Introduction to biochemistry

Moshtaghi-Kashanian Associated professor Kerman University of Medical Sciences

What is Biochemistry
Biochemistry is mother of different field in medicine
1. 2. 3. 4. 5. 6. 7. 8.

Anatomy Physiology Pharmacology Genetic Immunology Bacteriology Immunology Parasitology

1. 2. 3. 4. 5. 6. 7.

Internal medicine Surgery Endocrinology Dentistry Psychology Sociology Nursing

Definition of Biochemistry
Chemistry of Life Living Things are composed of lifeless molecules Doesnt fully take into account what chemistry is Biochemistry- Study of the structure, properties and changes of bio-matter

Special Considerations
1. Complex and highly ordered 2. Everything has a function 3. Living things transform their environment (extract energy) 4. Self-replicating 5. Reactions occur at constant temperature, pressure and pH; in an aqueous environment

Biomolecules - Elements
C, H, O, N 99% of mass of most cells

P, S Mg2+, Na+, K+, Ca2+, ClFe, Zn, Mn, Co, Cu

Biomolecules - Macromolecules
1. Carbohydrates- made up mostly of 7 monosaccharides 2. Proteins - 5 106, made up of 20 amino acids 3. Nucleic Acids - 1,000, made up of 4 nucleotides 4. Lipids

Water

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

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 barrier Present in all cells Further consideration in lipid material.

Nucleus
Bounded by a porous nuclear membrane Function: contain DNA Present in all eukaryotic cells 1 per cell Often 1-4 nucleoli

The nucleus and the nuclear envelope

Cell Wall & cell membrane

Thick, tough wall Function: rigidity Present 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 cells Structure: compartments Further consideration in metabolism.

Endoplasmic Reticulum Rough and Smooth

Phospholipid bilayer surrounding a lumen ribosomes Function: 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 see Function: degradation of proteins Present in animal cells, plant cells have similar organelle called peroxisome Number per cell varies enormously

Chloroplasts
Stacks of grana grana composed of thylakoid disks Function: photosynthesis Present in photosynthetic cells 50-200 per cell

Cytoplasm
Aqueous, solute-containing contents within the plasma membrane Contains soluble proteins, salts, organelles Cytosol- 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

Macromolecules: Carbohydrates

Glucose isomers

Macromolecules: Carbohydrates

Carbohydrates

Polymerization

glucose

fructose

sucrose

Making & breaking polymers

Storage polysaccharides starch

glycogen

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

Primary structure is due to strong covalent peptide bonds joining amino acids together.
lysozyme

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.

due to hydrogen bonds between amino acids backbones.

lysozyme

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 doesnt 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 Dissociation Keq 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.

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

pH = pKa + log [A] [HA] or pH = pKa + log [salt] [acid]

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.