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Molecular Interactions. Or, Chemistry class in one lecture!. Key Concepts. Elements, Atoms, Isotopes etc. Chemical formulas, Chemical bonds pH scale, acids/bases Organic Chemistry / Biochemistry. Element = Building block of matter. In human: 11 major essential elements C, O, H

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Molecular Interactions

Or, Chemistry class in one lecture!

Key Concepts

  • Elements, Atoms, Isotopes etc.
  • Chemical formulas, Chemical bonds
  • pH scale, acids/bases
  • Organic Chemistry / Biochemistry
Element = Building block of matter
  • In human: 11 major essential elements
    • C, O, H
  • Trace Elements (in smaller amounts but still essential)
    • Na, Se, P, Mg, Mn, K, Ca, Fe
Structure of Atoms(AKA elements)
  • Some Terminology for you to know:
    • Isotope
    • Atomic Number
    • Atomic Mass
    • Ion
Isotopes = Atoms of an element that have different numbers of neutrons. Same Atomic Number, variable Atomic Mass

Much rarer

Most common

Heavy water = ?

Some isotopes are unstable: Radioisotopes

3 types of radiation:

  •  radiation – An alpha particle is made up of two protons and two neutrons bound together.
    • Generally not dangerous to life unless inhaled or ingested
    • Does not travel far
some isotopes are unstable r adioisotopes
Some isotopes are unstable: Radioisotopes

radiation - In beta decay, a neutron in the nucleus spontaneously turns into a proton, an electron, and a third particle called an antineutrino. The nucleus ejects the electron and antineutrino, while the proton remains in the nucleus. The ejected electron is referred to as a beta particle.

  • Relatively harmless
  • Medium penetrating power
  • Can mutate DNA if struck
  • Used to kill cancer cells
Nuclear Medicine: use of radioisotopes in

diagnosis & treatment of disease.

127I is “normal” iodine

131I has 4 extra neutrons

 and  radiation

r adioisotopes


  • In spontaneous fission, an atom actually splits instead of throwing off an alpha or beta particle.
  • Gamma rays are made of energy, not moving particles like alpha and beta particles.
  • Gamma Radiation can penetrate thick material
  • Since Gamma Radiation is more penetrating it can cause the most damage to the human body
  • Gamma knife
    • Used for benign or malignant tumors of the brain
Alpha radiation consists of helium-4nucleus and is readily stopped by a sheet of paper.

Beta radiation, consisting of electrons, is halted by an aluminium plate.

Gamma radiation is eventually absorbed as it penetrates a dense material. Lead is good at absorbing gamma radiation, due to its density.

the chemistry of life
The Chemistry of Life
  • Elements = Atoms
    • Nucleus
      • Protons
      • Neutrons
    • Orbit
      • Electrons

Atoms must be neutral

Atoms/molecules that are stable will not bond with other atoms/molecules.

  • Atomic number
      • The number of protons, usually also equals the number of electrons.
  • Atomic mass
    • The sum of the number of neutrons and protons in the nucleus.
shells or orbits
Shells or Orbits

Each electron shell can hold a specific number of electrons

  • Shell 1 = 2e
  • Shell 2 = 8e
  • Shell 3 = 18e
electron bonding
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
  • 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
Chemical Bonds
  • Ions
    • More (or less) electrons than protons
  • Ionic Bonds
    • Anions
      • Negative
    • Cations
      • Positive
ionic bonds
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
chemical bonds1
Chemical Bonds
  • Covalent
    • Polar
    • Non-polar
covalent bonds
Covalent Bonds
  • Strong bonds that occur when two atoms share electrons in order to become more stable
covalent bonds1
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
Polar Covalent Bond: Water

The electrons are shared equally

If two electrons are shared, that is a “double bond.”

Polar covalent molecules

Non-polar covalent molecules

Consequence: ions and polar molecules dissolve well in water

Are call Electrolytes

chemical bonds2
Chemical Bonds
  • Hydrogen Bonds
    • Surface tension
    • Attractive force between water molecules that causes water to form spherical droplets
    • Quickly forms and quickly breaks
  • Types of Reactions
    • Synthesis Reaction--Anabolic
      • A + B C
    • Decomposition Reaction--Catabolic
      • AB A + B
    • Exchange Reaction
      • AB + C AC + B
chemical reactions
Chemical Reactions
  • Reactants form Products
    • First Type of Reaction
      • Anabolic or Synthesis Reaction
chemical reactions1
Chemical Reactions
  • Decomposition Reaction
    • Catabolic
acid base reactions
Acid Base Reactions


    • The concentration Hydrogen ions free in solution
      • Protons
        • H+
  • Bases
    • Are proton acceptors
      • Bind with hydrogen ions
      • Hydroxyl ion = OH-
      • Bicarbonate ion = HCO3-
  • 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
  • CO2 + H2O H2CO3 H++ HCO3-
  • Carbohydrates
  • Fats
  • Proteins
organic compounds
Organic Compounds
  • Carbohydrates
    • A group that includes things like table sugars and starches.
    • Includes Simple and Complex groups
simple carbohydrates
Simple Carbohydrates
  • Simple
    • Monosaccharides
      • Fructose
      • Glucose
    • Disaccharides
      • Sucrose
      • Lactose
simple carbohydrates1
Simple Carbohydrates
  • Examples
    • Candy Bar
    • Soda
    • Table Sugar
    • Fruit
    • Cake
complex carbohydrates
Complex Carbohydrates
  • Examples
    • Wheat
    • Rice
    • Corn
    • Cellulose
    • Potato
organic compounds1
  • Complex Carbohydrates
  • Polysaccharides are long branching chains of glucose molecules.
    • Starch is a carbohydrate stored in plants.
    • Glycogen is a storage carbohydrate in animals.
      • Stored in liver and all muscle types
  • 4 categories:
    • Fatty Acids can be (un)saturated
      • Mono-, di-, and triglycerides
    • Phospholipids (polar)
    • Steroids
    • Eicosanoids (prostaglandins)
organic compounds2
Organic Compounds
  • Lipids, Fats or Triglycerides
    • 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
    • Composed of Glycerol backbone plus 3 fatty acid chains
Unsaturated (mono- &

polyunsaturated) fats

are liquid at room temp.

Trans fats have added hydrogen (hydrogenated)

Triglycerides: 3 FA + Glycerol

Saturated Unsaturated Polyunsaturated

In cis bonds, the two pieces of the carbon chain on either side of the double bond are either both “up” or both “down,” such that both are on the same side of the molecule.
  • In trans bonds, the two pieces of the molecule are on opposite sides of the double bond, that is, one “up” and one “down” across from each other.
  • Naturally-occurring unsaturated vegetable oils have almost all cis bonds, but using oil for frying causes some of the cis bonds to convert to trans bonds.
If oil is used only once like when you fry an egg, only a few of the bonds do this so it’s not too bad.
  • However, if oil is constantly reused, like in fast food French fry machines, more and more of the cis bonds are changed to trans until significant numbers of fatty acids with trans bonds build up.
  • The reason this is of concern is that fatty acids with trans bonds are carcinogenic, or cancer-causing.
  • Modified triglycerides
    • Phosphorous head and two fatty acid tails
  • 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
  • Amphipatic
    • Hydrophilic, as well as Hydrophobic
organic compounds3
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
      • Attaches directly to DNA
      • Starts Transcription of proteins
        • Such as enzymes
    • Cholesterol can be produced through de-novo synthesis

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

organic compounds4
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
    • Made up of 20 amino acids
organic compounds5
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 bonds
Peptide Bonds
  • Two united amino acids form a peptide bond or dipeptide.
  • 50 or more amino acids are called a protein or polypeptide.
    • Less than 50 amino acids are called a peptide
  • Most proteins contain from 1500 to 50,000 amino acids in the human body.
structural levels of proteins
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


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 structure1
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
protein structure2
Protein Structure
  • Change in shape of protein =
    • Change in conformation = Change in configuration .
protein structure3
Protein Structure
  • 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
denature proteins
Denature Proteins
  • Denatured
    • When globular proteins lose their shape they can’t perform their function any longer
    • Proteins are denatures when:
      • pH drops too far
      • Temp rises above 40°C (104°F)
  • 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
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
adenosine triphosphate
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
  • 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.
  • The shape of the active site changes when the protein is denatured so the substrate can no longer bind.
some more characteristics of enzymes
Some more characteristics of enzymes:
  • Usually end in –ase
  • Inactive form: -ogen
  • in few cases RNA has enzymatic activity (eg: rRNA  peptide bond)
naming of enzymes
Naming of Enzymes

mostly suffix -ase

first part gives info on function

  • Kinase
  • Phosphatase
  • Peptidase
  • Dehydrogenase


enzyme biol catalyst
Enzyme = Biol. Catalyst

Some important characteristics of an enzyme:

  • Enzymes are proteins
  •  Rate of chemical reaction by lowering activation energy
  • Is not changed itself
    • It may change DURING the reaction
  • Does not change the nature of the reaction nor the result
  • Is specific
protein molecules
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
  • 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
enzyme activity depends on
Enzyme Activity depends on

Proteolytic Activation (for some)

Cofactors & coenzymes (for some)



Other molecules interacting with enzyme

  • Competitive inhibitors
  • Allosteric modulators
Which of the following statements about proteins is false?

Which of the following statements about proteins is false?

  • All proteins are enzymes
  • A given protein may contain over twenty different amino acids
  • The tertiary structure of a protein results from interactions between its amino acids
  • Proteins are gigantic polypeptides
  • All of the above statements are true.
fatty acids with one or more double bonds are
Fatty acids with one or more double bonds are
  • Unsaturated
  • Have less hydrogen than fatty acids with no double bonds
  • Generally found in plants
  • All of the above
Cholesterol, while it is not an energy molecule, has importance in the body because:
  • It is a stabilizing component of the plasma membrane and is the parent molecule of steroid hormones
  • It helps provide essential nutrients to the brain and lungs
  • It helps mobilize fats during periods of starvation
  • It enters the glycolytic pathway without being altered
When ketone bodies are present in the blood and urine in large amounts, it indicates increased metabolism of:
  • Amino acids
  • Fatty acids
  • Glycogen
  • Lactic acid
The atomic mass of an atom indicates the average total number of
  • Protons
  • Neutrons
  • Electrons
  • Protons, neutrons and electrons
  • Protons and electrons
Elements that have full outer shells of electrons
  • Will form many compounds
  • Will normally form anions
  • Will normally form cations
  • Frequently form hydrogen bonds
  • Are inert, and don’t bond readily with other atoms
Deuterium and Tritium are examples of
  • Elements
  • Ions
  • Buffering compounds
  • Isotopes
  • None of these
When a molecule is referred to as polar, it means that
  • The positive and negative charges of the molecule are unevenly distributed
  • The molecule is ionized and now carries a charge
  • The molecule is likely to dissolve in water
  • A and C are true
  • All of the Above
When a molecule is referred to as polar, it means that
  • The positive and negative charges of the molecule are unevenly distributed
  • The molecule is ionized and now carries a charge
  • The molecule is likely to dissolve in water
  • A and C are true
  • All of the Above
The number of protons in the nucleus of an atom constitutes the
  • Atomic weight
  • Atomic number
  • Atomic mass
  • Nuclear number
a sodium ion with 11 protons but 10 electrons is
A sodium ion, with 11 protons but 10 electrons is
  • Neutral
  • Positively charged
  • Negatively charged
  • Isotope
Suppose you dissolve a little acid in water and determine that the pH of the solution if 5.2. Now you add 100 times as much acid to the solution. Which of the following is the best estimate of the new pH?
  • 3.2
  • 6.2
  • 7.2
  • 8.2
A polypeptide consists of 100 amino acids. How many peptide bonds does it contain?

A polypeptide consists of 100 amino acids. How many peptide bonds does it contain?

  • 50
  • 100
  • 99
  • 101
  • Impossible to say without knowing the exact amino acid composition
Each of the following is a function of proteins except one. Identify the exception.

Each of the following is a function of proteins except one. Identify the exception.

  • Support and structure
  • Transport
  • Carrying of messages
  • Body defense
  • Storage of genetic information
A fatty acid that contains three double bonds in its carbon chain is said to be

A fatty acid that contains three double bonds in its carbon chain is said to be

  • Saturated
  • Monounsaturated
  • Polyunsaturated
  • Hydrogenated
  • Carboxylated
carbohydrates are stored in the liver and muscles in the form of
Carbohydrates are stored in the liver and muscles in the form of:
  • Glucose
  • Triglycerides
  • Glycogen
  • Cholesterol
the subunits of proteins are called
The subunits of proteins are called
  • Fatty acids
  • Carboxyl groups
  • Sugars
  • Amino acids
The bond between an oxygen and a hydrogen atom in a water molecule is a(n)
  • Non-polar covalent bond
  • Polar covalent bond
  • Hydrogen bond
  • Ionic bond
4 molecules interacting with enzyme cont d
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

4 molecules interacting with enzyme
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)

active site
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

isoenzymes different models of same enzyme differ in 1 or few aa
Isoenzymes = different models of same enzyme (differ in 1 or few aa)


  • Amylase
  • 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/LOptimal Adult Reading: 125

Catalyze same reaction but under different

conditions and in different tissues/organs

1 proteolytic activation
1) Proteolytic Activation
  • Also
  • Pepsinogen Pepsin
  • Trypsinogen Trypsin
2 cofactors coenzymes
2) Cofactors & Coenzymes


Inorganic molecules

Cu, Fe, Mg


conformational change of

active site


Organic molecules (vitamin

derivatives, FADH2 ....)


act as receptors & carriers

for atoms or functional

groups that are removed

from substrate

Importance of Electronsin Physiology
  • Ion formation = gain or loss of electrons
  • Bond formation between atoms  molecules
  • Energy capture & transfer
  • Free radical formation

Ions are often called electrolytes!


See Fig 2-7

  • Basic formula ? (see name!!)
  • Monosaccharides
    • examples ??
  • Disaccharides
    • examples ??
  • Polysaccharides
    • examples ??

= simple sugars

= complex CHOs

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

Names of the 2 functional groups ?


  • Made up of amino acids
    • Amino = - NH2
  • Peptide → oligopeptide → polypeptide → protein
  • Most versatile of biomolecules in structure and function

Learn these