Introduction to biochemistryIntroduction to biochemistry

MoshtaghiMoshtaghi--KashanianKashanianAssociated professor Associated professor

Kerman University of Medical SciencesKerman University of Medical Sciences

What is Biochemistry

1. Anatomy2. Physiology3. Pharmacology4. Genetic5. Immunology 6. Bacteriology7. Immunology8. Parasitology

1. Internal medicine2. Surgery3. Endocrinology4. Dentistry5. Psychology6. Sociology7. Nursing

Biochemistry is mother of different field in medicine

Definition of Biochemistry

“Chemistry of Life”Living Things are composed of lifeless moleculesDoesn’t fully take into account what chemistry isBiochemistry- Study of the structure, properties and

changes of bio-matter

1. Complex and highly ordered2. Everything has a function3. Living things transform their environment

(extract energy)4. Self-replicating5. Reactions occur at constant temperature,

pressure and pH; in an aqueous environment

Special Considerations

Biomolecules - Elements

C, H, O, N 99% of mass of most cells

P, SMg2+, Na+, K+, Ca2+, Cl-

Fe, Zn, Mn, Co, Cu

Biomolecules - Macromolecules

1. Carbohydrates- made up mostly of 7 monosaccharides

2. Proteins - 5 × 106, made up of 20 amino acids3. Nucleic Acids - 1,000, made up of 4 nucleotides4. Lipids

• 70% of most organisms• polar

• favors solubility• directionality holds macromolecules in given

conformations

Water

• hydrogen bond• half-life < 1/1,000,000 sec• holds water together without being viscous

• high specific heat• colligative properties• weakly ionizable

Water

Sizes of living things

Cell Structure

Cell Membrane

• Appears as 3 layers by EM• 7.5-10 nm thick• “Unit membrane”These three things are explained on

a molecular level as a phospholipid bilayer

Function: osmotic barrierPresent in all cellsFurther consideration in lipid

material.

Nucleus• Bounded by a porous

nuclear membraneFunction: contain DNAPresent in all eukaryotic

cells• 1 per cell• Often 1-4 nucleoli

The nucleus and the nuclear envelope

Cell Wall & cell membraneThick, tough wall

Function: rigidityPresent in plant and prokaryotic cells

Animal cell anatomy

Plant cell anatomy

Mitochondria

• Shape varies, size varies• 500-2,000 per cell

Mitochondria

Function: “powerhouse of the cell”Present in all eukaryotic cellsStructure: compartmentsFurther consideration in metabolism.

Endoplasmic ReticulumRough and Smooth

Phospholipid bilayer surrounding a lumen ± ribosomesFunction: protein synthesis (rough) lipid synthesis (smooth)Present in all eukaryotic cells (lots)

Rough Endoplasmic Reticulum

Surface looks rough because of the presence of ribosomes, another organelle (present in all cells)

Golgi Apparatus

Historically cis, medial and trans: trans-golgi network

Function: protein processing and secretion

Present in all eukaryotic cells (lots)

Lysosomes

• About as big as a mitochondrion

• not much to seeFunction: degradation of

proteinsPresent in animal cells, plant

cells have similar organelle called peroxisome

Number per cell varies enormously

Chloroplasts

• Stacks of “grana”• grana composed of

thylakoid disksFunction: photosynthesisPresent in photosynthetic

cells50-200 per cell

CytoplasmAqueous, solute-containing contents within the plasma

membraneContains soluble proteins, salts, organellesCytosol- is the supernate of a centrifugation process

Microtubules• Polymer of a protein called actin• Gives shape to cell, also functions in transport

around the cell

4 classes of macromolecules

Carbohydrates: Energy, structure

Lipids: Energy, membranes

Proteins: Catalysts, structure, etc.

Nucleic Acids: Information

Glucose isomers

Macromolecules: Carbohydrates

Carbohydrates

Macromolecules: Carbohydrates

Polymerization

glucose fructose sucrose

Making & breaking polymers

starch

glycogen

Storage polysaccharides

Cellulose: A structural polysaccharide

Chitin: a structural polysaccharide

Fatty acids & triacylglycerol

Cholesterol: a steroid

Polar & charged amino acids

Nonpolar amino acids

Macromolecules: Proteins

Structural proteins

Protein Structure: 4 Levels

Primary

Secondary

Tertiary

Quaternary

Primary structure of protein:the amino acid sequence

lysozyme

Amino Acid Structure

R is different for different amino acids.

Polymerization is peptide bond

formation

Primary structure of protein:the amino acid sequence

lysozyme

Primary structure is due to strong covalent peptide bonds joining amino

acids together.

Secondary structure:group of amino acids folded repetitively to

make a discrete shape.

lysozyme

Secondary structure:group of amino acids folded repetitively to

make a discrete shape.

lysozyme

due to hydrogen bonds between

amino acids’backbones.

Tertiary structure:

the overall 3-d conformation of a polypeptide.

lysozyme

Tertiary structure

involves several kinds of bonds.

Tertiary Structure

Most proteins are hydrophilic outside, hydrophobic inside.

Macromolecules: Nucleic Acids

Deoxyribonucleic Acid

Nucleic Acids are Polymers

pH and Buffers

Water is Weakly Ionizable

• 2 H2O <===> OH– + H3O+

• Weakly means this doesn’t happen often• [OH–] = [H3O+] = 1 × 10-7 M,• [OH–] × [H3O+] = 1 × 10-14, the basis of the pH

scale

Equilibrium Constants Mathematically Represent Degree of

DissociationKeq’ is used in biochemistry to denote modified standard state.

pKa’ Values are Used to Describe Ionization of Acids

• CH3COOH + H2O <===> CH3COO– + H3O+

• Keq’ =• Ka’ = 1.74 x 10-5 =• pKa’ = 4.76

Graphical Determination of pKa’• The pKa’ is the pH at the

point where buffering occurs

Buffers

Buffer- a compound that does not allow the pH to change even if acid or base is added to the system.

Amphiprotic compounds are also good buffers.

Amphiprotic compound- a compound that can act as a proton donor or as a proton acceptor.

[HA]

[A–]pH = pKa’ + log

[acid]

[salt]or pH = pKa’ + log

The Henderson-Hasselbalch Equation is Used to Determine the pH of

Buffered Solutions

When pH = pKa’, There is Equal Amounts of A– and HA

• Proof on board

pH Problems

What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of H2O?

What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 1 M HEPES initially at pH 7.6?

What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 50 mM HEPES initially at pH 7.6?

Choosing a Buffer

• pKa ± 0.5 pH units• ionic strength: use 50 or 100 mM• metal ion chelation, etc.