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117 Cards in this Set

  • Front
  • Back
what is the common structure of an amino acid?
a central alpha carbon,
an amino group, a carboxy group, a hydrogen and a sprecif r group that is unique to each amino acid.
how many standard amino acids are there?
20
what is a standard amino acid?
one used in direct protein synthesis
what naming system is used for amino acids?
the greek nomenclature for lipids
what is absolute configuration?
it is based on the position of the four substituent groups. if the amino acid is located on the left side of the alpha carbon then it is a L- amino acid, if it is on the right side then it is a d- amino acid. All amino acids that occur in nature are L-amino acids
which of the nonpolar amino acids can we make?
glycine, alnine and proline
which of the nonpolar amino acids are considered to be "essential"?
valine, leucine and isoleucine
What are the three branched chain amino acids?
valine, leucine and isoleucine
what types of bonds do two cysteines form?
disulfide
What is important about methionine?
it has a sulfur group attached to a methyl group. this make the mthyl group a good leaving group and therefor is a good methyl donor in the body.
what is special about Asparagine and glutamine?
they have amide side chains that are very stable. they do not ionize and are very good N donors in the body. Glutamine is a very good N carrier in the body.
where would you find non polar amino acids?
in the interior of the protein waya from and water because it is hydrophobic.
where would you find polar amino acids?
on the outdie of the protein because it is hydrophilic
What is the purpose of aromatic amino acids?
they make protein detectable at 280mn.tryptophan absorbs light the best.
How is tyrosine made?
it can be made from phenylalinine using phenylalinine hydroxylase. if there is no phenylalinine hydroxylase present then you get a consition known as PKU
Which basic amino acid is neutral at physiological pH?
histadine
What amino acid is the immediate precursor to urea?
Arginine.
Acidic amino acids are the best known connection between what?
protein and carbohydrate metabolism
What is trans-amination?
it converts a double bonded oxygen to a NH3 group and visa versa.
Collagen has what nonstandard amino acid precursors?
4-hydroxyproline and
5-hydroxylysine
Myosin contains what nonstandard amino acids?
N-methlylysine
prothrombin contains what nonstandard amino acids?
gamma- carboxyglutamate
elastin contains what nonstandard amino acids?
desmosine
explain the mechanism behind scurvy.
scurvy occurs from a collagen defiency. a prolyl residue needs ro react with O2 but it cannot without the help of ferrous oxygen. it uses the cofactor vitamin C to maintain ferrous (FE++) iron to bind to O2 to allow the O2 and prolyl residue to react forming 4-hydroxyprolyl which is a component of collagen.
What is desmosine?
it is made from 4 lysine residues. all but one looses a N groups from their R groups and combine to make desmosine. this contributes to the strechiness of elastin.
what is the henderson-hasselbalch equation?
pH= pKa + log ([A-]/[HA])

when pH=pKa then the congugate base and cong. acid concentrations are equal
What is pKa?
it is a dissociation constant. it tells how likely a acid or base will give up a proton. for strong acids (they want to give up protons) it is very low, but for strong bases (they dont want to give up protons) it is very high.
What are the equations for the calculation of isoelectric point of neutal and charged amino acids?
pI (neutral)= 1/2 (pK1 + pK2)
pI (basic)= 1/2 (pK2 + pKr)
pI (acidic)= 1/2 (pK1+ pKr)
How are peptide bonds formed and where are they located?
they form between the amino a carboxy terminus of two amino acids. they form via a dehydration rxn. the charge of both is lost when a peptide bond forms, thus the overall charge of a protein at physiological pH is based upon the charges of the R groups present.
how do you calculated the molecular weight of a protein?
MW= # of amino acids x 110
what is ion exchange chromotography?
this technique separates proteins on the basis of electric charge.

an anion exchange column binds anions using a cation bound resin.

a cation exchange column will bind cations using an anion resin.

whichever is bound will wash out LAST and whichever is repelled will be washed out FIRST
what is affinity chromotography?
this technique purifies proteins based on binding specificity. the resin uses a ligand that is specific for the protein and binds only to it. all others are washed through the column. highly specific.
What is molucular seive chromotography?
this technique separated proteins based on molecular size. proteins are washed through beads with holes in them. the smaller ones get stuck but the larger one just wash through. does not pruify protein but separates based on molecular size.
what is Gel Electrophoresis?
this technique separates proteins on a size basis. Using SDS page (a dentauring deturgent) it gives all the proteins a very large neutral charge . the proteins are then run basd on size. the large rones will get stuck on top and smaller will migrate quickly down.
what is Isoelectric focusing?
this technique separates based on the isoelectric point of proteins. this uses ampholytes to charge different positions of a gel tube and then as you run a sample, the sample will stop where it is neutral.
What is 2D gel electrophoresis?
it combines pI and gel electro. first you separate by pI and then by GEP. this gives individual proteins because it is very uncommon for two proteins to have both the same pI and molecular size.
What is proteonomics?
uses 2D gels to compare two separate protein samples. uses mass spectroscopy to identify the two separate proteins from the 2D gels.
What are ELISAs and Immunoblots?
these utilise antigen/antibody interactions to characterize a protein. in an elisa a protein is added to a well that has an antigen attached. if the protein is present it will bind and attach. a color indicator is then added and the amount of protein can be classified by the amount of color change that has occured. these can be troblesome because anything that is close will cross react and cn cause a color change
How are small proteins sequenced?
the N terminus is labeled with PTH and then mild hydrolysis releases both the the PTH and the amino acid. this is then repeated until all the amino acids have been released.
what two compounds are used for analyzing large protein sequences?
trypsin (cleaves at K or R) and chymotrypsin (F or W)
what is and how does Merifield synthesis work?
It is a way to bulid proteins in the lab. It builds backwards from in vivo building. it builds form the C to the N terminus. first the N terminus is protected so it cannot react. then it reacts with a resin at the C terminus. the N terminus is then unprotected and the processs repeats itself until all the amino acids have been added. and then is rleased using HF
What determines the 3D structure of proteins?
the amino acid sequence.
it is unique to each protein and also determines the function of that specific protein. the 3D structure is stabilized by weak non covalent interactions.
What are the four levelsof protein structre and what dies each intail?
primary: the amino acid sequence and any disulfide bonds. held together by covalent interactions.
secondary: regular reoccuring arrangements of adjacent amino acids. ( such as alpha helicies, beta pleated sheets and beta turns)
tertiary structure: arrangement of the total protein. the final 3D structure.
Quatrananry: arrangement of multiple protein subunits.
What is a proteins primary structure?
it is derived from the primary structure of the protein. includes peptide and disulfide bonds ( are included because both are covalent bonds). peptide bonds are planar. ridged bonds that hold the primary structure together.
What is the secondary structure of a protein?
the repeating arrangement of adjacent amino acids.
What are the characteristics of an alpha helix?
peptide bonds align along a long axis.
R groups stick out of the sides
each turn has the perodicity of 3.6 amino acid residues.
every 3-4 amino acids in close proximity will stabilize the structure through hydrogen bonding,
what are some alpha helix destabilizers?
a sting of several acidic/basic amino acids all in a row (like charges will repel)
a string of several amino acids with bulky side chains ( such as aromatic or branched chain amino acids)
amino acids 3-4 residues apart that cannot interact.
proline residues are ALWAYS alpha helix breakers!!!!
a string of glycine residues (because they are so small they make turns that are too tight to stabilize a tradititonal helix structure- important to collagen helix though)
What are some characteristics of Beta pleated sheets?
they are extended arrangements of polypeptides.

are stabilized by hydrogen bonds.

chains can be parallel or antiparallel. ( parallel if all the same on one side or antiparallel if they alternate on either side)
What are some characteristics of Beta turns?
all contain a proline in the cis conformation.

proline requires proline isomerase to convert it form the trans configuration to the cis configuration in order to make a beta turn.
what are the two major types of tertiary structure in proteins?
globular and fibrous.
What are some characteristics of fibrous proteins?
they are water insoluble.

they are all structural proteins.

they all have simple arrangements.

they are usually long chains or sheets.
what are some characteristics of globular proteins?
most are enzymes and proteins horomones.

they sec. structure is more complex.

the entire folding process is driven by the increased entropy of water. as the protein folds into a arrangement the water molecules get randomly dispursed around it causing it to be the most favorable conformation.
what are the three types to tertiary structure bonds?
H+ bonds: happens in an electronegative atom where the O or N actsas a H acceptor.

ionic bonds: attraction between opposite charges ( also called salt bridges)

hydrophobic interactions: forces that hold together nonpolar regions.
What are the proteins that help with the folding of teritary structure?
chaperone proteins.

the most famous is the heat shock proteins.
What are prions?
also called spongiform encephalitis. they are proteins that are folded incorrectly and cause disease.

causes: mad cow, scrapie, kuru (tribal), and creutzfeldt-Jacob.

If an abonmal prion comes into contact with a normal protein then it converts it to its infectious state which progresses along the disease.

first discovered by stanley pruizner.
What is cystic fibrosis?
a disease caused by a defective protein folding,

a codon triplet gets deleted (Phe is deleted) and results in the deletion of a vital chloride channel.

cuses mucous build up in the lungs and other effects
What are some characteristics of a proteins quartranary structure?
not all proteins exhibit this.

found only in proteins with more than one subunit
What is protein denaturation?
it is the disruption of the secondary to quatranary structure of a protein.

denaurants can be: heat,pH, detergents, or organic solvents ( such as SDS page and urea)

it ONLY disrupts weak interactions ( not covalents bonds)

proteins that have been denatured can be renatured when the denaturing agents are removed.
What are invariant amino acids?
amino acids that are crutial for the proper formation and folding. if disrupted these effects can be harmful.
Explain the Anfinsen Experiment.
found out that primary structure dictates tert. structure.

first he introduced urea (dentaured) and the BME (a reducing agent to break disulfide bridges).

then removed uream and then removed the BME. this caused normal protein formation
what is the layer of collagen left by a hand piece called?
smear layer
What are characteristics of Collagen?
it is a fiberous protein. it is a left handed nonstandard helix made of glycine and proline molecules. is tested for by measuring for hydroxyproline of hydroxylysine. has a perodicity of about 3 amino acid residues per turn.
is made from tropocollagen (3 helical strands that wrap around each other) and then arrange in an arrange of parallel bundles.
these bundles of tropocollagen croslink via lysinonoeleucine.
What is the structure of lysinonorleucine?
two lysine residues that are connected.
production involves enzyme lysyl amino oxidase. which uses vitamin B6 as a cofactor.
What are the two collagen related disorders?
Ehlers Danlos (defective type III collagen)

Osteogenesis Imperfecta (defective Type I collagen)
What are characterisics of Ehlers Danlos Syndrom?
defective type III collagen

stretchy skin and hyper mobility of the joints.
What are some characteristics of Osteogenesis Imperfecta?
Defective type I collgen

unmineralized skull and bones, blue sclera.
What enzyme is used t break down collagen?
collagenase
What are MMPs?
a type of collagenase.
a family of metal-dependent endopeptidases (must have Zn molecule to be active)
Degrades extracellular matrix proteins.
What are some characterics of alpha-keratin?
found in hair, nails and feathers.
is a classic right handed alpha helix with many hydrophobic amino acids ( because it is a structural protein)
makes a two stranded superhelix= protofilament that crosslink via disulfide bonds.
2 helix=2 chain coiled coil. 2x 2 chain coiled coil= protofilament. 4x protofilament= protofibril. 4xprotofibril= intermediate filament.
What are some characterics of Elastin?
found in smooth muscle, arteries, bladder, uterus.
triple stranded helicies= tropoelastin which are rich in gly, ala, and lys, but is not a true alpha helix. these tropoelastin filaments crosslink via desmosines.
What is neutrophil elastase?
Protein that degrades elastin that is found in the white blood cell. belongs to the family serine proteases and is deavtivated by alpha-1- antitrypsin which is a serpin.
alpha-1-antitrypsin defiency results in emphysema because elastase degrades the lining of the lungs before they can be rebuilt.
What are some characteristics of fibrillin?
found in arterial lining, and heart valves. coats elastin fibers.
defects result in Marfan syndrome and dissecting aortic aneurysm.
what is done for dissecting aortic aneurysm?
a gelatin coating of Dacron (gortx) is done for the ascending aortic replacement.
What is Marfans syndrome and wht causes it?
is caused by mutations in the fibril gene that effects Ca++ binding sites, disulfide bond formation, and hydrophobinc packing regions of the protein.
What are some characteristics of globular proteins?
sequester all the hydrophobic regions within the protein and place all the hydrophilic groups on the outside of the structure.
What are some characteristics of myoglobin?
a globular protein that serves as a oxygen storage molecule. Is made from a single ferrous heme group sequestered within a hydrophobic pocket. stabilized by hydrophobic interactions. is found in the muscles and is similar in structure to the beta chain of hemoglobin.
What is Heme?
heme is the structure that binds to oxygen within hemoglobin and myoglobin. it is made up of four pyrol rings liked by methene bridges (porpheryn ring) and then synthetic groups attached. then ferrous iron is sequestered in the middle to make heme. each heme molecule can bind to one O2 molecule.
Why must heme be protected?
because it ha a much higher affinity for CO than for O2. (20,000 times greater) and when prteted in the hydrophobic pocket this decreases to about 200 times the affinity.
What is the structure of myoglobin?
it has 8 alpha helical structures that are similar to the beta chains of hemoglobin. the distal histadine molecule gives steric hinderence to the heme group from CO while the proximal histadine group binds with Iron.
What is the structure of the Mb oxygen saturation curve?
it is a hyperbolic curve meaning that whatever one molecule of Mb does it does not affect the rest. it only releases O2 when at a critial point.
What are RBC and how are they important?
they are mode from hemipoietic stem cells from the horomone erythropoietin (EPOa) and loose all mito and ribosomes when mature. rely on glycolysis for energy and carry massive amounts of O2 to the tissues.
What is hemoglobin?
foun in RBC. has two alpha and 2 beta chains. exhibits cooperativity. has 4 heme groups and thus can carry 4 O2 molecules. cooperativity allows for both carring and delivery capacity.
What is the structure of the hemeglobin oxygen stauration curve?
It has a sigmoidal curve because it exhibits cooperativity. this allows form both carrying and delivery capacity at the proper conditions.
What is the differences in Hb during human development?
embryonic- are only expressed during the first trimester (zeta [alpha like] and epislon [beta like] chains)
fetal-has adult alpha chain and a gamma chain [beta like] chain which favors the oxy conformation for more O2 carrying capacity
adult- has alpha and beta chains.
What factors affect Hb's affinity for O2?
pO2, pCO2, pH, and 2,3 bisphosphoglycerate (2,3 BPG)
What is the Bohr effect?
Higher H+ (lower pH), high pCO2 (lower pH) and high 2,3 BPG lower O2. favors the deoxy form and shifts the affinty curve to the RIGHT which causes increased delivery to the tissues,
High pO2 levels (like in the lungs) shift the affinty curve to the LEFT and favors the oxy form which increases O2 loading.
Why do acidic conditions favor the deoxy form of Hb?
when the pH is acidic then the histadine molecules then become positivly charged allowing it to form salt bridges with 2,3 BPG. these salt bridges then cause the heme group to take on a puckered conformation. which wants to release O2
why do high pO2 conditions favor the oxy for of Hb?
because as heme binds to O2 it unpuckers and break the salt bridges favoring the oxy conformation.
explain how cooperativity in Hb works.
as O2 binds/releases in one Hb subunit, it shifts conformation to either the oxy or deoxy form. as it shifts conformation the other subunits also shift also allowing them to either bind or release O2.
How is CO2 considered acid?
because most is converted to bicarbonate which switches to carbonic acid via carbonic anhydrase. if there is excess acid in the blood then it can lead to acidosis.
Explain the chloride shift
as carbonic anhydrase difuses from RBC to blood a chloride ion is pumped the opposite direction in order to maintain charge neutrality of the system.
Where do we get 2,3 BPG?
It is a biproduct of glycolysis ( which is where RBC get there energy). 1,3 bisphosphoglycerate to 2,3 BPG via bisphosphoglycerate synthase.
How does altitude affect Hb?
as altitude increases the pO2 decreases to hypoxic levels (very low O2) and causes respiratory alkilosis. this causes an increase of 2,3 BPG to be made. this shifts the O2 curve to the right (favoring the deoxy form) and increases the delivery of O2 to the tissues. this allows for around the same amount of O2 to be delivered to the tissues even though not as much O2 has been loaded in the lungs.
What makes Fetal Hb favor the oxy form?
there are regions where there is decreased affinity for 2,3 BPG thus lowering salt bridge formation allowing for the oxy form to be favored.ths shifts the curve to the LEFT and allows for more O2 to be carried. this happens because the amino termini is acetylated and masks any positive charge that might bind to 2,3 BPG.
What is/causes sickle cell Hb (HbS)?
a glutamate is substituted for a valine on the beta chain at position 6. this causes a hydrphobic sticky spot on the Hb. these precipitate and causes deformation of the RBC. these lodge in capillaries and impair circ. this causes a decrease in malaria infected RBCs and gives immunity.
What is/causes Methemoglobin (HbM)?
this happens when ferrous (Fe++) iron in heme is oxidized to ferric (Fe+++) iron. this causes heme to bind to H2O instead of O2 causing cyanosis. can be induced by procaine (oxidizing agent in dentistry) and patients need to be treated with a reducing agent.
What is/causes glycosylated Hb? (HbA1c)
when Hb is glycosylated in bloodstream by glucose. excess glucose suh as in diabetes cancaue this to be increased. can be useful in quantifing diabetic control levels.
What is/causes COHb?
Hb has much higher affinty for CO. once CO binds to Hb it causes a higher affinity for O2 so it does not want to let it go to deliver it to the tissues. this causes hypoxia. must treat with 100% O2 at 3atm to force O2 replacement of CO. can cause death from carbon monoxide poisoning is CO levels reach 60%
What is the basic unit of muscle?
the sarcomere. muscle becomes a single syncytium ( a single multi nucleated cell)
What are thick filaments of muscle made up of?
supercomplexes of myosin (6 polypeptide chains [2 heavy chains and 2 light chains])
heavy chains are fibrous two stranded alpha helicies with a globular head
the light chains complex with the globular heads.
the M-line is where the muscle thick filaments are joined
What is the structure of myosin?
it has two heavy chains that coil from the carboxy terminus and the amino terminus forms the globular head. the light chains assoicate with the head region.
What are thin filaments of muscle made up of?
made up of complexes of actin, tropomyosin and troponin.
actin has two subunits: G actin (individual actin molecules) and F actin (fiberous complex of G-actin molecules).
tropomyosin- regulates actin/myosin interaction
troponin- binds Ca++
Actin does not hydrolyse ATP but the self polymerization of F actin does which is why there ADP residually bound to the molecule. each G-actin molecule had APD bound.
Name all the lines associated with the muscle structure
the m line- thick filament attachement. (H band= only thick filaments. A band= thick and thin filaments mixed)
the z line- point of attachment of the thin filament (I band- thin filaments only).
from the z line to z line= sarcomere.
What is Titin?
protein that extends half the length of the sarcomere and regulates sarcomere length and prevents overextention.
cardiac titin= largest single polypeptide ever to be identified.
How do muscles contract?
by sliding thick and thin filaments past one another. The sarcomere gets smaller, the Z disks get closer together when contracted.
nerve impulses signal muscle cell to release Ca++ from the sarcoplasmic reticulum. Ca++ binds to troponin and chages its conformation which in return changes the conformation of tropomyosin. tropomyosin then exposes myosin binding sites on the actin filament allowing for the power stroke.
what is a power stroke?
is based on the affinity of myosin for actin. alone, myosin has a high affinity for actin. as ATP binds to myosin it rleases from the actin molecule, and to had a conformational shift to an upward positon shifting the binding site of the actin. myosin is an ATPase and breaks down ATP increasing the affinity for actin again and then rebinds in the new conformational postion allowing for movement. this is called the power stroke.
What is the diffierence in smooth muscle and striated muscle contraction?
smooth muscle does not contain troponin. tropomyosin is therefore regulated with a Ca++calmodulin (CaCM) regulated protein called caldesmon.
smooth muscle has a unique light chain called myosin p-light chain
CaCM activates the myosin light chain kinase (MLCK) which phospholoryates myosin p-light chain and activates it for contraction.
What is Amelogenin and what is special about it?
is self polymerizes and fors into nano spheres that then linearize. this is thought to form parallel bunches of apatite during enamel formaion and regulates calcium phosphate crystal growth
What is the first law of thermodynamics?
the total amount of energy in any reaction remains constant, it cannot be created or destroyed.
what is the second law of thermodynamics?
In all natural processes the entropy of the universe increases
What is entropy?
(S) is the measure of disorder in the universe. must be greater than 0.
What is enthalpy?
(H) is the measure of heat enegry reflented in bond formation and breakage.
H>0 it is endothermic: requires heat
H<0 then it is exothermic: it releases heat
What is the gibbs free energy equation?
(G) the total energy available to do work.
G>0: endergonic and requires energy
G<0 exergonic: releases energy
dG=dH-TdS
how do you calc the eqiliubrium constant?
Keq= products/reactants.
does not predict the rate of a reaction.
What is the equation and values for the gibbs free energy at standard conditons?
dG=dG*' +RT ln Keq

T=25C (or 298 K) P= 1atm
Conc= 1 Molar
R is the gas constant which will be given.
What is the equation and values for the gibbs free energy at standard biological conditons?
dG=dG*' +RT ln Keq

T=25C pH=7 and differing conc.
What are the four ways that electrons are transferred?
directly as electrons, as hydrogen atoms, as a hydride ion, is direct combination with oxygen