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1. What does biochemistry translate to?
2. When was the origin of life?
3. What underlies all biodiversity?
4. How does life express itself?
5. Give examples?
- 1. The study of the chemistry of life
- 2. 3 billion years ago
- 3. Chemical unity
- 4. Through biomolecules: monomer--->polymer-->life
- 5. Glucose/nucleotides/AAs --> glycogen/DNA/proteins/enzymes --> life
Name the 4 main types of biomolecules and two other things.
Name examples for each.
- 1. Proteins (enzymes, polypeptides)
- 2. Nucleic Acids (DNA/RNA)
- 3. Lipids (fatty acids, etc)
- 4. Carbs (glycogen, starch, cellulose)
- 5. Ions (Na,K+, Cl-)
- 6. Small molecules (CoA, FAD, NAD+, NADP+)
1. What does biology obey?
2. What influences the behavior of biological systems?
3. Which rxns are highly exergonic?
4. List the three rxns that determine the tendency for a chemical rxn to proceed in a certain direction
- 1. Laws of thermodynamics
- 2. Physical forces (entropy, etc)
- 3. Rxns converting ATP --> ADP + Pi and ADP --> AMP + Pi.
1. What are other laws followed by biology? (3)
2. Which organisms require water?
3. What are interesting things about water? (3)
4. Additionally, what are physical properties of water due to hydrogen bonding? (3)
5. Molecular geometry? Bond angle? Why?
- 1. Henderson Hasselbalch, electrochemistry, and Keq
- 2. ALL
- 3. Influences 3D structures of macromolecules, most rxns take place in aq solutions, and water can be an active participant in a rxn
- 4. High BP, MP, and heat of vaporization
- 5. Tetrahedral, 104.5 (instead of 109.5) b/c of crowding by lone pairs on O.
1. Define a hydrogen bond
2. What are examples of biologically important H bonds? (4)
3. Why is ice denser than water?
4. What is stronger? Linear H bonds or non-linear?
- 1. A weak chemical bond between an EN atom (FON) and H bound to another EN atom.
- 3. B/c ice has more H-bonds (4 vs. 3.4) --> less density.
- 4. Linear. Non-linear (bent) is weaker b/c of strain.
1. Compare bond strength of H bond vs. C-C bond?
2. How can H-bonding play an important role in the interactions of biomolecules?
3. How does water interact w/ polar solutes?
4. W/ salts (crystalline lattices?) Why?
5. How does water interact w/ nonpolar solutes?
- 1. 20 kJ/mol (weak) vs. 350 kJ/mol (strong).
- 2. Individually, H-bonds are fairly weak (relative to noncovalent/covalent intx), but mayn H-bonds together can yield great stability (strength & flexibility) --> DNA.
3. Readily dissolves most biomolecules (b/c most biomolecules are polar/charged)
4. Dissolves salts easily b/c increase in entropy contributes to a negative dG (overcomes energy needed to break the bonds)
5. Nonpolar compounds force energetically unfavorable changes in structure of water --> increases dH --> dS decreases b/c H2O in the immediate vinicity of the nonpolar solute are constrained in their possible orientations forming water "cage."
1. How does water interact with amphiphillic solutes? Are these molecules static?
2. What is the key to hydrophobic collapse? what is this important for?
3. What allows for ordered formation of micelle?
1. Formation of micelles with water surrounding polar head group w/ CHO tails on the inside. NO they are in motion
2. Coalescence of nonpolar groups on the inside of aqueous solution --> why proteins fold.
3. Overall increase in entropy in water from containing nonpolar solutes allows micelle formation.
1. What mediates almost every process?
2. What is the most abundant biomolecule in the cell? At what %? What is the most abundant molecule in the cell?
3. Can we make all of our proteins and nucleic acids de novo?
- 1. Proteins
- 2. Proteins 15%, H2O (40%)
- 3. No. Bacteria can, but we can't. We need 8 essential amino acids.
1. Name 7 roles of protein - what does this show?
- 1. Ligand transport
- 2. Enzymes
- 3. Transcription factors
- 4. Redox reactions (ex., ETC)
- 5. Immune response (immunoglobulins)
- 6. Cytoskeleton structure
- 7. Membrane transport/receptors
It shows that proteins play a role in just about every biological process.
1. Draw the basic structure of an amino acid and describe each part. What are the charges at physiological pH?
2. What is deprotonated first?
3. How does charge of the amino acid change as pH increases?
It's a zwitterion at phys pH (7.2).
2. COOH (carboxylic ACID) is always deprotonated first!
3. Becomes increasingly more negative.
- a. I
- b. II
- c. IV
- d. II
- e. IV
- f. II & IV.
- g. III
- h. III
- i. V
- j. III
- k. V
- l. II
- m. III
- n. V
- o. I, III, V
1. What are the three types of amino acid side chains? What is Pk1 usually? Pk2?
2. What is the henderson hasselbach equation?
3. What is the only thing that makes amino acids unique?
4. What type of amino acids are found in living things? What type of monosaccharides?
5. Draw L-alanine, given D-alanine below
1. Nonpolar, polar uncharged, and charged (can be positive or negative)
- 2. pH = pKa + log [A-]/[HA]
- 3. Their side chains
- 4. L, D
1. How are amino acids classified?
2. Which structures contain S?
3. Which two non-charged amino acids have a pK value?
- 1. Based on the structure and chemical properties of their R groups
- 2. Methionine (nonpolar) & cysteine
- 3. Tyrosine (10.7 - OH group) and Cysteine (8.18 SH group), both originally neutral.
1. At what nm do nucleic acids absorb light at? 2. What about aromatic compounds?
3. Why do aromatic compounds absorb light?
4. Are aromatic R groups polar or nonpolar? Except?
5. Which absorbs more intensely, tyrosine or tryptophan? Why?
6. Which charged amino acid is most useful for acid base conditions under physiological conditions? Why?
- 1. 260 nm
- 2. 280 nm
- 3. Because they have conjugated rings and double bonds which can absorb light
- 4. Relatively nonpolar, except tyrosine which is polar uncharged at phys pH.
- 5. Tryptophan (4x more intensely at280 nm) b/c of extra conjugated ring.
- 6. Histidine bc its pR value is ~6 (close to phys pH).
1. Which molecules are negatively charged at pH = 7? Which are positively charged?
2. How do peptide bonds combine? Draw picture
3. What is the key to peptide bonding?
4. What causes directionality? How are proteins written?
1. Acidic amino acids; basic AAs
2. COOH + HNH
3. the C-N bond has 40% partial double bond character due to resonance.
4. terminal charges