BCHEM Block A

chemical changes (conversions) required to sustain life

• biosynthesis
• gluconeogenesis: generation of glucose in response to decreased blood glucose levels metabolic opposite of glycolysis

• biodegredation
• glycolysis: breakdown of glucose into pyruvate for energy (RBCs have no mitochondria)
• urea cycle: breakdown of protein into nitrogenous wastes for excretion

• protein catalysts
• increase the rate at which a reaction reaches equilibrium but do NOT alter the ratios of a chemical reaction's products and substrates
• not altered themselves by the reaction in which they participate

• substrate availability: high concentration necessary
• allosteric modulation of enzyme activities: alters the dynamics at an enzyme's active site by binding with a secondary site on the molecule
• covalent modification: usually phosphorylation; alters an enzyme's activity
• changes in enzyme protein levels

• glucose & amino acid delivery: absorbed by the intestine, carried by portal vein to liver
• fat packed by enterocytes in the gut as chylomicrons, carried by lymphatics into general circulation

carbohydrates, lipids, and proteins

energy availability as represented by levels of ATP, NADH, &  NADPH

• liver: glycogenesis will store glucose as the polymer glycogen for easy access later (through glycolysis)
• in other tissues: adipose tissue (fat); muscle (storage & energy); brain (ATP production); RBCs (glycolysis)
• lactate & pyruvate from glucose metabolism by other tissues incorporated into fatty acids by the liver

• hydrolyzed in the intestine so they can be absorbed as amino acid monomers or short polypeptides (asp, asn, glu, gln)
• the rest pass through the liver & will be used throughout the body for protein synthesis
• excess amino acids will be processed into fatty acids in lipogenesis or processed into urea & excreted

predominantly manufactured in the liver & exported as very low density lipoprotein (VLDL)

absorbed by the intestines and packaged into chylomicrons

breaks down VLDL and chylomicrons into fatty acids (triacylglycerols) for storgage in adipocytes

• liver responsible for maintaining blood glucose levels
• glycogenolysis will release glucose from glycogen
• lipogenesis is curtailed
• gluconeogenesis will produce glucose in preparation for the depletion of liver glycogen stores (~12 hours of fasting)

• glycerol from lipolysis in adipose tissue (minor source for gluconeogenesis)
• amino acids from muscle protein proteolysis (major contributor)

• large increase in lipolysis resulting in increased levels of fatty acids in the blood
• fatty acids are used by many tissues in preference to glucose (brain needs glucose)
• liver will increase fatty acid oxidation

• blood glucose decreases to a constant lower level (minimum requirement)
• free fatty acid levels increase somewhat
• ketone bodies increase dramatically in the blood
• total urinary nitrogen decreases
• urinary ammonia increases as a way to pull protons from the blood & counter the acidity of ketone bodies

• hereditary hemochromatosis (1 in 300)
• adult polycystic kidney disease (1 in 900)
• a1-antitrypsin deficiency (1 in 1700)
• cystic fibrosis (1 in 3000)
• neurofibromatosis 1 (1 in 3000)

• an increasing number of companies can provide DNA testing direct to consumers
• testing can be for paternity, disease gene identification or even for the appropriate diet
• it is not clear how that information will be used or even whether it will be understood

the observed expression of the genes of an individual (expression can be biochemical, physiological or morphological)

• the genetic constitution of an individual
• the alleles present at a particular locus

alternative forms of a gene, or of a DNA sequence, at a specific position on a chromosome

a specific location on a chromosome; often a specific gene

both alleles at a locus are identical

if the alleles at a locus are different

• 99.6% of DNA sequence is identical between two people
• the difference between any two people is about 24 million bp
• sequence variations are polymorphisms
• changes in the DNA that are pathologic are mutations

sequence variations

changes in DNA that are pathologic

• single nucleotide polymorphism (>1% abundance)
• human genome has ~3 million SNPs distributed randomly

• different mutations can cause different or similar phenotypes
• allelic heterogeneity: different mutations at the same gene cause the same phenotype (cystic fibrosis)
• locus heterogeneity: different mutations at different loci cause the same phenotype (breast cancer BRCA 1 & 2)

• the frequency with which the observable expression of a mutant gene manifests itself
• affected by: modifier genes, carcinogens, response to DNA damage & hormonal/reproductive factors

• caused by mutations in genes that affect several organ systems & functions
• may involve modifier genes that alter the affect/expression of the mutation
• ex - Neurofibromatosis 1 (severity of affected parent does not indicate extent to which child will be affected)

• neurofibromatosis 1
• myotonic dystrophy

• single gene: CF, achondroplasia, hemophilia
• chromosomal: trisomy 21
• complex: diabetes, heart disease

• mendelian diseases are the result of a mutation in a single gene
• the mutation alters the protein product in such a way that in can no longer function normally or may even be toxic
• the mutation can arise spontaneously (de novo) or it can be inherited

eye color, hair color, weight

• open square: unaffected male
• open circle: unaffected female
• open square with diagonal line: deceased male
• open circle with diagonal line: deceased female
• any symbol with an arrow pointing to it: propositus
• filled-in square: affected male
• filled-in circle: affected female
• circle with a dot in the middle: carrier for X linked condition
• diamond: sex unspecified
• single line: mating
• double line: consanguineous mating

• autosomal: inheritance of a gene located on any of the 22 chromosomes other than X or Y
• X linked: inheritance of a gene located on the X chromosome
• Y linked: inheritance of a gene located on the Y chromosome

• identifying all the genes in humans
• sequencing the DNA in the human genome (6 billion bases)
• studying the genomes of model organisms
• identifying the ethical and social issues caused by genomics

• personalized, predictive, preventive, and participatory
• better diagnoses and earlier interventions
• more efficient drug development
• more effective therapies

genetic influence on response to certain foods, vitamins, etc.

• microbial flora can affect our body and health
• normal microbial flora in the human body outnumber human cells by 10:1

large scale study of proteins

study of chemical processes involving metabolites

• drug dosing/use based on genetics
• genetic variations in enzymes that metabolize the pro-drug into the active drug
• enzymes that metabolize drugs into a form that is inactivated/elimination
• variation in target receptors

• heredity is determined by units or "factors"
• the units come in pairs
• the units come in different variant forms
• a form can be either dominant or recessive
• different factors are inherited independently of one another

• conditions that are expressed when just one allele is present (Aa)
• therefore, these conditions are expressed in heterozygotes
• direct transmission from an affected parent to an affected child
• transmission can occur from affected father to affected son
• approximately a 1:1 ratio of affected verse unaffected progeny with one affected parent
• equally transmitted by men & women
• no skipped generation
• each child has a 50% chance of inheriting the mutation

• achondroplastic dwarfism
• adult polycystic kidney disease
• Marfan's syndrome
• polycystic kidney disease
• neurofibromatosis 1 & 2
• polydactly
• Huntington's disease

• affected individuals often choose similar mates (selective mating)
• when two affected individuals mate, there is a 50% chance of affected child, 25% chance of homozygous lethal, 25% chance of child with normal stature
• most common cause of dwarfism
• mutation in the fibroblast growth factor receptor 3 gene (FGFR3)
• normal intelligence
• recurrence risk is low if parent is not affected

• autosomal dominant
• adult onset
• one of the most common inherited disorders in humans (1:900)
• accounts  for 10% of all dialysis patients
• cysts form throughout the kidney
• causes progressive renal dysfunction and ultimately renal failure

• symptoms begin in mid adulthood
• pain in the abdomen
• blood in the urine
• hypertension
• intense pain from kidney stones
• ~50% of patients with ADPKD have hypertension at the time of diagnosis

• hepatic cysts (focal expression)
• cerebral aneurysms
• cardiac abnormalities

• subarachnoidal hemorrage
• hypertension & stroke
• mortality due to intracranial aneurysms
• stroke

• neurofibromas: two or more, or one plexiform neurofibroma
• cafe au lait macules: six or more measuring 1/5 cm in their greatest dimension
• freckling: in axillary or inguinal areas
• sphenoid dysplasia: thinning of the cortex of the long bones

• connective tissue disorder - molecular defect in  Fibrillin 1 gene
• tall with long extremities
• archnodactyly
• hyperextensible joints
• dissecting aortic aneurysms
• subluxation of lens

• phenotype only seen in individuals homozygous for the mutant allele
• males & females equally affected
• most often seen - two individuals who are clinically normal produce an affected child
• heterozygous individuals are called "carriers"
• 1 in 4 chance of producing an affected child

• cystic fibrosis
• phenylketonuria
• hemochromatosis
• sickle cell anemia
• Tay-Sachs disease
• thalassemia

• most common genetic disease (13% of all Americans are carriers)
• about 1 in 200 people are affected
• iron overload syndrome: excess iron deposition in liver, pancreas, heart & other tissues
• no physiologic process to reduce excess iron
• symptoms begin at 30-50 years
• men more likely to be diagnosed and are affected at a younger age
• develop type 1 diabetes, liver sclerosis and cardiovascular problems

• autosomal recessive inheritance
• most common genetic disease of African Americans (1/700)
• caused by mutation in hemoglobin B subunit
• skeletal problems
• infarctions
• anemia & repeated infections

• abdominal pain
• bone pain
• breathlessness
• fatigue
• fever
• delayed growth

glutamate --> valine substitution (point mutation)

• in order to achieve balanced dosage for X linked genes, one of the two X chromosomes is inactivated
• begins as early as the 8 cell stage
• is always random, unless there is a structural defect in one of the Xs
• once the pattern of inactivation is set, it is preserved in subsequent cell divisions
• can be visualized as a Barr body
• female mammals are mosaics

• sons of carrier females have a 50% chance of inheriting the mutant allele
• examples include hemophilia, G6PD deficiency, Duchenne Muscular Dystrophy, and red/green color blindness

• more affected males than affected females
• affected grandfather to affected grandson transmission through a carrier female intermediate
• no male to male transmission

• X linked recessive inheritance
• primarily males affected
• caused by mutations in either factor VIII or factor IX
• clotting disorder that causes bleeding into soft tissues

• most common form of MD
• mutation in the dystrophin gene
• largest gene
• males have 50% chance of being affected

• fatigue
• muscle weakness (begins in legs & pelvis, but occurs less severely in arms, neck & other areas)
• progressive difficulty walking (lose ability by age 12)

• 50% of the children (both sexes) of an affected mother will be affected
• NONE of the sons of an affected man will be affected (they get the Y from him)
• males are usually more affected than females

• X linked dominant disorder
• most frequently encountered form of rickets
• consists of a genetic defect in the handling of phosphate in the proximal tubules of the kidney
• short stature, leg bowing, tooth anomalies

• decreased reabsorption of phosphatate by the renal tubule (otherwise renal function is normal - BUN and Cr)
• decreased absorption of calcium & phosphorous from the GI tract

• X linked dominant neurodevelopmental disorder
• male fetuses rarely survive
• slowed growth (microcephaly)
• loss of movement & coordination
• abnormal hand movements
• unusal eye movement
• irritability, seizures & scoliosis

genes involved have distinct function in males and females (ex. prostate cancer & milk production)

• passed from father to sons
• genes on the Y chromosome

• mitochondrial homoplasmy: all mutant or all normal
• mitochondrial heteroplasmy: mixture of mutant & normal

• mitochondrial genome codes for only 37 genes and containing only about 16,600 base pairs
• mutation rate is about 20X higher than for nuclear genome (limited DNA repair capacity)
• damages: brain, heart, liver, skeletal muscles, kidney (tissue that have high energy capacity)

• nervous system: seizures, tremors, developmental delays, deafness, dementia, stroke before age 40, poor balance, problems with peripheral nerves
• heart: cardiomyopathy (heart failure, conduction block)
• liver: liver failure uncommon except in babies with mitochondrial DNA depletion
• kidneys: fanconi syndrome (loss of essential metabolites in urine)
• eyes: drooping eyelids (ptosis), inability to move eyes from side to side (external ophthalmoplegia), blindness (retinitis pigmentosa)
• skeletal muscle: muscle weakness, exercise intolerance, cramps
• digestive tract: acid reflux, vomiting, chronic diarrhea, intestinal obstruction
• pancreas: diabetes

• trinucleotide expansion disorders
• tandem repeats of three base pairs (trinucleotides) that often change size upon transmissioin to children
• Fragile X syndrome: outside the gene
• Huntington's disease: middle of gene
• Machado-Joseph Disease: intron
• myotonic dystrophy: end of gene

• trinucleotide repeats expand with each successive generation
• age of onset becomes younger with each successive generation
• severity of disease increases with each generation

• autosomal dominant inheritance (1/20,000)
• late age of onset (usually in 40s)
• symptoms: dementia, memory loss, choreic movements
• death of cells in the caudate nucleus
• mutation is a triplet repeat expansion of CAG
• diagnosis with PCR
• new mutation rate is 3%

• the most common heritable form of moderate mental retardation
• affected individuals have "fragile site" at Xq27.3 that can be observed with cytogenetic analysis
• moderately retarded males & mildly retarded females
• patients have behavior problems, hyperactivity and autistic features
• triplet repeat is CGG and is in the 5' untranslated region of the gene
• most physical features develop after adolescence; long face with prominent jaw, large ears & macroorchidism
• normal lifespan

• inherited as autosomal recessive
• trinucleotide repeat of GAA
• symptoms begin in adolescence
• dysarthria: slowness and slurring of speech
• ataxia: impaired muscle coordination starts in legs & spreads to arms and trunk
• heart problems, muscle weakness & fatigue
• degenerative of peripheral nerves and spinal cord

• 20 common amino acids in proteins
• amino group (NH3+): protonated at physiological pH
• carboxyl group (COOH): unprotonated at physiological pH (forms the negatively charged carboxylate ion COO-)
• hydrogen ion
• R groups: side chains; distinctive for each amino acid; most important for charge characteristics of proteins

• nonpolar or hydrophobic
• polar or hydrophilic
• acidic (proton donors - negatively charged)
• basic (proton acceptors - positively charged)

• GAVLIMP-FW
• glycine: gly, G (simplest & smallest, only non-chiral)
• alanine: ala, A (methyl group side chain)
• valine: val, V
• leucine: leu, L
• isoleucine: ile, I
• methionine: met, M (sulfur side chain)
• proline: pro, P (secondary amine group; changes ability to fold)
• phenylalanine: phe, F
• tryptophan: trp, W (biggest side chain)

• serine: ser, S
• threonine: thr, T
• tyrosine: tyr, Y
• asparagine: asn, N ("carboxamide" amino carbonyl)
• glutamine: gln, Q ("carboxamide" amino carbonyl)
• cysteine: cys, C (forms disulfide bond, interacts with water)

• aspartic acid: asp, D
• glutamic acid: glu, E
• side chains act as proton donors
• fully ionized (negatively charged) at physiological pH 7

• histidine: his, H (largely uncharged)
• lysine: lys, K
• arginine: arg, R
• side chains act as proton acceptors
• at physiological pH, lysine & arginine are positively charged

• hemoglobin is a tetramer of two alpha & two beta subunits
• point mutation (glutamate to valine) at position 6 in the beta-globin chain causes sickle cell anemia
• RBCs become misshapen & too rigid to move in the microvasculature

• chiral carbon (optically active): carbon that has four different moieties attached to it (all amino acids but glycine)
• D & L forms (mirror images): optically active pair called stereoisomers, optical isomers & enantiomers
• L form: eukaryotes
• D form: some bacterial proteins

those amino acids that cannot be synthesized by humans & must be obtained from diet

serine, threonine & tyrosine

glutamate & aspartate

arginine, lysine & histidine

methionine & cysteine

proline

• GAVLIMP-FW
• glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan

ONLY cysteine

glycine (just a hydrogen)

serine, threonine, tyrosine, asparagine, glutamine, cysteine

• amino acids have a weakly acidic alpha carboxyl and weakly basic alpha amino group
• acidic & basic amino acids have ionizable side chains
• free amino acids & those in proteins can act as buffers

• a solution that resists changes in pH after addition of a strong acid or strong base
• created by mixing a weak base (A-, proton acceptor) & its conjugate acid (HA, proton donor)
• system capable of resisting pH changes

• when pH = pKa
• effective when pH of solution is +/- 1 of the pKa

• Ka = [H+][A-] / [HA]
• a weak acid is mostly intact (weakly ionized)
• a strong acid is mostly dissociated
• bigger Ka: stronger acid
• smaller Ka: weaker acid

• pH = pKa + log [A-]/[HA]
• pH: -log of [H+]
• pKa: -log of Ka

• useful in diagnosing metabolic or respiratory acidosis and alkalosis
• determining when a drug is charged will help determine best route of administration/dosing

• the sequence/chain of amino acids linked by peptide bonds
• crucial in determining a protein's structure
• abnormal sequence can lead to misfolding/lack of function/disease

• primary structures linked by hydrogen bonds
• ex: alpha helices, B strands & B pleated sheets, B turns, non repetitive structures, supersecondary structures

condensation reaction: condensation of amino group (NH3+) of one amino acid with the carboxyl group (COO-) of another amino acid; removal of H2O molecule

• "partial double bond"
• no free rotation around peptide bond
• rigid & planar
• almost always trans
• uncharged but polar (hydrogen bonds possible)
• R group rotation around alpha-carbon is possible (exception - proline)

• HCl hydrolysis: at high temp, breaks all peptide bonds (alters/destroys some amino acids)
• cation exchange chromatography: separates amino acids based on charge; eluted with solution of increasing ionic strength and pH
• heat with ninhydrin: measure purple color with spectrophotometer

• beginning with N-terminal of protein, react with phenylisothiocyanate (Edman's reagent)
• forms unstable phenylthiohydantoin (PTH) amino acid derivative that can be released from protein without interupting other peptide bonds
• different PTH-aa derivatives can be identified
• reaction is sequentially repeated to ID first 100 aa in protein (NOT COMPLETE SEQUENCE)

• enzymatic cleavage or chemical cleavage - specificity of peptide bonds broken
• trypsin: carbonyl (carboxyl) side of lysine & arginine (basic residues)
• chymotrypsin: carbonyl side of tryptophan, tyrosine, phenylalanine, methionine, leucine (hydrophobics)
• elastase: carbonyl side of alanine, glycine, serine (small side chains)
• cyanogen bromide (CNBr): breaks bond on carbonyl side of methionine

• carbon double bonded to an oxygen
• ex: aldehyde, keton, carboxylic acid

• used to determine whether there are differences in charges of proteins/peptides
• molecules placed in an electric field - separated by charge at pH used
• no denaturation

• set up a pH gradient in a gel (or chromatography column)
• different proteins will stop migrating in an electric field when they reach their isoelectric point
• denaturation not necessary

• separates proteins by their size using gel electrophoresis
• denaturation
• uses antibodies to ID proteins involved in HIV, Lyme disease & BSE, etc.

• most common secondary structure
• spiral structure, tightly packed, coiled
• held together by H bonds that are parallel to helical axis

• proline: imino structure; introduces "kink"
• highly charged amino acids: aspartate, glutamate, histidine, lysine, arginine introduce ionic bonds that disrupt the helix
• amino acids with bulky side chains: tryptophan physically impair formation of helix
• amino acids with branched side chains: valine, isoleucine physically impair formation of helix 

• composed of beta-strands
• stabilized by H bonds perpendicular to polypeptide backbone
• antiparallel: N terminal next to C terminal of other strand
• parallel: N terminals next to one another, C terminals too

hydrogen bond between two different polypeptide chains, each containing their own N & C termini

hydrogen bond between amino acids in the same polypeptide chain

• B-turn
• reverses the direction of a polypeptide chain
• helps form compact globular shape
• almost exclusively found on surface of protein
• composed mainly of charged amino acids - glycine & proline

less regular coils or loops

• regular packing of other higher order structures
• "supersecondary structures"
• ex: beta-alpha-beta unit, Greek key, beta-meander, beta-barrel

preferentially bind to the T state

preferentially bind to the R state

• 2,3 bisphosphoglycerate
• most common organic phosphate in RBCs (alternative intermediate in glycolysis)
• decreases oxygen affinity of hemoglobin
• binds to deoxyhemoglobin NOT to oxyhemoglobin
• stabilizes T form of hemoglobin
• released when oxygen binds

• oxygen released from hemoglobin increased by lower pH or higher pCO2
• causes decreased O2 affinity & right shift of dissociation curve
• higher pH & lower pCO2 increases O2 affinity of hemoglobin

pH < 7.4

pH > 7.4

• last oxygen is bound with 300X higher affinity than first oxygen
• lets more oxygen get to tissues with smaller change in pO2

• myoglobin: binds one O2; hyperbolic curve
• hemoglobin: binds 1-4 O2; sigmoidal curve
• amount of bound oxygen depends on partial pressure of O2 (pO2)

• T: taut, deoxyhemoglobin; dimers bound tightly together (ionic, H bonds); low affinity for O2
• R: relaxed, oxyhemoglobin; less tightly bound, more movement; high affinity for O2

• RBCs: transport oxygen from lungs to capillaries; brings CO2 from tissues to lungs
• HbA: major adult form; tetramer of 4 polypeptide chains (alpha-beta)2 in a quaternary structure
• heme binding pocket & alpha helical structure of each subunit similar to myoglobin
• binds allosteric effectors & exhibits cooperative binding

• heart & skeletal muscle: reservoir & transporter of oxygen in tissue
• one polypetide chain - 80% alpha helic (8 stretches)
• interior: all nonpolar amino acids; heme sits in crevice
• surface: charged amino acids
• proximal histidine: binds to iron in heme
• distal histidine: stabilizes binding of oxygen to heme

• tightly bound prosthetic group
• a porphyrin with bound ferrous iron (Fe2+)
• six bonds of iron: four bind to nitrogens in porphyrin ring; 2 available

• creutzfeld jakob (humans)
• scrapie (sheep)
• bovine spongiform encephalopathy (cows)
• infectious agent - misfolded PrP protein

• abnormal proteolytic cleavage can generate protein fragments that form beta pleated sheets & then associate to form long fibrous aggregates called amyloids
• ex. Alzheimer's  & neurofibrillary tangles

chemical reactions, heat, changes in solvent, heavy metals - disrupt the interactions of the secondary & tertiary structures

• relationship of subunits to each other
• MUST HAVE MORE THAN ONE POLYPEPTIDE

• all proteins are synthesized as linear sequence of amino acid residues
• N terminal to C terminal
• some polypeptide chains fold during synthesis to take up the native conformation
• protein folding can be complicated - may require chaperone proteins

• disulfide bonds
• hydrophobic interactions
• hydrogen bonds
• ionic interactions (salt bridges)

• final 3D shape of protein (single polypeptide chain) built from secondary structure elements
• hydrophobic side chains interiorly, hydrophilic side chains on exterior (soluble proteins)

combination of motifs that form globular units of the protein

• form of hemoglobin that carries CO2 from tissue to the lungs
• when CO2 is expelled in the lungs, Hb reverts to R form

• CO binds tightly to iron in hemoglobin (affinity is 220X greater than O2)
• stabilizes R form (high O2 affinity) of hemoglobin - but does NOT release oxygen as it should
• O2 binding curve is shifted to the left

• HbA: major adult form
• HbA2: minor adult form; (alpha-delta)2
• HbA1c: minor adult form to monitor glucose; (alpha-beta - GLUCOSE)
• HbF: fetal (alpha-gamma)2
• HbS: sickle cell

• nonenzymatic glycosylation occurs by Schiff's base formation between the alpha amino group at the N terminus of Hb beta chains & C1 carboxyl group of glucose
• C2 hydroxyl of glucose allows a subsequent Amadori rearrangement to irreversibly link glucose to the protein

• alpha gene family: cluster; a1, a2
• beta gene family: cluster; embryonic & fetal

• three exons (protein coding regions) are spliced together
• removal of two introns (noncoding sequences)
• spliced mRNA codes for globin proteins

• glu 6 -> lys 6
• makes HbC migrate slower than HbA and HbS
• mild, chronic hemolytic anemia

• double mutant: one HbS beta chain gene & one HbC beta chain gene
• usually undiagnosed until infarctive crisis occurs (childbirth or surgery)
• can be fatal

• oxidation of ferrous (Fe2+) iron to ferric (3+)
• cannot bind O2, binds H2O instead
• caused by environment (drug) or inherited mutation
• leads to formation of HbM - methemoglobinopathy (BLUE PEOPLE)
• can be reduced by NADH cytochrome b5 reductase (can now bind O2)
• BINDS CYANIDE

• methemoglobin is dark in color leading to brownish blue color in skin and membranes
• blood is chocolate colored
• symptoms: anxiety, headache, dyspnea

• hereditary hemolytic diseases (common in humans)
• synthesis of defective alpha or beta chains (unbalanced hemoglobin chain synthesis)
• gene deletions, substitutions or deletion in nucleotides, defect in splicing

• decreased of absent beta chains - only two copies of beta chains (only seen after birth; shift from fetal to adult hemoglobin)
• beta thalassemia minor: one normal, one defective beta chain gene (not life threatening)
• beta thalassemia major: both genes defective; develop severe anemia by age 2; iron overload (hemosiderosis), death b/w 15-25 years

• decreased or absent alpha chain synthesis
• four copies of alpha gene --> severity of disease depends upon the number of defective genes
• 0 defective: normal
• 1 defective: silent carrier of alpha thalassemia; no symptoms
• 2 defective: alpha thalassemia trait; mild symptoms
• 3 defective: moderately severe hemolytic anemia
• 4 defective: hydrops fetalis (fetal death)

• looks at the statistical distribution of genes in a particular population
• looks at how the frequency of genes is maintained or changes
• is the basis for understanding how different disease genes are more common in different populations

• encodes a cell surface cytokine receptor which is the entry point for HIV
• a 32 bp deletion results in nonfunction protein
• homozygotes for the mutation do not have the receptor and are resistant to HIV infection - autosomal recessive
• the normal allele can be distinguishes from the 32 bp deletion using PCR

• p+q=1
• p² + 2pq + q² = 1
• p = frequency of dominant allele
• q = frequency of recessive allele
• 2pq = frequency of heterozygote

• can be used to help estimate the frequency of carriers in a population
• usually put all disease-causing alleles together (whether compound heterozygotes or homozygotes)

• for rare recessive traits, p = 1 (approximately)
• 2pq is approximately 2q
• the number of carriers in the population is much larger than the number of homozygous affected individuals

• 1 - random mating
• 2 - a large population size
• 3 - no mutations
• 4 - no new alleles are introduced/lost
• 5 - no natural selection
• if all these assumptions are correct, then the population is in genetic balance (Hardy Weinberg equilibrium)

• mutation
• gene flow
• genetic drift
• nonrandom mating
• natural selection

• human populations do NOT randomly mate
• populations are large, but often distributed in small groups
• frequently have new mutations
• human populations are highly mobile and introduce new alleles
• populations are under a variety of natural selection stressors (malaria, HIV, etc.)

• stratification: when a population has subgroups that are relatively genetically separate (Cajuns, Amish)
• assortive matings: choice of mate is made based on possessing a particular trait (deafness & achondroplasia)
• consanguinity & inbreeding: higher risk of producing homozygous offspring

• affects the genetic makeup of the population but, unlike natural selection, through an entirely random process
• mechanism of evolution that does not work to produce adaptations

• occur when a population's size is reduced for at least one generation
• genetic drift acts more quickly to reduce genetic variation in small populations

• occurs when a new colony is started by a few members of the original population
• the small population size means that the colony may have reduced genetic variation from the original population & a nonrandom sample of the genes in the original population

• any movement of genes from one population to another
• gene migration includes people moving to new cities or countries
• important source of genetic variation

• quantitative trait loci: traits whose phenotypic characteristics vary and are caused by two or more genes
• quantifiable traits (bp, height, etc) that may not be genes, but are tightly linked by SNPs
• statistical methods are used to determine the degree of association
• can be used to identify candidate genes in that region

genome wide association studies: look for variation across the entire human genome in order to identify genetic associations with observable traits

large scale variations in gene copy number are common & suspected to underlie genetic diversity & susceptibility to certain diseases

• very regular, organized linear secondary structures that is crucial to its function
• ex. collagen, elastin, keratin
• unique mechanical properties

• three alpha chains wound in a triple helix (NOT an alpha helix)
• most abundant protein in body; rigid, insoluble
• gel: extracellular matrix (ECM), vitreous humor (eye)
• parallel fibers: tendons, great strength
• cornea: stacked to allow light transmittal
• bone: angled arrangement to prevent shearin any direction

• twenty types, differ in structure & function
• three alpha chains for a triple helix held together by H bonds
• fibril forming collagen
• network forming collagen
• fibril associated collagen

• type I: high tensile strength
• type II: cartilage
• type III: less rigid
• forms regular overlapping fibril that contribute to tensile strength 

• type IV: major component of basement membranes that support adjacent cells
• type VII
• form meshlike supports

• type IX & XII: located on the surface
• link collagen fibrils together

• amino acid sequence (gly-X-Y)333
• X: usually proline
• Y: usually hydroxyproline or hydroxylysine
• triple helical - R groups on outside
• posttranslations modifications: hydroxylation of proline (prolyl hydroxylase - requires ascorbate and oxygen) & glycosylation

• made in fibroblasts, osteoblasts & chondrocytes
• enzymatically modified
• aggregate & cross link
• secreted into extracellular matrix

• numerous collagenases degrade collagen to allow remodeling of the ECM
• high collagenase expression is seen in metastatic cancer cells

• lack necessary tensile strength
• defects in synthesis, mutations in collagen genes, etc.
• Ehlers-Danlos syndrome
• Osteogenesis imperfecta

• heterogenous group of disorders arising from defects in the synthesis or mutations in collagen types I, II & V (fibrillar collagens)
• characterized by stretchy skin, loose joints & thin transparent skin

• brittle bone syndrome
• various enzyme deficiences and mutations in type I collagen
• mostly autosomal dominant; some spontaneous cases
• blue sclera, slow wound healing, bones bend easily & fracture

• type I: decreased production of alpha1 and alpha2 chains
• fractures early in infancy, sometimes predicted in utero (long bone bowing seen on ultrasound)

• type II: severe mutations involving the substitution of bulky amino acids for glycine in the proalpha1 or proalpha2 chains
• death in utero or as neonate from pulmonary hypoplasia

• precursor: tropoelastin
• lots of proline, lysine, but no hydroxylysine
• found in lungs, walls of large blood vessels, ligaments
• stretch 2-4 times normal length; recoil to original length
• interacts with fibrillin

• mutations in fibrillin
• irregular interchain crosslinks (lysine involved)
• symptoms: tall, loose jointed, heart murmur, etc.

• a ringed structure made of lysine/allysines
• joins separate elastin polypeptides
• allows stretching and bending in all directions (elasticity)

• alpha1 antiproteinase: inhibits family of proteases that degrade protein (includes trypsin)
• inhibits neutrophil elastase: degrades elastin
• protects lung alveolar elastine & prevents loss of lung elasticity
• mutation in alpha1 antitrypsin may cause inherited emphysema

• proper balance between clot formation and dissolution is required for hemostasis (maintenance of correct blood flow)
• platelets form a "plug" and send out pro-clotting signals (begins when tissue is damaged)
• a cascade of proteolytic reactions occurs that results in thrombin production and a "hard" blood clot (begins when tissue is damage)
• clotting cascade is inactivated, clot is dissolved (begins when tissue is damaged!)

• proenzyme: an inactive enzyme precursor
• enzyme is in a self-inhibitory conformation
• may be partially activated by contact (with another molecule/surface) or fully activated by proteolysis

• extrinsic: blood contacts tissue in injury; requires extravascular component
• intrinsic: initiated by damaged blood vessels endothelium - all necessary components are present in blood
• common: common to both intrinsic & extrinsic pathways
• pathways activate proteolytic zymogens in a cascade that greatly amplifies procoagulation signals upon blood vessel damage
• result in production of thrombin (serine protease) that converts fibrinogen to fibrin & "feeds back" into the coagulation cascade pathways

• I: fibrinogen
• II: prothrombin (SP)
• III: tissue factor/thrombokinase
• IV: Ca 2+
• V: proaccelerin
• VII: proconvertin (SP)
• VIII: antihemophilic factor
• IX: christmas factor (SP)
• X: stuart factor (SP)
• XI: plasma thromboplastin antecedent (SP)
• XII: hageman factor (SP)
• XIII: fibrin stabilizing factor
• prekallikrein/kallikrein (Fletcher factor - SP)
• HMWK
• vWF

• soluble plasma glycoprotein synthesized by the liver
• 340kDa hexamer consisting of 2 sets of alpha, beta & gamma chains linked to each other by disulfide bonds
• the fibrinogen alpha & beta chains have small peptides that prevent fibrinogen from forming polymers (FpA + FpB)
• thrombin cleaves the alpha & beta chains releasing FpA, FpB creating fibrin
• fibrin associates end-to-end to create fibrils & then makes lateral associations to create fibers and then a fibrin "gel"
• the transglutaminase factor XIII then creates covalent crosslinks between fibrin monomers using lysine & glutamine residues

• serine protease zymogen precursor of thrombin synthesized in liver
• glycoprotein - contains gamma carboxyglutamate residues (become vitamin K later)
• gla residues bind to Ca2+ and allow membrane association
• two cleavage events are required to generate thrombin
• thrombin's degradation of fragment 1.2 is a means of self regulation
• inhibited by antithrombin, a serpin, that plugs active site (competitive inhibitor) - strongly potentiated by binding to heparin

• serpin inhibitor of thrombin (factor IIa)
• glycoprotein produced in the liver
• plugs active site (competitive inhibitor)
• inhibits IIa, IXa, Xa, VIIa, XIa, XIIa, kallikrein
• strongly potentiated by binding to heparin

• membrane bound glycoprotein found in subendothelial tissue, activated platelets & WBCs
• bind to and partially activates factor VII

factor III (tissue factor, thrombokinase) + surrounding membrane

• plasma protein cofactor
• activated by thrombin
• degraded by active protein C: protein S
• Factor V Leiden: mutation resistance to protein C:S cleavage; activated Protein C resistance

• serine protease zymogen produced in the liver
• contains gla residues (gamma carboxyglutamate) necessary for binding calcium & membranes
• partially activated by binding to factor III (tissue factor) in context of negatively charged membrane
• fully activated by thrombin
• can auto-activate to VIIa
• inactivated by tissue pathway factor inhibitor ONLY when Xa is present
• also inactivated by antithrombin

• binds to von Willebrand factor which stabilizes VIII
• upon cleavage by thrombin, VIIIa dissociated from vWF and forms a complex with IXa
• inactivated proteolytically by protein C:S complex & IXa
• deficiency results in hemophilia A (X linked recessive)
• Rx: recombinant VIII

• serine protease zymogen synthesized in liver
• contains gla residues (gamma carboxyglutamate) for calcium & membrane binding
• converted to IXa by factor XIa and VIIa/TF
• inhibited by antithrombin
• deficiency: hemophilia B (Christmas disease - X linked recessive)

• serine protease zymogen synthesized in the liver
• contains gla residues (gamma carboxyglutamate)
• converted into active Xa by IXa/VIII (intrinsic pathway) and VIIa/TF (extrinsic pathway)
• inhibited by tissue factor pathway inhibitor (TFPI), antithrombin & protein Z dependent protease inhibitor
• deficiency is rare autosomal recessive

Xa, Va, IIa, and I

• serine protease zymogen produced in the liver
• coverted to XIa by XIIa, thrombin & autocatalysis
• binks to high molecular weight kininogen which brings XI to negative surfaces
• inhibited by protein Z dependent inhibitor but does not require protein Z (like Xa inhibition)
• deficiency: hemophilia C (autosomal recessive; esp. Ashkenazi Jews)

• serine protease zymogen synthesized in the liver
• partially activated by negatively charged surfaces
• fully activated by kallikrein & autocatalysis
• XIIa & kallikrein are important for fibrinolysis (convert plasminogen to plasmin which cleaves fibrin & vWF)
• deficiency is autosomal recessive; essentially asymptomatic

• heterotetramer composed of 2 B chains and 2 A chains
• activation by thrombin - results in dissociation of B chains (leaving catalytic A chain homodimer)
• platelets only have XIIIa (2 A chain form)

• gamma carboxyglutamate
• "two headed" glutamate
• perfect for grabbing Ca2+ ions which bind to negatively charged membrane surfaces
• necessary for proper membrane association of clotting factors
• Factors II, VII, IX, X & protein C:S complex & Protein Z

• coumadin
• inhibits the necessary reduction of vitamin K
• competitive inhibitor of VKOR (Vitamin K epoxide reductase)

• heparin: highly sulfated glycosaminoglycan; binds to & activates antithrombin; complex inhibits Xa, IIa, VIIa, XIa, XIIa, kallikrein, plasmin
• dabigatran atexilate: direct thrombin inhibitor
• edoxaban: Factor Xa inhibitor (Phase III trial in Japan)

• widespread clotting in the bloodstream
• symptoms: impaired coagulation (thrombosis then ischemia), organ failure and bleeding
• causes: bacterial infections (sepsis), major trauma, malignancies, others
• tissue factor (III) exposed to the bloodstream activates extrinsic pathway (then intrinsic)
• uses up clotting factors & platelets (thrombocytopenia) resulting in predisposition for hemorrhage -- hard to treat hemorrhages & thromboses simultaneously

• blood vessel damage exposes circulating plasma factors and platelets to collagen, tissue factor & some negative charges (damaged membranes)
• factor VII binds to tissue factor (III) and is partially activated making some Xa
• Xa finds factor V and is able to make some thrombin
• thrombin then converts VII --> VIIa, V --> Va, XI --> XIa, VIII --> VIIIa, XIII --> XIIIa
• VIIa/TF converts IX --> IXa and X -->Xa
• platelets are activated & provide negative membrane for collecting Gla-containing coagulation factors
• IXa/VIIIa and Xa/Va on membranes make LOTS of thrombin
• thrombin cleaves fibrinogen to fibrin
• XIIIa (activated by thrombin) crosslinks Lys & Gln residues in fibrin

nitric oxide (NO) & prostacyclin (PGI2) produced by the endothelium

• upon endothelial cell injury, collagen & vWF are exposed
• platelets adhere to vWF via GP Ib/X/V and collagen via GP VI
• adhesion activates platelets resulting in shape change, release of ADP, TxA2, thrombin, vWF and activation of integrins GPIIb/IIIa  (bind to fibrinogen)
• PF3 moves to outer leaflet of platelet membrane (negative surface)
• when blood vessels are injured, platelets adhere to molecules in the subendothelial tissues
• aggregate to form the primary "plug"
• platelets stimulate the local activation of other platelets and plasma coagulation factors

• glycogprotien present in plasma, endothelium, subendothelial connective tissue
• processed by ER and Golgi (furin) into very large multimers
• domains that bind to platelets (GP Ib/X/V and GP IIb/IIIa), heparin, collagen, Factor VIII
• deficiency: von Willebrand Disease; most common hereditary coagulopathy

• cyclooxygenase inhibitors: aspirin
• ADP receptor inhibitors: clopidogrel (plavix), prasugrel (effient), ticlopidine (ticlid)
• phosphodiesterase inhibitors: cilostazol (pletal)
• glycoprotein IIb/IIIa inhibitors (IV use only): abciximab (ReoPro), eptifibatide (integrillin), tirofiban (aggrastat)
• adenosine reuptake inhibitors: dipyridamole (persantine)

• heparin: IV, short acting coagulant; binds to & activates antithrombin III which inactivates IIa, IXa, Xa, XIa, XIIa and plasmin
• coumarins: vitamin K analogue; blocks the action of vitamin K (causes gamma glutamyl carboxylation of clotting factors)
• plavix: ADP receptor agonist; blocks ADP mediated platelet activation
• ReoPro: blocks GPIIb-GPIIIa which bind fibrinogen
• aspirin: cyclooxygenase inhibitor; COX required for TxA2 production (increases platelet aggregation & vasoconstriction)

• clot ultimately dissolved by plasmin - activated by a cascade
• plasminogen activator inhibitor I inhibits clot dissolution
• with time, tissue Plasminogen Activator (tPA) becomes active
• tPA and urokinase convert plasminogen --> plasmin
• plasmin converts fibrin --> fibrin degradation products
• clot dissolves; replaced by connective tissue (scar)

• recombinant tPA used to treat patients with thrombosis
• streptokinase (bacterial protein) inactive by itself; complexes with plasminogen & converts it to plasmin (then dissolves the clot)
• urokinase (uPA) can also be used

• X linked recessive: only males typically affected
• defective fibrin formation
• symptoms: joint & muscle hemorrhage, easy bruising, prolonged bleeding from wounds
• high in European royalty - inbreeding causes recessive genes to be manifested more often in homozygous state
• absence of deficiency in factor VIII (antihemophilic factor)

• X linked
• defective fibrin formation
• same symptoms as Hemophillia A
• mutations in Factor IX gene

• most common coagulopathy; autosomal chromosome 12 mutation
• mild form: deficiency in factor
• severe form: abnormal factor produced

• type I: quantitative deficiency in vWF (mild, heterozygous)
• type II: qualitative deficiency (normal levels, but poor/unusual function); may bind GP too tightly and not stabilize VIII
• type III: qualitative or quantitative homozygous - no function or no detectable vWF (severe)
• autoimmune form: body develops antibodies against vWF

• replace missing factor by injecting with factor isolated from donor blood
• problem: possibility of transmitting viruses through contaminated blood
• recombinant protein: produced in bacteria from human gene sequence; good alternative but very expensive

• bleeding time (BT)
• prothrombin time (PT)
• thrombin time (TT)
• activated partial thromboplastin time (aPTT)
• Russell's viper venom test (RVVT)
• clot stabililty
• ELISA assay

• the "instantaneous" plugging of a hold in a blood vessel wall (primary hemostasis)
• vasoconstriction plus platelet adhesion & aggregation (does not require fibrin clot formation)
• requires independent platelet count for interpretation of defects
• abnormally long in thrombocytopenia (low platelet count) & von Willebrand disease (platelet function disorders)
• normal in hemophilia

• measure the functional state of both the extrinsic and common pathway
• plasma - add thromboplastin plus Ca2+ - measure time to clot formation
• this reaction requires vitamin K, often used to monitor coumadin treatment
• also used in pre-op screening

• functional evaluation of fibrinogen concentration and polymerization
• add purified thrombin to plasma and measure time to clot formation
• heparin in the plasma of the patient prolongs TT

• measure intrinsic & common pathway components
• stage 1: citrate anticoagulated blood is preincubated with a surface activator to produce activated factor XII
• stage 2: Ca2+ is added to initiate activation of Factor XI and the rest of the intrinsic pathway
• aPTT is prolonged in hemophilia A, B (Christmas disease), and C, von Willebrand Disease & other deficiencies in the intrinsic pathway

• dilute RVVT
• venom directly activates Factor X
• test detects deficiencies in X, V, I (fibrinogen) and II - the common pathway

• put patients clotted plasma into an acidic solution
• if clot rapidly dissolves, there is a XIII deficiency

• ristocetin mimics endothelial substratum
• causeds GP Ib to bind to large multimers of vWF in plasma
• assesses vWF function by measuring binding of vWF to GP Ib/IX/V on platelets
• mix ristocetin, patient plasma & formalin fixed platelets
• measure amount of platelet aggregation (will require vWF)
• detects: Bernard-Soulier syndrome, Glanzmann's thrombasthenia

• deficiency in GP Ib/IX/V
• autosomal recessive

• autosomal recessive disease
• patient lacks GP IIb/IIIa
• platelets cannot bind to fibrinogen

• oxidoreductase: catalyzes oxidation-reduction reaction
• transferase: catalyzes transfer of C-, N-, or P-containing groups
• hydrolase: catalyzes cleavage of bonds by the addition of water
• lyase: catalyzes cleavage of C-C, C-S, and certain C-N bonds
• isomerase: catalyzes racemization of optical or geometric isomers
• ligase: catalyzes formation of bonds between carbon and O,S,N coupled to hydrolysis of high energy phosphate

• protein catalyst that increases the velocity of a reaction without being consumed in the reaction
• rarely for RNA = ribozymes

• active site: a cleft or pocket lined with amino acids that form a 3D surface that is complementary to the substrate
• catalytic efficiency: faster reactions than without enzymes
• turnover number: Kcat, the number of substrate molecules converted to product per enzyme molecule per second **
• specificity: a single molecule or a group of structurally (closely) related substrate molecules
• cofactors: non protein component needed for enzyme activity
• regulation: positively or negatively
• subcellular localization: separates reaction pathways, allows macromolecular enzyme complexes to form that favor overall pathways

the enzyme protein plus its non-protein component

enzyme protein without its non-protein component

• metal ions (Ni++)
• coenzymes - organic molecules (TPP)
• cosubstrate - organic, changed
• prosthetic groups - very tightly (usually covalently) attached to the protein

• energy barrier separating the reactants and the products
• the energy difference between that of the reactants and a high energy intermediate that occurs during the formation of product
• represents the transition state

• T*: structure that reactant must be converted into to allow product formation
• formation of the transition state requires input of free energy of activation (slow reaction if uncatalyzed)

• proportional to number of molecules in T*
• the lower the energy of activation, the faster the reaction proceeds
• enzyme catalyzed rate of reaction is increased, but the equilibrium of the reaction is not changed

• stabilization of the transition state: enzyme binds substrate in a structure that resembles T*; lowers free energy of activation & puts more molecules into T* form --> accelerates reaction rate
• catalytic groups: help T* formation; acid/base catalysis (donation & acceptance of protons) or form covalent enzyme-substrate complex

• substrate concentration: more substrate present, more product formed; can be saturated (maximal velocity)
• temperature: increased velocity with increased temp (provides energy); denatured at too high temp
• pH: each enzyme has characteristic pH optimum suited for its environment; extreme pH can denature enzyme

number of substrate molecules converted to product per unit time (umol P formed/min)

• describes how intial velocity varies with substrate concentration
• can ONLY be used with simple (hyperbolic) enzyme curves, NOT with allosteric sigmoidal curves

• hyperbolic: simple binding kinetics (Michaelis-Menten kinetics)
• sigmoidal: allosteric binding (like hemoglobin)

• the concentration of substrate is MUCH greater than the concentration of enzyme
• the reaction is at a STEADY STATE
• the initial velocity is used in the analysis of enzyme reaction (k2 is VERY SMALL and ignored)

• Km: the substrate concentration at which the initial rate is half the maximal velocity
• small Km: reflect high affinity of the enzyme for substrate (low concentration of substrate needed to half saturate enzyme)
• large Km: reflects low affinity of enzyme for substrate (high concentration of substrate needed to half-saturate the enzyme)
• reaction rate is directly proportional to the enzyme concentration at all substrate concentrations
• order of reaction can be determined

when concentration of substrate is much less than Km, the velocity of the reaction is roughly proportional to the concentration of substrate

when the concentration of substrate is much greater than Km, the velocity (reaction rate) is constant and equal to Vmax

• linear transformation of Michaelis-Menten equation
• double reciprocal plot
• x axis: plot 1/[S]
• y axis: plot 1/Vo
• x intercept: -1/Km
• y intercept: 1/Vmax

• slows down the velocity of the enzymatic reaction
• may be reversible or irreversible
• competitive and noncompetitive most common

• inhibitor binds reversibly to the same site on the enzyme that binds the substrate (active site)
• competes with substrate binding to the enzyme

• Vmax: unchanged in competitive inhibition; effect of inhibitor reversed by adding more substrate
• Km: increased; [S] must be higher to achieve same 1/2Vmax as uninhibited reaction
• Lineweaver-Burke plot: y axis intercepts are the same for the inhibited & uninhibited reaction (Vmax is unchanged)

• statin drugs (antihyperlipidemic drugs)
• inhibitors of the binding HMG CoA substrate to the rate-limiting enzyme of cholesterol biosynthesis (HMG CoA reductase)

• inhibitor & substrate bind at different sites
• the noncompetitive inhibitor can bind either to free E or to the ES complex
• ex: ferrochelatase

• Vmax: lowered (enzyme cannot reach Vmax; noncompetitive inhibition cannot be reversed by adding more substrate)
• Km: no effect
• Lineweaver-Burke plot: y intercept changes; x intercept stays the same (Km is unchanged)

• five of the 10 most commonly prescribed drugs in the US are enzyme inhibitors
• aspirin: irreversible inhibitor of cyclooxygenase used to synthesize prostaglandins
• NSAIDS: other non-steroidal anti-inflammatory drugs; reversible inhibitors of cyclooxygenase

• concentration of substrate for many enzymes is near Km
• changes in reaction rates affected by alterations in substrate levels
• allosteric binding sites: homotropic effectors & heterotropic effectors
• covalent modification: phosphorylation, dephosphorylation
• induction & repression of enzyme protein synthesis

• bind effectors, modifiers, or modulators
• binding of effectors can change binding affinity (Km), maximum enzyme activity (Vmax) or both
• negative effectors reduce enyme activity
• positive effectors increase enzyme activity

• substrate itself (binding at a different site than the active site) affects enzyme activity on other substrate molecules
• most often this is positive effector
• positive cooperativity is shown - sigmoidal curve seen for enzyme
• at high [S], allosteric effector stimulates its own metabolism to a faster rate

• the effector is different from the substrate
• VERY OFTEN the product of a reaction pathway causes feedback inhibition
• most often occurs at an early step in the reaction path involving the rate-limiting, commited step (enzyme) in the biochemical pathway

• phosphorylation: protein kinases (usually highly regulated themselves), use ATP as phosphoryl group donor
• dephosphorylation: phosphoprotein phosphatases (usually constituitive); hydrolases that remove phosphate group

• cells are damaged & lyse due to disease
• serum levels of intracellular enzymes increase above the normal range
• plasma enzyme levels in serum correlates to severity of the disease
• many enzymes are specific for a certain tissue - helps pinpoint site of disease

• enzymes that catalyze the same reaction but have different physical properties
• different organs have different isoenzymes
• can be distinguished physically by electrophoresis
• CK: creatine kinase
• LDH: lactate dehydrogenase
• (S)GOT: serum glutamate oxaloacetate transaminase
• commonly used to diagnose myocardial infarction

• different subunits (B & M chains) are mixed in different combinations; have different electrophoretic mobilities
• CK1: BB
• CK2: MB
• CK3: MM

• heart tissue - only tissue with significant amount of CK2 (MB form of CK)
• CK2 increases at 4-8 hr after chest pains; peaks at 24 hrs
• LDH peaks at 2-3 days after a myocardial infarction (better indicator after 48 hrs)
• NEVER DIAGNOSE BASED SOLELY ON SERUM ISOZYME LEVELS

• troponin T & troponin I: cardiac specific contractile proteins
• high levels of these proteins indicate more severe disease and poorer prognosis than CK2

• loss of function mutations: mutated product has a reduced or no function
• gain for function mutations: mutated product has a new and abnormal function

• replace one amino acid with another in the same gene product
• alters the protein product & its function

• replace an amino acid with a stop codon
• result in production of a truncated protein

produced by deletions, insertions or splicing errors

create or destroy splice donor or acceptor, altering RNA splicing

changes the codon but does not alter the amino acid encoded

tandem repeats that often expand in size

• enzymes involved in metabolism
• transport proteins
• cell structure
• extracellular homeostasis
• development
• growth & differentiation
• metabolism & communication

• amino acid metabolism: phenylalanine hydrogenase (PKU)
• carbohydrates: G-1-uridyl transferase (galactosemia)
• complex lipids: hexomonidase A (Tay Sachs)
• purines: HPRT (Lesch-Nyan syndrome)

• enzyme defects nearly always inherited in an autosomal recessive fashion
• the defect causes either an accumulation of the substrate or a deficiency of the product
• there can be loss of multiple enzyme activities: enzymes may share the same cofactors, a common subunit or activating protein, or may be processed by a common modifying enzymes
• phenotypic homology: diseases due to enzymes in the same area or metabolic pathway can cause very similar phenotypes

• autosomal recessive mutation in phenylalanine hydrogenase (PAH - chromosome 12)
• significant allelic heterogeneity & ethnic/geographic differences in incidence & mutation
• PAH converts phenylalanine into tyrosine
• PKU patients are unable to degrade phenylalanine --> accumulate in tissues
• hyperphenylalanemia: toxic to developing neurons; can cause mental retardation
• Rx: dietary restriction of phenylalanine intake

• congenital heart diseasae
• microcephaly (small head size)
• low birthweight
• mental retardation
• slow development
• language deficit

• autosomal recessive mutation in the gene for the alpha subunit of hexosaminidase A gene
• fatal disease: affected infants appear normal until about 6 mos; progressive neurological deterioration & eventual death around 2-4 years
• carrier testing: HexA levels in WBCs

• seizures
• noticeable behavior changes
• feeding difficulties
• cherry red spot on retina
• abnormal body tone
• loss of motor skills
• blindness
• deafness
• loss of intellectual skills

• autosomal recessive
• enzyme deficiency caused by mutation in tyrosinase
• visual acuity is not normal & cannot be corrected completely (lack of development of the fovea)
• more prone to skin cancer

• glucose 6 phosphate dehydrogenase: enzyme normally involved in producing NADPH
• X linked recessive: more common in AA males
• most common human enzyme deficiency
• results in hemolytic anemia

• hemolytic anemia in states of oxidative stress
• paleness especially in mouth (lips, tongue)
• rapid breathing or shortness of breath
• extreme tiredness
• rapid heartbeat
• jaundice
• enlarged spleen
• dark, tea-colored urine

• defect in LDL receptor protein
• autosomal dominant inheritance of mutation in gene that codes for LDL receptor
• Aa & AA develop premature heart disease
• patients have xanthomas (cholesterol deposits in skin & tendons)
• gene dosage effect: homozygotes have symptoms earlier

• cystic fibrosis: chloride transport
• Menke's/Wilson's syndrome: copper transport
• hemoglobin thalasemmia: iron transport?

• cystic fibrosis transmembrane regulator (CFTR): chloride ion channel
• mutation (deletion) in codon 508 is present on 70% of CF chromosomes
• more than 900 mutations IDed
• carrier incidence in caucasians is about 1 in 25

sinuses, lungs, skin, liver, pancreas, intestines, reproductive organs

• X linked recessive inheritance
• elevated creatine kinase levels (100X elevated)
• modest decreaase in IQ
• develop muscle weakness age 3-5; progressive muscle degeneration that begins with hip girdle muscle
• patients usually die of respiratory or cardiac failure

• the Duchenne Muscular Dystrophy gene
• largest gene known in any species
• high mutation rate
• structural protein
• roles: maintaining muscular cell membrane integrity & required for assembly of synaptic junction

• AKA "brittle bone" disease
• autosomal dominant inheritance of defect in type I collagen gene
• eight types
• severity depends on which procollagen chain is affected & the location of mutation
• mildest: type I due to decreased production
• most severe: type II due to structure defect in procollagen

the study of energy transformations that occur in biological systems

• 1: the total energy of a system & its surroundings is constant
• 2: the total entropy of a system & its surrounding always increases for a spontaneous process
• 3: as temperature of a system is decreased, entropy of the system is decreased

• the sign of deltaG predicts the direction of a reaction
• less than zero: there is a net loss of energy by the system to the surroundings; the reaction occurs spontaneously (exergonic)
• greater than zero: there is a net gain of energy by the system from its surroundings; the reaction does NOT proceed spontaneously (endergonic)
• equals zero: the reactants are in equilibrium

• is predictive ONLY under standard conditions (concentration of products and reactants at 1mol/L, pH = 7 & P = 1 atm)
• Keq = 1: standard free energy equal zero (reaction is in equilibrium)
• Keq greater than 1: standard free energy is negative (reaction will proceed A --> B; spontaneous forward)
• Keq less than 1: standard free energy is positive (reaction will proceed A <-- B; spontaneous reverse)