Intermolecular
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Hydrogen bonds
Ionic and covalent bonds
Molecules: atoms held together by
covalent bonds
 Salts: molecules held together by ionic
bonds
Q: What are the strongest type of bonds?
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Importance of water
The body is mostly water (~2/3rds of
total body weight) so all chemical
reactions in the body occur in water
Covalent bonds are much stronger than
ionic bonds in water
Water properties
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Water can dissolve organic and
inorganic molecules making a solution
Water is needed for chemical reactions
Water can absorb and retain heat
Water is an effective lubricant
Water properties
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Water has all these amazing
properties due to their ability to form
hydrogen bonds
Hydrogen bonds: weak bonds
between molecules
Mixtures and Solutions
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Mixtures – two or more components
physically intermixed (not chemically
bonded)
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Solutions – homogeneous mixtures of
components
Colloids (emulsions) – heterogeneous mixtures
whose solutes do not settle out
Suspensions – heterogeneous mixtures with
visible solutes that tend to settle out
Essential Molecules
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Nutrients:
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essential molecules obtained from food
(you have to eat them to get them)
Metabolites:
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molecules made or broken down in the
body
Organic vs. inorganic
Organic molecules:
 Always contain carbon with hydrogen, and
sometimes oxygen
 Often soluble in water
Inorganic: Electrolytes, minerals, and
compounds that do not contain carbon with
hydrogen.
 Important examples: oxygen, carbon
dioxide, water, inorganic acids and bases,
salts
Vitamins and Minerals
Vitamins and minerals are essential
nutrients that are required in very small
amounts for healthy growth and
development.
Examples?
 They cannot be synthesized by the
body and are essential components of
the diet.
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Vitamins
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Organic substances necessary for
metabolism
There are 13 known vitamins (e.g. A,
B1, D, K)
Some are fat soluble while others are
water soluble
Are Coenzymes that help carry out
the reactions of metabolism
Minerals
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Inorganic compound (often salts or
elements) necessary for proper body
function
Can be bulk or trace minerals
Are Cofactors in metabolic reactions
Electrolytes
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Inorganic ions (usually minerals) that
conduct electricity in solution
Electrolyte balance is maintained in all
body fluids; imbalance seriously disturbs
vital body functions
Electrolytes
Biological Macromolecules
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Life depends on four types of organic
macromolecules:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Can you think of an example of each?
1. Carbohydrates
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Contain carbon, hydrogen and oxygen
in a ratio of 1:2:1
Account for less that 1% of body
weight
Used as energy source
Called saccharides
Glucose is a monosaccharide
Disaccharides
Sucrose
Lactose
Polysaccharides
Starch
 Glycogen
 Cellulose
All are long strings of glucose molecules
Difference lies in how they are bonded
together
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Polysaccharides
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Polysaccharides or polymers of simple
sugars
Polymers
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A polymer is any molecule made up of
several repeating units. Starch is a
polymer of glucose.
2. Lipids
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Contain carbon, hydrogen, and oxygen
but the ratio of C:H is 1:2 (much less
O)
May also contain other elements,
phosphorous, nitrogen, and sulfur
Form essential structures in cells
Are important energy stores
Lipids: Triglycerides (Fats and
Oils)
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Consist of 3 fatty
acids and glycerol
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Insulation
Energy
protection
Q: What ‘s the
difference
between
saturated and
unsaturated?
Lipids: Steroids and
Cholesterol
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All consist of a
complex ring
structure
Lipids: Phospholipids
Amphipathic
3. Proteins
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Consist of chains of
amino acids liked
together by peptide
bonds
Enzymes are
proteins
Protein Chemistry
Proteins
are very important
biological molecules that
play crucial roles in
virtually all biological
processes
BIOLOGICAL FUNCTIONS OF PROTEINS
1. Catalytic function:
Nearly all chemical reactions in biological systems are catalyzed
by specific enzymes.
2. Transport and storage:
For example;
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Hemoglobin transports oxygen in erythrocytes
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Myoglobin carries & stores oxygen in muscle.
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Albumin transports free fatty acids in blood.
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Transferrin transports iron in blood.
3. Coordinated motion:Actin and myosin are contractile proteins in
muscle.
BIOLOGICAL FUNCTIONS OF PROTEINS (cont.)
4. Structural and Mechanical support:
For Example; collagen, a fibrous protein in skin and bone.
5. Defense function:
For Example Clotting factors prevent loss of blood.
Immunoglobulins protects against infections.
6. Generation and transmission of nerve impulses:
For example, rhodopsin is the photoreceptor protein in retinal
rod cells.
7. Control of growth and differentiation:
For Example
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growth factor proteins.
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hormones such as insulin and thyroid-stimulating
hormone.
General structure of protein
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All biologically known protein are polymers of a
set of twenty known amino acids.
All biologically known amino acids are α L
amino acids.
They are composed of carboxylic end COOH
and amino end NH2 and α carbon attached to
both of them and special side chain (R)
attached to this α carbon .
This side chain is characteristic of every amino
acid.
AMINO ACIDS
are the basic building
blocks of
PROTEINS
Each AMINO ACID
has
An amino group,
A carboxyl group,
A hydrogen atom and
a specific side chain (R group)
Bonded to
the α-carbon atom
Classification of amino acids
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Side chain reaction classification
Biological classification
Metabolic classification
Side chain classification
1- Hydrophobic (nonpolar) R-group)
Glycine (Gly-G)
Alanine (Ala-A)
Valine (Val-V)
Leucine (Leu-L)
Isoleucine (Ile– I)
Methionine (Met– M)
Proline (Pro– P)
Phenylalanine (Phe– F)
Tryptophan (Trp–W)
2- Hydrophilic (polar) R-group
Uncharged
Aspargine
(Asn – N)
Glutamine
(Gln – Q )
Serine
(Ser – S)
Threonine
(Thr – T )
Tyrosine
(Tyr – Y)
Cysteine
(Cys – C )
Positively
charged
Lysine
(Lys – K )
Arginine
(Arg – R)
Histidine
(His – H )
Negatively
charged
Aspartic acid
(Asp – D)
Glutamic acid
(Glu – E )
Non polar (hydrophobic) amino acids
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Side chains of non polar (hydrophobic) a.a. can not
participate in hydrogen or ionic bonds, but they form
hydrophobic interactions.
In aqueous environment, non polar a.a. tend to be
present in the interior of proteins.
They include:
Amino acids with aliphatic R group (glycine, alanine,
Amino acids with aliphatic branched R group (valine,
leucine and isoleucine).
Amino acids with aromatic R group (phenylalanine,
tryptophan)
Amino acids with sulfur group (methionine) and
Imino acid (proine).
Polar (hydrophilic) amino acids
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Side chains of polar (hydrophilic) a.a. can participate in hydrogen or
ionic bonds.
Therefore, in aqueous environment polar a.a. tend to be present on
the surface of proteins.
Polar (hydrophilic) amino acids are classified into:
- Polar charged amino acids include
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acidic (Negatively charged): (aspartic and glutamic a.) and
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basic (Positively charged group): (arginine, lysine, histidine)
amino acids.
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Polar non charged amino acids include:
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Amino acids with OH group (serine, threonine, tyrosine)
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Amino acids with SH group (cysteine)
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Amino acids with amide group (glutamine, asparagines)
Biological classification
1- Non essential amino acids: These are
Glycine, Alanine, Serine, Tyrosine,
Cysteine, Arginine, Asparagine, Aspartic,
Glutamic acid , Glutamine and Proline.
2- Essential amino acids:
They include Valine, Leucine, Isoleucine,
Threonine, Methionine,, Lysine, Histidine,
Phenylalanine and Tryptophan.
Metabolic classification
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Glucogenic amino acids: These amino acids
could give intermediates which finally can give
glucose.
Purely ketogenic amino acids: They include
Leucine & Lysine. They give ketone bodies after its
degradation in the body, but no glucose.
Mixed amino acids: These are amino acids that
can give both ketone bodies and glucose
intermediates. These are Phenylalanine, Tyrosine,
Tryptophan, Isoleucine and Lysine.
* The rest of amino acids are all purely
glucogenic.
Ionic properties of amino acids
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Amino acids have amphoteric properties .
They contain acidic (COOH) and Basic (NH2) groups.
The amino acids are usually ionized at physiological pH .
In acidic medium ; amino acid is positively charged (
behave as a base : proton acceptor )
In alkaline medium ; the amino acid is negatively charged (
behave as an acid: Proton donor)
Isoelectric point or “pI”
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At certain pH “ specific for each amino acid “ the
amino acid can exist in the dipolar from : fully ionized
but with no net electric charge .
The characteristic pH at which the net electric charge
is zero is called the Isoelectric point or “pI”.
The amino acid at the isoelectric pI is called
“ Zwitter Ion “ and is electrically neutral not migrating
in an electric field
“Zwitter in German means hybrid or hermaphrodite”.
Isoelectric point or “pI”
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At certain pH “specific for
each amino acid” the amino
acid can exist in the dipolar
from : fully ionized but with
no net electric charge.
The characteristic pH at
which the net electric
charge is zero is called the
Isoelectric point or “pI”.
The amino acid at the
isoelectric pI is called
“Zwitter Ion” and is
electrically neutral not
migrating in an electric field.
Zwitter ion
Amide links
H
R
R
CH
CH
N
C
H
O
OH
An  -amino acid
R''
R'
N
C
N
H
O
H
R'''
CH
CH
R''''
CH
CH
C
N
C
N
C
N
C
O
H
O
H
O
H
O
A portion of a protien molecular
Primary structure: the exact sequence of the different α-amino acids
along the protein chain.
Second and tertiary structure: the folding of the polyamide chain
which give rise to higher levels of
complexity.
Although hydrolysis of natural occurring proteins may yield as many
as 22 different amino acids, the amino acids have an important
structural feature in common.
Protein Structure
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Proteins are the most abundant and
important organic molecules
Basic elements:
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carbon (C), hydrogen (H), oxygen (O),
and nitrogen (N)
Basic building blocks:
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20 amino acids
Protein Structure – 4 levels
Primary: amino acid sequence
Secondary: Hydrogen bonds form spirals
or pleats
Tertiary: Secondary structure folds into a
unique shape
Quaternary: several tertiary structures
together
Protein structure
Shape and Function
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Protein function is based on shape
Shape is based on sequence of amino
acids
Denaturation:
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loss of shape and function (due to heat,
pH change or other factors)
Protein Functions
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support:
 structural proteins
movement:
 contractile proteins
transport:
 transport proteins
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buffering:
regulation of pH
metabolic
regulation:
 enzymes
coordination and
control:
 hormones
defense:
 antibodies
Proteins: Enzymes
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Enzymes are catalysts:
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proteins that lower the activation energy of a
chemical reaction
are not changed or used up in the reaction
Other factors that speed up reactions:
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Increased temperatures
Smaller particles
Higher concentrations
Activation Energy
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Chemical reactions in cells cannot
start without help
Activation energy gets a reaction
started
Characteristics of Enzymes
Energy In, Energy Out
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Exergonic reactions:
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produce more energy than they use
Endergonic reactions:
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use more energy than they produce
KEY CONCEPT
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Most chemical reactions that sustain
life cannot occur unless the right
enzymes are present
How Enzymes Work
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Substrates:
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reactants in enzymatic reactions
Active site:
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a location on an enzyme that fits a
particular substrate
Active site
Amino acids
+
How
Enzymes
Work
Enzyme (E)
Substrates (S)
Enzyme-substrate
complex (E-S)
H2O
Free enzyme (E)
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
4. Nucleic acids
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Contain C, H, O, N,
and P
DNA and RNA are
nucleic acids
Nucleotide consists
of
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Sugar
Phosphate group
Nitrogenous base
Structure of
DNA
A nucleotide: ATP
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Energy storage for
cells
Many enzymes use
ATP
Provides a way to
run reactions that
are otherwise
endergonic
(require energy)
Membrane
protein
Pi
P
Solute
ATP is the
energy currency
of the cell
Solute transported
(a) Transport work
ADP
+
Pi
ATP
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
(b) Mechanical work
Pi
X
P
X
Y
+ Y
Reactants
Product made
(c) Chemical work
Compounds Important
to Physiology
Summary
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Energy and matter
Atoms, molecules, and chemical bonds
Importance of organic and inorganic
nutrients and metabolites
Structure and function of carbohydrates,
lipids, proteins, and nucleic acids
Enzymes and ATP help run the metabolic
reactions of the body