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167 Cards in this Set

  • Front
  • Back

Hydrophobic

Alanine, Proline, Glycine, Valine, Isoleucine, Leucine, Cysteine

Hydrophilic

Arginine, Glutamine, Asparagine, Histidine, Aspartic acid, Serine, Cysteine, Threonine, Glutamic acid

Amphipathic

Lysine, Methionine, Tryptophan, Tyrosine

isolated system

cannot exchange matter or energy with itssurroundings

closed system

may exchange energy, but not matter, with the surroundings

open system

may exchange matter, energy, or both with the surroundings

Living things are typically ___________ system.

open

first law of thermodynamics

states that thetotal energy of an isolated system is conserved

internal energy

commonly designatedE or U, and it includes all the energies that might be exchanged in physical orchemical processes, including rotational, vibrational, and translational energies of moleculesand also the energy stored in covalent and noncovalent bonds

state function

depends only on the present state of a system

independent of path

does not depend on how the system got there

internal energy depends only on ________ and not on _________.

present state of the system, how the system got there

Internal Energy (E) will not change if _____ is returned to its original state.

the system

Mechanical work

movementthrough some distance caused by the application of a force

Both ______ and _______ are required for work to have occurred.

movement, force

enthalpy

H, a function that is especially suitable forconstant pressure processes

van’t Hoff plot

A plot of R(ln Keq) versus1/T

second law of thermodynamics

1. Systems tend to proceed from ordered (low-entropy or low-probability) states to disordered(high-entropy or high-probability) states.2. The entropy of the system plus surroundings is unchanged by reversible processes;the entropy of the system plus surroundings increases for irreversible processes.3. All naturally occurring processes proceed toward equilibrium, that is, to a state ofminimum potential energy. Energy flows spontaneously so as to become diffused ordispersed or spread out. Energy dispersal results in entropy increase

entropy
ameasure of disorder and randomness in the system
energy dispersion
the dispersion of energy amonga large number of molecular motions relatable to quantized states (microstates)

For solutes in a solution, the standard state is ____________.

normallyunit activity (often simplified to 1 M concentration)

Consensus value of Delta G° of ATP in biological systems

-30.5kJ/mol

Why does the G° of ATP hydrolysis depend so strongly on Mg 2+ concentration?

The answer lies in the strong binding of Mg 2+ by the triphosphate oxygens of ATP. The binding of Mg21 to ATP is dependent on Mg 2+ ion concentrationand also on pH. At pH 7 and 1 mM [Mg2 +], approximately one Mg 2+ ion is boundto each ATP. The decrease in binding of Mg 2+ at low pH is the result of competition byH+and Mg 2+ for the negatively charged oxygen atoms of ATP.

thermodynamic potential

in the direction of positive Delta G

Many of the reactions necessary to keep cells and organisms alive must run against their __________.

thermodynamic potential

The anti-thermodynamic potential reactions are driven in the unfavorable direction by _______.

coupling

Important anti-thermodynamic potential reactions

intermediarymetabolism, oxidative phosphorylation, and membrane transport

Human consumption of ATP

11,700 kJ

standard reduction potential

Eo, quantitates the tendency of chemical species to be reduced oroxidized

reaction half-cells

A half-cell consists of a solution containing 1 M concentrationsof both the oxidized and reduced forms of the substance whose reductionpotential is being measured and a simple electrode

redox couple

the oxidized and reducedforms of the substance

Energy represents _____________.

energy dispersion.

free energy

a thermodynamic quantity equivalent to the capacity of a system to do work

Free energy depends on __________ and __________ concentrations

reactant, product

Free energy is pH-dependent if protons are __________________ ina reaction.

produced or consumed

ATP

is an intermediate energy-shuttle molecule

zwitterion

carboxyl group exists as OCOO2 and the amino group as ONH31, amino acid contains one positive and one negative charge

peptide bond

eliminating a water molecule and forminga covalent amide linkage

The repetition of a reaction forming a peptide bond creates ________ and _______.

polypeptides, proteins

peptide bond

remove H2O




form CO-NH bond

remove H2O










form CO-NH bond

y-Aminobutyric acid/GABA

amino acid produced by the decarboxylation ofglutamic acid and is a potent neurotransmitter

Histamine

synthesized by decarboxylationof histidine

serotonin

derived from tryptophan, similarlyfunction as neurotransmitters and regulators

Epinephrine/adrenaline

derived from tyrosine, is an important hormone

glycine hydrochloride

glycine, at low pH, boththe amino and carboxyl groups are protonated and the molecule has a net positive charge.If the counterion in solution is a chloride ion.

glycinate

increase in pH eventually results in dissociationof the amino group to yield the negatively charged

Edman reagent

A number of reactions of amino acids are noteworthy because they are essential to thedegradation, sequencing, and chemical synthesis of peptides and proteins. The reaction with phenylisothiocyanate,

glycine

only achiral amino acid

Serine, Threonine, and Tyrosine

they can become phosphorylated/ acetylated because of the (-OH)

Proline

only secondary amine

Histidine

will form in both positive and negative forms

Methionine and Cysteine

two with sulfur in them

Methionine and Cysteine can created and __________ bond.

disulfide

Phenylalanine, Tyrosine, Tryptophan, and Histidine

4 are aromatic

aromatic amino acids can:

1.) absorb light in the UV range


2.) Tryptophan will fluorescence

Seleno Cysteine/ Pyrrolysine

-C-Se-H

-Not in higher organisms



hydroxylysine & hydroxyproline

-in collagen


-the hydroxylation only occurs post translation


-turns into the protein of each

Pyroglutamic Acid/Bacterorhodopsin

-converts to glutamate

Gamma-aminobutyric acid (GABA)

-neurotransmitter


-neuromuscular junction involved in muscular tension


-CNS- inhibitor

histamine

r-antagonist-anti-histamines

Serotonin

-derivative of Tryptophan


-CNS neurotransmitter


-causes feeling of well being and relaxation



epinephrine/adrenaline

-released from the adrenal grands


-flight or fight response


-derivative of Tyrosine


-a techolamine



IR is looking at the _______ vibrations.

bond

NMR is observing Nuclear magnetic residence which looks for ____________________.

H+, C13, N15, P31

NMR

-will not observe a diamagnetic ion


-D20 will cause a large signal


-alaphatic protons lower than 4.84


-aramatics at 6 & 8

Negative charge near an amino acid causes________.

the amino acid to not let go of the proton, even 3 times as many.

Wobble Hypothesis

position three doesn't matter you'll get the right nucleic acid

dimeric enzyme

-homo dimer = two copies of the same chain

homoglobin heterotetramer

4 copies of the gene

primary structure

backbone & sequence of side chains held by covalent bonds

How to break a primary structure? Why?

hydrolyze it- 6M HNO3, no air, cook it


because they are really stable

secondary structure

regular repeated patterns in the structure of the backbone are held by hydrogen bonds from amide H-----carbonyl O

Why was x-rays used with secondary bonds?

-used to map the molecules within the structure

- found to map all the molecules in the structure but H





tertiary structure/domain structure

-held by intramolecular EaH (H-bonds, H0, e-statics) btwn side chains


-noncovalent except cys-s-s-cys = everything is in equilibrium nothing can change that

Quaternary structure

- just like tert but between different chains


-conformational change vs configuartional change

conformational change

moving

configurational change

breaking and forming of covalent bonding

Isoelectro Point

pI= pH of protein at no net charge

N-term

amino

C-term

carboxyl

enz

ase

trypsin & chymotrypsin

serine proteases, breaking the peptide the amine bond

Serine invariant residue

cannot be replaced w/out destroying the function

silent mutation

no change

innoculous

not much effect

deleterious

causes the whole thing to unravel

post translation modifications

PO4-ylated, acetylated, fatty acid esterification

golgi apparatus

puts sugars on the proteins called glycosylation

prosteketic groups

cofactors (inorganics) Zn 2+, Mg 2+, Mn 2+, PO4 2-

coenzyme

(organic) rhodopsin, NAD+,

Amino acids link to form_______.

polypeptide chains

The polypeptide backbone is __________.

relatively polar

dipeptide

two amino acids

tripeptide

three amino acids

tetrapeptide

four amino acids

oligopeptides

12 - 20 amino acids

polypeptide

several dozen amino acids

protein

broadly defines molecules composed of one or morepolypeptide chains

monomeric proteins

Proteins with one polypeptide chain

multimeric proteins

Proteinscomposed of more than one polypeptide chain

homomultimeric

Multimericproteins may contain only one kind of polypeptide

heteromultimeric

Multimeric proteins composed of several different kinds of polypeptide chains

homodimer

an alpha-type protein is adimer of identical polypeptide subunits

The peptide bond has partial _______________ character.

double bond

The amide plane of the peptide backbone includes all the atoms EXCEPT:

a. Cα-carbon.


b. amide nitrogen.


c. side chain carbons.


d. carbonyl carbon.


e. none, all are included.

c. side chain carbons

Hemoglobin is an α2, β2 _______ whereas, glutamine synthatase from E. coli is an α12 _______________.

heteromultimer, homomultimer

Collagen serves as what roll in the cell?

structural

Globular proteins are usually all EXCEPT:


a. Insoluble in water.


b. Roughly spherical.


c. Folded so that the hydrophobic amino acids are in the interior of the molecule.


d. Hydrophobic side chains are exposed to the water.



a. insoluable in water

10. Molecules of a given protein have all EXCEPT:


a. a fixed amino acid composition.


b. a defined amino acid sequence.


c. a sequence read from C-terminal end to N-terminal end.


d. an invariant molecular weight.


e. a nucleotide sequence from which they are encoded.

c. a sequence read from c-terminal end to n-terminal end.

Disulfide bond is formed in which levels of protein structure?

tertiary, quaternary

Which of the following levels of protein structure is correctly defined?


a. primary: interaction between subunits of a protein


b. secondary: hydrogen bond arrangement of polar R-groups


c. tertiary: three dimensional arrangement of all atoms in a single peptide


d. quaternary: order of amino acid residues in the peptide chain


e. none of the above are correct

c. tertiary: three dimensional arrangement of all atoms in a single peptide

22. The amino acid sequence is NOT:


a. a distinctive characteristic of a polypeptide.


b. encoded by the nucleotide sequence of DNA.


c. a form of genetic information.


d. read from N-terminal end to C-terminal end.


e. constant for proteins with the same function from different organisms.

e. constant for proteins with the same function from different organisms.

Edman degration

will determine the N-terminal amino acid

What is the product formed from the acid hydrolysis of a simple amide?

acid & amine

The C-terminal residue of a polypeptide can be determined by first cleaving the polypeptide with:
carboxypeptidase

Proteins that do NOT perform any obvious chemical transformation, but control the ability of other proteins to carry out their physiological functions are:

regulatory proteins.

Heparin

a naturalanticoagulant substance

Proline acts as a _______.

helix breaker

beta form

stretched helical structure that are uncoiled and extended

alpha form

protein structure in unstretched fibers was a helix

denaturation

loss of protein structure and function

helixcapping
providing H-bond partners for the otherwise bare NOH and CPO groupsand folding other parts of the protein to foster hydrophobic contacts with exposed nonpolarresidues at the helix termini
polyamino acids
polymers in which all the amino acids areidentical
Beta-pleated sheet
structure commonly observed in proteins also forms because of local,cooperative formation of hydrogen bonds
parallel beta-pleated sheet
adjacent chains run in the same direction
antiparallel beta-pleated sheet
adjacent strands run in opposite directions
Each single strand of the beta-sheet structure can be pictured as a twofold helix, that is,a helix with ________________.
two residues per turn

beta-turn

which the peptide chain forms a tight loop withthe carbonyl oxygen of one residue hydrogen bonded with the amide proton of theresidue three positions down the chain. Is a relatively stable structure.

Type I beta-turns are __________ than type II.

more common

Type 1 beta turn has _________ in position 3 while Type 2 has ________ in position 2 and _________ in position 3.

proline, proline, glycine

chaperones

proteins that assistin the process of protein folding in the cell

______________ are not needed in diluted solutions, proteins can fold and unfold themselves without their assistance.

Chaperones

Proteins are typically a mixture of _________ and _________ amino acids.

hydrophilic, hydrophobic

Why do proteins fold?

Because its made of both hydrophilic and hydrophobic amino acids

hydrophobic effect
inducesformation of a compact structure—the folded protein

Keratin

claws, fingernails, hair,and horns in mammals. structure is dominated by alpha-helical segments of polypeptide

Globular proteins

so named fortheir approximately spherical shape

amphiphilic helix
consists mainly of polar andcharged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues
domains or modules
larger globular proteins are usually made up of two or more recognizable and distinctstructures, compact, folded protein structuresthat are usually stable by themselves in aqueous solution
hydrophobiccollapse
Nonpolar residues may aggregate or coalesce in a process termed
flexibility and motion
All chemical bonds undergo a variety of motions, includingvibrations and (for single bonds) rotations. This propensity to move, together with themarginal stability of protein structures, means that the many noncovalent interactionswithin a protein can be interrupted, broken, and rearranged rapidly.
Atomic fluctuations
such as vibrations typically are random, are very fast, and usually occur oversmall distances
Conformational changes
involve motions of groups of atoms (individual side chains,for example) or even whole sections of proteins
metamorphic protein
exists naturally in an equilibriumbetween two diffferent three-dimensional structures under physiologicalconditions (Keq ~1). Example (chemokine* protein lymphotactin)

Hairpins

connect adjacent antiparallel beta-strands

Cross-overs

necessary to connect adjacent (or nearly adjacent) parallel beta-strands

betaalphabeta-loop

In many cross-over structures, the cross-over connectionitself contains an alpha-helical segment

alpha/beta proteins

in which helices and sheets are intermingled

alpha+beta proteins

in which a-helical and b-sheet domains are separated forthe most part

all alpha proteins and all beta proteins

in which the structures are dominated bya-helices and b-sheets, respectively

molecular chaperones

are essential for the correct folding of certainpolypeptide chains in vivo; for their assembly into oligomers; and for preventing inappropriate liaisons with other proteins during their synthesis, folding, and transport

natively unfolded proteins

do not possess uniform structural properties butare nonetheless essential for basic cellular functions

heat shock proteins

which are induced incells by elevated temperature or other stress

oligomers

complexes composed of (often symmetric)noncovalent assemblies of two or more monomer subunits

Orthologous proteins
are proteins that perform the same functionin different cells
Paralogous proteins
are proteins found within the same speciesthat have homologous amino acid sequences; paralogous proteinsarise through gene duplication
Related proteins shared a ________ evolutionary origin.

common

A __________ protein is a protein with a slightly different amino acidsequence.

mutant

Coupled processes
Enzymatic coupling of a thermodynamically unfavorable reaction with athermodynamically favorable reaction to drive the unfavorable reaction. Thermodynamically favorable reactionis often hydrolysis of high-energy molecule
High-energy molecules
 Phosphoric anhydrides (ATP, ADP, GTP, UTP, etc.)

 Enol phosphates (phosphoenolpyruvate a.k.a. PEP)


 Phosphoric-carboxylic anhydrides (1,3-bisphosphoglycerate)


 Guanidino phosphates (creatine phosphate)

Transfer of proton reaction equation:

pKa= ∆G/2.303RT

Why is hydrolysis of high-energy bonds favorable?
 Destabilization of reactant due to electrostatic repulsion

 Product isomerization and resonance stabilization


 Entropy factors

Thermodynamics of ATP hydrolysis influenced by:
pH, cation concentration, reactant and productconcentrations

Anion exchangers

Matrix is positively charged so anions bind
Cation exchangers
Matrix is negatively charged so cations bind
Carboxyl group + amino group – water =

peptide bond

Sulfur containing amino acids
cysteine, methionine