FOM Comp I: Biochemistry, Microbiology, Clinical Correlations, and Embryology

Sickle Cell Anemia

G6V Substitution, leads to hydrophobic patch on Hb. Unstable hemoglobin leads to red cell breakdown, anemia, capillary occlusion, and pain in the extremities

Protein Conformational Disorders

Proteins have altered confirmations resulting in cellular toxicity, functional deficiency, or dominant negative effects. Eg Alzheimer’s Disease, Parkinson’s, BSE

Marasmus

Deficient in protein and calories; no edema

Kwashiorkor

Protein deficient but enough calories

Phenylketonuria (PKU)

Cannot process Phenylalanine; Tyrosine replaces it as an essential Amino Acid

Effects of Starvation

Spike in Gluconeogenesis, Increase in ketone bodies in blood, TCA cycle intermediates cannot be made

Hb Hammersmith

F42S, breaks the hydrophobic barrier around the heme and allows water access to the pocket, leading to heme loss

Hb Savannah

G24V, leads to unstable Hemoglobin

Hb Milwaukee

V67E, stabilizes Methemoglobin (causes blue skin and anemia)

HbC disease

E6K leading to mild anemia

Scurvy

Low Vitamin C leads to low hydroxylation of proline and lysine. Poor assembly and crosslinking of collagen, leading to weak blood vessels and poor wound healing

Ehlers Danlos Syndrome (EDS)

Type 3 Collagen affected (either by mutations in genes or defective collagen processing enzymes) leading to weak bones and muscle, hyperextensible skin, hypermobile joints and skin, and easy bruising

Menkes Disease

Impaired Copper absorption. Less copper leads to lower lysyl oxidase activity (collagen processing enzyme) leading to poor collagen crosslinking. Floppy muscle, kinky hair, intellectual disability.

Osteolathyrism

Caused by toxic osteolathrogens that inhibit lysyl oxidase (collagen processing enzyme), soft deformed bones and weak muscles

Collagen Vascular Diseases

Autoimmune diseases, the body’s collagen is not recognized as native leading to immune response. Eg Ankylosing spondylitis, Dermatomyositis, Polyarteritis nodosa, Psoriatic arthritis, Rheumatoid arthritis, Scleroderma, Vasculitis

Osteogenesis Imperfecta

Mutation in Type 1 Collagen gene, causing inability of triple helix and imperfect formation of bones (aka brittle bone disease), leading to a group of genetic disorders where bones easily bend and fracture

Marfan Syndrome

Mutations in the FBN1 gene, which encodes Fibrillin-1. Clinical manifestations include elongated limbs, flexible joints, scoliosis, aortic aneurysm

Emphysema

AAT counteracts Elastase and preserve Elastin. In AAT deficient patients elastase is unopposed, causing destruction of the connective tissues of alveolar walls
-smoking could prevent binding between AAT and Elastase

Biological Markers of Liver Damage

AST and ALT

Biological Markers of Muscle Damage

Aldolase from Gluconeogenesis is high, AST and ALT, Creatine Kinase

Biological Markers of Heart Attack

Cardiac Troponin, CK-MB

Effects of Rotenone and Amytal

Inhibit Complex 1 of ETC

Effect of Antymycin A

Inhibit Complex 3 of ETC

Effects of Cyanide and Azide

Inhibit Complex 3 & 4 (Cytochrome Oxidase) of ETC

Effects of Ionophores

Collapse the proton gradient, resulting in increased cellular respiration and inhibiting ATP production

Effects of Arsenate Poisoning

Incorporated into Glyceraldehyde-3-P instead of Phosphate, eliminating substrate level phosphorylation in glycolysis. No net gain of ATP.

Effects of Fluoride

Inhibits enolase (and lactate production by bacteria)

Pyruvate Kinase Deficiency

Normally adds a Phosphate to produce ATP; RBCs that have no mitochondria (for ETC) and rely entirely on glycolysis for ATP can experience hemolytic anemia.

Lactic Acidosis

Elevated concentrations of Lactate in blood, lowering pH. Causes include failure to regenerate NAD+ from NADH

Leigh Syndrome

Mutation in Pyruvate Dehydrogenase or Pyruvate Carboxylase causing lactic acidosis

Pyruvate Dehydrogenase Complex (PDH)

Converts Pyruvate to Acetyl-CoA for biological processes

Lactate Dehydrogenase

Converts Lactate to Pyruvate for energy in the body

Berberi Disease and Wernicke-Korsakoff Syndrome

Deficient in Thiamine (Vitamin B1) which is a cofactor of PDH

Pompe Disease

Accumulation of glycogen in certain organs impairing their ability to function normally. Symptoms include excessive glycogen in lysosomes, massive cardiomegaly

von Gierke Disease

Glucose-6-Phosphatase deficiency, cannot release glucose into the blood so it accumulates in liver and kidney

Cori Disease

Deficiency in de-branching enzyme so glycogen has abnormal structure, causing fasting Hypoglycemia

McArdle Syndrome

Deficiency of Glycogen Phosphorylase particularly in skeletal muscle, therefore glycogen cannot be broken down to glucose during exercise

Fructosuria

Fructokinase deficiency

E1 Deficiency

congenital lactic acidosis occurs because pyruvate is shunted to lactic acid via LDH. X-Linked Dominant

Effects of Arsenite Poisoning

Inhibits enzymes requiring lipoic acid (including PDH, α-ketoglutarate dehydrogenase, branched-chain amino acid α–keto acid dehydrogenase) by forming stable complex with lipoic acid

Effects of Fluoroacetate

Inhibits Aconitase, a protein used for TCA Cycle

Pyruvate Carboxylase

Catalyzes the first reaction of gluconeogenesis. Activated by Acetyl-CoA (which is produced by PDH)

PDH kinase regulation of TCA Cycle

Inhibits E1, a component of PDH

PDH Phosphatase regulation of TCA Cycle

Activates E1, a component of PDH

ATP, acetyl CoA, and NADH regulation of TCA Cycle

Activates PDH kinase, which inhibits E1 (cofactor of PDH), thereby also inhibiting PDH via feedback inhibition

Pyruvate regulation of TCA Cycle

Inhibits PDH Kinase, allowing PDH to convert Pyruvate to Acetyl-CoA, thereby allowing TCA cycle to occur

Ca2+ regulation of TCA Cycle

Released in skeletal muscles during contraction, stimulates PDH and energy production by activating PDH phosphatase

Citrate, NADH, and Succinyl CoA regulation of Citrate Synthase

Inhibits Citrate Synthase via feedback inhibition

Citrate Synthase

Synthesizes Citrate from Acetyl CoA and Oxaloacetate. 1st Rate-Determining enzyme of TCA Cycle

Isocitrate Dehydrogenase

Oxidative decarboxylation reaction, yields the 1st NADH of TCA cycle and releases the 1st CO2. 2nd Rate-Determining Enzyme of TCA Cycle

Activation of Isocitrate Dehydrogenase

ADP (a low energy signal) and Ca2+ (muscle contraction)

Inhibition of Isocitrate Dehydrogenase

ATP and NADH (sufficient energy signals)

α-ketoglutarate dehydrogenase

Causes oxidative decarboxylation and produces Succinyl CoA (which contains a high energy bond), the 2nd CO2, and produce the 2nd NADH

Activation of α-ketoglutarate dehydrogenase

Ca2+ (muscle contraction)

Inhibition of α-ketoglutarate dehydrogenase

ATP, GTP, NADH, and succinyl CoA (feedback inhibition)

Function of Kinases

Adds Phosphate to Enzyme

Function of Phosphorylases

Adds a phosphate to an enzyme which INACTIVATES the enzyme

Cofactors of PDH and α-ketoglutarate dehydrogenase

thiamine, Lipoic acid, Coenzyme A (CoA), FAD, NAD

Cofactors of Pyruvate Carboxylase

Contains biotin and requires ATP and Mg2+

Effect of Increased 2,3-BPG

Stabilizes T form of Hb to decrease its O2 affinity. Right shift SpO2 Curve

Hyaline Cartilage

Type of cartilage found in long bones, epiphyseal plates, and articular surfaces of synovial joints

Fibrocartilage

Type of cartilage found in discs within joints (e.g. menisci) of knee, glenoid labrum of shoulder

Elastic cartilage

Type of cartilage that is highly flexible (e.g. auricle of ear, epiglottis)

Nonpolar, aliphatic Amino Acids

Glycine, Leucine, Alanine, Methionine, Valine, Isoleucine, Proline

Nonpolar, aromatic Amino Acids

Phenylalanine, Tryptophan

Polar, uncharged Amino Acids

Glutamine, Cysteine, Asparagine, Threonine, Tyrosine, Serine

Basic Amino Acids (positively charged)

Histidine, Arginine, Lysine

Acidic Amino Acids (negatively charged)

Aspartic acid, Glutamic acid

Essential Amino Acids

Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Alanine, Leucine, Lysine

Amino Acids with -OH (can be phosphorylated)

Serine, Threonine, Tyrosine

Underweight BMI

<18.5

Normal BMI

18.5-24.9

Overweight BMI

25-29.9

Obesity Class I BMI

30-34.9

Obesity Class II BMI

35-39.9

Extreme Obesity BMI

40 and above

Type I Collagen

Collagen found in Bone, Skin, Tendon. Defective in Osteogenesis Imperfecta

Type II Collagen

Collagen found in Cartilage

Type III Collagen

Collagen found in Reticulin (skin, blood vessels) and hollow organs

Type IV Collagen

Collagen found in Basement membrane. Defective in Alport Syndrome

Function of Thyroid Hormones

stimulates partial uncoupling of mitochondria to allow transfer of electrons to ETC

Diabetes

lack of/low sensitivity to insulin resulting in higher blood glucose (hyperglycemia) levels, lower intracellular sugar availability

Lysyl Oxidase

Cross-links staggered tropocollagen molecules into collagen fibrils through covalent lysine-hydroxylysine cross-links

Procollagen Peptidase

Removes C & N terminal extensions of procollagen to produce tropocollagen

Stickler Syndrome

group of hereditary conditions caused by mutations in the collagen genes. Characterized by distinctive facial appearance, myopia, hearing loss, joint problems

Cholestasis

Disease in which flow of bile from liver is slowed or blocked

Rickets

lack of vitamin D, calcium, or phosphate

Biological Markers of Cholestasis and Rickets

Alkaline Phosphatase

Biological Markers of Pancreas Damage

amylase

Mechanism of SDS-PAGE (E.g. Electrophoresis)

Mix SDS with proteins and heat to denature. Apply electricity. The mobility of a protein on an SDS-PAGE is proportional to its molecular mass (E.g. small travel fast, large travel slow). Use to identify protein of interest

Mechanism of Chromatography

Gel filtration column is specially coated. Protein is loaded on column. Proteins are eluted with different buffers. Larger molecules elute first, smaller molecules elute last.

Enzyme needed for Preprocollagen → Procollagen

Prolyl/Lysyl Hydroxylase, and Vitamin C as a Cofactor

Enzyme needed for Procollagen → Tropocollagen

Procollagen Peptidase

Enzyme needed for Tropocollagen → Collagen

Lysyl Oxidase, and Copper as a Cofactor

Effect of Increased Lactic Acid in tissues

Hb needs to unload O2 to Myoglobin in tissues. Right shift SpO2 Curve

Normal BP

<120 SBP and <80 DBP

Elevated BP

120-129 SBP and <80 DBP

Hypertension Stage 1

130-139 SBP or 80-89 DBP

Hypertension Stage 2

140 or higher SBP or 90 or higher DBP

Hypertensive Crisis

<180 SBP and/or <120 DBP