Lecture 1 Flashcards
define cytoplasm
the internal volume enclosed by the plasma membrane
define plasma membrane
the periphery of the cell, separating its contents from the surroundings
define cytosol
an aqueous solution, highly concentrated with enzymes and the RNA molecules that encode them, etcs., that makes up the cytoplasm
define genome
the complete set of genes, composed of DNA
what are the 6 simple elements that are essential to an organisms’s existence and function?
carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur
why are cellular organism carbon based?
bonding versatility
true or false? if false, correct the statement
Single bonds can rotate freely
true
freedom of rotation around single bonds allows for _____ _____ and different _____
freely interconvertible; conformations
what type of bonds do not have free rotation?
double bonds
what do the restricted rotation of double bonds produce?
isomers with different configurations
what do geometric isomers need to be interconverted? does anything need to break?
they require energy to break the double bonds
a atom that is attached to 4 different groups has a ….
chiral center
if a molecule is chiral it cannot be ______ on its mirror image
superimposable
all chiral molecules have at least how many chiral center?
1
find the word: something can be placed on top of another object and align exactly with it, so that no difference is noticeable
superimposable
what is the biggest difference between a molecule being chiral or achiral?
achiral molecules are superimposable
if a molecule is superimposable, it has to be ______
achiral
are enantiomers mirror images or not mirror images?
mirror images
are diastereomers mirror images or not mirror images?
not mirror images
what formula gives you the amount of stereoisomers based on the chiral carbons?
n chiral carbons gives 2^n stereoisomers
what functional group is this?
hydroxyl
what functional group is this?
methyl
what functional group is this?
carbonyl (ketone)
what functional group is this?
carboxyl
what functional group is this?
ester
what functional group is this?
phenyl
what functional group is this?
sulfhydryl
what functional group is this?
disulfide
what functional group is this?
amino
what functional group is this?
phosphoryl
what functional group is this?
phosphoanhydride
as an open system, what can a living organism exchange with its surroundings?
matter and energy
where do organisms derive energy from?
their surroundings
what is the first law of thermodynamics?
conservation of energy
i.e. energy cannot be created or destroyed but can change forms
what is the second law of thermodynamics?
the entropy of the universe increases
what is entropy?
a measure of a system’s disorder or randomness
what state will a spontaneous process proceed towards?
one with the least potential energy
does the disorder in the universe increase or decrease in a spontaneous process?
increase
what does thermodynamics ultimately tell us?
if a reaction is possible and whether it will occur spontaneously
does the building of organisms require energy?
yes
how is Gibbs free energy defined?
usable energy content of a biological system
match the word to the definition
enthalpy
entropy
measure of disorder
heat content of the system
entropy - measure of disorder
enthalpy- heat content of the system
what must be the overall charge in free energy for a process to occur?
negative
true or false? if false, correct the statement
free energy of the reactants must be greater than the free energy of the products
false; Free energy of the products must be less than the
free energy of the reactants
fill in the blanks
fill in the blanks
as the volume of a substance increases so must its….
entropy
entropy is a function of …
concentration
true or false? if false, correct the statement
The free energy change of a chemical reaction depends
on the concentrations of reactants and products
true
what are three main points about a reaction being at equilibrium?
- rate of product formation equals the rate at which product is converted to reactant
- no net change in [ ] of reactants
- equilibrium does not mean that the [ ] of reactants and produsts are =
what two things does a reaction’s free energy change depend on?
- a constant term dependent only on the reaction itself
- a variable term dependent on the concentration of reactants and products
fill in the blank:
what does delta G tell us?
which direction and how far a reaction must go to reach equilibrium when initial concentrations of each component is 1.0M
delta G is a function of ….. and measures the ….
a function of the actual concentrations of reactants and the temperature; a measure of the distance from equilibrium
important formula to know
fill in the blank:
what are two ways we can drive unfavorable reactions to occur?
- you can make an unfavorable reaction favorable by adjusting the concentrations of reactants and products
- couple endergonic reactions with exergonic reactions
are endergonic reactions favorable or unfavorable?
unfavorable
are exergonic reactions favorable or unfavorable?
favorable
molecules that differ in configuration cannot be:
chiral centers that can be interchanged by the rotation of a single bond
what does a large (» 1) Keq mean?
the formation of products is favored at equilibrium
what are hydrogen bonds the result of?
the attraction between the oxygen atom of 1 h2O molecule and the hydrogen atom of another h2O molecule
true or false? if false, correct statement
h2o molecules are in continuous motion a and hydrogen bonds are randomly breaking and forming
true
N-H, O-H are common H bonds. what atom formed to hydrogen doesn’t form hydrogen bonds?
C-H
which of these structures show a strong and weaker hydrogen bond? what detail make one stronger than the other?
hydrogen bond geometry affects bond strength
what are the two types of bonds in biochemistry?
covalent and noncovalent
what do atoms in a covalent bond do?
share electrons
hydrogen bonds, ionic interactions, hydrophobic interactions, and van der Waals interactions are all examples of what type of bond?
noncovalent bonds
what are five types of noncovalent bonds?
hydrogen bonds, ionic interactions, hydrophobic interactions, and van der Waals interactions
true or false? if false, correct statement
Non-covalent interactions are individually strong but weak in large numbers
false; Non-covalent interactions are individually weak but strong in large numbers
what type of molecules are hydrophilic, soluble in water and charged or able to H bond
polar molecules
what types of molecules are hydrophobic and insoluble in water
nonpolar molecules
what types of molecules contain both polar and nonpolar components?
amphiphilic
what type of compound is oil?
nonpolar
what type of compound is cholesterol?
amphiphilic
what happens in the hydrophobic effect?
it drives the nonpolar components to cluster away from the water and effectively increases the amount of disordered water
what is one thing the affects the structure and activity of biological molecules?
pH
the product of [H+] and [OH-] in any solution must be equal to _____
10^-14
neutral solution = [H+]=[OH-]= ___
10^-7
Acidic solution =[H+] > ____
10^-7
Basic solution = [H+] < _____
10^-7
changes in the [_____`] are balanced by changes in the [____]
[H+]; [OH-]
what defines pH?
the concentration of hydrogen ions
pH= -log [___]
[H+]
pOH= -log [___]
OH-
pH + pOH = ___
14
between acids and bases, which are the proton (H+) donors?
acids
between acids and bases, which are the proton (H+) acceptors?
bases
____ acids and bases — _____ completely
strong; ionize
weak acids and bases don’t dissociate completely in _____
h2O
tendecy of an acid to lose its proton is defined as ….
Keq or Ka
true or false? if false, correct the statement
The larger the acid’s Ka, the smaller it’s pKa
true
true or false? if false, correct the statement
the stronger the tendency to lose a proton- The weaker the acid
false; the stronger
the tendency to lose a proton- The stronger the acid
defined buffer
aqueous systems that resist changes in pH when small amounts of acids (H+) or bases (OH-) are added
the flat zone around the pKa of a solution is the _______
buffering region
why are buffers important in biological systems?
-various aspects of biological systems work best at well-defined pH
-buffers help maintain pH within well-defined ranges
what is the Henderson- Hasselbalch equation?
what in our body have optimum pH range for function and if they don’t function, reactions are slow and the organism dies?
enzymes
