biochem lecture 1

definition of life? NASA?

no singular definition. NASA = self-sustaining chemical system capable of Darwinian evolution

4 properties of all cells

1. PM,

2. cytosol,

3. dsDNA genes,

4. take up/use E:

   1. energy = photo/chemotroph

   2. carbon = auto/hetero

jacques monod

biochemist that said "what is true for e coli is true for the elephant"

prok v. euk:

1. size

2. complexity

3. gene location

4. structures

1. proke

   1. small 2 um

   2. simple, unicellular,

   3. nucleoid and plasmids

2. euk

   1. large 10-100 um

   2. complex, multicellular,

   3. nucleus and membrane bound organelles

the inside of cells are jam packed w/ mCs. how are precise reactions possible in this environment?

compartmentalization: localized chemical conditions created in organelles

angstrom

1E-10 m , 0.1 nm

1. # of mCs required for life? why do we all share these?

protein specifically?

2. how did first biomolecules form

1. 33

2. protein = L-amino acids

2. "primordial soup" of H2, H2O, CH4, NH3, SO2, and HCN in a reducing environment

3 fundamental properties of all cells

1. have PM

2. have cytosol

3. genes contained in nucleoid or nucleus

size of cell limited by

need to deliver oxygen to all parts of cell

size/ distance b/t:

1. peptide bond

2. 1 turn DNA

3. distance b/t bp DNA

1. 1.3 Angstroms

2. 34 Angstroms

3. 3.4

1. 4 major types of biomolecules?

2. which 3 can form polymers and why?

3. what bonds hold polymers together?

3. why doesn’t 1 form polymers?

1. proteins = polymer of AA = covalent peptide bond

2. nucleic acids = polymer of nucleotides = covalent phosphodiester bond

3. polysaccharides = polymer of sugars = covalent glycosidic bond

4. lipids dont = bc large lipid molecules like membranes aren't covalently bonded

3 main carbon the base element of life?

1. can form 4 highly stable covalent bonds

2. high functionality (single, double, trip bonds w/ C,O,N,S,H

3. can form long C-C chains

oxide is a soluble gas that is chemically available

why carbon not silicon

1. C-C bond stronger

2. C-C stable to H2O

3. oxide CO2 is a gas not solid... you can get rid of it

biochemist's periodic table:

1. how many elements essential for life?

2. what 4 elements make up >99% of cell mass

3. # bulk elements v trace elements

4. importance of trace elements

1. 30

2. C H O N

3. 10 and 12

4. important roles

what makes water special

1. liquid

2. polar

a. dissolves ions and polar compounds,

b. doesn't dissolve nonpolar -> lipid membranes

3. can be a reactant in chemical processes

why is water a liquid

Liquid water is a fluid due to the constant forming and breaking of relatively weak hydrogen bonds

high dielectric constant of water allows? how?

1. dissolve ions and polar compounds

2. forms solvation shell around ions through electrostatic interactions

hydrogen bonds:

1. what are they

2. 2 reasons why special?

3. where do they form/how drawn?

1. relatively weak electrostatic interactions, neither ionic nor covalent

2a. makes water a liquid bc strong enough to order itself into water but still relatively weak

b. allow water to dissolve polar uncharged molecules,

c. allow lipid membranes

b. can mediate interactions b/t molecules

2. triple horizontal lines b/t H (hydrogen donor) and almost any other electronegative atom (hydrogen acceptor)

why are hydrophobic groups not soluble in water? 3 steps?

1. driven by an increase in entropy of water

2a. lipids dispersed in H2O = highly ordered lattice of H2O, low entropy

b. lipids begin to cluster due to hydrophobic interactions = fewer ordered H2O mCs, higher entropy

c. more hydrophobic interactions cause Micelles to form = minimal ordered H2O shell, high entropy

3 ways water is a reactant in biochemical processes:

1. acid/base properties (ionization)

a. 2H2O <-> H3O+ + OH-

b. H3O+ <-> H2O + H+

2. often a direct participant in reactions

a. condensation/hydrolysis reactions

-condensation = water forms (like condensation) and 2 mCs condense into 1 big one

-hydrolysis = split a H2O mC

b. oxidation/reduction reactions

-oxydation forms O2 from 2 O-containing mCs

4 non-covalent bonds that are important in biological structure and function

1. ionic

2. hydrogen

3. hydrophobic/hydrophillic interactions = protein folding

4. van der Waals interactions = lipid bilayers

why does water buffer against pH changes? 2 reasons why important

1. mixture of weak acid/base and its salt resist changes in pH thus acts as a buffer

2a. phosphate and other salts keep bodily pH near 7.4 and that's where macromolecules retain their structural function. also,

b. enzymes work best at certain pH and enzymes that work in certain cellular compartments show greatest actiity at those pH values

ender v exergonic? reactions that convert ATP to P + ADP? hydrophobic reactions?

1. exergonic = free energy released = -deltaG = happens spontaneously

2. both exergonic