introduction to biochemistry
TRANSCRIPT
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.