Střední doba kamenná Mladší doba kamenná Pozdní doba kamenná
Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon...
-
Upload
georgina-jordan -
Category
Documents
-
view
223 -
download
3
Transcript of Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon...
![Page 1: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/1.jpg)
Foundations of Biochemistry
Doba Jackson, Ph.D.
Dept. of Chemistry & Biochemistry
Huntingdon College
![Page 2: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/2.jpg)
What distinguishes living organisms from other forms of matter?
• High degree of chemical complexity and organization (muscle tissue)
• System for extracting energy from the environment (bird)
• The ability to self-replicate (zebra)
• Ability to sense changes in the surroundings and respond
• Defined functions of each component and regulated interactions
• The ability to adapt with time (evolution)
![Page 3: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/3.jpg)
Chemical Foundations
“What are the common chemical principals important to all cells”
![Page 4: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/4.jpg)
Only 30 of the 90 naturally occuring elements are found
in biological systems
![Page 5: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/5.jpg)
Components of macromolecules: the ABC’s
of BiochemistryProteins Nucleic Acids Lipids
Carbohydrates
![Page 6: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/6.jpg)
You must remember all of these functional groups!!!!!
Biomolecules are hydrocarbons with attached
functional groups
![Page 7: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/7.jpg)
What do these have in common?
Hydrocarbons
![Page 8: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/8.jpg)
What do these have in common?
All have carbon-oxygen bonds
![Page 9: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/9.jpg)
What do these have in common?
All have carbon-nitrogen bonds
![Page 10: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/10.jpg)
What do these have in common?
All have carbon-sulfur bonds
![Page 11: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/11.jpg)
What do these have in common?
All have carbon-phosphate bonds
![Page 12: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/12.jpg)
Some Definitions
• Chiral center- a carbon atom with four different a substituents (ie.- asymmetric carbon)
• Enantiomers- pairs of stereoisomers that are mirror images of each other.
• Diastereomers- pairs of stereoisomers that are not mirror images of each other.
![Page 13: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/13.jpg)
4 substituents 3 substituents
Enantiomers Same molecule
![Page 14: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/14.jpg)
Example: 2,3 disubstituted butanes
![Page 15: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/15.jpg)
Stereoisomers distinguisable by taste
Aspartate
Phenylalanine
![Page 16: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/16.jpg)
Summary of chemical foundations
• Only 30 of the 90 naturally occuring elements are found in biological systems
• 99.9% of biomolecules are considered organic compounds
• Most biomolecules have more than one functional group
• Conformation, configuration, and constitution are all important factors for determination of biological activity
![Page 17: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/17.jpg)
Aqueous SolutionsBy Doba D. Jackson, Ph.D.
Dept. of Chemistry & BiochemistryHuntingdon College
![Page 18: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/18.jpg)
Why study Water
• Water is the most abundant chemical in living systems making up to 70% of the mass of most organisms.
• The attractive forces between water molecules and the slight tendency of water molecules to ionize are of crucial importance to the structure and function of biomolecules.
![Page 19: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/19.jpg)
Outline of Discussion
• Weak interactions in aqueous solution– Hydrogen Bond– Nonpolar compounds and water insolubility– Hydrophobic interactions, van Der waals interactions
• Ionization of water, weak acids and bases– Review acids, bases, Kw and pKa
• Buffers, pH changes in biological systems– Phosphate, Carbonate buffers in living organisms– Tris, HEPES buffers commonly used in laboratories
![Page 20: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/20.jpg)
![Page 21: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/21.jpg)
Structure of a water molecule
Less than 109.5º
- The Oxygen bears two partial negative charges each aligned with the p-orbitals.
- Each Hydrogen bears a positive charge
aligned 104.5º from the OH bond.
![Page 22: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/22.jpg)
The Hydrogen Bond
“I believe that as the methods of Structural chemistry (x-ray crystallography) are further applied to physiological problems, it will be found that the significance of thehydrogen bond for physiology is greater than that of any other single structural feature” -Linus Pauling, The Nature of the Chemical Bond (1939)
![Page 23: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/23.jpg)
The Hydrogen Bond
- The hydrogen atom becomes between covalently bound oxygen and the oxygen aligned from its neighbor.
- The hydrogen bond has a dissociation energy of 23 kJ/mol (compared to 470 kJ/mol).
- Based on orbital overlap, the hydrogen
bond is 10% covalent and 90% electrostatic.
- The total hydrogen bond length is
approximately 2.8 Ǻ (~ 3 Ǻ).
![Page 24: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/24.jpg)
Hydrogen bonding in ice
- Solid ice
2 covalent bonds 4 hydrogen bonds 6 total bonds
- Liquid water
2 covalent bonds 2.4 hydrogen bonds 4.4 total bonds
![Page 25: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/25.jpg)
Hydrogen Bonds other than water
Any electronegative atom (usually N, O) with a pair of electrons can attract a hydrogen attached to another electronegative atom.
![Page 26: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/26.jpg)
Examples of Biologically important hydrogen bonds
Alcohol & water
Ketone & water
Between amino acids in proteins DNA
strands
![Page 27: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/27.jpg)
Water as a solvent
- Polar solutes: compounds that have polar bonds; usually dissolve easily in water.
- Nonpolar solutes: compounds that do not have polar bonds; usually difficult to dissolve in water but dissolves easily in nonpolar solvents (hexane, chloroform or benzene).
- Amphipathic solutes: compounds with polar and nonpolar groups; solubility will vary.
![Page 28: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/28.jpg)
![Page 29: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/29.jpg)
![Page 30: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/30.jpg)
– Water at a hydrophobic surface loses a hydrogen bond.
– Water molecules compensate for this by creating a low-density water network with lower entropy directly surrounding the hydrophobic solute.
– Water covers the surface with clathrate-like hexagons, so avoiding the loss of most of the hydrogen bonds.
What happens to the structure of water at a hydrophobic
interface?
![Page 31: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/31.jpg)
![Page 32: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/32.jpg)
Hydrophobic Effect
![Page 33: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/33.jpg)
Release of ordered water can drive the formation of an enzyme-
substrate complex
![Page 34: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/34.jpg)
Review weak (noncovalent) molecular interactions
• Electrostatic (ionic) interactions- The attractive forces between oppositely charges molecules or functional groups.
• Hydrogen Bonds- an interaction between a hydrogen covalently attached to an electronegative atom and the electron pair of another electronegative atom.
• Hydrophobic interactions- the strong tendency of water to minimize the surface area surrounding nonpolar groups or molecules.
• Van der Waals forces- are the result of induced electrical interactions of closely approaching atoms as their negative electron clouds fluctuate with time.
![Page 35: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/35.jpg)
Van der Waals forces
![Page 36: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/36.jpg)
Van der Waals forces .4 – 4.0 .3 - .6
Hydrogen bonds 12 – 30 .3
Ionic interactions 20 .25
Hydrophobic interactions
<40 >1
Strength(kJ/mol)
Distance(nm)
Weak chemical forces and their strengths and distances
Hydrophobic interactions can act across very large distances which makes these interactions very dominant
in determining macromolecular structure and function
strength
![Page 37: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/37.jpg)
“Proton hopping” common in enzymes that translocate protons
across cell membranes
Cytochrome f; in photosynthesis
![Page 38: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/38.jpg)
Weak interactions are crucial to macromolecular structure and function
• For macromolecules (DNA, RNA & proteins) the most stable structure is one that maximizes the weak bonding possibilities.
![Page 39: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/39.jpg)
![Page 40: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/40.jpg)
Titration curves can reveal dissociation constants (pKa) and buffer ranges
![Page 41: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/41.jpg)
Henderson-Hasselbalch Equation: relationship between pH, pKa and buffer concentrationsCH3COOH CH3COO- + H+
3
3
3
3
3
3
3
3
3
3
a
a
a
a a
a
a
CH COO H
CH COOH
CH COO HLog K Log
CH COOH
CH COOLog K Log Log H
CH COOH
pK Log K
pH Log H
CH COOpK Log pH
CH COOH
CH COOpH pK Log
CH COOH
K
![Page 42: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/42.jpg)
![Page 43: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/43.jpg)
Typically a buffer is best when it is within .5 units of
its pKa
![Page 44: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/44.jpg)
Blood, Lungs and extracellular fluid is
buffered by carbonateVigorous Exercise(lactic acid)
Blood, extracellular Fluid
Lungs, Air space
Vigorous Exercise
Typical catabolismraises pH
Typical catabolismraises pH
![Page 45: Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College.](https://reader035.fdocuments.net/reader035/viewer/2022062409/5697c01b1a28abf838ccfa04/html5/thumbnails/45.jpg)
Enzymes have specific pH optimums due to the combination of many
functional groups