L: the bottom -OH group is on the LEFT.

D: the bottom -OH group is on the RIGHT.

- phenylalanine

- tyrosine

- tryptophan

these guys are aromatic; aromatic amino acids absorb in the UV spectrum, not just the infrared spectrum like other amino acids. 

- they also display weak fluorescence

TRYPTOPHAN ONLY displays phosphorescence (which means it emits light for a long time.)

oligomeric: it contains at least two polypeptide chains that are identical.

protomers: polypeptide chains which are identical.

resin beads with a certain charge stick to proteins with an opposite charge, keeping them from eluting as fast as those proteins with a similar charge.

a CATION exchanger attracts cations (is negatively charged)

an ANION exchanger attracts anions (is positively charged) 

define: 

- activity

- specific activity

activity: the number of enzyme units in a solution

specific activity: the number of enzyme units/milligram of total protein

- specific activity is a measure of enzyme purity

1. react N-terminus with Sanger's Reagent

2. cleave all the bonds

3. check with amino group is bound to Sanger's Reagent

amino acid reacted to PITC; cleaves N-terminus amino acids one by one

- becomes less accurate the bigger the protein is

- and you basically have to guess where the disulfide bonds are

- reduction and oxidization

- reduction (turning into -SH) must be followed by carboxymethylaton to keep the -SH from reacting again into another disulfide bond

1. protect the N-terminus of aa with Fmoc

2. bind C-terminus to reactive Cl-CH2-bead resin

3. protect N-terminus of a second aa and activate it's C-terminus with DCC

4. take of Fmoc from first aa

5. react N-terminus of first aa to activated c-terminus of second aa

6. remove Fmoc protective group from second aa

7. repeat

weaknesses: small differences in STEPWISE yield can strongly lower OVERALL yield.

the C-N bonds of a polypeptide chain have double bond character, making the =O (carbonyl oxygen) and the -H (hydrogen on the N) planar to each other, where they share electrons and therefore cannot rotate freely. Rotation is only possible between the Calpha and C=O carbons, and the N and C carbons.

this limits the number of conformations a polypeptide chain can have!

- 5.4 angstroms

- 3.6 residues

1. how likely each aa is to form an alpha helix

2. the interactions between the R-groups of aa making up the alpha helix, particularly those 3 or 4 residues apart

3. the bulkiness of adjacent R groups (if they are two big they push on each other and destabalize)

4. the more proline (ring that can't H-bond) and glycine (-H is -R so too flexible to reliably helix), the less likely to form an alpha helix

5. interactions between the aa at the ends of the chain and the overall dipole charges

four amino acid residues

the carbonyl oxygen of the first forms a hydrogen bond with the nitrogen of the fourth

mostly happens with glycine (flexible) and proline (cis configuration is easy)

happen near the surface

- made of two alpha helixes matched parallel (with n-terminus at the same end) and coiled together lefthandedly in a supracoil (quartenary structure)

-strength enhanced by covalent cross-linking: disulfide bonds

- forms hair, horn, etc.

- made of three ALPHA CHAINS, which are NOT the same as alpha helixes. These guys have a lefthanded twist.

- they wrap around each other righthandedly.

- forms tendons, cartilage

hydrophobic side chains inside; hydrophilic side chains outside (and most are hydrated)

- the hydrophobic side chains are so closely packed that van-der-waals forces between them play a huge role in stabilizing the protein structure

these are two enzymes that catalyze protein folding.

PDI: messes with the sulfide bonds until the right ones are formed.

PPI: changes proline from cis to trans and back, speeding the unfolding process

- protein with aromatic proteins making up a beta sheet

- these start to self associate

- then are joined by other proteins, lengthening the beta sheet/amyloid structure

present in heme proteins like myoglobin and hemoglobin. Is made of protoporphyrin IX, with a bound Fe²⁺ atom in the middle. It is bound between four N, which donate electrons to keep the Fe from oxidizing and not being able to bind oxygen anymore.

in addition, Fe has two available bonds not taken up by N. One of them is occupixed by a His residue, because two oxygens binding at once will also oxidize it.

explain the location of the following protein based on the name:

His⁹³

His F8

His⁹³: the histidine residue 93 residues away from the amino terminus

His F8: the eighth his residue in the F alpha helix

the association constant of a protein for a ligand. Ka = [PL]/[P][L]

Therefore the larger Ka is, the more the protein likes to stick to the ligand. 

units: M^-1

Ka is also equal to k_a/k_d, which are the association/dissociation rate constants.

first order reaction (depends on concentration of one thing): s^-1

second order reaction (depends on the concentration of two things): M^-1s^-1

homotropic allosteric protein: the molecule that binds to the protein and changes its ligand affinity IS the ligand

heterotropic allosteric protein: the molecule that binds to the protein and changes its ligand affinity is a different molecule entirely than the ligand

- must have multiple binding sites

- must have subunits that are able to interact with each other (usually stable next to unstable segments)

hydrates carbon dioxide in the blood to bicarbonate (with H+ as a product). This is needed because carbon dioxide isn't very soluble in blood and otherwise would form bubbles. 

This causes the tissues to become more acidic.

hemoglobin transports all three molecules. When there is a lot of carbon dioxide and hydrogen (low pH), they both bind to hemoglobin and lower the affinity for oxygen, causing oxygen to be deposited in the tissue.

In the lungs, however, carbon dioxide is breathed out of the body. This stops its conversion to bicarbonate and stops the production of H+, raising pH. Therefore oxygen is free to bind to hemoglobin - until it leaves the lungs, and carbon dioxide concentration increases again in the tissues/pH goes down, the oxygen is dropped off again in the tissues.

reduces affinity of hemoglobin for oxygen; BPG concentration changes based on altitude (when you go higher up, you have more of it, so more oxygen is released into your blood.)

It binds to the T state and is NEGATIVELY charged, binding to the positively charged amino acids and stabilizing the T state. 

When oxygen binds, the cleft where BPG binds becomes smaller, expelling it, and raising oxygen affinity.

Glu-->Val mutation

Val, unlike Glu, has no negative charge.

- this creates a hydrophobic contact point on the outside surface

- and when hemoglobin is deoxygenated, these spots cause it to stick to other hemoglobins.

- this forms long, insoluble aggregates.

- these block capillaries

- and rupture easily, destroying a lot of the body's hemoglobin

normal protein side-chains: low affinity for oxygen

transition metals: generate free radicals in solution

heme group: would become oxidized to Fe³⁺ in solution, and stop binding oxygen

so you use a PROTEIN-BOUND HEME GROUP

myosin thick filament inside six actin thin filaments

myosin head: binds to actin.

atp binds to myosin --> myosin lets go of actin

 bound ATP hydrolized --> ADP + Phosphate still attached to myosin head

--> myosin changes conformation --> binds to actin filament further down the line --> phosphate is released

--> phosphate release causes myosin and actin to move relative to each other --> causes ADP to be released

--> now myosin head is holding tightly again

- cofactor (an inorganic metal ion)

- coenzyme (a complicated organic or organometallic molecule)

- prosthetic group - if either of these is covalently (or else very tightly) bound to the enzyme, either a cofactor or a coenzyme is called a prosthetic group

holoenzyme: enzyme + cofactor/coenzyme/prosthetic group

apoenzyme: the enzyme without its cofactor/coenzyme/prosthetic group

identify the functions of the following enzyme groups:

- oxidoreductases

- transferases

- hydrolases

- lyases

- isomerases

- ligases

oxidoreductases: transfer electrons (OH^- or H⁺)

transferases: group transfer reactions

hydrolases: hydrolysis reactions 

lyases: cleavage resulting in elimination, or addition of groups to double bonds

isomerases: rearrangement of groups to yield isomeric forms

ligases: formation of organic bonds by condensation reactions - coupled to ATP or other cofactors

ΔG° is the change in free energy; i.e. the net energy difference between the substrate and the product of a reaction. 

ΔG‡ is the energy it takes to reach the TRANSITION STATE. This is what the reaction rate depends upon, NOT on ΔG°!

affected: the rate of reaction is much faster.

NOT affected: the reaction equilibrium remains the same.

the relationship betwee rate constant k of a reaction and ΔG‡ is INVERSE and EXPONENTIAL.

This means that a higher activation energy means a slower reaction rate.

- covalent

- noncovalent (this produces BINDING ENERGY)

specific: when water is the electron donor and acceptor that stabilizes the reaction

general: when an enzyme does it

1. the metal ions that are bound to the enzyme can interact with the substrate and orient the substrate for reaction, or stabilize charged transition sites. 

2. metals can become oxidized or reduced to mediate oxydization/reduction reactions.

1. the rate constant of the rate-limiting step in an enzyme-catalyzed reaction

2. the TURNOVER NUMBER - kcat is the number of substrate molecules converted to product in a given unit of time on a SINGLE enzyme molecule, when enzyme is saturated with substrate.

the unit is s^-1

kcat/km : turnover rate (how many molecules of substrate are turned to product for one enzyme unit in one time unit at enzyme saturation) over michaelis-menton constant ([S] when v = 1/2 vmax.

between 10⁸ and 10⁹ is the ideal value for specificity constant; the nearer it is to this value (which is a maximum value), the more efficient catalysis is of an enzyme.

1. enzyme binds S1 and then S2 (must be in this order) and then releases them in a specific order

2. enzyme binds S1 and S2 in no specific order, and then releases them in no specific order

3. enzyme binds S1, then releases it, in the process having its conformation changed. This enables it to pick up and release S2, changing its conformation back to its original state.

intersecting lines: it's ordered or non-ordered, but it involves a ternery complex (both substrates bound to the enzyme at once.)

nonintersecting lines: ping-pong mechanism - there's no ternery complex; first one S binds, changes the conformation, is released, second S binds, returns conformation to normal upon release

1. competitive inhibition; K_I (the smaller this is, the better the inhibitor is at sticking); binds to E (in the active zone)

2. noncompetitive inhibition; K'_I (the smaller this is, the better the inhibitor is at stickin); binds to ES complex, NOT just the enzyme!

3. mixed inhibition; this does NOT bind at the active site, but can bind either to the enzyme or the ES complex.

- appears to raise Km

- lowers Vmax

- is a protease (catalyses hydrolytic cleavage of peptide bonds)

- cuts after aromatic amino acids (Trp, Phe, Tyr)

- has a two-step mechanism:

1. peptide bond cleaved --> enzyme bound by ester linkage to the carbonyl carbon (fast)

2. this linkage is hydrolized and the enzyme is regenerated (slow)

aldose sugar: ACETAL

ketose sugar: KETAL

what you get when you oxidize the aldehyde carbon of a sugar HO-C=O

          |

homopolysaccharides/heteropolysaccharides (contains one repeated monomer or different kinds)

branched/unbranched

molecules made up of alternating:

- uronic acids

- amino sugar residues (N-acetylglucoseamine or N-acetylgalactoseamine)

they are VERY negatively charged and hang out in the extracellular matrix. To keep the negative charges (uronic acids and esterified sulfide groups) away from each other, it winds into a helix with these charges on opposite sides.

starch: stores energy in plants. It's a homopolysaccharide for glucose. Amylose is linear, amylopectin is branched.

glycogen: energy storage in aminals. Homopolysaccharide for animals. branched.

cellulose: structural support in plants. Homopolysaccharide for glucose. Branched.

one or more oligosaccharides bound covelently to a protein. Found on outer face of plasma membrane, in ECM, and in the blood; also sometimes inside the cell on the organelles. 

- form highly specific recognition sites for binding by lectins

1. conformational activation --> binding to the NS domain changes the conformation of protein, allowing it to accept a factor

2. enhanced protein-protein interaction --> binding of each protein to NS holds them in a way that makes it easier to bind to each other

3. coreceptor for extracellular ligands --> NS binds both a cofactor and its ligand, bringing them together

4. cell surface localization/concentration --> NS ionically attracts positively charged molecules and holds them in a certain place they need to be

1. O-linked

the carbohydrate is attached by its anomeric carbon to the -OH of a SER or THR

2. N-linked

the carbohydrate is attached by its anomeric carbon to the AMIDE NITROGEN of ASN

1. covalently attached lipid

2. transmembrane protein

triacylglycerols (fats) have more reduced double bonds than carbohydrates, so when you oxidize them you get lots more energy than glycogen breakdown. 

Also! 

they are hydrophobic, so you don't carry the extra water weight when storing them as you do with glucose.

[image]

is an example of what kind of membrane lipid?

[image]

what kind of membrane lipid is this?

- sphingosine backbone

- C2 has a long chain fatty acid with an AMIDE linkage

- C3 has either a phospholipid or a sugar attached

[image]

what kind of membrane lipid is this?

primary active transport: transfer of something against its electronic or concentration gradient is coupled directly to an energy-generating reaction

secondary active transport: when endergonic "uphill" transport of one thing is coupled to exergonic "downhill" transport of another, that was originally pumped "uphill" by primary active transport.

PROTON HOPPING

protons being transferred between water molecules in a chain causes a NET movement of a proton (or OH^-) over a long distance very quickly.