Biochem- Exam 1
A buffer can only compensate for influix or removal of H ions within __ pH unit of pKA
1. Outside of this range, the pH will rise or drop rapidly because there is little conjugate base or H+ left.
At 1 pH unit above hte pka of a buffer, ratio of A- to HA changes from
1:1-->10:1
1 ph unit below hte pka, the ratio of A- to HA cahnges from
1:1==>1:10
Cells in the kidney generate ___ and excrete it in the urine in proportion to the acidity of the blood.
NH4+ (when is it increased more...?) ( i think that the more acidic the blood, the more of it is excreted...)
In urine you also have ammonium ions-
NH4+-->NH3+H+
Do ALL proteins in the cell fold into their NATIVE confirmations on their own?
NO!
Is the tst for myoglobin specific to cardiac or skeletal muscle?
NO!
Can a pH of 1-2 BREAK peptide bonds?
NO! but it does disrupt the native confirmation of the protein making it a better susbtrate for digestive enzymes!
Protein structure is governed by ____ interactions
NON COVALENT (? what about disulfide bond)
Breaking the salt bridges in the contacts between subunits is an energy __ process, therefore, the binding rate for the first O2 is very __
REQUIRING; LOW
Proline is a ___ amino acid
RING
Every molecule of the same protien (ex/ myoglovbins) fold into the SAME 3D structure; this is called native confirmation. T/F
TRUE!
How many water molecules are bound to the H?
2
How many water molecules are bound to the O?
2
Hemoglobin is referred to as :
2 alhpa-beta promoters
Adult hemoglobin is composed of:
2 alpha and 2 beta chains- and is a tetramer- (alpha2beta2)
Aspartate protease family enzymes use:
2 aspartate residues int he active site for acid-base catlaysis of peptide bond.
PkA1 of phsophate buffer system?
2.12
Each water molecule in hydration shell of water lastss:
2.4 nanoseconds (1 nanosecond=10^-9 seconds-->so 10^-9*2.4)
HCO3- to H2CO3 of __ to __ is required for blood plasma to be maintained at 7.4
20:1
Creatinine kinase is composed of __ subunits: with __ to __ % sequence homoloy
2; 60-70
PrPc- C terminal region: contains:
3 substantial helices, and 2 three residue beta strands joined by 2-3 H bonds. (mostly alpha (40%) almost no beta)
Typically, CtNt is detected in an acute MI within __ to ___ hours after the onset of symptoms:
3-5; positive in 8 hours mostly; 100% sensitivity in 10-12 hours; remains elevated for 5-10 days
If H+ is 3*10-5 use shortcut to calculate the pH
3.0 x 10^-5....5-(0.3+.1)= 5-(0.4) = 4.60.....real answer is 4.52
pKA carbonic acid is
3.8
Usually, optimal temp. of enzyme=
37 degres C.
Native confirmation refers to a proteins ___ structure
3D
One water molecule is bound to ___ neighboring molecules
4
N terminal region of a prion binds:
4 Cu2+/chain
Strength of H bond between 2 water molecules is only:
4 kcal
Hydrogen bond strength:
4 kcal- 1/20th of covalent bond
Heme is made of __ __ rings w. __ __ concentrated in center
4 pyrole; 4 Ns
When the next O2 binds, many of the Hb molecules are in thsi state:
4 subunits in the R state= raise the rate of binding. Continues to increase with further binding
But PrPsc (bad)- mostly alpha or beta?
40%-50% beta 20-30% alpha promotes aggregation
Cooperative binding of O2 in hemoglobin comes from changes in ___ structure that takes place when O2 binds.
Tertiary
Describe the hydration shell of water molecules-
The H atom is closest to the anion
When is fCJD present in life?
4th decade
What is the minimum urine PH?
5.0
What is the pH of urine?
5.5-7.0
pKA=pH in which?
50% of the acid has dissociated
Widest possible range of pH with function?
6.8-7.8
Water composes how much % of the body:
60
Normal INTRACELLULAR pH?
7.1
Relevant pkA of phospahte buffer system?
7.2
pKA2 of phosphate buffer stystem
7.2
Normal pH of blood is what- extracellularly
7.36-7.44 (extracellularly)
Blood pH is
7.4
AGEs tend to accumualte with?
age!
How does thiamine def. happen?
alcoholism; ethanol inhibition of thiamine transort through the itnerstinal mucosa
PrPc vs. PrPsc energy level...
almost same! BUT- to get from PrPc-->PrPsc= LARGE energy barrier; makes conversion SLOW
Proline involves the ___ carbon
alpha
Secondary protein structure
alpha and beta helix
What is the main difference between alpha and beta helices?
alpha- H bonding on SAME strand Beta- H bonding on adjacent strand
Hemoglobin is made of 2 __ and 2 __ polypeptide chains
alpha; beta
acetylation of lysine residues in histone protein can:
alter DNA
Why is myoglobin NON specific for MI:
amino acid sequences of cardiac and skeletal muscle myoglobins are identical
Ammonia is produced from ____ catabolism, or absorbed through the _____.
amino acid; intestine
Primary protein structure linear sequence of __ __ in a __ __.
amino acids; polypeptide chain
Back bone of a pepdie bond is:
amino group, carboxyl group, alpha carbon
HIGH pH disrupts H bonds and ionic bonds formed by
amino groups!
Glycosylation: addition of ___
an oligosacchride at O or N linkages
A protein WITHOUT a prosthetic group attached:
apoprotein
3 basic amino acids:
arginine, lysine, histidine- their charge is POSITIVE
All amino acids are __ amino acids- means
L; nitrogen is to the LEFT when carboxyl group is up top
Glycine has the ___ amount of steric hindrance
LEAST
PrP-sc has __ beta structure
LOTS
Polar uncharged amino acids:
aspargine, glutamine, serine, threonine
Acidic amino acids:
aspartate and glutamate (both are negative)
2 acidic amino acids- what is their charge in phys. pH?
aspartate, glutamate- their charge is NEGATIVE
heat shock proteins use the energy provided by __ ___ to assist in folding process
atp hydrolysis
concentration of glycoslyated proteins is proprotional to concentration of:
available glucose
Ammonia is a __ that combines with protons to produce ___.
base; ammonium (NH4+)
at very alkaline pH, hydrogen and ionic bonds formed by __ __ __ would be disrupted
basic amino acids
arginine, lysine, histidine
basic amino acids/ positive
Glycine is found in the _____ of many proteins
bend
Glcine is found at ___ or tightly packed chains of __ __
bends; fibrous proteins
Thiamin deficinecy causes?
beri beri <3 disease
In what chain is sickle cell glutamate-->valine?
beta 2
Penicillin contains a strained peptide bond in the __ __ __ that looks like __ __ of nromal cleavage reaction
beta lactam ring; transition state. So then glycopeptide transpeptidase tries to cleave the pencillin peptide bond, and ends up covalenetly attached to tehe nzyme's active-site serine. This inactivates the enzyme
Amyloid fbril structure is made of repeated __ __ aligned perpindicularly to the axis of the fibers;
beta sheets
As the renal tubular cells transport H+ into the urine, they return ____ anions to the blood
bicarbonate
Long chain fatty acids and other highly hydrophobic molecules have their own __ __ in the cell
binding proteins
th side group sticks out of the backbone and folds into distinct regions called:
binding sites- where ligands bind
Gout- genetic or env? What happens?
both! Accumulatiion of URIC ACID in blood; leads to preciptiation in joints/ severe pain discfomrt
disulfide isomerase:
breaks and remakes disulfide bonds between SH groups of 2 cysteine residues
fatty acid acetylation: is when you___ attach a ___ __ on a __ __
covalently attach a lipid group on a membrane protein
At physiological pH most of the carboxy groups are____
deporotonzated
How do isozymes differ among one-another?
different PRIMARY structure
Amyloid can be derivde from __ __ that have changed their confrimation state based on different dsiease processes.
different proteins
What does urea do?
disrupts H bonding patterns of both PROTEIN and WATER
H2CO3 is in equilibriumw ith?
dissolved CO2
Within the tertiary structure are physically independent structures called:
domains
Acids _____ a H atom
donate
Three D structure is _____
dynamic and flexible
Because the H bonds are relatively weak, water is
dynamic- has many strained bonds that are continuously breaking and reforming!
How do you get PrpSC into your system
eat it
Malathion poisoning: genetic or env?
env
In the induced fit model, as the substrate binds to the enzyme..
enzyme undergoes confirmational change- this change repositions the sidechains of the enzymes aa int eh active site thus icnreasing the number of binding interactions.
Who is glycosylation common in:
enzymes that turn over SLOWLY in body
40% of the water in your body is?
extracellular
Where sulfuric acid comes from:
foods, metabolism of sulfur containinga mino acids, cyestine, methionine
Glycoslyation - occurs when __ __ is in the interstitum OR __ __ binds to an exposed __ __ on a protein
free glucose; intracellular fluid; amino group
pH < peak
functional group's aren't fully ionized; can't be productive in catalyzing the rxn. i.e. pH< pKA- so everything is protonated.
Transferases: catalyze the transfer of __ __ between mmolecules.
functional groups
pH must be contained in a __ __ for the ind. protein
functional range
Amyloid fibers are pathological insoluble fibrillar proteins; from where are they derived?
gamma or K immunoglobulin LIGHT chains
Physiologically, proteins are denatured by __ __ of stomach
gastric juice; 1-2
primary structure is dicatated by
genetic code
Water is a good solvent for who?
glucose and electrolytes.
Long chain fatty acids inhibit many enzyme catalyzed reacitons by binding nonsepcifically to:__ __ in proteins, thereby disrupting __ __
hydrophobic pockets; hydrophobic interactions
Covalent inhibition is ______ and does the affeccted enzyme work anymore?
irreversible;no
Water is a dipole molecule; why?
it contains two hydrogen molecules with + charge and 1 oxegyn molecule with negative charge. The O has 2 unpaired electrons with a negative charge. This allows water to form H bonds making it a good solvent.
What ist he problem with PrPsc-
it is NOT degradable- results in AGGREGATION of proteins- causing neurodegenrtuiave disease
Why aspirin works:
it looks like the prostaglandin precursor that is a substrate for COX
Weak acids dissociate to a limited extent..... in the body these are?
ketone bodies, acetoacetic acid, Beta hydroxybuteric acids (all of the above are carboxylic acids)
As the protein folds and refolds, it is searching for its native low energy state, and it passes through many high energy confirmations that slow down this process called: ____ ____
kinetic barriers
One of the first proteins released into the blood during an acute MI:
myoglobin- from damaged cardiac tissue-
Myoglobin measurements have high ___ value within 2-6 period
negative predictive value; i.e. if myglobin isn't elevated, then MI didn't happen
Blood contains high content of ___ charged proteins
negatively
Ammonia is toxic to ___ tissues.
neural
Transmissable spongiform encephalopties are __ ___ characterized by :
neurodegenerative diseases; 1. spongiform degeneration 2. astrocytic gliosis in CNS
Are ketone bodies normally presnet in urine?
no
Does xanthine oxidase work Guanine-->Xanthine
no
Nonpolar substances- do they dissolve inw ater?
no! WATER CLUSTERS IN NONPOLAR ENVIRONMENT
You have a pt. with constant blood clots, and you hear someone say that they give them streptokinase all the time- is that okay?
no! streptokinase can only be used once. it causes immune response after first use.
Is the amount of myoglobin released during an acute MI ENOUGH to cause myoglobinurea?
no! that is red tinged urine and that happens with skel. muscle damage
Van der waals forces work even between:even between:
non polar amino acids
Urine is a _____ produced by metbaolism
non volatile acid
Most of the nonvolatile acid hydrogen ion is excreted as ______ acid- generally buffering the urinary pH between:
nonvolatile; 5.5-7.0
3 aromatic amino acids:
phenylalanine- nonpolar tyrosine- polar. alchohol tryptophan- amine
To maintain metabolic homeostasis, we must exfrete, the same aount of ___ in teh urine that we injest with food as ___ anions or ___ phosphates such as phospholipids.
phosphates; phosphate; organic
Dissolved Co2 is ine quilibrium with Co2 in the air of the alveoli of the lungs. The availability of Co2 can be increased or decreased by:
rate of breathing, or amount of CO2 expired.
Lower than 37 degrees celcius, enzyme has not....
reached maximium velocity of reaction
Hb is a ______ composed of 2 different subunits polypeptide chains
tetramer; 2 alpha; 2 beta
Collagen adn other glycoslyated proteins in tissues are further modified by non enzymatic oxidation adn form additional______ and make ___.
cross links; ages! (advanced glycsolyation end products)
Between what amino acids do disulfide bonds exist?
cysteine amino acids ONLY.
When you heat water, hydrogen bonds
decrease
glutamine
Q
Arginine
R
Ex of inorganc cations
K+
What determines chemical properties of amino acid?
R
2,3,BPG is made here:
RBC
Prion disease acquired throughs poradic or inherited mutation
CJD
Inside a cell you have what compounds:
K+, phosphates, HPO42-
Proline puts a ___ in the peptide backbone
KINK
Fore tribes people;ritual canabilism causes this prion disease:
KURU!
Buffers work by keeping the __ constant
Ka
Henderson Hasselbach equation:
Ka=H*A/HA
Amine
NH2RO
at pH >>8.5, what happens?
NH3+ is deprotonated!
disulfide bond is a _____ bond between
covalent; sulfahydride
Which can bind to O2 at lower Po2- myoglobin or hemoglobin?
myoglobin!
Enzymes you can look at for MI:
(what about alt and ast??? ask) 1. Myoglobin- nonspecific 2. cTnT 3. CK-MB
ionic bond is betwen
+ and -
Each amino acid is made of:
- central alpha carbon - amino group - carboxylate group - side chain R
What is a promotor?
- part of quatenary structure - unit structure within protein composed of multiple NON identical subunits
Both hydrolases and oxidases:
1. O from O2-->substrate 2. O from O2-->water 3. O2- both-->water
ph=
-log H+
pka=
-log Ka
Gertsmann Strausller Scheinker disease
...
Buffers only work within __ ph unit of its corresponding pKA
1
Clinical sequale of amylodisis:
1. Bence jones protein in urine 2. Mild renal failure 3. cardiac arytmia 4. loss of weight 5. constipation diarrhea 6. disease goes fast 5. proceeds fast!
Causes of respiratory acidosis:
1. COPD 2. Asthma 3. CHF 4. Pneumonia 5. Alchohol 6. Narcotics (downers)
What are cuases of metabolic acidosi:
1. DKA - diabetic ketoacidosis 2. Kidney failure 3. chronic diarrhea 4. lactic acidosis 5. aspirin
Forces that maintain tertiary structure:
1. H bonding 2. ionic bonding 3. van der waals 4. hydrophobic effect 5. disulfide bonding
Side group determines:
1. How protein folds 2. What ligands bind 3. how proteins interact wtih its environment
Outside a cell you have what contents:
1. Na/Cl 2. interstitial fluids 3. Blood/plasma 4. Lymph
Dehydrogenases:
1. accept and donate e- 2. involves e- trasnferring enzymes: NAD/NADH
What are the 4 acids produced in body:
1. acetoacetic acid 2. ketone bodies 3. lactic acid
DFP forms a covalent intermediate in the active site of:
1. actylcholinesterase; pt. presents with too much ACH. Activity of ACHesterase is only recovered with forming NEW ACHesterase not bound to DFP. 2. Serine proteases; inhibition not as leathal. These enzymes use SERINE for hydrolytic cleavage
2 lyases cleaving C-C bond:
1. aldolase decarboxylase; CO2 released from substrate 2. thiolase- S containing nucleophile of cyestine or CoASH braeks C-C bond
What are the acids present in urine?
1. ammonium, phosphate, uric acid 2. dicarboxylic acid 3. TCA- citric acid
What are the POLAR UNCHARGED amino acids
1. aspargine 2. glutamine 3. serine 4. threonine 5. cyestine
4 uncharged polar amino acids:
1. aspargine- amide 2. glutamine- amide 3. serine- alch 4. threonine- alch
What are polar charged amino acids:
1. aspartate 2. glutamate 3. arginine 4. lysine 5. histidine
2 polar charged amino acids:
1. aspartate- amine 2. lysine- amine 3. histidine- amine
hsp70 proteins job:
1. bind to new polypeptide chains as they are being made to stop them from folding prematurely. 2. unfold proteins before their insertion throught he membrane of mitochondria and other organelles
3D structure is designed to serve all aspects of protein function through creating
1. binding sites for ligands 2. maintains amino acids on the surface appropriate for proteins cellular location 3. flexibiility
Tissue plasminogen activator: 1. Where does recombinant human t-PA come from? 2. tPA is used to dissolve? 3. tPA has the same activity as____, but it is the same as ___ t-PA, so it elicits no immune response
1. bioengineered 2. blood clots after MI 3. streptokinase; endogenous
Polymerization of Hb molecules is dependent on
1. concentration of HbS 2. O2 content- low O2 content= polymerization, high O2 content= no polymerization
3 types of oxidoreductases:
1. dehydrogenase 2. hydroxylases 3. oxidases
Chronic respiratory alkalosis:
1. from years of decreased CO2 and compensatory decreases in HCO3-?
Alpha helix is common for the following proteins:
1. globular 2. membrane spanning 3. DNA binding
2 non enzymatic ways a protein can be denatured:
1. glycosylation 2. oxidation
C-N cleaved by:
1. hydrolases 2. lyases 3. ligases
Respiratory alkalosis is caused by?
1. hyperventiliation (getting rid of CO2 too much) 2. exercise 3. fever 4. stroke 5. increased altitutude
Advantages of multisubunit structure ( does this include Hb or no?)
1. increasing stability 2. cooperativity between subunits in binding ligands 3. form binding sites with high affinity for larger molecules 4. diff. subunits= diff activities and cooperate in common function
Heterozygous sickle cell anemia
1. infected cells with malaria= form aggregates 2. Aggregates form long fibers 3. cause cell to be distorted 4. distorted cells containing malarial parasite- preferentially recognized by the spleen and destroyed 5. life of parasite ends
Improper form of proteins in prion disease (PrPsc) can be introduced via:
1. infeection- mad cow 2. inherited mutation: creutzfeldt-jakob
Changes in env. can disrupt these bonds:
1. ionic 2. hydrogen 3. hydrophobic bonds
The 5 ways protein structure is governemd:
1. ionic bonding 2. hydrophobic effects 3. disulfide bond 4. hydrogen bond 5. Van der walls
Group transferred exists as good leaving group on donor molecule:
1. kinase 2. glycosyltransferase 3. acyltransferase
C-C cleaved by:
1. lyases 2. ligases
What if pt is not candidate for stem cell transplant and immunosuppresion?
1. melphalan; atineoplastic agent 2. dexamathasone; steroid
Streptokinase: 1. is it a pure enzyme? 2. What does it activate? 3. What is used for?
1. no; mixture from streptococcus 2. fibrinolytic system 3. break down blood clots
Why is it important to understand that 3d structures wiggle or shake?
1. occur without unfolding 2. allow water to diffuse though the structure 3. provide alternative confirmations for ligand binding
xanthine oxidase can work as either:
1. oxidase 2. dehydroenase
What is soluble in water?
1. polar organic molecules 2. inorganic salts 3. inorganic anions 4. inorganic cations 5. organic with electronegative charges- N and O
What 2 things are frequently seen in prion diseases:
1. protein aggregates 2. amyloid oplaques
Homozygous sickle cell anemia symptoms:
1. sickling of RBC 2. vessels= occluded 3. painful ischemia from LACK of O2 4. enhanced destruction of sickled cells by spleen 5. anemia
When we say neurodegenerative disease in prions we are discussing: (2)
1. spongiform degeneration 2. astrocyte gliosis in CNS
Transfer of N from aa to an alpha keto acid forming a new amino acid and an alpha keto acid corresponding to the donor amino acid:
1. transaminase 2. aminotrasnferase 3. req. enzym pyridoxal phosphate
What are the best indicators for a MI for marking CARDIAC dysfunction:
1. troponin (I and/or T) 2. creatine kinase
Asparginase: 1. breaks down aspargine which is the preferred metabolic susbtrate for certain ____ 2. used in trt. of some kinds of __ __.
1. tumors 2. adult leukemia
Protein precipitates cans ometimes be dissolved by amphiphatic agents:
1. urea 2. guanidine hydrochloride -HCL 3. SDS- sodium dodecylsulfate forms extensive H bonds and hydrophobic interactions with the protein
Kd of water
1.8*10^-16 M
Carboxyl group pKA:
1.8-2.4 But app.= 2 ph < pka, all are protanated: COOH ph=PKA- 50% of COOH are dissociated ph>pKA: more than 99% are COO-
The average H bond between water molecules lasts:
10 picoseconds
Duration that the H bond lasts:
10 picoseconds (1 picosecond=10^-12 seconds)
1 picoscond is
10^-12 seconds. so water's H bonds last 10*10^-12 seconds
1.8*10^-16*55.5=
10^-14M- ion product of water=Kw
MB creatinine kinase reaches its peak __ to __ hours after infarct and decreases __ to __ days after.
12-36; 3-5
pKA3 of phosphate buffer system
12.67
___ intx. between myoglobin amino acids adn different groups of porphyrin ring.
16
Lyases: cleave:
C-C, C-O, C-N - not by oxidation or hydrolysis
Hydrolases: break:
C-O, C-N, C-S bond by adding H2O
Water composes how much % of body in kids
75%
Tertiary structure of myglobin is made of __ __ __, connceted together by __ __ known as the __ __
8 alpha helices; shrot coils; globin fold
The covalent O-H bond in water is ___ k/cal making the H bond...
80 k/cal- only 1/20th of the strength of the O-H bond
What is normal serum glucose level?
80-110- not higher than 200
Sporadic form of CJD accounts for __ % of all cases of the disease
85%
NH3+ H+-->NH4+ this reaction occurs at a pKA of?
9.25
Amino group PKA=
9.5 Phys pH=7.4(?) protonated at physiological pH
at LOW O2 levels, the % saturation of O2 of Hb is ___ than that of Myoglobin
<
When you have 2,3, BPG, O2 is ___ readily bound, more readily _____
<; released
In the emergency room, Dianne (Di) Abietes was rehydrated with intravenous saline, which is a solution of 0.9% NaCl. Why was saline used instead of water?
A 0.9% NaCl is 0.9 g NaCl/100 mL, equivalent to 9 g/L. NaCl has a molecular weight of 58 g/mol, so the concentration of NaCl in isotonic saline is 0.155 M, or 155 mM. If all of the NaCl were dissociated into Na+ and Cl− ions, the osmolality would be 310 mOsm/kg water. Because NaCl is not completely dissociated and some of the hydration shells surround undissociated NaCl molecules, the osmolality of isotonic saline is approximately 290 mOsm/kg H2O. The osmolality of plasma, interstitial fluids, and ICF is also approximately 290 mOsm/kg water, so no large shifts of water or swelling occur when isotonic saline is given intravenously.
Amylidosis/AL: Extracellular deposits of pathological insoluble __ __ called amyloid fibers get on organs or tissue
A term used to describe lots of diseases fibrillar protein
ADP ribosylation can transfer:
ADP-ribose to target protein on cell surface - this process is sued by pathogenic bacteria to produce bacterial toxins (ADP ribosyl transferase) ultiamtely altering the human cell
When do post translational mods occur?
AFTER the protein is folded into its 3D confirmation
glycoslated proteins can form crosslinks and large protein aggregates called ___
AGES! (adavanced glyucosylation end products)
Phosphate buffer system is present where?
ALL cells
WHAT IS THE DIFFERENCE BETWEEN AMIDE AND AMINE:
AMIDE:NR3 Amine: NH2RO
WHICH AMINO ACIDS CONTAIN AMINES?
ARGININE, LYSINE, HISTIDINE, TRYPTOPHAN
Why did they make the conjugate base with a +?
ASK
WHICH AMINO ACIDS CONTAIN AN AMIDE
ASPARGINE GLUTAMINE
WHICH AMINO ACIDS CONTAIN CARBONYLS?
ASPARTATE, GLUTAMATE
Normally: ACH-->
Acetylcholline+ acetate
At first, aspirin causes
Acetylsalcilyc acid-->salciylc acid+ acetic acid. To get rid of the acid, you breath faster. When you breath faster you expel CO2 faster (Co2 is an acid)-->therefore you have a lack of acid, and then you have alkalosis at frst. (respiratory alkalosis) But then the salcilyc acid will break down into salciylate. Thismakes your body have a lot of base. You want to increase the acid in your body, so you get metabolic acidosis *must go over difference
Allopurinol:-->
Allopurinol-->xanthine oxidase-->alloxanthine (oxypurinol)-->allxanthine enzyme complex Why? xanthine oxidase performs the first oxidation step. It converts xanthine-->alloxanthine. But then alloxanthine remains bound to the Molybdenum (Mo-S). This prevents the next step of the rnx.
What is a water lattice?
An extensive area of H bonds that are constantly forming and breaking.
Water's heat capacity adn heat of vaporization are really high... what does this mean?
As liquid water-->gas, it evaporates from the skin, and we feel a cooling effect.
In pts. with amylydosis, you find fragments of light chains in urine called:
Bence-Jones proteins
In the case of a patient who suffers from insulin-dependent diabetes mellitus, describe how a lack of insulin leads to metabolic acidosis and low arterial blood CO2 values (see case of Di Abietes).
Blood insulin falls too low-- so it means sugar isn't being transported into the cells-- means that free fatty acids leave her adipocytes and are converted by the liver to the ketone bodies: acetoacetic acid+ Beta hydroxybuteric acid. These acids accumulate in the blood,a dna metabolic acidosis happens called diabetic ketoacidosis. (DKA). Until insulin is adminstered, a respiratory center is stimualted in the hypothalmus (induced by acidosis)- this makes you breath mroe deeply and frequently- this is called Kussmaul's respiraton. Co2 is expired more rapidly than normal and blood pH rises. Pt presents with LOW arterial blood pH, LOW bicarbonate, and HIGH ketone bodies in blood and urine.
Skeletal muscle form of creatinien kinase: Brain form of creatinine kinase: Heart form of creainine kinase: Mitochondrial creatinine kinase:
CK-MM CK-BB CK-MB (also produces homodimers) Heart mitochondrial CK (CK-MB?) universal isoform found in all tissues.
Peptide bond is between:
COOH of one AA and the amino group of another
Aspirin inhibits this enzyme:
COX
Hydrogen bonds in alpha helix are between
Carbonyl O atom and H (attached to the N atom) four amino acids down the chain.
Low PH disrupts: H bonds and ionic bonds formed by:
Carboxylic acid groups
Normally xanthine oxidase:
Hypoxanthine--->xanthine-->uric acid (urate)
AMP-->
Hypoxanthine-->xanthine oxidase-->xanthine-->xanthine oxidase-->urate
Myoglobin, hemoglobin, Cyt-C affinity for O2- in increasing order:
Cyt C- Myoglobin- Hemoglobin
Aspartate
D
Ex. of organophosphate:
DFP: diisopropylphosphofluoridate
Metabolic acidosis : initial chemical cahnge and compensatory response:
Decrease HCo3- Decrease PCO2
Respiratory alkalosis initial chemical cahnge and compensatory response:
Decrease PCO2- initial Decrease HCO3- compensatory
In the emergency room, Dianne (Di) Abietes was rehydrated with intravenous saline, which is a solution of 0.9% NaCl. Why was saline used instead of water? ****
Dianne (Di) Abietes has an osmotic diuresis. Because her blood levels of glucose and ketone bodies are so high, these compounds are passing from the blood into the glomerular filtrate in the kidneys and then into the urine. As a consequence of the high osmolality of the glomerular filtrate, much more water is being excreted in the urine than usual. Thus, Di has polyuria (increased urine volume). As a result of water lost from the blood into the urine, water passes from inside cells into the interstitial space and into the blood, resulting in an intracellular dehydration. The dehydrated cells in the brain are unable to carry out their normal functions. As a result, Di is in a coma.
Glutamate
E
Pheynalanine
F
Glycosylation- reversible or not?
IRREVERSIBLE
The laboratory reported that Dianne (Di) Abietes's blood pH was 7.08 (reference range = 7.37 to 7.43). What was the [H+] in her blood compared with the concentration at a normal pH of 7.4?
From inspection, you can tell that her [H+] is greater than normal, but less than 10 times higher. A 10-fold change in [H+] changes the pH by 1 unit. For Di, the pH of 7.08 = −log[H+], and therefore her [H+] is 1 × 10−7.08. To calculate her [H+], express −7.08 as −8 + 0.92. The antilog to the base 10 of 0.92 is 8.3. Thus, her [H+] is 8.3 × 10−8 compared with 4.0 × 10−8 at pH 7.4, or slightly more than double the normal value.
Six nonpolar hydrophobic amino acids:
GAVLIP! 1. glycine 2. alanine 3. valine 4. leucine 5. isoleucine 6. proline- cyclic all others are aliphatic
ka=
H*A/HA
Kd= dissociation constant for water:
H*OH/H2O at eq H20=55.5M because water dissocaites to small extent
Kw=
H+*OH-=1*10^-14
Acidic cell- ___ is transported OUT of the cell, and __ is transported INTO the cell.
H+; Na+
Organic molecuels containing a lot of electronegative atoms like O or N, are soluble in water because....
H- bond with water molecules
Carbonic acid
H2CO3
Things that happen at pkA 7.2 in phosphate buffer system
H2PO4- --> H2PO4(2-) + H+ (has high buffering capacity)
The equation involved in the phosphate buffer system:
H2PO4--->H+ + HPO4(2-)
What is the MAJOR acid present in urine?
H2SO4 ( from amino acids/food etc.) it is present in urine as H2SO4 or HPO4- (?)
ph=pka means
HA=A- (weak acid is 50% dissociated)
Ex/ of strong acids in the body:
HCL and H2SO4
Bicarbonate
HCO3-
Chronic respiratory alkalosis
HCO3- decreases
Chronic respiratorya cidosis
HCO3- increases
____ molecules can denature proteins by disrupting ___ interaction present in proteions
HYDROPHOBIC
ex of protein exhibiting cooperativity between subunits in bdining ligands
Hb
SICKLE CELL abb.
HbS
Lysine
K
Example of multisubunit protein forming binding sites with high affinity for large molecyules
IgG
Why histidine in chymotrypsin is not okay in the stomach as an enzyme like aspartate in pepsin
In order for an enzyme to participiate in general acid- base caltaysis, the amino acid side chain must be able to extract a proton at one end of the rection and donate it at the other. histidine's pka=6.0, but aspartate's pka (found in pepsin) is 2.0. When pH< pKA= enzyme is protonated. When pH> pKA enzyme is deprontoanted. So here ph=2=>> pka, so it is going to be able to release an H. On the other hand, 2.0 (pH) <<< (pKA) 6.0, so it would be PROTONATED in the case of histidine; therefore, since it is protonated, it can't extract a H from a nucleophile (?). Aspartic acid with a pKA of 2 can release protons at a pH of 2. The two asprtates work together to activate water through the removal of a proton to form the hydroxyl nucleophile.
In the kidney what happens to HCO3-?
It loses 2 negative charges: turns into CO32- and H+, the CO32- goes back into the blood and the H+ is excreted as urine
Which reaches its peak 12-36 hours after infarc and decreases 3-5 days later
MB creatinine kianse order?
WHICH AMINO ACIDS ARE SULFURE CONTAINING?
METHIONINE, CYSTEINE
Water's thermal conductivity is high... what does that matter?
Makes it easier to move heat from high energy using areas like the brain into the blood and total body water pool.
Xanthine oxiase contains ____ complex. This binds to substrates adn transfers __ required for __ recations.
Mo-S; electrons; oxidation
Aspargine
N
ex of organic with electronegative charges
N and O
Technically carbonic acid should...
NOT be able to act as a buffer. Because the pH is > pKA so it would be HCO3- only all the time. You wouldn't be able to replinish teh H2CO3 because by the time you made it, it would already be turning into HCO3-, and tehrefore, it wouldn't make a good buffer. BUT the coencentration of dissolved CO2 in body fluids is 400 times higher than H2CO3. So you have a LOT of CO2 in your body. So when you add a base, and you remove an H from carbonic acid (H2CO3) and you get HCO3-, CO2 will react with the water (H+ from carbonic acid and OH- from the base added)- and it will REPLINISh teh H2CO3 that is being eaten up because the pH? pKA, and when that happens an H is removed from carbonic acid.
Amide:
NR3
Ex of inorganic anion
Na-
When xanthine oxidase works as a dehydrogenase:
Nad accepts 2e- NAD is reduced to NADH
What do Na and K do in water?
O atom interacts w/ them and forms hydration shell
When xanthine oxidase works as a oxidase:
O2 accepts 2e- O2 is REDUCED to H2O2
Cytochrome oxidase a transports-__ to eventually make ___
O2; ATP
Why water doesn't dissociate a lot
OH and H cocnentration are EQUAL! can be used in proportion to one another as a constant- this is called Kw.
When the osmolaity of blood and interstital fluid is too high, water moves ______ the cells.
OUTSIDE
In hyperglycemia, water moves _______ the cell.
OUTSIDE- because tons of sugar in the blood increases the osmoallity of the blood!
Chronic metabolic acidosis
PCO2 decreases (Hyperventilation- gets rid of CO2 fast so you end up having alkalsois)
Chronic metabolic alkalosis
PCO2 increases
Beta doesn't have to be carboxy to amino or amino to carboxy. In fact, the beta sheets can be parallel or nonparallel. Parallel vs. nonparallel
Parallel: polypeptide strands run in same direction Anti: polypeptide strains run in opposite directions
Prion protein normal in brain:
PrP (c)
Prion protein improper confirmation in brain:
PrP (sc)
PrP(sc) vs. PrP (c) Which has lower activation energy?
PrP(sc)- bad- lower activation energy PrP(c)-good- higher activation energy
Prion disease exists when PrPc-->
PrPsc- which has a lower activation energy
WHICH AMINO ACIDS ARE ALHOHOLS?
SERINE, THREONINE, TYROSINE
Describe the development of the disulfide bodn
SH--SH-->S-S H atoms are removed during OXIDATION
Trascellular water:
SMALL, specialized portion of extracellular water that includes GI secretions, urine, sweat, fluid, that has leaked out of capillary walls because of processes like increased hydrostatic pressure or infalmmation
One of the major sources of nonvolatile acid in the body:
Sulfuric acid (H2SO4)
If you add base to a buffer system (weak acid and its conjugate base)
The base takes away the H from HA (the conjugate?? (weak) acid. And you have lots of water (what if not water...) So only a small increase in PH happens. If you add H+ to the buffer system, it combines with the conjugate base (A-) and almost no decrease in pH hapens.
In MI, why do certain enzymes show up in the blood?
The cells of the heart can't make ATP, so the membranes become damaged and leak enzymes frm teh cells into the blood.
What does it mean that body water is inversely related to fat?
The less fat you have, the more body water % you have.
Phosphorylation, aceytlation, ADP ribosylation:
UPREGULATEES activity
Tryptophan
W
Thiamine deficiency can lead to this syndrome:
Wernike Korsakoff
Aspirin method of inhibiton:
covalent acetylation
Tyrosine
Y
Can ribonuclease refold spontaneously on its own if carefully brought back to phsyiolgoical conditions?
YES
Can van der waals forces exist between NON POLAR amino acids?
YES
What does it matter if water's heat of fusion is high?
a large drop in temperature is needed to convert liquid water to solid.
buffer is
a weak acid and its conjugate base. Together, resist change in pH when OH or H is added.
Oxegynase enzymes: where both O2 atoms are incorp. into?
acceptor
Base ___ hydrogen ions
accepts
Malathion poisoning inhibits
acetylcholinesterase at the NMS; ACH is up; overtimulation of autonomic NS
Urinary excretion of H2PO4- helps remove____
acid
Where does DFP bind?
active site- serine on ACHesterase; this active site CANNOT be hydrolyzed by water. Whereas DFP without ACHesterase CAN be hydrolyzed by water.
Acyltrasnferase; transfers:
acyl group
Example of an enzyme with O linkage:
adenylyl cyclase
Organophosphates use _____ to function:
covalent inhibitors
Alanine, valine, luecine, isoleucine have __, __ __, ___ side chains
bulky non polar aliphatic
Which appears first in 3-5 hours, then 8 hours, then 100% in 10-12 hours?
cTnT
What seperates interstitial fluid and plasma?
capillaries
Polymerization of Hv is most llikely initiated here:
capillary beds
glycosyl transferase: transfers:
carbohydrate residue
In beta sheets what is connected:
carbonyl O+ H (attached to the N =) on the ADJACENT strand!
When is myoglobin released?
cell damage
2,3, BPG binds to:
central cavity of Hb
hsp60- called: shape:
chaperonins; barrel
In a hydration shell, where are the H atoms located?
closest to anion
Witihin the polypeptide chain, ______ and ____ form bound susbtrate into products.
cofactors; functional groups
Proteins that turn over very slowly in body are glycosylated in high percent. What are these proteins:
collagen and hemoglobin
Strong acids dissociate______
completely
At HIGH PO2, Hb is:
completly saturated with o2
Rate of glycoslyation proprotional to:
concentration of glucose present BECAUSE the reaction is NOT enzymatic
Osmolality=
concentration of solutes- i.e. total concentration of ALLLLLL dissolved molecules in a compartment
Weak acids dissocaite into
conjugate acid and a conjugate base.
The buffering capacity is maximal when
conjugate base concentration= conjugate acid concentration; i.e. when pH=pKA
What is the signficance of the water lattice:
continuous dissoication allows polar substances to move through water.
cis-trans isomerase:
converts cis-->trans before a proline
Glycopeptidyl transferase catalyzes a partial reaction with penicllin that:
covalaently attaches penicllin to it's own active site serine
Fatty acid acyetelation is what kind of bond:
covalent
All amino acids are assymetric except:
glycine
Allopurinol is used to treat this disease:
gout
Hydrolases: the enzyme class name specifies:
group being cleaved chymotrypsin is a protease; a protease is a hydrolase that cleaves peptide bonds in protiens
GMP-->
guanine-->xanthine-->urate xanthine oxidase works at xanthine to urate
Why is myoglobin unusual for a globin
has NO BETA sheets (globisn usually have beta sheets)
kinetic barriers are overcome by:
heat shock proteins
Cytochrome oxidase: a __ containing enzyme in the __ __ __
heme; electron transprot chain
Relaxed state of Hb has __ affinity for O2
high
Water's heat capacity is?
high
Water's heat of fusion is?
high
Water's heat of vaporization is?
high
Water's thermal conductivity is high or low?
high
BPG is commonly associated with __ __ __
high altitutde adjustment
kinase- transfers:
high energy phosphate
high concentration of solutes=
high osmolality
People with hyperglycemia have___ rate of glycosylated proteins than people with normal glycose levels
higher
Result of alpha helix:
highly compact+ rigid!
Water's heat of fusion is high or low?
hihg
a protein with its prosthetic group attached=
holoprotein
Anionsa re surrounded by a ___ __ of water molecules.
hydration shell
What does Cl- and HCO3- do in water?
hydration shell
Polar organic molecules and inorganic salts can readily dissolve in water because water forms?
hydrogen bonds and electrostatic intx. with these molecules
Ligases cleave everything ___ do, except:
hydrolases; except ligases also cleave C-C C-S, C-O, C-N; cleaved by both
Alanine, valine, leucine, isoleucine are all considered.....
hydrophobic
Long chain fatty acids can inhibit some enzymes by bonding to their ___ binding sites
hydrophobic
Helices in myoglobin create a __ __ ___ ___ containing __ and __ atom in the center
hydrophobic O2 binding pocket; containing HEME and Fe2+ atom in the center
Generally, the final structure of a folded protein results in a __ __ on inside, and __ __ amino acids on outside
hydrophobic core, polar hydrophilic
Sickle cell is when there is THIS aa not THIS ONE in the ___ chain, creating a __ __
hydrophobic valine in place of glutamate; beta 2; hydrophobic knob on surface of deO2 Hb. Fits into hydrophobic binding pocket of B1 subunit of a different Hb molecule. Then, a third Hb molecule binds to the first and second Hb molecules through polar intx. Then the third Hb molecule binds to a fourth Hb molecule with its valine knob. Polymerization continues till long fibers are formed.
Myoglobin exhibits a ___- curve
hyperbolic
Myoglobin has a ___ curve, but hemoglobin has a ___ curve
hyperbolic; sigmoidal
Where xanthine oxidase works:
hypoxanthine-->xanthine Xanthine-->urate
Prion disease acquired through growth hormone inoculations in USA and france:
iatrogenic or doctor induced CJD
In prion disease, proteins act as a template for:
improper proteinf olding
When you cool water, hydrogen bonds
increase
Respiratory acidosis- initial chemical cahnge and compensatory response:
increase PCO2- intial Compensatory: Increase in HCO3
2,3, BPG does what?
increases the energy required for hte confirmational change of Hb from T to R.
The structural features of each domain can be discussed ___ of another domain int he same protein AND the structural features of ONE domain may not __ that of other domains in the same protein
independently; match
Quatenary strcutres are associateions of
individual polypeptide chain subunits in a geometrically and stoichometrically specific manner.
Familial Creutzfeltd Jakob's disease arises from an __ __ and has __ __ pedigree
inherited mutation; autosomal dominant AKA: fCJD
Metabolic alkalosis: initial chemical cahnge and compensatory response:
initial: increase HCO3- Compensatory: increase PCO2
pH > peak
innapropitate ionization (i.e. H is coming off) of enzyme's amino acid residues. Inhibits them from aiding in catalysis. (Ph>>> pKA, so it is deprotonated)
Strong acids in the body are ____ acids
inorganic
When the osmolality of blood and interstitial fluid is too low, water moves ____ the cells
inside
As water is passed from blood into the urine to balance the excretion of ions, the blood volume is repleted with water from?
interstitial fluid
60% of the water in your body is:
intracellular
Treatment of type 1 diabetes mellitius
intravenous saline- to replace fluids lost with osmotic diuerisis and hyperventiliation - osmotic diuerisis because there's a lot of sugar AND ketone bodies in the urine so water follows - hyperventilation- Co2 is expired more rapidly than normal, and blood pH rises. This happens because there is acid in the blood andstimualtes hte matabolic central respiratory center in the medulla, increasing the rate of breathing adn the expiration of Co2.
Prostehtic group is an __ part of the protein, and doesn't ___ unless the protein has degraded
intrinsic; dissoicate
Body water is _________ related to fat
inversely
CtnT- late or early specific marker of myocardial injury:
late, but highly specific
Adding base will combine with the conjugate acid, and the equilibrium shifts ___ and reaction shifts__
left; right
Fat has ___ water associated with it
little- so the fatter you are, the less your water content
Prp-C has ___ beta structure, and is ___ alpha strucutre
little; 40%
In sickle cell, the Hb proteins form __ __ within the RBC, and cause the RBC to be sickle celled
long polymers
Protein denaturing: modfication of a protein that results in __ of __
loss of function
Ammonia is kept at a very ___ concentraiton in the blood.
low
At LOW PO2- saturation of Hb is ___
low
Tense state of Hb has __ affinity for O2
low
Low concentration of solutes=
low osmolality
so water moves from
low to high osmolality
Water moves from compartment with ___ concentration of solutes to compartment with ___ concentration of solutes
low-->high
Strong acids have a ___ pka and a ___ ka
low; high
Weak acids have a ___ ka and a ___ pka
low; high
Older have __ water then younger
lower
Women have __ water than men
lower
RBC sepnds most of its time in the _ __ concentrations of the venous capillary bed. This is where ____ is initiated
lower O2; where polymerization is initiated
fCJD does what?
lowers the energy required for the protein to fold into the PrPsc confirmation- therefore, the conversion occurs more readily
Prion disease acquireed through infection
mad cow aka NEW VARIANT CJD
Why cis-trans isomerase is cool:
makes hair pin turns
Phosphorylation of OH group:
makes neg. charge that alters activity of protein
Most hydrolases and oxidases require:
metal ions; Fe2+; for electron transfer
2 sulfur contianing amino acids
methionine and cyestine
osmolality= is
moles/kg
osmolarity=
moles/liter
Multimer: somtimes used as a mroe generic term to designate a complex with many subunits of
more than one ype
Bc PrP sc has a lot of beta structure, it favors the aggregation of PrPsc into _____ complexes
multimeric compelxes
But as PrPsc causes the normal proteins to become it, it aggregates, and its level goes down... 1, aggregates into ____ assembly resistant to proteolytic digestion
multimeric; once aggregate forms-->cooncentration of FREE prpsc decreases, adn shfit the equilibrium to MAKE MORE PrPsc!!! Leads to further aggregation.
Each subunit of hb is similar to:
myoglobin
Which appears first in MI?
myoglobin
___ binds well at low Po2
myoglobin
What is the molecular basis of cystiniuria:
normally, amino acids are filtered out of the blood and into the urine by glomoerular capillaries. The amino acids DON'T stay in the urine- they are instead reabsorbed into the blood by transport proteins. But in cystinurina- there is an inherited amino acid SUBSTITUTION in the transport protein that reabsorbs CYSTEINE, ARGININE, LYSINE- therefore, the pts. urine is filled with LARGE amounts of these aa. But cystine is the one we care about because it is teh LEAST soluble; preciptiates to form renal stones.
F actin is an ___ and a multisubunit protein composed of identical __ __ subunits.
oligomer; G actin
O linkages- attach
oligosacchrides to serine or threonine hydroxyl group in secreted protein
point mutations are changes in __ __ in DNA nucleotide sequence
one base
Proteins may be dimers, tetramers, oligomers, in which 2,4, or more subunits have combined to make __ __ __
one functional protein
In antiparallel sheeth- atoms involvbed in hydrogen bonding are directly __ to one another
opposite
Water moves throughout the compartments according to:
osmolality
Hyperglycemia induces __ ___
osmotic diuerisis- gotta pee a lot! this means dehydration and hyperosmolality (not osmolarity) of her body fluids
The force it takes to keep the same amount of water on both sides of a membrane?
osmotic pressure
Alkaline cell; bicarbonate transported _____of cell and __ is transported INTO cell.
out; Cl-
Oxidoreductases catalyze....
oxidation-reduction reactions
Xanthine oxidase does WHAT to allopurinol:
oxidizes!-->oxypurinol- binds tightly to Mo-S in the active site of xanthine oxidase.
Pka= what?
pH at which A=B
Isoelectric point:
pH at which net charge on mlecule is 0 and will NOT nmigrate into elecric field.
Parallel sheets vs antiparallel hydrophobic sides?
parallel: hydrophobic residues are on BOTH sides of sheet Antiparallel: have 1 side= hydrophobic other= hydrophilic
The penicllin reaciton is favorede because
penicllin's peptide bond in the beta lactam ring and the transition state complex of the natural transpeptidation reaction look similar
Primary protein structure is formed by __ ___
peptide bonds
1 non polar amino acid that isn't hydrophobic (is it hydrophilic?)- also aromatic:
phenylalanine
So each pH profile for an enzyume depends on the __ __ of the spcified enzyme. Stomach's 1-2 pH is good for? Not good for?
physiological range good for: pepsin! (aspartate residues of pepsin are good for acid-base catalysis of peptide bonds) Bad for: histidine
Heme is a __ __ ring
planar porphyrin
Trts. of amylodisis: may be directed againts:
plasma cell proliferation! and the symtoms that come from organ dysfunction! it's only partially succesful!
Familial prion diseases: caused by __ __ in gene encoding Pr. protein
point mutations
Is glucose polar or non polar?
polar
Tertiary structure maintains residues ont he surface appropriate for hte protein's cellular location- for cytosolic proteins you have ___ resideus for transmembrane proteins you have ___ resideues on surface (ex/)
polar hydrophobic- beta 2 adrenergic
H bonds are strong enough to dissolve __ __ in water, and to __ __
polar molecules; seperate charges
Painful vasoocclusive crisis are caused by :
polymerization of sickle cell hemoglobin molecules into LONG FIBERS that distort te shae of the RBC into sicle cells
The phosphate buffer system is ______, undergoing __ titration steps.
polyprotic;3
Active site:
portion of enzyme's surface polypeptide chain where catalytic reaction occurs
Van der walls forces are forces between __ __ nucleus of one atom and __ __ of the other.
positively charged; electron cloud
Once PrP sc is introduced, it takes over as the __ __ __
primary folded confirmation becasue of its LOWER activation energy
Tertiary structure is dictated by
primary structure
What determines the folding pattern of a protein?
primary structure
WHAT determines the folding pattern of the three D structure AND the assembly of subunits into QUATENARY structure
primary structure, but SPECIFICALLY the sequence of aa. side chains
Scrapies
prion disease in sheep
1 cyclic amino acid:
proline
What amino acid canNOT form alpha helicies?
proline
One alpha beta pair can be considered a ____
promoter
Heme group is positioned in the protein by interaction of its negatively charged ___ groups with positively charged __ and __ sidechains from hb.
propionate arginine histidine
Heme groups fall into a group of tightly bound organic ligands called __ __
prostehtic groups
Increased heat can lead to loss of __ __ and shape.
protein bonds
Higher than 37 degrees C, will cause __ __ which will grossly inhibit the reaciton.
protein degradation
PRION stands for:
proteinacious infectious agent
Prion disease represents a ___ ___ agent
proteinacious infectious agent
isoprenoids:
proteins that are acetylated fatty acids: they are involved in regulation
What is true about protein aggregates and amyloid plaques: resistant to __ __
proteolytic degradation
At physiological pH, most of the amino groups are_____
protonated
Allopurinol is involved in the degradation of ___ nucleotides ___ and ___ to ____ ___
purine; AMP;GMP;uric acid (urate)
Xanthine oxidase helps degrade _____
purines
Sickle cell anemia is caused by wrong ___ stx.
quatenary
.Sickle cell anemia is a problem with THIS level of protein folding structure:
quaternary
Selenocytesine:
rare amino acid found in some proteins and enzymes. To make selenocystine- modify serine while serine is bound to tRNA. This is NOT a post translational modification
Other trts. of amylodisis:
renal and cardiac transplants!
How do Lyases cleave C-C?
require C=O (carbonyl carbon)- to stabilize the carbanion that is formed transiently when C-C breaks (acts as electron sink)
Ex/ of a protein disrupted by urea
ribonuclease
Adding acid will combine witht he conjugate base molecules- the equilibrim shifts __ and reaciton shifts __
right; left (means what?)
Alpha helix has __ __ conformation maximizing hydrogen bonding, while allowing ___
rigid, stable rotation
Acetylsalcilyc acid-->
salcilyc acid int he body (which is the base in this case???)
How are isozymes the same:
same function; but different properties from tissue to tissue
Antiparallel beta strands:
same polypeptide chain folded back on itself -simple hair pin turns - long runs of polypeptide chain conencting the strands
What seperates the extracellular and intracellular comparmtents:
semipermeable cellular membrane
Where aspirin inhibits:
serine in enzyme prostaglandin endoperoxide synthase
Glycoprotein transpeptidase normally does what: 1. What kind of enzyme 2. Cleaves what?
serine protease; cleaves peptide bond between 2 D-alanine residues
What is the cause of metabolic alkalosis?
severe vom. and antiacid use
Van der walls forces are ONLY effective for __ ___ with many atoms.
short distances
Homozygous sickle cell=
sickel cell disease
Curve of sat. of hb wrt to Po2 is a ___ curve. Indicative of __ binding.
sigmoidal; cooperative
Myoglobin is a ___ polypeptide chain; binds ___ o2
single;1
M form of creatinine kinase is produced in __ __, and B polypeptide chains are formed in ___
skeletal muscle; brain
Where is myoglobin released from?
skeletal or cardiac muscle
In parallel beta sheet, atoms involved in H bonding are slightly __ frome onw another
skewed- one amino acid is H bonded to TWO OTHERS in the opposite strand
Sporadic CJD comes from __ __ __ or __ __ __ that initiates a cascade of refolding into the ___ confirmation
somatic cell mutation; rare spontaneous refolding; PrPsc
2,3, BPG _______ Hb.
stabilizes
MOST SUCCESFUL treatment of amylodisis:
stem cell transplants+ immunosuppresion
What prevents everything but the intended susbtrate to bind int eh lock and key model?
steric hindrance; charge repulsion
In a lock and key model, the _________ is what provides specificity.
substrate binding site
What kind of inhibitor is penicllin:
suicide inhibitor- becasue it inhibits the active site; and undergoes a partial reaction; to form irreversible inhibitors in hte active site
If the sugar is added at N linkage, it attaches to?
surface proteins; prevents protein from attack or proteolysis
When a reaction makes a important compound: called:
synthase
The structure of water allows it to resist:
temperature change
PrPsc- act as a ___ for refolding other molecules
template
hsp60 job:
template for protein folding
Hb changes from __ to __ state when O2 binds
tense- relaxed
Folding into 3 D confirmational elements:
tertiary
Subunits of a partiocular protein always comine int he same number and same way becasue bdinign between subunits is dictated by:
tertiary structure
Hemoglobin is a ____ composed of __ different subunits:
tetramer; 2
Hy organic molecules containinga lot of electronegative atoms like O or N are soluble inw ater?
these atoms participate in H bonding with water molecules
Tetrameric structure of Hb facilitates the efficient binding and transfer of O2 to the _-
tissues
Becuase Hb does NOT bind well at low Po2 it realses the O2 at the ___ where Po2 is low
tissuesl it is bound by myoglobin in the skel. muscles nad heart. At this point, myoglobin stores O2 for later use during contraction
Beta sheets maximize hduogen bodnming between peptide backbones while allowing:
torsion angles (like still allow rotation)
Glycogen synthase:
transfers glucosyl residue from UDP-glucose to the end of a glycogen molecule
Xanthine oxidase commits suicide by converting allopurinol to:
transition state analog
Prion diseases are categorized as ___ __ ___
transmissable spongiform encephalopthies
penicillin is a __ __ analog
transtion state; binds to glycopeptidyl transferase; bacteria use this enzyme to MAKE the cell wall. So if its not working, bacteria can't make the cell wall.
most POLAR amino acid:
tryptophan
Allopurinol decreases __ __ by inhibiting __ __
urate production; xanthine oxidase
How can proteins be denatured?
urea
When have allopurinol- can't make this:
uric acid
Whether phsophate is present in urine as H2PO4- or HPO4- depends on?
urinary pH and pH of blood
Ammonium ions are major contributors to buffering ___ pH but not ___ pH
urinary; not blood
Sickle cell is sub of: ___ for ___ in this chain __ __.
valine for glutamte in BETA 2 chain
Sickel cell anemia causes a __ __
vasoocclusive crisis
H bonds are weak enough to allow movement of __ and __.
water and solutes
Why polar organic molecuels and inorganci salts can dissolve in water?
water forms H bonds and electrostatic intx. with tehse molecules
All amino acids are__ __ at physiological pH
water soluble
Is glucose water sol. or not water sol?
water soluble
Polar substances and inorganic salts.... do they dissolve in water?
yes! into things that form H bonds with water. These H bonds are constantly breaking and reforming. This allows these polar substances to move through water. Remember! like dissolves like!
Does water interact wtih cations like it does with anions?
yes- hydration shells form both