Molecular Interactions
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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

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

Molecular interactions

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

Molecular interactions

Structure of Atoms(AKA elements)

  • Some Terminology for you to know:

    • Isotope

    • Atomic Number

    • Atomic Mass

    • Ion

Molecular interactions

Isotopes = Atoms of an element that have different numbers of neutrons. Same Atomic Number, variable Atomic Mass

Much rarer

Most common

Heavy water = ?

Molecular interactions

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

Molecular interactions

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

Molecular interactions

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.

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Molecular interactions


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!

    Molecular interactions

    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

    Molecular interactions

    Ionic Bonding

    Molecular interactions

    Important Ions in Physiology



    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

    Covalent bonds2

    Covalent Bonds

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    Molecular interactions

    Polar Covalent Bond: Water

    The electrons are shared equally

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

    Molecular interactions

    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


    • 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-

    Molecular interactions

    End of Inorganic Chemistry



    • 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

    Molecular interactions


    • 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



    Molecular interactions

    Unsaturated (mono- &

    polyunsaturated) fats

    are liquid at room temp.

    Trans fats have added hydrogen (hydrogenated)

    Triglycerides: 3 FA + Glycerol

    Saturated Unsaturated Polyunsaturated

    Trans fats

    Trans Fats

    Molecular interactions

    • 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.

    Molecular interactions

    • 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



    Molecular interactions


    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

    Molecular interactions


    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

    Amino acids

    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.

    Molecular interactions


    Protein structure

    Protein Structure

    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

    Molecular interactions



    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.

    Activation energy

    Activation Energy

    Fig 4-3

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    The atomic mass of an atom indicates the average total number of

    • Protons

    • Neutrons

    • Electrons

    • Protons, neutrons and electrons

    • Protons and electrons

    Molecular interactions

    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

    Molecular interactions

    Deuterium and Tritium are examples of

    • Elements

    • Ions

    • Buffering compounds

    • Isotopes

    • None of these

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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

    Molecular interactions

    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 sitechange 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

    Reversible reactions follow the law of mass action

    Reversible Reactions Follow The Law of Mass Action

    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

    • PepsinogenPepsin

    • TrypsinogenTrypsin

    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

    Molecular interactions

    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!

    Molecular interactions


    See Fig 2-7

    • Basic formula ? (see name!!)

    • Monosaccharides

      • examples ??

    • Disaccharides

      • examples ??

    • Polysaccharides

      • examples ??

    = simple sugars

    = complex CHOs

    Molecular interactions

    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

    Molecular interactions

    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

    Peptide bond

    Peptide Bond

    Molecular interactions

    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

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