Introductory Biochemistry

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Introductory Biochemistry
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Instructors

• Dr. Nafez Abu Tarboush
• Dr. Mamoun Ahram
• Dr. Said Ismail

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Recommended textbooks

• Biochemistry Mary K. Campbell and Shawn O.
  Farrell, Brooks Cole 6th edition

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Recommended electronic web address

• NCBI Bookshelf
• (http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?db
  Books)
• The Medical Biochemistry Page (http//web.indstat
  e.edu/thcme/mwking/home.html)
• Biochemistry, Garret and Grishan, Second Ed.
  http//web.virginia.edu/Heidi/home.htm

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Outline (Ahram)

• Introduction
• Acid, base, and pH
• Macromolecules and carbohydrates
• Lipids
• Amino acids
• Polypeptides and proteins structure
• Protein analysis

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Outline (Abu Tarboush)

• Protein structure-function relationship (part I
  fibrous proteins)
• Protein structure-function relationship (part II
  globular proteins)
• Enzymes (introduction)
• Enzymes (kinetics)
• Enzymes (mechanism of regulation)
• Enzymes (cofactors)

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Outline (Ismail)

• Nucleic acids structure
• Replication, synthesis, and repair of DNA
• Transcription, synthesis of RNA
• Translation, synthesis of proteins
• Regulation of Gene Expression
• Oncogenes and tumor suppressor cancer
• Recombinant DNA Technology
• Gene Therapy
• Stem cell technology

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Office hours

• Location Faculty of Medicine, first floor
• Time Daily 2-4
• Note If I am not in my office, then try the lab
  in the third floor. Simply ask for me.

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Introduction into biochemistryChemical
composition of living organisms

• Dr. Mamoun Ahram
• Lecture 1

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Reference

• Campbell and Farrell, Page 35-43

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Physiology and biochemistry
Anatomy
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What is biochemistry?

• Biochemistry is the chemistry of living organisms
• It seeks to describe the structure, organization,
  and functions of living matter in molecular terms

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Understanding life

• Know the chemical structures of biological
  molecules
• Understand the biological function of these
  molecules
• Understand interaction and organization of
  different molecules within individual cells and
  whole biological systems
• Understand bioenergetics (the study of energy
  flow in cells)

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Biochemistry and medicine

• diagnose and monitor diseases
• design drugs (new antibiotics, chemotherapy
  agents)
• understand the molecular bases of diseases

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The chemical elements
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Chemical elements in living creatures

• Living organisms on Earth are composed mainly of
  31 elements

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Abundant elements

• Four primary elements carbon, hydrogen, oxygen,
  and nitrogen
• 96.5 of an organism's weight
• The second groups includes sulfur and phosphorus
• Most biological compounds are made of only SIX
  elements C, H, O, N, P, S

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Others

• Minor, but essential, elements
• Mostly metals

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Dalton

• The atomic weight of an atom, or the molecular
  weight of a molecule, is its mass relative to
  that of a hydrogen atom
• Specified in Daltons
• One Dalton equals to the mass of a hydrogen atom

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Chemical bonds
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Types of chemical bonds

• There are two types of chemical bonds between
  atoms
• an ionic bond is formed when electrons are
  donated by one atom to another (example NaCl)
• a covalent bond is formed when two atoms share a
  pair of electrons

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Important properties of bonds

• Bond strength (amount of energy that must be
  supplied to break a bond)
• Bond length the distance between two nuclei
• Bond orientation bond angles determining the
  overall geometry of atoms
• The three-dimensional structures of molecules are
  specified by the bond angles and bond lengths for
  each covalent linkage

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Covalent bonds
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Properties of covalent bonds

• Bond strength The strongest bonds
• Bond length variable
• Bond orientation specific bond angles
  determining the overall geometry of atoms
• The three-dimensional structures of molecules are
  specified by the bond angles and bond lengths for
  each covalent linkage

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Single and double bonds

• Most are single bonds
• Some are double bonds

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Single vs. double bonds

• O, N, S, P, and C atom allow double bonds
• Double bonds are shorter and stronger
• A single covalent bond allows rotation of a
  molecule

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Polarity of covalent bonds

• Covalent bonds in which the electrons are shared
  unequally in this way are known as polar covalent
  bonds

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Examples

• Oxygen and hydrogen
• Nitrogen and hydrogen
• Not carbon and hydrogen
• Oxygen and nitrogen atoms are electronegative
• Water is an excellent example of polar molecules

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Non-covalent interactions
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What are they?

• Reversible and relatively weak
• Electrostatic interactions, hydrogen bonds, and
  van der Waals interactions

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Electrostatic interactions(charge-charge
interactions)

• Formed between two charged particles
• These forces are quite strong in the absence of
  water

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Hydrogen bonds

• The hydrogen atom in a hydrogen bond is partly
  shared between two relatively electronegative
  atoms

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Donor and acceptor
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van der Waals interactions

• The distribution of electronic charge around an
  atom changes with time
• The strength of the attraction is affected by
  distance

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Hydrophobic interactions

• Not true bonds

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Carbon
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Why is carbon important?

• It can form single, double, or triple bonds
• Different geometries
• Rotation
• Stable
• Internediate electronegativity
• Hydrophilic vs. hydrophobinc
• Chains and rings
• backbone
• Versatile three-dimensional structure

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Water
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Polarity of water

• Water accounts for about 70 of a cell's weight
• In the water molecule, oxygen is more
  electronegative than hydrogen therefore, the
  oxygen side of the molecule has a negative charge
  and the other side has a positive charge

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Hydrogen bonds

• Each water molecule can form hydrogen bonds
  through its two H atoms to two other water
  molecules, producing a network

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Properties of water

• Polar molecule
• Bent, not linear, the charge distribution is
  asymmetric
• An excellent solvent
• It weakens electrostatic forces and hydrogen
  bonding
• Small size
• Highly cohesive
• Networks of hydrogen bonds
• Reactive
• Nucleophile
• Ionization

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Organic compounds and functional groups
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Functional groups

• Groups of atoms attached to carbon skeleton
• Usually hydrophilic

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Functional groups

• Hydroxyl group (-OH)
• -Alcohols. eg. ethanol, sugars, phenol
• -Dissolve in water (sugars)
• Carbonyl group (CO)
• aldehyde
• ketone
• Carboxyl group (-COOH)
• Carboxylic acids
• formic acid, acetic acid, amino acids

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Functional groups

• Amino group (-NH2)
• Amines. eg. amino acids
• Sulfhydryl group (-SH)
• Thiols
• Phosphate group
• Phosphate is formed by dissociation of an acid
  called phosphoric acid (H3PO4)