Studied by 4 people
Ch 1-4 (only half of 4)
How do we know when reverse or forward rxn is favored?
Where are phosphate groups found in activated carriers? Where are they not?
NADP+ and NADPH = phosphate groups
NAD+ and NADH = none
Anabolic rxns vs Catabolic rxns
NAD+ NADPH
What does ATP transfer in a high energy linkage?
phosphates
primary structure
amino acid sequences
secondary structure; where does bonding occur
a helices and b sheets in proteins
held together by non covalent bonds such as hydrogen bonding (C=O and N-H)
local folding pattern of polymeric molecules
hydrogen bonding occurs between atoms of two peptide bonds
tertiary structure
3D structure of fully folded protein
disulfide bonds, hydrogen bonds, ionic bonds and non polar hydrophobic interactions
quaternary structure; what determines them
multiple polypeptide chains to form larger complexes
held and determined by noncovalent bonds
what are amino acids held together by?
peptide bonds
how are peptide bonds created? what atoms of amino acids join them?
condensation rxns; C and N terminus
what is a protein comprised of?
polypeptide chains linked together
what part is not involved in forming peptide bonds?
backbone/ side chain (R group)
how are dipeptide bonds formed?
when two amino acids join by 1 peptide bond
when charge is unevenly distributed, it is
polar
what holds amino acids together?
peptide bonds
what is a protein aggregate? Solubility?
abnormal proteins formed into larger aggregate structure
tends to be insoluble
what do chaperones do? what is required for function?
binds newly synthesized or partially folded chains to help them fold through most energetically favorable pathway
Chaperone function requires ATP binding and hydrolysis
what are isolation chambers? what is required for function?
Where a single polypeptide chain within barrels of chaperones can fold without risk of forming aggregates in the crowded cytoplasm
requires input of energy (ATP hydrolysis) mainly for association and subsequent dissociation of cap that closes off the chamber
What is ATP hydrolysis?
releases energy present in high energy terminal phosphate bonds
provides energy needed for processes
What cleaves DNA?
deoxyribonuclease
what are alpha helices ?
stabilized by hydrogen atoms in every 4th amino acid
what a b sheets?
side by side hydrogen bonds with flat, ridgid structures
what are a helix and b sheets common folding patterns? what structures do they form?
result from hydrogen bonds that form between N-H and C=O (NO SIDE CHAIN INVOLVEMENT OF HYDR BONDING)
secondary structure
where are side chains found in a helix vs b sheets?
a helices: on the sides
b sheets: above and below
Hydrogen bonds in a helixes are created every
4th amino acid, linking C=O of one peptide bond to the N-H of another
where are a helix abundant?
proteins embedded in cell membranes such as transport proteins and receptors
ex: portions of transmembrane protein that cross the lipid bulayer usually form an a helix
How are a helices embedded in transmembrane proteins that cross the lipid bilayer?
amino acids w nonpolar side chains
polypeptide backbone (hydrophilic) is hydrogen bonded to itself INSIDE the a helix where its shielded by the hydrophobic lipid environment of the membrane, and had protruding nonpolar side chains on the OUTSIDE
hydrophilic and hydrophobic in a helix vs b sheets:
a helix: interior (hydrophilic) exterior (hydrophobic)
b sheets: interior (hydrophobic) exterior (hydrophilic)
what is a coiled coil?
a helices wrapped around one another forming stable structures
formes when a helices have most nonpolar side chains along one side so they can twist around to have their hydrophobic chains facing inward
what 2 varieties of b sheets are there?
parallel and anti
what are unstructured sequences?
continually bend and flex due to thermal buffering ; unstructured lengths of polypeptide chains
what is a subunit?
each completely folded polypeptide chain in a quaternary structure
what is a globular protein? fibrous proteins?
when a polypeptide chain compacts into a ball shape (irregular shape)
elongated 3D structures
what helps bind cells together to form tissues?
extracellular matrix
what are disulfide bonds? when are they formed?
sulfhydryl groups (S-S bonds) of two cysteine side chains used to reinforce structures of secreted proteins
formed in tertiary structures, but also before a protein is secreted by an enzyme in the ER that links the 2 -SH groups together that are adjacent in the folded protein; does not change a proteins conformation
quaternary structures will always have 2 or more…
protein domains
what are domains ? what are motifs?
multiple polypeptide chains or subunits; 3D protein structures independent folding unit (can fold on their own)
commonly repeated sequence patterns of secondary structures
is protein folding energetically favorable or unfavorable?
favorable bc it does not require energy input
are chaperones always needed?
Although chaperone proteins assist in protein folding, they do not provide the energy needed for a protein to fold into the correct conformation.
what forms disulfide bonds/ sulfide bridges?
cysteines
what do proteins outside of the cells start their life?
in the ER
how do peptide bonds join amino aicds?
condensation rxns
Nitrogen and carboxyl groups form
peptide bonds
How can we tell if an AA will span the membrane?
alpha helix spans them
1 turn helix =
0.54 nm
how many amino acids are found in 1 turn?
3.6 amino acids
what are motids?
constructed of secondary structure folds
domains are repeated
MOTIFS ; you can have multiple domains in one polypeptide chain
what binds something specific or has some kind of conformation allowing for a certain function?
motifs and domains
many motifs create
polypeptide chains (domains)
combo of many domains makes final
tertiary structure
each subunit is a fully folded
tertiary polypeptide
How far apart would hydrophobic residues have to be if you wanted to assemble a coiled coil?
Roughly 4 amino acids - every 4 has to be hydrophobic (creates a strip)
Hydrophobic side groups must congregate more towards one side
Allows to make hydrogen bonds above each
between 1st and 5th = 2 residues in the backbone that are creating the box
Nonpolar 3x (must be on outside) Polar 1x (every 4th = polar)
what are condensation reactions? what type of rxn and characteristics?
creates peptide bonds/ polymers and releases and H2O
anabolic rxn / nonspontaneous / unfavorable
hydrolysis
breaks polymers or peptide bonds and consumes H2O
catabolic rxn / spontaneous / favorable
what is glycolysis? what kind of pathway
where each glucose is broken down into 2 molecules of pyruvate; involves the generation of 3 carbon sugar (pyruvate) from breakdown of glucose (6 carbons)
catabolic pathway
results in formation of active carrier ATP to then be used by cell to drive anabolic rxns
anabolic vs catabolic rxns
large molecules are made by smaller ones
complex molecules degredated into simpler ones
As O2 atoms are (+) or H atoms are (-), central carbon..
becomes more oxidized
decrease in electron density due to electroneg atoms present in molecule
what is an example of oxidation of carbon? reduction of carbon
formic acid —> CO2 or methane —> methanol
formladehyde —> methanol or formic acid —> formaldehye
the more reduced the molecule, the energy amount
increases from released oxidation process
what are enzymes?
lowers activation energy for one specific rxn leading to one product
specific for one desired pathway and end product
How do you overcome activation barriers?
molecules energy increase OR barrier decrease before reaction proceeds
What is free energy?
harnessed to do work
delta G = 0 @ equilibirum and no work can be done
free energy of rxn at its lowest point at equilibrium
what do high energy bonds allow for?
can be broken to yield energy (drives lifes metabolic processes)
contains phosphates
what maintains a balanced OH and H+ concentration?
buffers
what forms acids and bases
polar molecules
*Bases = charged molecules
what is pKa?
= topH at which half molecules are dissociated and half are neutral or undissociated
pH =
pKa + log[A-]/[HA] - products over reactants
what does pKa tell us?
allows us to understand how biological systems control acidity of aq fluids
pH above pKa =
deprotonated
pH below pKa =
protonated
what happens as pH increases
carbonic acid gives away its protons as it increases
what is an example of a buffer used in cells?
carbonic acid
carboxylate group
COO-
amino group
NH3+
guamodonium group
+H2N=C-NH2
what is the isoelectric point? how is it calculated?
pH at which molecule carries no net electric charge
pl = (pKa1 + pKa2) / 2
what is the chemical character of each amino acid side chain NH2
polar h
what does the pKa tell you about a molecule? how do you determine the pl?
protonation; pl = (pKa1 + pKa2) / 2
which amino acids would naturally be found on the inside of a protein? why?
nonpolar side chains of a protein tend to join on the inside to withstand the aqueous environment and hydrophilic forces
what do cells use to catalyze oxidation of organic molecules?
sequences of rxns that allow energy to be harvested from
what makes up a cells metabolism?
anabolic and catabolic pathways
do favorable rxns increase or decrease disorder?
increase disorder; unfavorable decreases disorder (more ordered)
how do cells obtain energy?
through oxidation of organic molecules
why do enzymes bind substrates to catalyze chemical rxns?
lowers activation barrier
specific to one rxn
remainds unchanged
what is free energy?
determines if a rxn will occur
decreased free energy = - delta G = favorable
increased free energy = + delta G = unfavorable
decreased free energy =
- delta G = favorable = less order (more disordered)
equilibrium constants
indicates the strength of noncovalent binding interactions
activated carriers
contains energy rich covalent bonds that store energy
store energy in an easily exchangeable form, either as a readily transferable chemical group or as high-energy electrons
biosynthesis
requires energy and can utilize stored energy from activated carriers
What does delta G help us determine?
whether or not a rxn is favorable and allows us to compare reactions
thicker arrow favors that direction
what do equilibrium constants tell us?
the direction of a given reaction AND indicates the strength of noncovalent binding interactions
what are coupling rxns?
to make unfavorable rxns possible
changes in bond energy cause…
heat to be released
enzyme substrate complexes, how are they stabilized?
by formation of many weak bond interactions
who locates who in enzyme and substrate?
substrate locates enzyme
when will 2 molecules bind? depending on what?
when free energy of resulting complex is less than sum of the free energies of the 2 when unbound
how do enzymes encounter their substrates?
diffusion and noncovalent bonding interactions (enzymes bind to specific molecules based on their chemical character)
Why would delta G change?
due to amount of energy stored in a molecule and concentration
changes as it proceeds to equilibrium
What yields more product for each molecule of substrate?
negative delta G
Note 
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