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159 Cards in this Set
- Front
- Back
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Dietary fuels and fates
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carbs = 4 kcal/g
protein = 4kcal/g fat = 9kcal/g cmpds are oxidized to CO2 and H2O via citric acid or aka krebs cycle during which e- are transferred to O2 leading to production of ATP via a process called oxidative phosphorylation excess dietary fuel -> fuel stores -> fat, glycogen, protein -> fasting -> oxidation = ENERGY |
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ATP
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critical for biosyn of
macromolec musc cont active ion transport thermogenesis cell signaling |
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major carbs in human diet
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starch - storage form of carbs in plants
sucrose & lactose - disaccarides fructose & glucose - monosaccharides glucose - predominant carb in human blood |
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Protein
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cmpsed of AA via peptide bonds
16% N by weight hydrolyzed to their constituent aa during digestion oxidation to CO2 and H2O - 4kcal/g |
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lipids
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consist of triacylglycerols (triglycerides) which are cmpsd of 1 glycerol to 3 fatty acids via ester linkage
common saturated fatty acids = palmitate and sterate common unsaturated - oleate more E b/c highly reduced |
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ethanol
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7kcal/g
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daily energy expenditure
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=
1. energy expended at rest + 2. energy expended in physical activity + 3.energy needed to process food we eat - diet induced thermogenesis & is equivalent to 10% of kcal ing. |
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basal metabolic rate
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measure of E needed to amintain life
determined by measuring O2 consumption OR heat produced by resting person recently awakened after 12 hr fast expressed in kcal/day depends on body weight, sex (F is lower), body temp ( inc 12%/deg C) and ambient temp BMR=24kcal/day/kg body weight * body weight in kg |
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physical activity relates to BMR
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30% of BMR of sedentary person
60-70% of BMR for person who engages in about 2 hrs of moderate exercise a day 100% for ppl who do several hrs of heavy exercise a day daily energy expenditure can be det. from BMR and approp. % of BMR req for phys act. daily energy expenditure = BMR+%ofBMR |
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diet induced thermogenesis
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E needed to process/store food we eat
10% kcal ing often ignored in daily energy expenditure calc |
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caloric balance
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to maintain body weight has to stay in this (E intake =E expenditure)
overweight ppl can be defined as weighing 20% more than ideal weight positive cb = consumption> expenditure cb = consumption =expenditure neg cb = consumption < expenditure |
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Body mass index
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BMI = weight/height^2 used to determine if weight is in a desirable range
- below 18.5 underweight above 25 are overweight |
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dietary req
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specific nut to remain healthy
carb - no essential fatty acids - linoleic and alpha-linoleic fatty acids b/c they are precursors for arachadonic acid and eicosanoids (these come from plants) -eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) from fish oils protein-0.8g/kgof ideal body weight 9 essential aa = Lys, Ile, Leu, Thr, Val, Trp, Phe, Met, and His Arg conditionally essential - req to support growth vit - sml quantites minerals - some req in lrg quantiteies like P or Ca others only trace amts Fe and Se |
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nitrogen balance
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when aa are oxidized N atoms exreted in urine as urea primarily but also as uric acid, creatinine, & ammonia
= N taken into body each day - amt of N cont cmpds lost in urine, sweat, feces, and cells that slough off neg N balance develops when a. too little protein in diet b. diet consists of lower quality prot. lacking essential aa |
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aliphatic cmpds
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carbon based cmpds that contain single or doublebonds and are either straight or branched
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sulfhydryl group
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c-sh
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quaternary amine
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ch3
| N-ch3 |ch3 |
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thioester
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o
|| c-s-ch2 |
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ester vs esther
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O
|| c-o-ch2 c-o-c |
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amide
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o
|| c-nh |
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conj bases of major biol relevant acids
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carboxylates, phosphates, or sulfates
dissociated form of an acid "ate" acid ends in "ic" |
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reactivity
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polar bonds are highly reactive b/c electronegative atoms can act as nucleophiles to attack electropositive atoms
electroneg atoms= good nucleophiles electropos atoms =electrophilic |
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monosaccarides
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cmpsd of 3+C that contain a carbonyl group and multiple hydroxyl groups
can be aldoses and ketoses "ose"=carbohydrate trioses = 3 C tetroses= 4C pentoses, hexoses , and so on glucose = aldohexose fructose=ketohexose |
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epimers
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stereoisomers that differ in the position of a hydroxyl group at only 1 chiral carbon
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mutarotation
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in solution the carbohydrate ring structure, the hydroxyl group attached to the anomeric C can undergo this process
the hydroxyl changes from the up (beta) to the down (alpha conformation) position or vice versa non-enzymatically or catalyzed by mutarotases |
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glycosidic bonds
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anomeric C react w.N or O to form these bonds
N-linked ones found in nt O-linked found in disaccarides or other sugar polymers have either an alpha or beta orientaiton and numered according to their positions of attachment |
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fatty acids
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long aliphatic chains w/COOH at one end and CH4 (w-carbon) at the other
cis unsaturated fatty acids are the most naturally occuring |
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phosphoacylglycerols
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linked to 2 fatty acids through ester linkages at positions 1 and 2 of the glycerol
phosphate group to position 3 via phosphodiester linkage can be linked to a polar head group like choline common components of lipid membranes |
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steroids
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major structural motif of steroids is 4 ring steriod nucleus
converted into amphpathic bile salts used by body to absrb poorly soluble chem/cmpds |
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nitrogenous bases
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possess either a purine, pyrimidine or pyridine ring
adenine, guanine, thymine, nicotinic acid liked to sugars through a N-glycosidic bond to form a nucleoside when these are phosphorylated on the ribose ring they are termed nucleotides (adenosine triphosphate) |
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water
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50-60% body weight of adults
75% " " " " kids obese = body weight is made up of a lower precentage of water 60% of total body water is intracellular and rest makes up extracellular fluid can make up to 4- H bonds - avg one lasts 10 picoseconds - constantly forming/breakinig/reforming good solvate for organic molec and inorganic salts high heat capacity and high heat of vaporization |
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electrolytes
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cations ECF ICF
Na+ 145 12 K+ 4 150 anions Cl- 105 5 HCO3- 25 12 Pi 2 100 numbers in mmol/L distribution maintained by energy req transporters ex/ Na+/K+ pump |
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osmolality
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proportional to the total conc of solute particles
water moves from a compartment w/low conc of solutes => one w/higher conc of solutes when water moves from one compartment to another it is replaced by fluid from diff. compartment to maintain a near constant osmolality |
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Woman could not be aroused from nap, taken to ER in coma. roommate reported that she had been feeling nauseated, drowsy, vomiting for 24hrs. she is clinically dehydrated and has a low BP. Resp. deep and rapid, breath has fruity odor of acetone.
what's wrong |
osmotic diuresis
-blood levels of glucose are so high b/c lack of insulin so body thinks it is starving so mobilizes fatty acids and metabolize it a metobolite is ketone bodies so there is an inc. in particles in blood so they are passing from blood into the glomerular filtrate kidneys=>urine b/c high osmolality of glomlar filtrate much more H20 is being secreted in urine than usual (polyuria) so H20 depleted from blood replaced from intracellular fluid so cells are dehydrated when brain stem is dehdrated unable to carry out normal fns = coma give her isotonic (0.9%) saline to rehydrate b/c osm of blood and intercellular fluid is 290 oms/kg .9g NaCl per 1mL = 155mMol NaCl <=> Na+ + Cl- if all the way => then 310 Osm/kg H2O so this saline rehydrates her w/minimizing swelling |
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dissociation constant in H2O
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Kd = [H3O+][OH-] / [H2O]
dissociation is small conc. of pure water is 55.5 M so use Kw= [H3O+][OH-] = 1*10^-14 |
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dissociation constant Ka
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the ability of an acid to donate a proton to a solution
Ka = [H3O+][A-] / [HA] stronger the acid the higher the Ka pKa = -log (Ka) The smaller the pKa the stronger the acid |
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acids produced during normal metabolism
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strong
Sulfuric acid lactic acid pyruvic acid citric acid weak - acetoacetic acid beta-hydroxybutryic acid acetic acid dihydrogen phosphate ammonium ions |
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ketone bodies
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acetoacetic acid and beta-hydrooxybutric acid
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henderson-hasselbalch equation
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when concentration of A- = HA then pH=pKa
so pH=pKa + log ([A-] /[HA]) |
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buffer
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mixture of a weak acid and conj base that resists changes in pH when an external acid or base added
factors that determine the effectiveness of a buffer 1. pKa relative to pH of solution buffers work best w/in 1 pH of their pKa 2. Its concentration the more concentrated the buffer the greater its capacity to accept or donate protons body fluids are all buffered if pH of buffered solution drops 1 unit in pKa the ratio of A-/HA- from 1:1 to 1:10 |
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how much acid does the body produce a day?
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22,000mmol of acid/day which if unbuffered would equal <1.
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pH of body fluids
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- blood pH is maintained btw pH 7.36-7.44 and intracellular pH is 7.1
- major organs operate btw pH 6.8-7.8 |
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mech. for maintaining body pH
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4 major buffering systems :
1. the bicarbonate-carbonic acid boffer system - extracellular fluid -open sys out via urine and lungs 2. the hemoglobin buffering system (red blood cells) 3. the phosphate buffer system (all cells) 4. the protein buffer system (all cells and plasma) |
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Bicarbonate buffer system
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CO2 produced during TCA cycle is major metabolic acid (about .5-1kg/day)
CO2 reacts reversibly w/ water to produce carbonic acid, which dissociates to form bicarb and a proton CO2 + H2O <=> H2CO3 <=> H3O+ + HCO3- occurs spontaneously - but occurs primarily in RBC where it is catalyzed by carbonic anhydrase concof CO2 in body fluids is about 400 times higher than carbonic acid dissolved CO2 is in eq w/ CO2 in air in the aveoli and avalibility of CO2 can be inc or dec by adjusting the rate of breathing carbonic acid (H2CO3) in blood can be reduced by deep breathing which leads to increased release of CO2 into the lungs -- useful for treating metabolic acidosis (dec in blood pH but shallow breathing can be used to treat metabolic alkalosis (inc in blood pH) b/c more CO2 is retained in blood dissolves into intercellular fluid - providing a buffer for interstitial fluid |
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Concentration of dissolved CO2 measured in ER
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expressed as a fractioin of partial pressure of CO2 in the arterial blood (PaCO2)
pH=3.5 + log([HCO3-]/[H3CO3]) -> pH= 6.1 + log([HCO3-]/ [CO2(d)]) -> pH=6.1 + log ( [ HCO3-]/ 0.03PaCO2) [HCO3-] and PaCO2 are expressed as mEq/mL and mm Hg the constant 0.03 reflects that only 3 % of gaseous CO2 is dissolved |
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hemoglobin buffer system
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near the tis. hemoglobin acts as a buffer b/c it is enriched in histidine (basic pKa=6.7) at a number of exposed positions
His combine reversibly w/protons to produced protonated and nonprotonated versions of hemoglobin can except a proton near the lungs where CO2 is released and shifts the eq and can accept a proton from carbonic acid |
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phosphate buffering system
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dihydrogen phosphate and its conj base is a major buffer of intracellular pH in all cell types
H2PO4- <=> H3O+ + HPO4- pKa=7.2 occurs in RBC |
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protein buffering system
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proteins and their conj bases are a major buffer of intracellular pH in all cell types
ex - serum albumin mantiains osm. balance H+ + protein - <=> H3O+ + Protein |
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3 yo boy brought to ER by grandfather. boy had taken a half full 500 tablet bottle of 325 mg asprin (acetylalicylic acid) from counter- grandfather found him taking them and made him spit out but he wasn't sure how many he already swallowed so brought him to ER now gramps is hyperventilating
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boys stomach was lavaged and white tablets where found but he was showing no signs of salicylate toxity ( resp stimulation, upper abd. distress, nausea, or headache
initial effect of asprin induces an alkalosis caused by an effect on the hypothalamus that inc. the rate of breathing and expiration of CO2 which is followed by a complex metabolic acidosis caused by dissociation of salicylic acid (salicyclic acid <=> salicylate +H+ pKa = 3.5) Salicylate is lipid soluble and has a dissociable proton. in high conc able to partially uncouple mitochondria so there is a decline in ATP conc in cell and consequent inc in AMP in cytosol which stimulates glycolysis overstimulation of glycolytic pathway results in inc levels of lactic acid in blood and metabolic acidosis salicylate may impair renal fn so accumulation of strong acids |
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usual level of serum salicylate
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therapeutic dosage 4-5 g/day
120-350 micrograms/ml and a level of 800 micrograms/mL is lethal |
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blood pH range
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7.36-7.44
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how do you test for ketone bodies
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blood ad urine
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normal blood glucose level
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no higher than 200 w/o regard to last meal
80-110 |
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reference level of PaCO2
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38-42 mmHg
this reflects carbonic acid level |
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reference serum bicabonate level
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24-28 mEq/L
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type 1 diabetes
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aka juvenile or insulin-dependent diabetes mellitus
if blood insulin levels fall too low - free fatty acids leave adipocytes and converted by liver to ketone bodies acetoacetic acid and beta-hydroxybutryic acid which accumulate in blood resulting in a metabolic acidosis known as diabetic ketoacidosis (DKA) until insulin is administered the resp center in brain is stimulated by acidosis to cause deeper and more frequent resp (Kussmaul's resp) .CO2 is expired more rapidly than norm and blood pH rises |
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what is the physiological pH
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about 7
at this level AA are protinated the amino group is protonated so has a + charge the carboxyl group is deprotonated so it has a neg charge so if R is uncharged a zwitterion predominates at physiological pH |
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D vs L forms of alpha AA
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enantiomers
glycine's alpha C is the only one that is not chiral so it doesn't have difefrent forms alpha AA in L config are used to syntehsize proteins D AA are rarer and occur in components of bacterial cell walla and a number of antibiotics |
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5 groups of AA
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nonpolar/aliphatic
aromatic polar/uncharged sulfur containing charged |
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nonpolar/aliphatic AA
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glycine
alanine proline valine leucine isoleucine |
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glycine
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simplest AA
greatest flexibility of all the AA b/c min steric hindrance |
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proline
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imino acid b/c of cyclic structure
secondary amine least flexible b/c side chain restricts conformational freedom |
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which AA have branched highly hydrophobic side chains?
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valine
leucine isoleucine |
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which AA are found on the interior of globular protein
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ala
val leu ile b/c they help stabilze the globular protein by excluding water |
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aromatic AA
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phenylalanine
tyrosine typtophan in each the aromatic ring is attached to the beta carbon |
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ring stacking
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forms strong hydrophobic interaction occur w/each of the side chains of the aromatic AA
hydrophobicity of the aromatic AA are Phe>Trp>Tyr (side chain is a weak acid) |
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aromatic AA and UV light
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can abs light in the near UV region btw 240 and 300 nm
abs of trp can be 4x that of tyr phe abs significantly lower amts of UV b/c it's lack of resonance this explains why most proteins abs light at 280 nm which is used to measure the conc of protein |
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polar/uncharged AA
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serine
threonine asparagine glutamine more soluble in water b/c they can H-bond w/water often located on exterior of protein |
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amide group of Asn and Gln
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do not donate or accept protons at physiological OH
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which AA can be phosphorylated by protein kinase?
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ser
thr tyr modification that is imp for cell signaling and cancer |
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Sulfur containing AA
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methionine also nonpolar
cysteine also polar |
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which AA is the first AA in the vast majority of proteins?
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Methionine
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charged AA
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aspartate
glutamate histidine lysine arginine side chains deprotonated and neg charged at physiological pH except lys and arg which are protonated participate in electrostatic interactions |
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histidine
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acts as an acid/base catalyst found in lots of enzymes
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a 4 month old female infant, emigrated from the soviet union w/her french mother and russian father 1 month ago. she was normal but in the last several weeks was less than norm. attentitive to her surroundings. her psychomotor maturation seemed delayed and a tremor of her extremities started. So she came to the ER when mother found her having gross twitching mvmts. Pediatrician examined and noted a musty odor to baby's wet diaper.
several phenyl ketones were found in her urine |
she has PKU
hyperphenylalaninemia which is mediated by autosomal recesive transmission of defective phenylalanine hydroxylase (PAH) gene causing accumulation of phenylalaine in bood (norm less than 1-2 mg/dL but in newborn it's twice this) people w/PKU have levels abv 16 mg/dL. PAH is req for the generation of Tyr phenyl ketones cause the musty odor liver biopsy det the level of activity of PAH tx - maintain levels of phenylalanine in blood through dietary restriction |
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isoelectric point
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pI - the pH at which molecule has no net charge
pI= (pKa (alpha-COOH) + pKa(alpha+NH3))/2 |
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van der waals
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weak non-convalent interactions
occurs btw two close atoms done by temporary dipoles |
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hydrophobic effect
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when 2 non-polar groups approach each other, water molecules become disordered so there is a net increase in entropy which results in a decrease in free energy which stabilizes the interaction
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Pi or ring stacking
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-forms a dipole-dipole iinteraction btw two neighboring aromatic groups
-possible bc of redistribution in electron density 2 orientations: off center stacking (DNA)or t-shapped stacking |
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cation-pi stacking
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forms an ion-dipole interaction btw aromatic group and a neighboring cation
common in proteins weaker than ioinc interactions but stronger than ring stacking |
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strength of a H-bond
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stronger when O-H-O is in a straight line and weaker when bent or at an angle
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electrostatic interactions in proteins
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at physiological pH arg, lys, and His are positively charged but asp, and glu are neg charged
can interact over longer distances than other types of interactions |
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disulfide bonds
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covalent bonds in proteins
help in protein stability cysteine can be oxidized to sulphenic, sulphinic and sulphonic acid |
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18 year old male brought to hospital by mother bc of the sudden onset of severe lft flank radiation around his left side toward pubic area. his urine was reddish-brown in color and urinalysis revealed presence of many RBCs. xray showed radiopaque stones(calculi) in both kidneys but no fam history of kidney stones. he passed a stone shortly after admitance w/immediate releif of pain. stone analysis revealed maj component to be cystein. whats wrong?
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norm AA filtered by renal glomerular caps into tubular urine but reabs from fluid back into blood.
he has cystinuria - genetically det. AA substitution in transport protein which nnorm reabs cystine, arginine, and lysine back into the blood. urine contains high amts of these aa and cysteine is less soluble than aa b/c of disulfide bonding and precipitates to form renal stones rare disorder 1 in 2500 to 1 in 15000 recessive mode of inheritance tx- dec amt of cystein w/in bod restricting dietary methionine which contributes to cystein formation. increase in volume of fluid drinks stones may be removed by surgical tech. - sonic fracture of stone and pass b/c of smlr size |
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characteristics of peptide bonds
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planar
O has a partial neg charge N has a partial pos charge free rotation around C-N bond does not occur but rotation around alpha C and C (called psi angle) and alpha C and N do occur (called phi angle) b/c of steric constraints alpha C are norm in trans conformation and so are side chains |
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tetrapeptide
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4 AA
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oligopeptide
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3-30 AA
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polypeptide
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many AA MW less than 10,000g/mol
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protein
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lots of AA MW greater than 10,000 g/mol
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peptide bond formation
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dehydration (condensation rxn)
AA favored over protein so carboxyl group on peptide is chem modified or activated in order to synthesize a new peptide bond |
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peptide bond formation - chemical method
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short peptides can be synthesized by solid phase peptide synthesis
uses dicyclohexylcarbodiimide (DCC) to activate the alpha- carboxylate of AA syn proceeds from c-terminus of peptide to N- terminus |
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peptide bond formation - biological method
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occurs in 3 steps
1. aminoacyl adeylate (aminoacyl-AMP) is formed by reaction of an AA w/ATP which is catalyzed by aminoacyl-tRNA synthetase specific for the AA during this reaction pyrophospahte (PPi)is formed the release and hydrolysis of PPi makes rxn energetically favorable 2. AA is transfered to ribose on a specific tRNA to form an aminoacyl tRNA 3. two tRNAs bind to the ribosome at adjacent sites alpha-amino group of a C termila AA (in A site) nucleophillically attacks the activated carboxyl of the N-teerminal AA (in P site) the A site tRNA then translocates to the P site and the next amino acyl-tRNA binds at the A site to extend the polypeptide chain syn proceeds from n- to c- terminal direction |
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peptide bond hydrolysis
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favored rxn but very slow
rate inc by incubating protein w/ 1. SA (6M HCl, 110 deg C for 24 hrs) 2. SB (40% aq NaOH, 110 deg C for 24hrs) 3. enzyme called protease |
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protesases
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exopeptidase (aminopeptidase) cleaves in between AA
endopeptidase cleaves w/in the AA btw NH and c=o |
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initiator codon
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AUG
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stop codons
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UAA
UAG UGA |
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wobble effect
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3rd AA most variable
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degenerate genetic code
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there are multiple codons for an individual AA
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alpha helix
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2dary structure
polypeptide wraps around imaginary helical axis side chains protrude away stabilized by internal Hbonds btwn amide of N of one peptide bond and carbonyl O of 4th AA from N terminal side of peptide bond - parallel to long axis of helix each turn held together by 3-4 H-bonds pro is a helix disrupter b/c shape and lack of amide H gly is destabilizing bc of high conformation flexibility poly Glu will not form a helix at pH 7 bc of destabilizing effect of adjacent neg charge bulk and shape of Asn, Ser, Thr, and Cys residues can also destabilize if they are close together stabilized by positive residues 3or 4 AA away from neg charge residues |
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factors affecting a- helix stability
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1. electrostatic repulsion/attraction btw adjacent AA
2. the bulkiness of the adjacent R groups 3. interactions btw R groups 3-4 residues apart 4. presence of Pro or Gly residues in sequence |
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beta sheet
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secondary structure
H-bonds btwamide H on one strand and carbonyl oxygen on other strand adjacent R groups in individual beta strands protrude from sheet in opposite directions above and below parallel or antiparallel when it makes a beta sandwich stacking R groups must be small |
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beta turn
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in globular proteins typically 1/3 of AA are in turns or loops that connect secondary structural elements to create tertiary structure
most common - connects two adjacent strands of an antiparallel beta sheet 180 degree turn only using 4AA carbonyl O on first residue H bonds w/amide N on 4th residue to help stabilize the turn |
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supersecondary structure
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commonly occuring recognizable combos of alpha helicies and/or beta sheets
zinc finger, helix turn helix, leucine zipper motifs commonly occur in DNA binding proteins in leucine zipper Leu residues interdigitate in zinc finger cys and his residues coordinate a zinc atom |
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tertiary structure
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electrostatic, H-bonding, van der Waals, hydrophobic and disulfide bonds stabilize tertiary structure
hydrophobic AA typically on int of protein hydrophillic on surface H-bond w/H2O to help solubilize protein |
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what denatures proteins?
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beta- metacaptoethanol - reducing agent cleaves disulfide bonds
urea disrupts hydrophobic interactions btw side chains heat, extremes of pH, detergents |
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protein folding
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defects in intracellular protein folding can contribute to dx like cystic fibrosis, creutzfeldt-jacob dx(mad cow dx), huntington dx, alzheimer's
once outside the cell many proteins cannot fold or refold into their native structures once denatured intercellular folding aided by molecular chaperones whose fn is conserved from bacteria ->humans inc. numbers of chaperone levels in cells exposed to cellular stresses (high temp) hydrophobic rich regions of unfolded proteins are bound w/in poockets in chaperonin complex to prevent aggregation conformational changes in chaperonin complex promote proper folding of the bound polypeptide |
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insulin
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a peptide hormone 51 AA sml protein
synthesized as a single chain precursor caled preproinsulin which contains a signal sequence that is removed during its insertion into the ER which results in the production of proinsulin w/3 disulfide bonds proinsulin packaged into secretory granules in pancreatic beta cells and converted to active insulin by specific proteases that cleave peptide bonds to form mature insulin elevated blood glucose triggers insulin secretion composed of chain A (21 AA) and chain B (30 AA) linked by 2 disulfide bonds |
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immunoglobulins
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IgG Ab are one of most abundant serum proteins
contains 4 chains : 2 heavy and 2 light made from diff genes light chains=220AA heavy chains = 440 AA held together by disulfide linkages and noncovalent forces IgG = Yshapped structure can be cleaved by proteases at the hinge region papain tx generates Fc fragment(crystalizes easily) and Fab fragment all have regions of fairly constant sequence CH1, CH2, CH3, and CL and variable secuence VL and VH constant domains adopt a characteristic structure called immunoglobulin fold heavy chain and light chain both have one region of variable sequence variable domains associate to from the antigen binding site 10^8 diff Ab antiparallel beta strands look like beta barrels which bind sml molecules |
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IgG
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- predominant Ab in serum - 4 additional classes of Ig somewhat related structures
- known as gamma globulin, readily traverse blood vessel walls and the placenta so can transfer immunity to developing fetus can activate complement system when it binds Ag |
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IgA
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principally found in body secretions (saliva, sweat, tears, milk, walls of intestine
occurs as a monomer or dimer conected by a J chain interacts w/Ag to prevent their binding to a particular cell helps get Ag out of body w/IgA |
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IgM
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produced during initial phases of an infection
consists of 5 Y-shapped IgG like chains largest Ig 5 chains are held together in pentameric form by a j chain b/c of size restricted to blood stream |
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IgD
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found on surface of B cells
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IgE
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plays imp role in allergic response by interacting w/phagocytic leukocytes in blood and histamine secreting cells in tis.
when binds Ag mast cells are stimulated to secrete histamine and other molecules that cause vasodilation. inc the permeability of blood vessels to facilitate mvmt of immune cells to sites of inflammation recognizes pollen or other allergens as foreign triggering immune response |
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fibrous proteins
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alpha keratin, collagen, and silk fibrin
elongated filamentous proteins that have structral roles in animal cells and tis major protiens in skin and CT and animal fibers like hair and silk dominated by secondary structure a-helix cross linked by disulfide bonds -tough insoluble protective structures of varying hardness and flexibility - ex - alpha keratin of hair, feathers and nails beta conformation - soft flexible filaments - silk fibrorin collagen triple helix - high tensile strength w/o stretch - ex collagen of tendons, bone matrix |
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alpha keratin
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major proteins of hair, wool, nails,claws, quills, and consitute major fraction of proteins in animal skin
Intermediate filament proteins which have important structural roles in cytoskeletal architechture of nuclei, the cytoplasm, and cell surface primarily alpha helical that can be more than 300 residues in length high content of Ser, Glu, Gln, and Cys pairs of helices twine about each other in parallel to form left handed coiled-coil - residues btw alpha helicies must interdigitate norm. hydrophobic rich in Ala, Val, Leu, Ile, Met, and Phe coiled coils associate to get protofilament which assoc to get protofibril mechanical strength depends on chemical intrachain crosslinking (disulfide bonds) the greater the number of disulfide bonds the greater the strength - nails have a higher number than hair |
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permanent waves
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heat and a reducing agent applied to hair to break H-bonds and disulfide bonds respectively
heat uncoils alpha helical structure removal of the reducing agent and addition of an oxidizing agent allows disulfide bonds to reform in a pattern determined by the stylist shuffled disulfide bonds |
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silk fibroin
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produced in insects and spiders
individual polypeptide chains are predominantly in beta conformation high content of Gly and Ala residues interdigitate to permit close packing of layered sheets each beta sheet is stabilized by H bonding btw peptide bonds intersheet interactions are predominantly van der waals interactions silk fivers do not stretch bc the polypeptide backbone is already in an extended conformation - but flexible bc it is held together by weak interactions |
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collagen
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collagen fibrils are present in CT, tendons, cartilage, the organic matrix of bone and cornea of the eye
strong as steal wire numerous proteins belong to this family distinct secondary structure collagen helix is: left handed, 3 residues per turn, composed of repeating tripeptide sequence Gly-X-Y where X is often pro and Y is often 4-Hydroxyproline individual polypeptide chain contains about 1000 AA each the pro and 4 Hyp residues allow form sharp twisting and Gly allows for close proximity of chains 3 collagen heilices called alpha chains are wrapped around each other -superhelical twisting is rt-handed triple helix stabilized by interchain Hbonds |
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tropocollagen
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individual triple helical collagen molecules
supramolecular assemblies of tropocollagen units arrayed in staggered , side-by-side allignment how they associate determines tensile strength of collagen molecule |
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collagen and tropocollagen post translational modified
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1. proline hydroxylation - vit C dependent rxn - uses prolyl hydroxylase and Fe+ too, 4-hydroxy proline plas imp role in stabilizing triple helix by formin H-bonds btw individual collagen helicies
2. lysine hydroxylation - vit C dependent rxn as well as Vit C and Lysyl Hydroxylase Hydroxy Lysine residues are sites of attachment for disaccharide moieties (glucose-galactose) 3. lysine oxidation to allysine req lysyl amino oxidase allysine can react w/another molecule of allysine to form an aldol cross-link covalent crosslinks such as these strengthen the collagen structure could also cross link w/lys or hydroxylysine in the absence of covalent modifications cross linking btw molecules of tropocollagen cannot occur and collagen molecules are largely unstable |
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2,3 - Bisphosphoglycerate
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BPG - produced by RBC in lrg amts from glycolysis
has a neg charge -reduces affinity of hemoglobin for O2 favors dissociation of O2 HbBPG + O2 <=> HbO2 + BPG central cavity of Hb is lined w/+charged residues that interact w/ BPG only one molecule binds to each hemoglobin tetramer in T state r state hs a low affinity for BPG b/c of conformational changes that reduce access to central cavity |
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fetal hemoglobin
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HbF is an alpha2 gamma 2 fetus synthesizes gamma subunits instead of beta
has lower affinity for BPG consequently has higher affinity of O2 imp bc fetus must be able to extract O2 from the blood of the mother |
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factors affecting O2 release
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HbO2 <=> Hb + O2
H+ -> BPG -> CO2 -> <- O2 |
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how can diff. forms of hemoglobin be separated by electrophoresis?
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bc differences in PIs
HbA pI = 6.87 HbS pI = 7.09 HbF pI = 6.58 - charged proteins migrate toward anode (+ electrode) + charged proteins migrate toward cathode (-electrode) HbA has a fastr rate of migration towards the anode b/c pI is lower least pI travels fartest and highest pI travels least HbA has a lower pI b/c Beta subuint of HbS contains a Glu6Val mutation so it has 2 fewer neg charged residues than HbA |
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apoenzyme
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protein by itself that is free of cofactor or prosthetic group
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how much can enzymes enhance rxn rate?
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10^16-10^17 fold
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holoenzyme
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complex of apoenzyme + prosthetic group, coenzyme, or cofactor
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what are the 2 most studied proteins?
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hemoglobin and myoglobin
myoglobin was the first 3D protein structure to be solved and hemoglobin was 2nd |
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hemoglobin vs myoglobin
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heme - transports O2 through blood , a tetramer
myo - stores O2 in mm so it can be used to provide E through oxidative phosphorylation, a monomer both contain heme group |
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six classifications of enzymes
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oxidoreductase - transfer of e- (hydride ions or H atoms)
transferases - group transfer rxns hydrolases - hydrolysis rxns lyases - addition of groups to dbl bonds or formation of dbl bonds by removal of groups isomerases - transfer of groups w/in molecules to yeild isomeric forms ligases - formation of c-c, C-s, C-o and C-N bonds by condensation rxns coupled to ATP cleavage |
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enzyme naming
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assigned a 4 part classification Num. by Enzyme Commission (EC num)
first number - denotes class name 2nd - denotes subclass(what it transfers) 3rd = denotes chem idenitiy of modified group 4th - denotes id of substrate also assigned a systematic name that IDs the rxn it catalyzes |
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pH optimum
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typical pH or pH range enzyme operates w/max activity
due to the fact tat aa have ionizable groups |
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active site
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AA residues create molecular surface that is complementary to substrate and are involved in catalyzing the rxn
once substrates is bound the conformation changes to isolate substrate from surrounding aq enviro |
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enzyme catalyzed rxn
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E + S <=> ES <=> EP <=> E + P
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rxn coordinate diagram
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progress of rxn plotted against free E (G)
starting pt = ground state and end point under standard cond: 298 K, 1 atm, 1 M , pH 7 biochem standard free E change = delta G prime knot = difference in S and P ground state if P is lower E state then free E is neg. b/c favorable but if P is higher free E is pos. top of curve - transition state things are changing activation E = delta G vertical 2 headed arrow - lower activation E = faster rxn |
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heme
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protein bound prosthetic group which iron is bound to carry O2 b/c if iron is free promotes formation of reactive O2 which damages O2
belongs to class of cmpds called porphyrins (protoporphyrin IX) binds to ferrous (Fe2+) six coordination bonds - 2 to N atoms in flat porphyrin ring and 2 perpendicular to porphyrin ring F3+ doesn't bind O2 heme deep in protein to prevent iron oxidation - in myoglobin 1 of the axial sites of coordination is bound to a HIs, the other site of coordination interacts w/O2 color of blood due to changes in electronic properties of heme when O2 binds CO and NO can coordinate to heme iron in place of O2 and have a higher affinity for heme iron than O2 - CO binding to heme prevents O2 from binding and is highly toxic |
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transition state theory
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the enzyme active site is complementary so iit binds most effectively to the TS for the rxn
the binding of ES should be weaker than the interaction btw enzyme and the TS for rxn if it binds to tightly to the substrate during the transition state then the activation energy is higher when going from ES to TS than when going from S to TS the complementary interactions btw the enzyme and the transition state of the rxn are maximized so the activation E is lowere when going from ES to TS than when going from S to TS enzyme binds TS 10^12 times tighter than to the substrate or products |
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induced fit
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conformational change when the enzyme binds substrate that excludes water
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hexokinase
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binds glucose to change into a conformational active enzyme - phosphorylates glucose b/c it undergoes conformational change upon glucose binding that converts the enzyme from inactive to active conformation that excludes water
ex of induced fit glucose + Mg-ATP --(hexokinase)--> phosphorylated glucose +Mg-ADP extensive H-bonding to glucose - induces the conformational change galactose the C-4 hydroxyl is in axial position so it can't bind productively to hexokinase b/c of loss 4- Hbonds so it cannot be phosphorylated by hexokinase but can be by galactokinase enzyme specifity |
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Inhibition of HIV protease
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HIV protease is an "aspartyl protease: that cleaves peptide bonds in proteins
2 closely spaced Asp residues make water nucleophilic so it can attack the carbonyl carbon in the peptide bond aspartyl proteases provide an example of acid base catalysis HIV protease cleaves newly snthesized viral protein at specific Phe-Pro bonds so it can package new virus for release into blood during the rxn cycle a tetrahedral intermediate is formed at the TS -most HIV protease inhibitors possess a tetrahedral hydroxyl group to maximize interactions with the enzyme at the TS TS analogues are generally competitive inhibitors that bind to enzymes 10^2 to 10^6 times more tightly than the normal substrate |
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TS state analogues of HIV protease
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Indinavir
Nelfinavir Ritonavir Amprenavir Saquinavir |
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3 main drugs target certain enzymes to control HIV
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HIV reverse transcriptase
HIV integrase HIV protease |
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factors that stabilize the TS and lead to rate enhancement include
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1. Decrease in ENtropy
2. Desolvation effects 3. induced fit 4. general acid-base catalysis 5. covalent catalysis 6. metal ion catalysis 7. use of coenzymes 1-5 used by chymotrypsin |
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decrease in entropy
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proper orientation of substrate in enzyme active site - increases the probability of productive collisions btw molecules - which in solution may be rare
also by proximity loss of rotational and translation entropy when substrate binds but loss is offset by favorable binding energy of substrate ES are now bound so now the rxn is 1st order instead of 2nd order ( an increase in effective molarity of rxn centers) |
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desolvation effects
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when an enzyme binds to substrate desolvation of substrate occur
H bonds btw substrate and water are replaced by interactions between enzyme and substrate - solvation shell stabilizes biomolecules - so rate enhancement in absence of this |
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general acid-base catalysis
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side chains of variety of AA can act as either proton donors or acceptors
positioned to max proton transfers rate enhancements of 10^2 -10^5 fold used bymost enzymes |
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covalent catalysis
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nucleophilic attack by an active site residues lead to the formation of a covalent intermediate which is more reacctive than the substrate
several AA can participate in this by acting as nuceophiles (Ser (OH), Cys, His) used to activate the substrate |
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chymotrypsin and trypsin
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pancreatic serine protease catalyzes the hydrolysis of peptidebonds C-terminal to an aromatic AA acit (Trp, Tyr, Phe)
- works in sml intestines - ex if how entropy effects, transition state stabilization, general acid-base catalysis and covalent catalysis contribute to rate enhancement enhances the non-enzymatic rxn by at least a factor of 10^9. Trypsin employs a virtually identical catalytic mechanism but trypsin cleaves peptides after Arg or Lys In trypsin the substrate recognized pocket contains an aspartyl residue(neg) which helps to promote bindng positively charged AA active site serine |
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RXN mechanism of Chymotrypsin
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1. substrate (unstructured region of protien) binds to the enzyme
2. His acts as a general base and deprotonates the Ser hydroxyl = alkoxide nucleophilically attacks the carbonyl C 3. Formation of tetrahedral acyl-enzyme intermediate . the neg charge on O is stabilized by H bonding to the electropositive amide protons in the oxyanion hole 4. collapse of the tetrahedral acyl-enzyme intermediate leads to the reformation of the carbonyl the breakage of the peptide bond and the loss of the C-term fragment His57 donates the proton that it removed from Ser195 to the departing N-term alpha amino group (covalent catalysis) 5. step 4 leads to the formation of the acyl-enzyme intermediate 6. a H2O molecule binds to active site. His57 again acts as a general base deprotonating the water molecule to generate hydroxide anion (-OH). Nucleophilic attack on the carbonyl carbon occurs 7. Nucleophilic attack on the carbonyl C results in the formation of a second tetrahedral acyl enzyme intermediate . The neg cha |
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summary of the rxn mechanism of chemotrypsin
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Asp - modulates the pKa of His os it is able to deprotonate Ser hydroxyl (pKa 4)
protonated His is stabilized by neg charge of nearby carboxyl group of the Asp residue catalytic triad the acyl-enzyme intermediate has a lower E level than the TS b/c it is more stable the last step has the highes E level and is the rate limiting step of rxn |
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catalytic triad
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this arrangement of Asp, His, and Ser is common to a number of proteases and called the catalytic triad - a good example of the cooperative interactions that occur btw the aa in an active site that occur to promote catalysis
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metal ion catalysis
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metal ions are often cofactors for enzyme rxns (1/3 of all enzymes use metal ions)
metal ions are either tightly bound by the enzyme or bound to the enzyme as a substrate metal ion complex Mg-ATP in the hexokinase rxn is an example which helps orient the substrate for nucleophilic attack and to help stabilize deveolping charge n the transition state in solution there is no free ATP so enzymes typically bind metal ion-ATP complexes |
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myoglobin
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153 aa - single polypeptide chain w/ 8 alpha helicies that comprise 78% of the aa residues in the protein - named A-H
the polar and charged residues are on the surface and the heme group is buried in a hydrophobic pocket in the interior there are 2 His residues present in the Heme binding pocket |
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myoglobin binding to O2
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binds and releases O2 based on its affinity for O2 - binds O2 in O2 rich environments and releases it in O2 deprived regions
equilibrium constant Ka is a association constant and is a parameter that indicates the affinity of a ligand for a protein expressed in terms of M-1 the larger the Ka the higher the affinity of the ligand(O2) for the protein P+L<=>PL Ka=PL/P*L the fraction of available binding sites that are occupided by a ligand = [PL]/[P]+[L] = binding sites occupided/total binding sites --- this is also equal to w/ the substatution of Ka = [L]/[L]+1/Ka dissociation constant Kd = 1/Ka with M as the units - equivalent to the conc of ligand(O2) at which half of the ligand binding sites are occupied. Smaller the Kd the higher the affinity of ligand for the protein so theta = [L]/[L]+Kd a hyperbola eqn -hyperbolic fn because O2 is a gas partial pressures replace the concentrations so theta = p[O2] / p[O2] +P50 P50 of myoglobin for O2 is 0.37 kPa or 2.8mm Hg CO binds to myoglobin 200 times |
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hemoglobin
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present in erythrocytes (34% by weight)
near the lungs hemoglobin is 96% sat w/O2 in peripherial tis hemoglobin is only 64% saturated an alpha2beta2 tetramer consisting of 2 alpha subuints 141 residues and 2 beta subunits w/146 residues mass 64,500g/mol diameter 5.5 nm roughly spherical exists in 2 major conformations tense T state (absence of O2 predominate of deoxyhemoglobin) or relaxed R state (O2 binds and stabilizes this conformation) ionic salt bridges stabilize the T state - porphyrin ring adopts a puckered conformation when O2 binds the ring adopts a planar conformation and pulls the proximal His residue and alters the conformation of attached Helix F cange causes conformational changes in other subuits and allows them to more readily bind O2 |
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why myoglobin is not good transporter of O2
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pO2 in lungs is abt 100 mm Hg (13.3 kPa) in lungs it is 30 mm Hg (4 kPa)
since P50 of myoglobin is 2.8 mm Hg it would not release the O2 to tis -so not a good O2 transporter any protein that bound O2 w/hyperbolic binding curve isn't good transporter b/c a. protein that binds O2 w/high affinity would be completely saturated w/O2 in lungs and would not release to tis. b. protein binds to O2 w/low affinity would release it to the tis but would not become saturated w/O2 in lungs hemoglobin overcomes this problem by binding to oxygen cooperatively - it undergoes transition from a low affinity state to high affinity state as O2 conc increases |
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hemoglobin binding to O2
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O2 binding to an individual subunit of alters the affinity of adjacent subunits for O2.
binding of first molecule of O2 binds weakly b/c bound to T state but affinity for second one is increased and subsequent binding of O2 to the remaining subunits helps to further convert hemoglobin from the T to R state - positive cooperativity -O2 sat. curve for hemoglobinis sigmoidal hemoglobin can only bind 4 molecules of O2 reversible binding of ligand to protein w/n binding sites described by eq expresion : P+nL<=>PLn Ka=[PLn]/[P][L]^n fraction of binding sites occupied by ligand (theta) = [PLn]/[P]+[L]^n = [L]^n/ [L]^n+Kd (eqn for a sigmodial curve) subs for partial pressures theta = p[O2]^n/p[O2]^n+kd when hemoglobin is half saturated w/O2 theta=0.5, Kd=p[O2]^n so for a sigmodial curve Kd does not equal the concentration of ligand that yields half max binding (P50) P50 = nth root of Kd for hemoglobin P50 = 26 mm Hg |
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hemoglobin transport of H+ and CO2
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hemoglobin responsible for transport to the lungs of 40% of H+ and 15-20% of CO2 produced by tissues
CO2+H2O <=>H2CO3 <=> H+ + HCO3- hydration of CO2 in tis decreases the pH of the surrounding solution the protons and CO2 produced in the tis do not bind the heme protons can bind to the AA residues in hemoglobin His 146 (His HC3) in the beta subunit makes a major contribution to the Bohr effect when protonated His146 forms a salt bridge to Asp94 (Asp FG1) that stabilizes the T state therefore protonation of His146 favors release of O2 CO2 produced in tis does not bind directly to heme CO2 forms a carbamate group w.the alpha amino groups on each of the individual hemoglobin subunits since the reaction produces protons it contributes to the bohr effect the higher concentration of O2 in lungs promotes O2 binding and the relase of CO2 |
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the bohr effect
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pH decrease the O2 saturation curves shift to the rt favor low affinity state
at at low pH 7.2 tis, the affinity for O2 dec. and O2 released at low pH CO2 and H+ bind to hemoglobin is favored proton binding to specific sites on hemoglobin cause conformational changes that favor a shift to the T state In the lung higher pO2 and a slightly elevate blood pH (7.6) promote release of CO2 and H+ which favors the R state consequently the affinity for hemoglobin for O2 increases binding in the lung favors release of protons wheras in tis where the proton concentration is higher the binding of a proton favors release of O2 The effects of CO2 and H+ on O2 transport were first noted in 1904 by christian bohr and is therefore called the bohr effect HHb+ + O2 <=> HbO2 + H+ |
