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what is pH?
- measure of acidity
- (activity of solvated hydrogen ions)
stong acid properties
completely dissociate and the amount added = amount dissociated.
weak acids properties
DO NOT completely dissociate and have a dissociation constant Ka. Have buffering regions
Buffers resist changes in pH.
what is a Buffering range
pKa +/- 1 unit
1st law of themro
total energy of a system and its surroundings is constant.
- delat H-measure of total energy of a system
- exothermic-release of heat (- delta H)
- endothermic-absorption of heat (+ delta H)
entropy and 2nd law of thermo
gibbs free energy
- (-) delta G-spontaneous-->products
- + delta G-non spontaneous-->reactants
- 0 delta G-equilibrium--> CONCENTRATIONS of products and reactants DO NOT change
realation of gibbs, enthalypy, entropy and themp?
- delta G=delta H-T delta S (goose hunters take shotguns)
- - = - + (prod)
- + = + - (react)
- - - (calc)
- + + (calc)
what is the standard state,
biological standard state
- standard state-298K, 1 atm, 1M
- biological SS (delta G prime)-has a H+ concentration of 10-7 (pH7)
calculation standard state free energy in biological systems
ΔG° = - RT ln Keq or -2.3RTlog Keq
purpose of coupled reactions?
Thermodynamically unfavorable reactions can be made facorable by coupling with favorable ones.
made of C, H, O with formula Cm(H2O)n
same molecular formula but diff. structures
same number of atoms different conectivity
same number of atoms, same connectivity, different orientation in space
isomers that are NOT mirror images
Nonsuperimposable MIRROR images
differ @ one of several ASYMMETRIC carbons
Isomers that differ at a new asymmetric carbon upon formation of a ring
almost all saccharides are in what form
glucose straight chain can make_____and____ when it closes
fructose and make what 4 stuctures when forming a ring?
2 strctures used to avoid steric hindrance in a 6 memberd ring.
what is a condensation raction?
What bond is formed between 2 sugars b/c of this bond?
- loss of H2O
- a glycosidic linkage
what bond is formed between two molecules of glucose?
apha, or beta -1,4-Glycosidic Bond
name the monosaccharides that makes the following Disaccharides.
- 1. glucose + fructose
- 2. glucose + galactose
- 3. glucose + glucose
what bonds are present in glycogen?
same for Amylose, and Amylopectin
glycogen- alpha-1-4 links and alpha-1-6 links at branch points, branch every 10 units
- Amylose-alpha-1-4 links and unbranched
- Amylopectin-alpha-1-4 and alpha-1-6 links at branch points, branc every 30 units.
What are the structures of Glucose, fructose, galactose?
What are the structures of Maltose, Sucrose, Lactose?
What bonds are involved in cellulose
beta 1-4- links and hydrogen bonds
what is a proteohlycan?
a protein that is heavliy glycosylated (carbohydrate bound to protein), they are major components of the ECM.
And is an example of a chain of polysaccharides.
Mucins are glycosylated as well.
What is the difference between Ribose and Deoxyribose
- In ribose it is a OH group, in DEOXYribose it is an H.
What Nucleotide Bases are found on DNA? RNA?
How do they match up?
How many Bonds?
- DNA- Adenine (A), Thymine (T), Guanine (G), Cytosine (C). AT, GC
- RNA-Adenine (A), Uracil (U), Guanine (G), Cytosine (C).
- AU, GC
- AT and AU- 2 hydrogen bonds
- GC- 3 hydrogen bonds
Which nucleotide bases are Purines? Pyrimidines?
- Purine-A, G
1. DNA polymerization occurs in which direction?
2. Exonuclease activity occurs in which direction?
How many forms of DNA are there?
What are they?
- 3 forms
- 1. A form (in vitro) right handed
- 2. B form right handed
- -major form of DNA
- 3. Z form left handed
What are 3 specificities to B form DNA
- has major and minor groves
- 10 base pairs per turn
- major form of DNA in body
What stabalizes DNA helix
base stacking ( van der Waals) and hydrogen bonds btwn bases.
what is the structure of RNA?
(tRNA was disscussed in class).
What is a Cofactor?
non-protein compound boud to a protein, and is REQUIRED for protein to function.
1. if cofactor is tightly bound it is a ?
2. if cofactor is loosely bound it is a ?
- 1. prosthetic group
- ex. FAD-->attached to an enzyme
- 2. coenzyme
- ex NAD--> free floating
ATP does what?
energy currency carries phosphoryl groups
Nicotinate (niacin) is a vitamin precursor for what Coenzyme?
what does it carry?
NAD+ and NADP+
Riboflavin (Vitamin B2) is a vitamin precursor for what Coenzyme?what reaction does it do?
- FAD and FMN
Pantothenic acid is a vitamin precursor for what Coenzyme?what reaction does it do?
what does Lipoamide carry?
Thiamine (vitamin B1) is a vitamin precursor for what Coenzyme? what reaction does it do?
Biotin is a vitamin precursor for what Coenzyme?what reaction does it do?
biotin-lysine adducts (biocytin)
ATP dependent carboxylation and carboxyl-group transfer (CO2)
Folic acid is a vitamin precursor for what Coenzyme?what reaction does it do?
transfers one carbon components and thymine synth.
Vitamin B12 is a Coenzyme precursor for
transfers methyl groups and intramolecular rearrangements
what does Uridine diphosphate glucose carry?
what does Cytidine diphosphate diacylglycerol carry?
what do Nucleoside Triphosphates carry?
Pyridoxine (vitamin B6) is a precursor for what Coenzyme? What reaction does it do?
Group transfer TO or FROM amino acids
Water soluble vitamins are?
B3, B2, B5 B6
Fat soluble vitamins
A, D, E, K
Vitamin A is a?
what is its function?
roles in vision, growth, reproduction
Vitamin C (ascorbic acid) is a?
what is its function?
Vitamin D is a? what is its function?
Regulation of Calcium, and phosphate metabolism
Vitamin E is a? what is its function?
Vitamin K is a? what is its function?
what is the structure of the 20 amino acids?
are they polar uncharged, Non-polar, polar charged, basic, or acidic.
I'm not drawing that mess you do it!
peptide bond formation occurs via?
define oligopeptide and polypeptide
- condensation reaction
- -done by ribosomes
- oligo-2-25 residues
poly more than 25
define primary structure
linear sequence of AA's in a peptide chain startin at N-terminus and ending at C-terminus.
peptide bonds have what kind of character?
they have partial double bond character and this makes them planar and not rotate.
What is the predominant side chain orientation?
Trans over cis with the excepton of Proline. Trans config. is most energetically favorable. with proline most energetically favorable is cis.
what secondary structures encompass polypeptide residues?
- 1. alpha helix-R groups face outward so can have different chemistry on different sides of each helix. There is a hydrogen bond btwn every 1st and 4th AA residue.
- 2. beta sheets or strands, can be parallel (same N and C termini) or anti parallel (opposing N and C termini) and are stabalized by hydrogen bonds above and below each sheet.
define Tertiary Structure
and give examples of some
- 3-D spatial arrangents of AA's and are made up of 2ndary structures.
- examples-ferritin (all alpha helicies), beta barrles, leucine zipper (coilied coil) in keratin, myosin and used for structure, collagen helix (stabilized by steric repultion of pro) it's in skin, bone, teeth, cartilage.
function of Prolyl hydroxylase and its mech
and where do the prolyl residues come from?
- aids in the production of collagen, and takes a prolyl residue and the enzyme prolyl hydroxylase takes O2 and alpha ketogulterte and makes 4-hydrosyprolyl residue (hydroxylated proline res.), CO2 and succinate
- The residues come from vitamin C. a dificiency leads to scurvy.
how is Hydroxylysine formed?
and what does it do?
need-vitamin C (ascorbic acid), iron , and a lysyl hydroxylase
forms intercain cross links in collagen and provides attachemnt sites for carbohydrates.
Define Quaternary Structure
spacial arrangement of tertiary subunits. can be homodimeric (cre protein) and heterotetrameric (hemoglobin)
What is a disulfide bond? what does it mean to the structure of a protein? What proteins have them?
an S-S bond betwn two SH containing residues (formation bia oxidation, and breakage via reduction)
they are used to stabalize tertiary structures offten connecting separate polypeptide chains to make one structure. example insulin
How do hydrophobicity effect protein structure?
it aids in the proper formation of the completed protein. the hydrophillic exterior will stay exposed while the hydrophobic interior will fold in.
how is it possible for a protein to unfold in the presents of urea, and then regain confirmation once urea is taken out?
the presents of disulfide bonds! they hold the structures together to a certain degree!
what is the purpose of chaperones and give two examples presented in lecture.
- they are proteins that help newly synthesized protiens fold.
- ex. Hsp70- prevent folding of nascent chain and promote refolding
and Hsp 60-surround unfoled protein and form a barrel shape to allow the protein to complete it's final confirmation and they requier ATP's.
What are Intrinsically unstructured proteins?
also termed metamorphic protiens, are not in final confirmation until binding of substrate or specific functional group.
proteins that convert structurs with function to structures without function
- ex Creutzfeldt-jakob disease or mad cow
- one protein two structures.
Name 3 characteristics of enzyme regarding rate, specificity, and overal reaction?
- A catalyst that speed up a favorable reaction by lowering it's activation energy.
- rate increase 106-1017
- have specificity in that one enzyme has a precise interaction with substrate to make ES complex
- It make the rxn reach equilibrium quicker. does not alter amout of products or reactants.
in an active site how does substrate binding occur?
it's stabalized by multiple weak interactions with in the unique microenvironment the active site presents.
what are two models that describe specificity binding?
lock and key model (fisher) and Induced fit model (Koshland)
-substrate binds to enzyme to make an ES complex
Describe the relationship of Apoenzyme, Holoenzyme, and cofactor
Apoenzyme is an enzyme that has no bound cofacor, once cofactor is bound it is deemed a holoenzyme.
-reaction type? Example?
- Lactate Dehydrogenase
- -catalyses the interconversion of pyruvate and lactate and uses NAD+/NADH as cofactor
- Tyrosine Hydroxylase
- -catalyses the syth of L-DOPA neurotransmitter precursor of dopamine, norepinephrine, and epinephrine. cofactor BH4
-reaction type? Example?
Nucleoside monophosphate kinase (NMP kinase)
Serotonin N-Acetyltransferase (SNAT) or AANAT cofactor of Acetyl-CoA
-reaction type? Example?
- Hydrolysis reactions (transfer of fuctional groups to water)
- -cleave C-O, C-N, or C-S bond with addition of water to make OH and H+
- and beta-galactosidase
-reaction type? Example?
- Addition or removal of groups to form double bonds
- -cleave C-C, C-O, and C-N bonds by double bond formation!
Fumarase, aldolase (used in glycolysis to split 6 carbon molecule into two 3 carbon ones.
-reaction type? Example?
- isomerization (intramolecular group transfer)
- -rearrange the bond structure of a compound.
- Triose phosphate isomerase
- -used in glycolysis to make Dihydroxyacetone phosphate into glyceraldehyde 3-phosphate.
-reaction type? Example?
- Ligation of two substrates at the expense of ATP hydrolysis.
- -make C-C, C-S, C-O, and C-N bonds coupled to ATP or nucleotide.
- Aminoacyl-tRNA synthetase
- Pyruvate carboxylase
- -1st step of making glucose from pyruvate in gluconeogenisis
what is V0 and how does it relate to KM, [S], and Vmax?
the initial reaction velocity- product/time
- Michaelis-Menten equation
- if [S]<<KM V0=Vmax----------- KMif [S] >>KM V0=Vmax
1/V0=KM/Vmax x 1/[S] + 1/Vmax
Y = m x + b
define KM and explain how it effects lineweaver-Burk plots.
KM is related to the affinity of enzyme to substrate. and when it increases the slope (KM/Vmax) increases as well as the x-intercept. (-1/KM) it is also equal to 1/2 Vmax.
define Vmax and describe how it affects lineweaver burk plots
- Vmax is the point to which all enzyme is bound to substrate and the maximal velocity for the reactino for the given amout of enzyme has been reached. Vmax changes only when you add more enzyme, adding more substrate does nothing. effects burk plot increase or decrease y int. if v max increases then y intercept goes down and vice versa and it also affects slope. the slope with go up when Vmax decreases slope increases.
1. reversible inhibition examples
2. irreverible inhibition examples
1. Substrate inhibitor to DHFR
- 2. Glycopeptied transpeptidase (penicillin)
- Aspirin in COX
define Competitive inhibition and how it effects Km, Vmax and the graphs/burk plots
- similar to substrate and binds at the active site, and is reversible. the way to overcome competative inhibition is to increase the amount of substrate so that it will out compete the competitive inhibitor.
- Vmax-not effected,
- Km- increases (and so does slope) and causes a less steep curve
Define Uncompetitive inhibition and how it effects Km, Vmax and the graphs/burk plots
- An uncompetitive inhibitor binds to a site that is closely assiciated to the active site but is not the active site. it only binds once the substrate has bound and formed the ES complex which increases affinity from substrate thus making Km decrease.
- Km decreases (b/c afinity increases)
- graphically slope relative similar but y int increases
Define Noncompetitive inhibition and how it effects Km, Vmax and the graphs/burk plots
- noncompetitive inhibitor binds to an allosteric site (site other than active site) and changes the confirmation of the acitve site so that the ES complex can not catalyze the reaction.
- Km-does not change
- graphically- slope increases and so does intercept, curve gets lower.
define Allosteric enzymes
- Binding of one substrate facilitates binding of a second. (cooperativity)
- do not have Michaelis-menton kinetics, produce sigmoidal curves, have multiple active sites, and show cooperative substrate binding.
- Tense (T)-low affinity binding, relaxed (R)-greater binding affinity.
what is the difference between concerted model and sequential model?
- concerted is all or nothingsay there are 4 binding sitesbinding at one site instantly changes the shape of the 3 other sites
- sequential is whenthere are 4 binding sitesbinding at one site activates the binding site next to it
What 3 enymes are in chymotrypsin? and what is their role in the reaction mechanism?
- Aspartate, Histidine, Serine (acts as alkoxide ion)
- Serine-residue attacs the peptied bond and is the alkoxide ion that does the nucleophilic attack on carboxyl group of peptied bond.
- Histidine-base catalyst that (it grabs proton from ser so that ser can attack the peptide bond. then later it acts as a acid catalyst when it gives it's proton to the amino group.
- Aspartate-helps orient the histidine residue to make it a better proton acceptor. (though hydroben bonding and electrostatic effects) All of this is done for the purpose of making the C on the substrate more susceptible for nucleophilic attack by water
explain serine proteases and specificity
the difference in each serine protease is the diferentiation in the active sites which leads to speificity.
- Chymotrypsin has a non polar pocket so it can cleave non polar residues (Trp,Tyr,Phe, Met, Leu)
- Trypsin has an additional Asp (negative charge on it) so it can cleave + charged residues (Arg, Lys)
- Elastase has two valine resitues wich make to pocked smaller and therefore can only acces small residues (Ala, Ser)
compare serine proteases, cysteine proteases, and Aspartyl proteases? what is similar in roles of the residues in the active site?
- Cysteine protease like serine protease has a histidine residue that acts as both a base and acid catalyst during different steps of the mech. main pupose still makes the C more susceptible to nucleopihlic attack by water. (takes proton to allow for tetrahedral intermediate then when water comes it takes water to allow for the release of the substrate then delivers proton back to cystine as before) examples: Papain, cathepsins, caspasees
- Aspartyl proteases are similiar to serine proteases in that they have aspartate residues (2 of them) one activates the substrate and the other will use engage water to allow for nucleophilic attac of activated substrate. The two residues make the C more susceptible to nucleophilic attack by water.
have metal ions that are used to make the carbon more susceptible to nucleophilic attack by water.
explain Uses of protease inhibitos in HIV, and High blood pressure.
HIV proteae cleaves HIV virus into active form and use the inhibitor Crixivan acts as a transition state analog.
Angiotensin converting enzyme (ACE)- captopril is a transition state intermediate and blocks the active site so angiotensin, which casues vasoconstriction which increases BP, can't bind.
What is an isozyme?
- protein that differs in amino acid sequence but it catalyzes the same reaction and have a different Km, regulatory propterties or localization. used in fine tuning specific reactions.
- ex glucokinase and hexokinase, protein kinase C, lactate dehydrogenase
Feed-forward regualtion vs feedback regulation
Feed-forward reg. is when something binds to an enzyme and causes and increase in production
Feed back regulation is when someting from down stream (usually in excess) will slow a given enzymes production.
How does Aspartate transcarbamolase exhibit allosteric activation, and allosteric inhibition?
Aspartate Transcarbamolase(ACTase) is allosterically inhibited by CTP which shifts the equilibrium to stabilize the T state, making it harder to bind substrate resulting in a shift to the right in the graph.
it is allosterically activated by ATP, which shifts the equilibrium the the R state making it easier for substrate to bind and results in a shift to the left in the graph!
Aspartate transcarbamoylase or ATCase consists of what subunits? which are regulatory, and which are catalytic, and what causes their dissociation?
- ATCace has 2 catalytic trimers and 3 sets of regulatory dimers (these bind CTP the allosteric inhibitor)
- ATCase dissociates when they bind a substrate analog PALA or ATP
ATCase exhibits which of the two allosteric models?
- Concerted Model "all or none"
- it's cooperative and has sigmoidal curve.
- CTP binding favors T state
- substrate or ATP binding favors R state
how is activation of protein Kinase A acheived? and how is activation of CaM kinase acheived? and what kind of regulation is it?
- both are considered to be regulation through interaction
- Protein kinase A has 2ndary messanger interactions when cAMP(released by hormones adrenaline) binds to the inhibitory subunit. it causes a release from the Active site of the catalytic subunit and it will phosphorylate things.
- CaM kinase has a protein protein interaction in which calmodulin a protein clamps the CaM kinase peptide, which changes the confirmation of the kinase making it active.
what are the different covalent modifications?
- Phosphorylation, ser, thr, tyr kinases (turn it on), phosphotase takes it off, muscle glycogen phosphorylase regulated by AMP and phosphorylation (both make it acitve)
- ADP-ribosylation, of arg, glu, or asp, similar effect of
- Acetylation, histones(makes the chromatin condense
- structural modification
- glycoslyation-in extracellular proteins
- lipid modification, anchor proteins to cell membrane
- Hydroxylation of AA residues, hydroxyproline, and hydroxylysine important in collagen structure and functions
- gama-caboxylation of AA res.
zymogens are active enzyme precursors that have an activation cascade are are regulated by either being turned completely on or completely off. the cleaveage of a Lys-Ile bond in tripsinogen to make trypsin allows for further activation of zymogens.
trypsin cleaves chymotrypsinogen to the active chymotrypsin and forms a N-terminal Ile which forms an ionic bond with asp. this then leads to a conformational change which forms the binding poket that was not there in zymogen form and an oxyanion hole is possible for the ability to stabalize the tetrahedral intermediate
how is gama-carboxyglutamic acid synthesized and what does it do?
- it is catalysed by the vitamin K dependent carboxylase
- it is a strong calcium chelator which is essential in blood clotting (activate prothrombin) and involved in mineralization (osteocalcin)
what is the Vitamin K cycle
it carboxylates a prozymogen with the vitamin K-dependent carboxylase to make a carboxylated zymogen.