Or, Chemistry class in one

lecture!

Key Concepts
 Elements, Atoms, Isotopes etc.

 Chemical formulas, Chemical bonds

 Solutions, Concentrations, pH

 Organic Chemistry / Biochemistry

 Element = Building block of
matter
Contains only atoms with same # of
protons

 Periodic Table of the Elements

 In human: 11 major essential elements

C, O, H, N, S, P, Mg, K, Ca, Fe =
trace elements

 Organic Chemistry = Chemistry of Carbon

Structure of Atoms (AKA elements)

• Some Terminology:
– Atomic Number
– Atomic mass
– Ion
– Isotope
Isotopes = Atoms of an element that
have different numbers of neutrons.
Same Atomic Number, variable
Atomic Mass

Most common Much rarer

Heavy water = ?
 Some isotopes are unstable:
Radioisotopes

3 types of radiation:
1.  radiation – protons and neutrons
1. (If protons are emitted, the element changes!)

2.  radiation - electrons

3. radiation: high energy waves, not particles

More stable
atom of same
element
 Nuclear Medicine: use of radioisotopes in
diagnosis & treatment of disease.

127
I is “normal”
iodine
131
I has 4 extra
neutrons
 and  radiation

Medical
Imaging ?
Treatment?
 Importance of Electrons in
Physiology
• Ion formation = gain or
loss of electrons

• Bond formation between

atoms  molecules

• Energy capture & transfer

• Free radical formation

Ions are often called electrolytes!

The Chemistry of Life
• Elements = Atoms
– Nucleus
• Protons
• Neutrons
– Orbit
• Electrons
Atoms
• Atomic number
• The number of protons,
usually also equals the
number of electrons.
• Atoms must be neutral
• Atoms/molecules that
are stable will not bond
with other
atoms/molecules.
Shells or Orbits
Each electron shell can
hold a specific
number of electrons
– Shell 1 = 2e
– Shell 2 = 8e
– Shell 3 = 18e
 Electron Bonding
• Outermost shell contains all pairs of
electrons
– Stable
• Outermost shell contains at least one
unpaired electron
– Unstable
• Lose, gain or share electrons to become stable
• An atom is most stable when each electron
is paired!
 Chemical Bonds
– Ionic: electrons pulled from one atom to
another: Na+ and Cl-
– Covalent: electrons shared equally: C
--- C
– Hydrogen: weak attraction between H
atoms and O, N, and Fl. Causes surface
tension in water.
– Van der Waal’s forces: weak attractions
between nuclei of atoms
 Chemical Bonds
• Ions
– More (or less) electrons than protons
• Ionic Bonds
– Anions
• Negative
– Cations
• Positive
 Ionic Bonds
• Give away or receive electrons to create
ions and for each ion to become more
stable
• Ions of opposite charge bind with each
other to form an ionic bond
• An ionic bond typically includes a metal
– NaCl
Ionic Bonding
 Important Ions in
Physiology

cations anions
 Chemical Bonds
• Covalent
– Polar
– Non-polar
 Covalent Bonds
• Strong bonds that occur when two atoms
share electrons in order to become more
stable
 Covalent Bonds
• Non-polar Covalent Bonds
– If the electrons are shared equally between
atoms
• Polar Covalent Bonds
– If electrons spend more time around one atom
than the other
– Molecules develop regions of partial positive
and negative charges
Covalent Bonds
Covalent bond: Water
The electrons are shared equally

If two electrons are shared, that is a

“double bond.”
 Polar covalent
molecule

Non-polar covalent
molecules

Consequence: ions and polar

molecules dissolve well in
water
Chemical Bonds
• Hydrogen Bonds
– Surface tension
– Attractive force between
water molecules that
causes water to form
spherical droplets
– Weak attractive force
between hydrogen and
oxygen, nitrogen or
fluorine atoms
– Quickly forms and
quickly breaks
 Reactions
• Types of Reactions
– Synthesis Reaction--Anabolic
• A + B ----> C
– Decomposition Reaction--Catabolic
• AB ----> A + B
– Exchange Reaction
• AB + C---->AC + B
• Oxidation-Reduction Reactions (REDOX)
 Chemical Reactions
• Reactants form Products
• First Type of Reaction
– Anabolic or Synthesis Reaction
 Chemical Reactions
• Decomposition Reaction
– Catabolic
The number of protons and
neutrons in a nucleus of an atom
constitutes the
The number of protons in a
nucleus of an atom constitutes the

A. Atomic weight
B. Atomic number
C. Atomic mass
D. Nuclear number
The number of protons in a
nucleus of an atom constitutes the

A. Atomic weight
B. Atomic number
C. Atomic mass
D. Nuclear number
 The bond between an oxygen and
a hydrogen in a water molecule is
a(n)

A. Non-polar covalent bond

B. Polar covalent bond
C. Hydrogen bond
D. Ionic bond
The bond between an oxygen and
a hydrogen in a water molecule is
a(n)

A. Non-polar covalent bond

B. Polar covalent bond
C. Hydrogen bond
D. Ionic bond
 Deuterium and Tritium are
examples of
A. Elements
B. Ions
C. Buffering compounds
D. Isotopes
E. None of these
Deuterium and Tritium are
examples of

A. Elements
B. Ions
C. Buffering compounds
D. Isotopes
E. None of these
 The atomic mass of an atom
indicates the average total number
of
A. Protons
B. Neutrons
C. Electrons
D. Protons, neutrons and electrons
E. Protons and electrons
The atomic mass of an atom
indicates the average total number
of
A. Protons
B. Neutrons
C. Electrons
D. Protons, neutrons and electrons
E. Protons and electrons
 Elements that have full outer
shells of electrons
A. Will form many compounds
B. Will normally form anions
C. Will normally form cations
D. Frequently form hydrogen bonds
E. Are inert, and don’t bond readily with
other atoms
Elements that have full outer
shells of electrons
A. Will form many compounds
B. Will normally form anions
C. Will normally form cations
D. Frequently form hydrogen bonds
E. Are inert, and don’t bond readily
with other atoms
 When a molecule is referred to as
polar, it means that
A. The positive and negative charges of the
molecule are unevenly distributed
B. The molecule is ionized and now carries a
charge
C. The molecule is likely to dissolve in water
D. A and C are true
E. B and C are true
When a molecule is referred to as
polar, it means that

A. The positive and negative charges of the

molecule are unevenly distributed
B. The molecule is ionized and now carries
a charge
C. The molecule is likely to dissolve in
water
D. A and C are true
E. B and C are true
 Acid Base Reactions
Acids
– The concentration Hydrogen ions free in
solution
• Protons
– H+

• Bases
– Are proton acceptors
• Bind with hydrogen ions
• Hydroxyl ion = OH-
• Bicarbonate ion = HCO3-
 Buffers
• Buffers resist abrupt and large swings in
the pH of body fluids.
• To resist large changes in pH, the body
releases hydrogen ions when the pH rises
and binds hydrogen ions with bicarbonate
ions when the pH drops.
• Blood pH = 7.35 – 7.45
 Buffers

• CO2 + H2O H2CO3 H++ HCO3-

 BIOMOLECULES
• Carbohydrates
• Fats
• Proteins
 Organic Chemistry /
Biochemistry
Biomolecules ( = organic molecules associated
with living organisms)
1) Protein
2) Fat (lipid)
3) CHO
4) Nucleotides

•2 common features of biomolecules ??

•Carbon Backbone
•Presence of C, H, O
Functional Groups

= partial molecules.

Frequently occur in
biological molecules.

Moved around as a
single units.

Often make a big

difference in the
strength or function
of a molecule
 Organic Compounds
• Carbohydrates
– A group that includes things like table
sugars and starches.
– Includes Simple and Complex groups
Carbohydrates

See Fig 2-7

• Basic formula ? (see name!!)

• Monosaccharides
– examples ?? = simple sugars
• Disaccharides
– examples ??

• Polysaccharides = complex CHOs

– examples ??
 Simple Carbohydrates
– Simple
• Monosaccharides
– Fructose
– Glucose
• Disaccharides
– Sucrose
– Lactose
Monosaccharides
Disaccharides
Polysaccharide
Organic Compounds
• Complex Carbohydrates
• Polysaccharides are long branching
chains of simple sugars, specifically
glucose.
– Starch is a storage carbohydrate in plants.
– Glycogen is a storage carbohydrate in animals.
• Liver and skeletal muscle
 Lipids
• Most diverse group of biomolecules
• Solid at room temp = fat;
– liquid at RT = oil

• Contain much less O2 than CHOs

– Often long chains of C
• 4 categories:
 Fatty Acids can be (un)saturated
 Mono-, di-, and triglycerides
 Phospholipids (polar)
 Steroids
 Eicosanoids (prostaglandins et al.)
 Functions?
Triglycerides
 Unsaturated (mono- &
polyunsaturated) fats
are liquid at room temp.

Trans fats have

added hydrogen
(hydrogenated) (p
29)
Triglycerides: 3 FA
+ Glycerol

Saturated Unsaturated Polyunsaturated

Organic Compounds
• Lipids, Fats or Triglycerides
– Composed of Glycerol backbone plus 3 fatty acid
chains
– Saturated Fats
• Contains only single bonds between the carbons on the fatty
acid chains
• Solid at room temperature
– Unsaturated Fats
• Contains one or more double bonds between the carbons on
the fatty acid chains
• Semi-solid or liquid at room temperature
• Mono, di- and polyunsaturated fats
– Will only dissolve in other lipids and insoluble in
water.
• Like Dissolves in Like
Phospholipid
Phospholipids
 Organic Compounds
• Phospholipids
– Modified triglycerides
– Phosphorous head and two fatty acid tails
– Amphipatic
• Hydrophilic, as well as
• Hydrophobic
– Found only in human cell membrane as a bi-
layer
• Hydrophobic – Tails on the inside of the membrane
• Hydrophilic – Heads on the outside of the membrane
Steroids

Cholesterol decreases
cell membrane
permeability to small
water-soluble
molecules.

Function?
Steroids
 Organic Compounds
• Steroids
– Parent compound is cholesterol.
– Used for the production of steroid hormones.
– Can dissolve in fatty substances.
– Dissolves through cell membrane and nuclear
membrane and attaches directly to DNA
• Starts Transcription of proteins
– Such as enzymes
– Cholesterol can be produced through de-novo
synthesis
 Organic Compounds
• Proteins
– composes 10 – 30% of cell mass and is the
basic structural material of the body.
– Some are structural.
• Bones, hair, connective tissue
– Some are functional.
• Antibodies, enzymes, protein hormones
 Names of the 2
functional groups ?

Proteins
• Made up of amino acids

– Amino = - NH2

• Peptide → oligopeptide → polypeptide → protein

• Most versatile of biomolecules in structure and function

Learn
these
Amino Acids
 Organic Compounds
• Amino acids.
– The Building Blocks of Protein
– Composed of
• an amine groups
• a carboxyl group
• a “R” or Functional group.
– 20 different types of amino acids
• 9 Essential
– Must acquire these through the foods we eat
• 11 Non-essential
– Can be produced through de-novo synthesis
Peptide Bond
 Peptide Bonds
• Two united amino acids form a peptide bond or
dipeptide.
• 50 or more amino acids are called a protein or
polypeptide.
• Most proteins contain from 1500 to 50,000 amino
acids in the human body.
Protein Structure
Structural Levels of Proteins
• Primary Structure
– Polypeptide chain
• Secondary Structure
– Alpha Helix
– Beta pleated sheet
• Tertiary Structure
– Alpha helix folds on itself.
• Quaternary Structure
– Hemoglobin molecule
 Proteins
• Hydrogen bonds are created within the
Functional Group of the primary
polypeptide chain
• Hydrogen bonds form and break quickly
and can thereby change the protein shape
and its function
 Protein Structure
• Fibrous Proteins
– Secondary structure
– Strand-like proteins
– Structural proteins
• Collagen
 Globular
protein

This picture illustrates

the hydrophobic core
of protein ras p21
The backbone is
colored purple, and the
hydrophobic
residues are colored
green. All the
hydrophilic residues in
the protein are colored
yellow.
 Protein Structure
• Globular Proteins
– Compact, spherical proteins
– Have tertiary or quaternary structures
– Also known as functional proteins
• Antibodies
• Hormones
• Enzymes (catalysts)
• Membrane Transporters
• DNA Regulatory Proteins for transcription
 Proteins
• Fibrous proteins are stable.
• Globular proteins are very unstable.
– Hydrogen bonds can form and break easily.
– Hydrogen bonds can break when:
• pH drops.
• Temperature rises above normal levels.
• Add a PO4 group or other molecules
 Adenosine Triphosphate
• The transfer of a high energy phosphate
group to an enzyme causes a change in
confirmation
• The change in enzyme shape allows the
enzyme to quickly catalyze the reaction
 Protein Structure
• Change in shape of protein =
– Change in conformation =
– Change in configuration
• Denatured
– When globular proteins lose their shape they
can’t perform their function any longer.
 Cellular Metabolism
• Energy as it relates to Biology
– Energy for synthesis and movement
– Energy transformation

• Enzymes and how they speed reactions

• Metabolism and metabolic pathways

– Catabolism (ATP production)
– Anabolism (Synthesis of biologically
important molecules)
 Enzymes
• Enzymes are globular proteins that
act as catalysts.
– A catalyst speeds up a chemical reaction
but it itself is not used up
– Enzymes are recycled
• The function of a globular protein depends on the
arrangement of the atoms
• A ligand is any molecule that binds to
another molecule
– A substrate is a ligand that binds to an enzyme
Mechanism of Enzymes

• Three Basic Steps

– The Enzyme binds with a substrate at its
active site.
– The Enzyme-Substrate Complex is
rearranged to form a product.
– The Enzyme releases the product and
goes back to its original shape
• The Enzyme can be used again to catalyze
another reaction
 Enzymes
– The shape of the substrate matches with the
shape of the active site.
– The shape of the active site changes when the
protein is denatured so the substrate can no
longer bind.
 Enzymes
• The job of an enzyme is to lower the
activation energy
– Some enzymes carry a helper of “cofactor”
such as iron or copper.
• Vitamins, especially B complex.
Activation Energy

Fig 4-3
 Enzyme = Biol. Catalyst
Some important characteristics of an enzyme:

1. Enzymes are proteins

2.  rate of chemical reaction by lowering activation

energy

3. is not changed itself

1. It may change DURING the reaction

4. does not change the nature of the reaction nor the

result

5. is specific
 Some more characteristics of
enzymes:

• Usually end in –ase

• Inactive form: -ogen
• in few cases RNA has enzymatic
activity (eg: rRNA  peptide bond)
• Isoenzymes may be produced in different
areas of the body
– E.g., LDH
 Naming of Enzymes
mostly suffix -ase
first part gives info on function
examples

• Kinase
• Phosphatase
• Peptidase
• Dehydrogenase
 Active Site:

Small region of the complex

3D structure is active (or
binding) site.

Enzymes bind to substrate

Old: Lock-and-key model / New: Induced-fit model

Reversible Reactions Follow The
Law of Mass Action
 Protein Molecules
• Specificity
– The ability of a protein to bind to a certain
ligand or a group of related ligands
– Some proteins are very specific about the
ligands they bind, others bind to whole groups
of molecules
 Affinity
• The degree to which a protein is attracted
to a ligand is referred to as its Affinity.
– High affinity proteins are more likely to bind a
certain molecule than a low affinity protein
Isoenzymes = different models of same
enzyme (differ in 1 or few aa)

Catalyze same reaction but under different

conditions and in different tissues/organs
Examples:
1. Amylase
2. LDH → importance in diagnostics
– (LDH) Lactate dehydrogenase  - Total LDH
will begin to rise 2 to 5 days after an MI; the
elevation can last 10 days.
• 140-280 U/L
• Normal Adult Range: 0 - 250 U/L
Optimal Adult Reading: 125
 Enzyme Activity depends on

 Proteolytic Activation (for some)

 Cofactors & coenzymes (for some)
 Temperature
 pH
1. Other molecules interacting with enzyme
1. Competitive inhibitors
2. Allosteric modulators
1) Proteolytic
Activation

Also
1. Pepsinogen Pepsin
2. Trypsinogen Trypsin
 2) Cofactors & Coenzymes

Structure:
Inorganic molecules Structure:
Cu, Fe, Mg Organic molecules (vitamin
derivatives, FADH2 ....)
Function:
conformational change of
active site Function:
act as receptors & carriers

for atoms or functional

groups that are removed
from substrate
 4) Molecules interacting with enzyme

Competitive inhibitors:
bind to active site

Fig 4-13
block active site

E.g.: Penicillin binds covalently (= irreversibly

to important bacterial enzyme active site)
 4) Molecules interacting with enzyme, cont’d

Allosteric modulators: bind to enzyme away from

active site change shape of active site
(for better or for worse)

Special case:
= end product inhibition
Which of the following statements
about proteins is false?
A. All proteins are enzymes
B. A given protein may contain over twenty
different amino acids
C. The tertiary structure of a protein results
from interactions between its amino acids
D. Proteins are gigantic polypeptides
E. All of the above statements are true.
Which of the following statements
about proteins is false?
A. All proteins are enzymes
B. A given protein may contain over twenty
different amino acids
C. The tertiary structure of a protein results
from interactions between its amino acids
D. Proteins are gigantic polypeptides
E. All of the above statements are true.
 A polypeptide consists of 100
amino acids. How many
peptide bonds does it contain?
A. 50
B. 100
C. 99
D. 101
E. Impossible to say without knowing
the exact amino acid composition
 A polypeptide consists of 100
amino acids. How many
peptide bonds does it contain?
A. 50
B. 100
C. 99
D. 101
E. Impossible to say without knowing
the exact amino acid composition
Each of the following is a
function of proteins except
one. Identify the exception.
A. Support and structure
B. Transport
C. Carrying of messages
D. Body defense
E. Storage of genetic information
Each of the following is a
function of proteins except
one. Identify the exception.
A. Support and structure
B. Transport
C. Carrying of messages
D. Body defense
E. Storage of genetic information
A fatty acid that contains three
double bonds in its carbon
chain is said to be
A. Saturated
B. Monounsaturated
C. Polyunsaturated
D. Hydrogenated
E. Carboxylated
A fatty acid that contains three
double bonds in its carbon
chain is said to be
A. Saturated
B. Monounsaturated
C. Polyunsaturated
D. Hydrogenated
E. Carboxylated
Magnesium atoms have two electrons
in the outermost shell and chlorine
atoms have seven. The compound
magnesium chloride would contain

A. 1 magnesium and 1 chlorine

B. 1 magnesium and 2 chlorine
C. 2 magnesium and 1 chlorine
D. 2 magnesium and 7 chlorine
E. Impossible to tell without more info
Magnesium atoms have two electrons
in the outermost shell and chlorine
atoms have seven. The compound
magnesium chloride would contain

A. 1 magnesium and 1 chlorine

B. 1 magnesium and 2 chlorine
C. 2 magnesium and 1 chlorine
D. 2 magnesium and 7 chlorine
E. Impossible to tell without more info
Which of the following nucleotide
bases in DNA can form H-bonds
with the base adenine?
A. Thymine
B. Uracil
C. Guanine
D. Cytosine
E. Both A and B
Which of the following nucleotide
bases in DNA can form H-bonds
with the base adenine?
A. Thymine
B. Uracil
C. Guanine
D. Cytosine
E. Both A and B