Exam 1: Ch. 1, 2, and 4 Flashcards
Name the 4 biological molecules
Amino acids (proteins)
Carbohydrates (polysaccharides)
Nucleotides (nucleic acids/polynucleotides)
Lipids
Amino Acids: What are the names of the two groups
amino group (-NH2) carboxylic acid group (-COOH)
Carbohydrate groups
Hydroxyl groups
Carbonyl group
(CH2O)n, where n > or equal to 3.
3 components of nucleotides
- 5-carbon sugar
- nitrogen-containing ring
- 1+ phosphate groups
Lipid qualities
poorly soluble in water due to bulk of structure and hydrocarbon-like chains
Ex: palmitate
monomers linked _____
What are monomers called once they’ve been incorporated into a polymer?
covalently
residues
Proteins are linked together by…
Peptide bonds
O=C —N
Nucleic acids linked by…
phosphodiester bonds
Polysaccharides linked by
glycosidic bonds
Starch vs. Cellulose
Starch- loose helical conformation
Cellulose- extended and stiff conformation
Proteins
Main: Carry out metabolic reactions, support cellular structures. (M S)
Minor: Store Energy (E)
Nucleic acids
Main: Encode information (I)
Minor: Carry out metabolic reactions, support cellular structures (M S)
Polysaccharides
Main: Store Energy, Support Cellular structures (E S)
minor: Encode information (I)
Gibbs Free Energy
A measure of the free energy of a system based on H and S
Units = J • mol-1
Enthalpy, H
The heat content of a system
Units = J • mol-1
Entropy, S
A measure of the system’s disorder or randomness
Units = J • K-1 mol-1
Exothermic reactions
Release heat into surroundings
Hfinal - Hinitial = delta H < 0
Endothermic reactions
Absorb heat from the surroundings
delta H > 0
In order for a process to occur overall change in free energy must be
negative
Spontaneous reaction
Exergonic
Delta G is less than zero
Nonspontaneous reaction
Endergonic
Delta G is more than zero
Decrease in enthalpy, increase in entropy is ___ at all temperatures
spontaneous, delta G less than zero
Enthalpy increase, entropy decreases
does not occur
Enthalpy and entropy increase or decrease
delta G depends on temp
What do cells do to ensure that net change in free energy is negative?
Couple unfavorable metabolic processes with favorable ones so that the net change in free energy is negative
When thermodynamically favorable reactions are coupled to unfavorable synthesis of monosaccharides from atmospheric CO2,
Carbon reduced
Reduction
gain electrons
Addition of H or removal of O
When animal eats plant
oxygen oxidized
Oxidization
Loses electrons
Addition of O, remove H
Carbon becomes CO2
Oxidation of carbon is
thermodynamically favorable
If a living organism has low entropy relative to surroundings, how does it maintain thermodynamically unfavorable state?
Obtains free energy from food
What is a dielectric constant? and is water’s high or low?
measure of solvent’s ability to diminish electrostatic attractions between dissolved ions.
High
The higher the dielectric constant, the less able
the ions are to associate with each other.
Hydrophilic
Ex: Glucose/ other hydrated substances
polar groups, soluble in water
Hydrophobic
insoluble
lacks polar groups
Adding nonpolar molecules to water
lowers entropy, can’t break/form hydrogen bonds
Intracellular
K+
Extracellular
Na+ and Cl-
Electronegative rankings
H < C < S < N < O < F
Has Charlie Seen Natalie’s Old Frock?
Proton Jumping
effective mobility of H+ in water is much greater than the mobility of other ions that must physically diffuse among water molecules.
Donate proton
Acid
Accept Proton
base
Organ which does buffering in humans
Kidney
Kidney Buffer
- Ion exchanger moves Na+ into cell and H+ out
- H+ combines with HCO3- to make CO2
- Kidney cell takes up CO2 and then does the reverse
How is HCO3- returned to bloodstream?
Cl- ion exchanger,
H+ pumped out
Acidosis
Blood pH less than 7.35
Alkalosis
blood pH greater than 7.45
Metabolic acidosis
accumulation of acidic products of metabolism
CNS depression, rapid deep breaths
Treated by administering sodium bicarbonate
Metabolic Alkalosis
Loss of HCl in gastric fluid
(overproduction of mineralocorticoids, abnormally high H+ excretion and Na+ retention)
prolonged vomiting
Treated by infusing NaCl
Stop breathing to minimize CO2 loss
Respiratory acidosis
pulmonary function caused by airway blockage
Kidneys increase synthesis of enzymes that break down glutamine to produce NH3.
Treatment: Excretion of NH4+
Respiratory Alkalosis
hyperventilation by fear/anxiety
N connected to C
amino group
C=N
imino group
O=C, then C-N
amido group
-OH
hydroxyl group
-SH
Sulfhydryl group
-O-
ether linkage
O=C, then C-O
Ester linkage
C=O
- No Side Chains
- Side Chain
- Carbonyl group
2. Acyl Group
O=C, then C-OH
Carboxyl group
O=C-O negative
carboxylate
Secondary Structure
Polypeptide backbone (exclusive of side chains)
Tertiary Structure
3D confirmation of polypeptide (including backbone atoms and all side chains)
Quaternary Structure
Spatial arrangement of all chains
How do peptide bonds form ?
Condensation reaction.
Water is lost, carboxylate and amino groups linked
N –> C
In cells, peptide bonds are broken/hydrolyzed by
exopeptidases/endopeptidases
The electrostatic properties of the polypeptide primary depend on…
identities of side chains (R groups) that project out the polypeptide backbone
_____ may alter a side chain’s polarity and tendency to lose/accept proton
microenvironment
Short polypeptides are called
oligopeptides
Is there rotation around C-N bond?
No, due to partial (40%) double bond character.
N-C alpha can rotate, though limited
Secondary structure’s goal is to minimize
strain
amino groups are hydrogen bond ___ whereas carbonyl groups are hydrogen bond ___
amino: H donor
carbonyl: H acceptor
Secondary: Alpha helix
Right-handed. Hydrophobic in the center.
Most 12 residues long
Secondary: Beta Sheets (parallel)
Jagged O-H bonds, align same direction
N –> C, loop out
longer linker
Secondary: Beta Sheets (antiparallel)
Ladder O-H bonds, opposite direction.
smaller linker
Largest force governing protein structure
hydrophobic effect
When a protein is misfolded ___ tags it with ______. Which is recognized by ___
Proteaosome
Ubiquitin
Ligase
Size and Exclusion Chromatography
Porous solution.
Larger proteins exclude from bead spaces and will pass faster
Ion Exchange Chromatography:
If want -, use + (vis versa)
uncharged/+ pass, whereas - binds. then use salt solution to dissociate the bound proteins.
Affinity Chromatography
Separation based on molecular interactions.
Ex: what proteins will bind to this small immobilized molecule ?
HPLC
High performance liquid chromatography
Analytical
Closed columns under high pressure
SDS
Gel electrophoresis
charge and size
SDS is -
All proteins move to + side, smaller proteins move faster.
SDS: what if you have dimers of proteins? Or disulfides?
Reducing condition: reduce disulfide bonds
Nonreducing: retain associations
Mass Spectrometry
Protein, ionization, fragmentation, and mass analysis (details?)
Magnet to apply force to charted particles
X-ray Crystallography/NMR
3D arrangement of atoms
H resonate in NMR
X-ray: diffraction images
Only trend that goes down
Ionic and atomic radii
Denaturation ruins
tertiary structure
