biochem - exam 1 Flashcards
bio vs chemistry
levels 1,2,3 & 4
levels 1-3 are chemistry
level 1: monomeric units: nucleotides, amino acids, sugars
level 2: macromolecules: DNA, Protein, cellulose
level 3: supramolecular complexes: chromosome, plasma membrane, cell wall
biology is level 4
level 4: the cell and its organelles
what are the parts of a cell
cytoplasm
plasma membrane
ribosomes
nucleus
nuclear membrane
membrane bound organelles
what is principle 1
All cells of the simplest and most complex organismsshare certain fundamental properties, which can beseen at the biochemical level.
what do the parts of the cell do
A place for chemical reactions/hold- everything together- cytoplasm
Something to separate in/out- plasma membrane
Something to make proteins- nucleus
Genetic material- nucleus
“Areas of specificity”- organelles
surface area to volume issue
solves by having many parts make up a whole
all cells have
Plasma membrane (lipids)
Cytoplasm/sol (all kinds of molecules!)
Regions of “specificity”
Organelles (Favorite?)
Inclusions (Pro)
“Supramolecular” structures
: Differences between plant and animal eukaryotic cells!
Animal cells each have a centrosome and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not.
Evolutionary and Genetic Foundations:We can/have tracked these differences through time using molecules!
Cell membranes are made of
DNA replication is
Genetic code makes
Glucose is a preferred
ATP is an
Aerobic and anaerobic organisms
Cell membranes are made of lipids
DNA replication is semi-conservative
Genetic code nucleic acids
Glucose is a preferred sugar source for energy
ATP is an energy currency
Aerobic and anaerobic organisms
Biochemistry: Small Differences Matter!
A- bacterial and Archean ribosomes are smaller than eukaryotic ribosomes, but serve the same function: protein synthesis from an RNA message
B- cell envelope: structure differ
C- nucleoid: contains one or several long, circular DNA molecules
D- pili: provide points of adhesion to surface of other cells
E- flagella: propel cell through its surroundings
gram positive bacteria
gram negative bacteria
methanothermus
gram positive bacteria: solid outer layer, glycoprotein, peptidoglycan, plasma membrane
gram negative bacteria: LPS, outer membrane, peptidoglycan, plasma membrane, lipoprotein, porin, periplasm
methanothermus (heat tolerant Archean) solid layer, glycoprotein, pseudopeptidoglycan, plasma membrane
carbons can
make all types of bonds!
what are the main organic elements
CHNOPS
Carbon
hydrogen
nitrogen
oxygen
phosphorus
sulfur
CHNO make up 99% of all atoms of the human body
light elements can form strong covalent bonds in a variety of ways
what re the 4 macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
How do macromolecules work?
functions groups!
what are the functional groups that are are supposed to know
methyl
ether
guanidinium
ethyl
ester
imidazole
phenyl
acetyl
sulfhydryl
carbonyl (aldehyde)
anhydride (2 carboylic acids)
disulfide
carbonyl (ketone)
amino (protonated)
thioester
carboxyl
amido
phosphoryl
hydroxyl (alcohol)
imine
phosphoanhydride
enol
N-substituted imine (schiff base)
mixed anhydride (carboxylic acid and phosphoric acid; also called acyl phosphate)
what functional groups make up acetyl coenzyme A
thioester
amido
hydroxyl
phosphoanhydride
imidazole-like
amino
phosphoryl
what atoms do
Blue
black
Red
gray/White
represent
and what model representations should know
Blue: Nitrogen
Black: carbon
red: oxygen
Gray/White: hydrogen
structural, ball & stick, space-filling
Geometric/Configurational Isomers
Double Bond!
Compare your big groups and your small groups
Cis- and trans- good only for disubstituted double bonds
E/Z for tri and tetra
Z/Cis; E/Trans
Diastereomers!
Optical Isomers
Need: CHIRALITY
Chirality 4 different substituents around the carbon
what should you know about chiral molecules
1- Chiral molecules are optically active - rotate plane-polarized light
2- n chiral centers means 2^n stereoisomers
3- Chiral molecules are not identicalto their mirror image.
4- Achiral molecules are identical to theirmirror image
how do you organize and identify CHIRAL MOLECULES
1- rank atoms attached to choral center according to atomic number
Br > Cl > C > H
2- Rotate the molecule such that the substituent ranked #4 is in the back
3- with #4 in the back, trace the path of the #1, #2 and #3 ranked substituents. if #1, #2 and #3 trace a clockwise oath, assign the chiral center as R
4- if #1, #2 and # trace a counter clockwise path assign the chiral center as S
R/S: L/D: +/-
L/S/(-) = Left (anti)
R/D/(+) = right (clock)
what are enantiomers
differ at all stereocenters, and are therefore mirror images of each other
diasteriomers
Diastereomers are non-mirror image stereoisomers. They occur when a compound has different configurations of one or more (but not all) of the equivalent stereocenters.
why care about Stereospecificity/Stereoselectivity
In nature, most chiral molecules exist in only one configuration
L-amino acids
D-glucose
Proteins and other biomolecules are able to distinguish between (react differently) with different stereoisomers.
Examples to the right have different smells/tastes one is sweet and one is bitter
Racemic Mixture (Racemates)
is an equimolar solution of two enantiomers (50% R/ 50% S)
racemates
The two enantiomers in a racemic mixture are called racemates, rotate plane-polarized light in opposite directions, so there is no net rotation.
Racemic Drugs!
One stereoisomer is usually active, the other inactive (or opposite), or has a different activity than the first form. Why?
Ideally…
So what happens to the dose if you have a racemic mixture, compared to enantiopure?
SSRI Antidepressant
Celexa (trade name) of Citalopram (racemate)
Lexapro (trade name) of Escitalopram (S)-Citalopram
Β2 adrenergic agonist
The (R)-(-) enantiomer is active
The (S)-(+) enantiomer is inactive
Equilibrium does NOT always
mean equal!
Reactions tend to go to completion, notto “equality”
Completion depends
on a specific set of concentrations, described by an Equilibrium Constant, Keq
what is Keq
concentration products/concentration reactants
One can compare where the reaction is going when you used Q and compare it to Keq. Given the concentrations of all of the constituents and the Keq.
put aA + bB goes to cC + dD in Keq form
Q = Keq = [C]^c [D]d / [A]^a[B]^b
Q =
Products/reactants = Keq
what happens if products>reactants
net rxn towards reactants or the left
Q>K
what happens if products<reactants
net rxn towards products or the right
Q<K
what happens if products = reactants
no net rxn
Q=K
What makes a reaction go?
Energetics/Thermodynamics
What is enthalpy
what is its symbol
what does the net change in enthalpy mean
what does it mean when net enthalpy is less than zero
what does it mean when net enthalpy is more than zero
what are the units
enthalpy: number & type of chemical bonds
the net change in enthalpy, delta H, for a rxn depends on the relative strengths of the bonds broken and formed
delta H < 0: exothermic: heat generated/released
delta H > 0: heat energy transformed
measured in kilojoules per mole (kJ/mol)
how do you calculate enthalpy change
Sum Enthalpy (Products)minusSu m Enthalpy (Reactants)
what happens as time moves forward In an isolated or closed system
As time moves forward, the net entropy (degree of disorder) of any isolated or closed system will increase.
It takes a lot of effort (energy?) to decrease entropy.
entropy (S)
randomness
delta S > 0: system becomes more random, less ordered (favored)
delta S < 0: system becomes more ordered, more ordered
what is Gibbs free energy (G)
Delta G < 0: exergonic, rxn releases energy
Delta G > 0: endergonic, must put energy into system to make rxn happen
It is the energy available to do work
exergonic
products predominate at equilibrium (occurs spontaneously as written)
reactants predominate at equilibrium (does not occur spontaneously as written [occurs spontaneously in reverse directional])
Rxn release energy
free energy change and delta H and delta S
Delta G = delta H - T delta S
Free energy change and equilibrium
delta G * = -RT*ln(Keq)
factors that contribute to making delta G more negative (less positive)
-negative delta H (exothermic rxn)
-postive delta S (increasing entropy [more random])
factors that contribute to making delta G more positive (less negative)
-positive delta H (endothermic rxn)
-negative delta S (decreasing entropy [more ordered])
thermodynamics of biosystems
left alone (w/o any energy input), biosystems would fall apart (entropy maximization)
to maintain order, and to grow, energy input is required
to accomplish this, exergonic rxns are couples to endergonic rxns
metabolism
The sum total of all chemical reactions in an organism.
Metabolism = Anabolism + Catabolism
Anabolism
Synthetic reactions.
Normally endergonic (+∆G)
Usually involves reduction (Entropy, too
Catabolism
Degrative Reactions
Normally exergonic (-∆G)
Usually involves oxidation (Entropy?- +)
Reaction Coupling
Some reactions are not energetically favorable. The first reaction of glycolysis, for example, wants to go in reverse.
In living organisms, an energy-releasing reaction can be coupled to an energy-requiring reaction to drive the otherwise unfavorable reactions.
more on rxn coupling
High-energy compounds are used by all organisms to provide a driving force for thermodynamically unfavorable reactions (entropy).
Two reactions are “coupled” when one reaction is energetically favorable and can provide energy which allows the second reaction (unfavorable on its own) to occur.
Energy released by the second reaction drives the first reaction!
Thermodynamically unfavorable reactions (anabolic?; ∆G > 0) create order andrequire work and energy. We gotta get that energy from somewhere.
what is chapter 2 about
water, weak forces and acids/bases
what percentage of an organism is composed of water
water it the universal what
drugs work in what environment
drugs targets are in what environment
how drugs behave is dependent on what and how they interact with what
what bonds do water molecules for with polar solutes (has a dipole)
are the forces of water weak or strong
water is the critical determinant of what
what do non polar things do when in contact with water
≥ 70% of weight of most organisms
Universal solvent Chemical reactions occur in aqueous environment
Drugs work in an aqueous environment (Pharmacy, right?)
Drug targets are in an aqueous environment (Pharmacy, right? Right?)
How drugs behave depends on their electrical charge, and this depends on how they interact with water
Water forms hydrogen bonds with polar solutes
Water and non-polar things have an interesting relationship
Weak forces!
Therefore, water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes! (Basically biochemistry, right here)
non polar elements will ball up in aqueous environment
what kind of Weak Forces/Interactions Exist in Aqueous Systems
what do these forces/interactions allow for
Hydrogen Bonds- strong association bwtn FNO
Ionic Interactions
Hydrophobic Interactions- hide from water and keep to themselves
Van der Waals Interactions
These weak interactions allow for dynamic (rapidly changing/temporary)molecular processes.
what is a hydrogen bond
what elements have
to be connected to a hydrogen bond in order for there to be a hydrogen bond
what is the pneumonic
unequal distribution of charge that results when a hydrogen is covalently bonded to an electronegative atom, such as oxygen or nitrogen interacts with a FNO somewhere else
H-Bonding is for F, O, N
Sulfhydryl (sulfur, below oxygen, behaves like oxygen ) groups too
Directional
Polarity!
A typical Hydrogen bond in bio-molecules is between H and _____
hydrogen bonding is
do not change
what kind of interaction is amphipathic
N or O
FNO
test question
amphipathic is a hydrophobic interaction
A carboxyl group is…
polar
nonpolar
amphipathic
polar
there’s lots of oxygens pulling electro density to itself leaving the hydrogen more positive and so there is a net negative and net positive end
A methyl group is…
polar
nonpolar
amphipathic
non polar
no FON
For the dissolving of a gas in water/in container, the entropy of the system…
decreases
we order it and put it in something
giving it order
not letting it run around me be free
which part of each molecule would make hydrogen bonds?
alcohol
ketone
polypeptides
DNA
alcohol: hydroxyl group and water
ketone: carbonyl and water
polypeptides: peptide groups in polypeptides
DNA: nitrogen and carbonyl
Water and Ionic Interactions
The salt crystal is ordered. It is _____________favorable for water to break it apart and surround the individual components of ____with _______ molecules.
Charge of the electron: _____. Add a negative charge: be ________. If you remove this then become positive
Charge of proton: ________
Opposites ________
________charge repel
This all may change the _______ a molecule so it is needed to know when something might be ________charged or ________
Salt in ________, Na and Cl _________and associate with water—entropy _________
The positive part of water _________Cl, negative part of water surrounds _______—this is a ________shell
Broken up ________ into bits and pieces—this is thermodynamic _________ because entropy increases. The universe tends towards __________
Ionization of water gives us ________—net H+ and OH-
The salt crystal is ordered. It is thermodynamically favorable for water to break it apart and surround the individual components of Na-Cl with water molecules.
Charge of the electron: negative. Add a negative charge: be negative. If you remove this then become positive
Charge of proton: Positive
Opposites attract
Like charge repel
This all may change the shape of something so it is needed to know when something might be negatively charged or positive
Salt in water, Na and Cl dissociate and associate with water—entropy increases
The positive part of water surrounds Cl, negative part of water surrounds Na—this is a hydration shell
Broken up solid into bits and pieces—this is thermodynamically favorable because entropy increases. The universe tends towards disorder
Ionization of water gives us acids and bases—het H+ and OH -
Water and Van der Waals Forces
it broke and _________
even though it is ________the cumulative effect is ________
think of ___________
it broke and reformed
even though it is weak the cumulative effect is great
think of velcro
are
hydrophilic
hydrophobic (lipophilic)
mixed
soluble in water
hydrophilic: yes
hydrophobic (lipophilic): no
mixed: partly
soluble in water
are gases soluble in water
polar gases–yes
non-polar gases—less
rank the Polar/Hydrophilic and Non-Polar/Hydrophobic (Solubility)
highest: polar solids, lipids, and gases
middle: non-polar solids, liquids
lowest: non-polar gases
entropy for:
Any gas in a container
Any gas in the universe
what is the eqn for Gibbs free energy?
Solid or liquid solute: if polar, becomes more ______; if non-polar becomes more_______
Gas
–entropy always_______, because the gas is confined to a small volume
–decrease is smaller if polar (molecules disperse), larger if nonpolar (molecules cluster)
Any gas in the container: entropy decreases because set at a volume
Any gas in the universe: entropy increases, more volume, more random
eqn: deltaG = deltaH - Temp deltaS
Solid or liquid solute: if polar, becomes more disordered; if non-polar becomes ordered
Gas
–entropy always decreases, because the gas is confined to a small volume
–decrease is smaller if polar (molecules disperse), larger if nonpolar (molecules cluster)
Amphipathic
Bulk water has little order what is the entropy
- Water near a hydrophobic solute is highly ordered: low entropy thermodynamically unstable low ______
- Lipids group together, increasing the amount of ______ in the system ___________ are _______ordered around individual lipids.
contain regions that are polar (charged/hydrophilic) and regions that are non-polar (hydrophobic)
Complex hydrophobic/hydrophilic interactions are thermodynamically favorable!
- Lipids group together, increasing the amount of entropy in the system water molecules are less ordered around individual lipids.
Water near hydrophilic solute: water in oil, tends to itself and does not mix—less entropy
Lipid organizes to itself-–water does not have to form hydration shell. Oil and water mixture is thermodynamically favorable—universe tends to thermo. The state, has to have entropy increasing, keep entropy high
do you know all the functional groups yet?
methyl
ether
guanidinium
ethyl
ester
imidazole
phenyl
acetyl
sulfhydryl
carbonyl (aldehyde)
anhydride (two-carboxylic acids)
disulfide
carbonyl (ketone)
amino (protonated)
thioester
carboxyl
amido
phosphoryl
hydroxyl (alcohol)
imine
phosphoannhydride
enol
N-substituted imine (Schiff base)
mixed anhydride (carboxylic acid and phosphoric acid; also called acyl phosphate)
Yes, I know all of them!!!!!! God is good!!!
Nah I don’t but I will go practice them!!!!!!!! God is STILL GOOD!!!!!!!!!
Polar/Hydrophillic and Non-Polar/Hydrophobic (Interactions!).
The association or folding of non-polar molecules in aqueous solution is one of the main factors behind:
Formation of lipid ______ (and membranes)
______folding
Protein-_______association
Binding of ________hormones totheir receptors
Drug/Ligand Receptor ________!
The association or folding of non-polar molecules in aqueous solution is one of the main factors behind:
Formation of lipid micelles (and membranes)
Protein folding
Protein-protein association
Binding of steroid hormones totheir receptors
Drug/Ligand Receptor Binding!
what is the Net Result of all these Forces?
what do weak forces maintain and determine what iinteractions
what do non covalent interactions permits
Dynamic Interactions and Functionality!
Weak forces maintain biological structure and determine biomolecular interactions!
Molecular Complementarity!
Mediated via noncovalent interactions – permits tight, highly specific binding of biomolecules!
Colligative Properties of Water
solutes decrease the concentration of what
what do properties depend on the number of what
what do colligative properties include
what is are the units for osmolarity
what are the units for osmolality
140mmol NaCl/kg = how many osmol
what is osmosis
water follows what
Osmotic pressure
solutes decrease the concentration of water
properties depend only on the number of solute particles not their size
colligative properties: vapor pressure, boiling point, melting& freezing point and osmotic pressure
osmolarity: moles solute particles/L solution
osmolality: moles solute particle/kg solution
140 mol NaCl/kg = 280 mOsmol NaCl/kg
osmosis: diffusion of solvent across a membrane along a solute concentration gradient
water follows salt
Osmotic pressure: forcing water through a membrane in an attempt to equalize concentrations; isotonic, hypertonic and hypotonic solutions
what happens to cells in the following salt solutions
isotonic
hypertonic
hypotonic
isotonic” no net water movement, cell stays at normal size because there is equal amount of water inside that outside
hypertonic: water moves out of cell and cell shrinks because there is more salt outside that inside and water follows the salt outside
hypotonic: water moves in the cell creating outward pressure ; cell swells and may burst because there is more salt inside that outside so water follows salt inside
Water (and Strong Acids) Ionize!
what happens when a water molecule dissociates and what is this called
what Is pH
pH + pOH =
In pure water (neutral), [H+] = [OH] so pH equals what
when [H+] > [OH], pH < 7.0 (____)
when [H+] < [OH], pH > 7.0 (_____)
when a water molecule dislocates: results in a proton and hydroxide
H + H30+ & OH- this is the ionization of water
pH = -log[H+]
pH + pOH = 14
In pure water (neutral), [H+] = [OH] so pH equals 7
when [H+] > [OH], pH < 7.0 (acidic)
when [H+] < [OH], pH > 7.0 (basic)
