BIOCHEM CH. 1: Overview
Terms in this set (46)
biochemistry is the study of ...?
which study intensified the study of biochemistry?
discovery that biological molecules such as urea could be synthesized in 1828
development of the ___ revealed a key ____ feature that underlies the diversity of life
microscope; unifying--everything is related
proteins and nucleic acids
low molecular weight molecules examples. these are referred to as ___. what happens to these molecules in biological processes?
glucose and glycerol; metabolites; they are transformed
besides structure and composition, what is another key unifying feature common to many organisms?
metabolic processes--for ex. how plants and animals acquire energy and convert it to more useful forms
DNA illustrates the interplay btw ___ and ___
know structure of DNA
why is DNA held together by weak bonds such as hydrogen bonds?
weak enough to reversibly broken in biochemical processes but strong enough to help stabilize structure of double helix
how structure of DNA explains heredity and storage of information (form and function)
1. structure compatible with any sequence of bases
2. sequence is how information is stored
3. since each strand complementary, if they should get separated, one strand can act as template
relationship btw resonance and stability
more resonance = more stability (covalent bonds)
4 noncovalent interactions
hydrogen, van der Waals, ionic and hydrophobic
another term for an ionic interactin
an attractive interaction has a positive or negative energy?
what are hydrogen bonds technically?
largely ionic interactions with partial charges on nearby atoms attracting one another. The H atom is partially shared by two electronegative atoms such as N or O.
what is the hydrogen bond donor?
group that includes both the atom to which the H atom is more tightly linked and the H atom itself
what is the hydrogen bond acceptor?
the atom less tightly linked to the H atom
describe van der waals interactions
the distribution of electronic charge around an atom fluctuates with time.
2 important properties of water
2. cohesive thru H bonds
what is the hydrophobic effect?
nonpolar molecules interact with each other and release H2O surrounding them in a "cage" causing more entropy vs order when they are in "caged" form. free H20 can interact with freely with bulk water.
importance of Na+ and Mg2+ in formation of DNA helix
initially, ionic interactions caused by negative charge of phosphate groups oppose the formation of helix. these repulsive ionic interactions are neutralized by high dielectric constant of water and through ionic species such as Na+ and Mg2+ which are positive and partially neutralize the negative charge on phosphates.
other important reason for H bonds in formation of double helix
important in determining complementarity of bases. contribute to specificity of binding when 2 strands of DNA break H bonds with water to form H bonds in helix.
describe base stacking in DNA. is there base stacking in ssDNA?
base pairs are parallel and stacked on top of one another with distances btw each other that corresponds nicely with van der Waals contact distance. there is base stacking in ssDNA but are more optimal in dsDNA.
hydrophobic interactions contribute to base stacking in DNA. what is the effect?
more complete base stacking moves the nonpolar surfaces of the bases out of water into contact with each other
how is surface complementarity a key feature in DNA?
when complementary surfaces meet, H bond donors align with H bond acceptors and nonpolar surfaces come together to maximize van der Waals interactions and minimize nonpolar surface area exposed to the aqueous envmt
definition of "system"
matter within a defined region of space
term for matter outside the "system"
First Law of Thermodynamics
total energy of a system and its surroundings is constant
Second Law of Thermodynamics
the total entropy of a system plus that of its surroundings always increases
when can entropy decrease in a favorable way?
entropy may be decreased locally if in the formation of such ordered structures only if the entropy of other parts of the universe is increased by an equal or greater amount such as releasing E in form of heat which increases entropy of the surroundings
Thermodynamics Equations pg 12
Gibbs Free Energy
free energy must be positive or negative for a process to take place spontaneously?
there is negative free energy change when and only when...?
the overall entropy of the universe in increased
formation of double helix leads to more organization and less entropy. How can double helix form without violating 2nd Law?
releases a lot of heat to surroundings increasing entropy in the universe
acid base formulas
what is the Ka?
what does the pKa indicate?
susceptibility of a proton to removal by reaction with a base
how does adding base disrupt the double helix?
OH- ions can react with bases in DNA base pairs to remove certain protons. The most susceptible proton is the one bound to the N-1 nitrogen atom in a guanine base. (pg 14)
when pH equals pKa, what does this tell you about concentrations of [H+] and [A-]?
the [ ] of the deprotonated form of the group or molecule is equal to the [ ] of the protonated form (pg. 15 has derivation of pH)
how does adding acid disrupt the double helix?
some of the H bond acceptors that participate in base-pairing become protonated. In their protonated forms, these bases can no longer form H bonds and the double helix separates.
what is titration?
the process of gradually adding known amounts of reagent to a solution with which the reagent reacts while monitoring the results
how does sodium acetate buffer the addition of HCl in water?
H+ from HCl react with acetate ions forming acetic acid until all acetate ions are bound leaving remaining H+ free in solution which lowers the pH
what is the important buffer in biological systems?
phosphoric acid (H3PO4) which can be deprotonated in three steps to form PO4^3-. physiological pH is about 7.4 and inorganic phosphate exists primarily as a nearly equal mixture of H2PO4- and HPO4^2- at this pH. so they function as elective buffers at pH 7.4. (pg 16)
differences btw DNA and proteins
1. proteins built from 20 building blocks and DNA from 4
2. proteins spontaneously fold into elaborate 3D structures determined by only by their AA sequences
what overcomes the entropy lost from the folding of proteins into 3D structures?
balance of H bonding, van der Waals interactions and hydrophobic interactions
definition of "genetic code"
set of rules that links the DNA sequence to the encoded protein sequence