biochem_mod3

MADE FROM FATTY ACIDS

TAGs ARE BROKEN DOWN INTO MAGs IN SMALL INTESTINE AND FORMED INTO MICELLES

MICELLES ABSORBED BY INTESTINAL CELLS AND MAGs CONVERTED (USING LONG/VERY LONG FATTY ACID CHAINS BACK INTO TAGs

TAGs PACKED WITH OTHER LIPIDS INTO CHYLOMICRONS AND RELEASED THROUGH LYMPH INTO BLOODSTREAM

BREAKS DOWN TAGs INTO FATTY ACIDS, MAGs AND DAGs

HELPS CONVERT FAT DROPS INTO SMALLER EMULSION DROPLETS THAT HAVE HIGHER SURFACE/VOLUME RATION

Pancreatic lipase: Triacylglycerol  Monoacylglycerol + 2 Fatty acids

Chylomicrons are secreted into the lymph and eventually reached the blood, where they are attacked by lipoprotein lipase. This enzyme attacks the triacylglycerols to release fatty acids and glycerol. Fatty acids are carried by serum albumin to adipose and other tissues.

The enzyme triacylglycerol lipase (also known as hormone-sensitive lipase) converts triacylglycerols into diacylglycerols by removing a fatty acid.

Other lipases break down the diacylglycerol into glycerol and three fatty acids.

Regulation of triacylglycerol lipase: This enzyme is activated by adrenaline, glucagon, and adrenocorticotropic hormone (ACTH). The enzyme is inhibited by insulin. In activation, the lipase is phosphorylated

Rationale: Adrenaline and ACTH promote response to stress. To cope with stress we need excess energy, hence, we need to break down fatty acids. Glucagon's role is to increase glucose levels in the blood. If we break down more fatty acids for energy, we will break down less glucose and, hence, glucose levels will be elevated.

Because of their insolubility, most lipids need to be transported in the blood in a complex with particular proteins.

Free fatty acids are transported by serum albumin

TAGs from the intestine are transported on chylomicrons.

TAGs made in the liver are transported on very-low-density lipoproteins (VLDL).

Straight-chain fatty acids (saturated and unsaturated) longer than 10 carbons are transported into mitochondria for degradation.

The fatty acid is carried across the mitochondrial membrane bound to carnitine.

carnitine is a metabolite of the amino acid lysine.

Stage 1. Oxidation by Acyl CoA Dehydrogenase to Give Enoyl CoA. LCAD > 12 Cs, MCAD 6-12 Cs, SCAD 4-6 Cs

Stage 2. Hydration of the trans Double Bond by Enoyl CoA Hydratase to Give L-3-Hydroxyacyl CoA

Stage 3. Oxidation by L-3-Hydroxyacyl Dehydrogenase to Give Ketoacyl CoA. This reaction converts the hydroxyl group to a ketone

Stage 4. Cleavage by Thiolase. Product of this step is acetyl CoA. Fatty acid is now 2 carbons shorter. The cycle will continue, releasing 2 carbons per cycle until the last cycle yields two acetyl CoA molecules:

16-carbon palmitic acid MAKES 8 acetyl CoA, 7 of FADH2 and 7 of NADH.

2.5 ATP's per NADH and 1.5 ATP's per FADH2 and processing of acetyl CoA via TCA MAKES 10 ATP's per acetyl CoA

7 x 1.5 + 7 x 2.5 + 8 x 10 = 10.5 + 17.5 + 80 = 108

Recalling that we used up 2 ATP equivalents in the initial activation reaction, the net yield of ATP for the β-oxidation of one molecule of palmitate is 106 ATP's.

Compare this with glucose, where we get about 30 ATP's per glucose.

Glucose and palmitic acid have molecular weights of 180 and 256, respectively.

(106/256)/(30/180) = 0.414/0.167 = 2.48

Therefore, per unit weight, fats are more fattening than carbohydrates.

Degraded in peroxisomes

H2O2 is a by-product

Step 1: Thiolase (an isozyme of the thiolase involved in β-oxidation) turns acetyl CoA into acetoacetyl CoA

Step 2: Hydroxymethylglutaryl CoA synthase reacts acetoacetyl CoA with acetyl CoA to form 3-hydroxy-3-methylglutaryl CoA

Step 3: Hydroxymethylglutaryl CoA lyase breaks down 3-hydroxy-3-methylglutaryl CoA into acetoacetate and acetyl CoA

Step 4: 3-Hydroxybutyrate dehydrogenase converts acetoacetate into D-3-hydroxybutyrate

Acetoacetate and D-3-hydroxybutyrate can freely diffuse out of the liver mitochondria and into the blood

WHEN oxaloacetate supplies are low and yet fatty acid oxidation is proceeding rapidly.

Cause a build-up of acetyl CoA, which cannot easily be transported between tissues

Cells cope by USING ketogenesis, turns acetyl CoA into a readily water soluble and transportable form.

The four enzymes in this pathway are located in the mitochondria. The products and intermediates in ketogenesis are referred to as ketone bodies

Certain tissues, such as cardiac muscle and the renal cortex prefer to use ketone bodies as fuel instead of glucose.

Important during exercisE AND starvation when glucose is not available

brain switches over to using ketone bodes BY convertING D-3-hydroxybutyrate into acetoacetate USING 3-hydroxybutyrate dehydrogenase

In uncontrolled diabetes and in starvation, supply of glucose inside cells is exhausted.

There is little oxaloacetate with which acetyl CoA can react. As acetyl CoA builds up, ketogenesis turns the acetyl CoA into ketone bodies.

Increased concentration of the acidic ketone bodies in the blood lowers the blood pH in a condition known as ketoacidosis.

The decreased pH can cause a coma

Fatty acids synthesized in the cytosol

The pathway not just the reverse of fatty acid degradation, but there are some interesting parallels between the two pathways

Two enzymes synthesize palmitate (16-carbons) from acetyl CoA (acetyl CoA Carboxylase and Fatty Acid Synthase)

For Acetyl CoA Carboxylase, a carboxyl group is added to acetyl CoA to generate Malonyl CoA.

biotin-containing enzyme catalyzes the committed step in fatty acid biosynthesis

subject to complex regulation

• Mobilization:
• 1. Acetyl Transacylase. Transfers the acetyl group from acetyl CoA to ACYL CARRIER PROTEIN (ACP)

2. Malonyl Transacylase. Transfers the malonyl group from malonyl CoA to ACP

• Elongation:
• 3. Acyl-malonyl ACP Condensing Enzyme. Reacts a malonyl ACP with the acetyl ACP. One ACP is discarded as is a CO2; this creates a 4-carbon acetoacetyl group

4. β-Ketoacyl ACP Reductase. Uses NADPH to reduce the ketone to a hydroxyl group

5. 3-Hydroxyacyl ACP Dehydratase. Removes a water

6. Enoyl ACP Reductase. Reduces the double bond to give the 4-carbon fatty acyl butyryl ACP

The elongation process will then resume at step 3. At the end of each cycle of elongation the fatty acid is 2 carbons longer

7. Thioesterase. When the fatty acyl group is 16 carbons long, this enzyme cleaves it to generate free palmitic acid and ACP

Citrate stimulates allosterically AND INACTIVATES by phosphorylation.

Phosphorylation catalyzed by AMP-activated protein kinase (AMPK).

AMPK is activated by AMP and inhibited by ATP.

Dephosphorylated by protein phosphatase 2A, WHICH IS in turn is inhibited by phosphorylation by protein kinase A. INSULIN ACTIVATES PROTEIN PHOSPHATASE 2A

PKA is activated by adrenalin and glucagon.

Three polypeptide chains, two of which are identical to each other.

The third is a very small polypeptide called acyl carrier protein (ACP), which contains a phosphopantetheine group that is identical to the one in Coenzyme A.

The other two polypeptides have 7 different enzymatic activities. First mobilizing malonyl CoA and acetyl CoA (attaching them to ACP). Then begins a cycle of reactions in which a fatty acid grows from ACP.

At the end of each cycle the growing fatty acid is 2 carbons long. When the fatty acid has reached 16 carbons in length, it is cleaved from the ACP.

The mitochondria and the endoplasmic reticulum are the sites where we make fatty acids longer than 16 carbons

• Mitochondria
• A single cycle of four different enzymes (analogous to the ones in fatty acid degradation) uses acetyl CoA to convert palmitoyl CoA to the 18-carbon stearoyl CoA.

NADH and NADPH are used as reductants.

• 2. Endoplasmic Reticulum (general)
• A single cycle of four different enzymes uses malonyl CoA to convert palmitoyl CoA to stearoyl CoA.

NADPH is the reductant.

• 3. Endoplasmic Reticulum (brain)
• Four different enzymes similar to those in other tissues, acting in multiple cycles, use malonyl CoA to convert palmitoyl CoA to longer-chain fatty acids, up to 24 carbons long.

Patients with this disease lack peroxisomes. They are unable to metabolize, not only fatty acids, but other lipids as well (e.g. plasmalogens).

They suffer severe abnormalities of bones, cartilage, brain, liver and other organs. They generally do not survive beyond 6 months of age

Generally due to a mutation in the very-long-chain acyl CoA dehydrogenase.

Boys who have this disease are generally normal for the first 4-8 years of life. Then they exhibit neurological symptoms that gradually progress to a vegetative state.

They have an accumulation of very long chain fatty acids, particularly hexacosanoic acid (26 carbons). There is no real cure.

There is some evidence that when patients known to have the biochemical lesion but who have not yet developed neurological symptoms are treated with a mixture of glyceryl trioleate and glyceryl trierucate, development of symptoms can be slowed down.

Glyceryl trierucate is a 22-carbon fatty acid found in rapeseed oil. The mixture of these two fatty acids is named "Lorenzo's oil"

Proteolytic enzyme of the stomach, derived from the zymogen pepsinogen.

Pepsinogen molecule is secreted into the stomach AND undergoes a conformational change that causes it to digest itself. This is called auto-activation.

Going from a pH of about 7-8 TO 1-2 in the lumen of the stomach. This changes the charges of all the glutamate and aspartate residues and causes the protein to undergo a major conformational change, creating the active site.

After the conformational change, the N-terminal region masks the active site. Then the active is cleaved off the N-terminus exposing the active site and creating the pepsin molecule.

Once one molecule of pepsin is activated, it can cleave the N-terminus of other molecules of pepsinogen, thereby creating more pepsin molecules. This is called auto-catalysis.

In auto-activation, a given molecule of a protein acts on itself. In auto-catalysis, one molecule of a protein acts on another molecule of that protein.

In serine proteases (such as trypsin, chymotrypsin, elastase, and some blood coagulation and complement factors), cleavage is generally between a hydrophilic area near the N-terminus and an adjoining hydrophobic area.

The hydrophilic area acts like a "buoy" pulling the hydrophobic area toward the surface of the protein molecule.

Following cleavage, the hydrophobic area, now free of the hydrophilic "buoy", sinks inside the molecule. The newly exposed N-terminal amino group makes a salt link with the carboxyl group of an aspartate or glutamate residue in the active site.

The movement of this aspartate or glutamate residue to form the salt link exposes and creates the active site. The hydrophilic portion that is cut off during zymogen activation is referred to as the activation peptide.

In certain cases, the activation peptide has no function; in others (such as complement) it acts as a messenger.

In pepsin, the active site is created by a conformational change and then unmasked by cleavage. In the second mechanism cleavage occurs first and causes a conformational change that creates the active site

• C1 (C1q, C1r, C1s)
• C2
• C3
• C4
• C5
• C6
• C7
• C8
• C9

IgG BINDS TO ANTIGEN AND CREATES A CONFORMATIONAL CHANGE IN ITS Fc REGION WHICH INCREASES AFFINITY FOR C1q

C1q IS PART OF C1 COMPLEX (1 MOL C1q, 2 MOL C1r, 2 MOL C1s, AND 1 MOL Ca)

C1q HAS 18 SUBUNITS AND CAN BIND 6 MOLS OF IgG

1) PATHOGENIC CELL ENTERS

2) IgG BINDS TO SURFACE AT LOCATION ARBITRARILY CALLED SITE 1

3) C1 COMPLEX BINDS TO IgG, WITH C1q BINDING TO THE C_H2 DOMAIN OF IgG

4) C1q UNDERGOES CONFORMATIONAL CHANGE CAUSING IT TO CLEAVE AND ACTIVATE ITSELF. C1r IS ACTIVATED AND CLEAVES OTHER C1r, WHICH CLEAVES AND ACTIVATES C1s

5) C1s IS A PROTEOLITIC ENZYME AND CLEAVES C4 AND C2. MANY C4 AND C2 MOLs CAN BE ACTIVATED BY C1s, ILLUSTRATING AMPLIFICATION

6) C4b AND C4a FORM C4,2 COMLEX THAT BINDS TO NEW SITE 2

7) C4,2 IS A PROTEASE SPECIFIC FOR C3. IT CLEAVES INTO FRAGMENTS C3a AND C3b

• 8a) C3b BINDS TO PATHOGENIC CELL DISTINCT FROM SITE 2
• 8b) 1 C3b BINDS TO C4,2 COMPLEX TRANSFORMING IT INTO C4,2,3 COMPLEX, WHICH IS NOW SPECIFIC FOR C5

9) C4,2,3 COMPLEX CLEAVES C5 INTO C5a AND C5b

10) C5b, C6, C7, C8 AND 6 MOLECULES OF C9 FORM MAC COMPLEX AT SITE 2

11) MAC OPENS CHANNELS IN SURFACE AND LYSES CELL

ANAPHYLATOXINS WHICH INCREASE VASCULAR PERMEABILITY, CONTRACTION OF SMOOTH MUSCLE, AND RELEASE OF HISTAMINES FROM MAST CELLS.

C3a AND 5a PARTICULARLY POTENT

C5a IS CHEMOTACTIC FACTOR

C3a

PRESENT AS POST-TRANSLATIONAL MODIFICATION (LINKING CYSTEIN AND GLUTAMINE) IN CERTAIN PROTEINS (C3 & C4)

FORMATION IS SPONTANEOUS (DOES NOT REQUIRE ENZYME)

WHEN THIOESTER IS CLEAVED, ENDS BECOME HIGHLY REACTIVE TO OH-R. C3b AND C4b USE THIS TO BIND TO BACTERIA

APPEARS DURING SEVERE INFLAMMATIONS

BINDS TO CERTAIN LIPIDS AND BACTERIAL POLYSACCHARIDES

ONCE BOUND, THEN BINDS C1q CAUSING ACTIVATION OF C1 AND REST OF COMPLEMENT COMPONENTS.

CRP CAN SUBSTITUTE FOR IgG

USED AS MARKER FOR CORONARY ARTERY DISEASE

• C3
• C5
• C6
• C7
• C8
• C9
• B, D, H, I, & P

DEFENSE AGAINST PATHS FOR WHICH THE HOST MAY NOT HAVE Ab. DOES NOT NEED Ab TO BEGIN

IgM CAN ON OCCASION INITIATE THE PATHWAY

IMAGINE PATHWAY CONTINUALLY GETTING STARTED AND ITS CONTINUATION ID DEPENDENT ON PRESENCE OF PATHOGEN

1) C3 REACTS WITH WATER (THIOESTER REACTION) PRODUCING C3-H₂0

2) C3-H₂0 BINDS WITH B & D FORMING C3 CONVERTASE. D BECOMES ACTIVE PROTEOLYTIC ENZYME

3) C3 CONVERTASE CLEAVES C3 MAKING C3a AND C3b USING D. C3b CAN EITHER BIND TO PATHOGEN, TO NON-ACTIVATING SURFACE, OR TO WATER. BINDING TO PATH CONTINUES ALT PATHWAY!!!

• 4a) IF C3b BINDS TO WATER, INACTIVATED BY H & I (H ENHANCES PROTEOLYTIC ENZ I)
• 4b) IF C3b BINDS TO NON-ACTIVATING SURFACE, INACTIVATED BY H & I

5) C3b BOUND TO PATHOGEN SETS UP SITE FOR B. D JOINS AND CLEAVES/ACTIVATES B, WHICH LAUNCHES REST OF PATHWAY. Ba FROM N-TERMINUS OF B AND IS BY-PRODUCT OF ACTIVATED COMPLEX IS CHEMOTACTIC FOR NEUTROPHILS

6) Bb BINDS TO C3b FORMING C3b,Bb COMPLEX WHICH IS PROTEOLYTIC ENZYME FOR C3

7) C3b,Bb COMPLEX CLEAVES/ACTIVATES MOLECULES OF C3

8) C3b FORMED IN 7 BINDS TO NEARBY SURFACE AND MEDIATES IMMUNE ADHERENCE, OR BINDS TO C3b,Bb COMPLEX TO FORM C3b_n,Bb COMPLEX SPECIFIC FOR CLEAVING C5

9) PROPERDIN (P) ADDS TO C3bn,Bb TO FORM C3bn,P,Bb WHICH STABILIZES THE COMPLEX

10) C3bn,P,Bb CLEAVES C5

11) C5b ACTIVATES REST OF COMPLEMENT PATHWAY AS IN CLASSICAL PATHWAY

12) PATHOGENIC CELL LYSES

• 1) RAPID DECAY
• C3 & C4 HIGHLY UNSTABLE DUE TO THIOESTER BOND

• 2) ENZYMATIC INACTIVATION OF C3a, C4a, C5a, AND Ba
• REMOVAL OF THEIR C-TERMINAL ARGININES BY SERUM CARBOXYPEPTIDASE B

• 3) INHIBITION OF COMPLEMENT BY SPECIFIC PROTEIN FACTORS
• H & I INHIBIT C3b

• 4) DECAY-ACCELERATING FACTOR (DAF)
• ERYTHROCYTES AND MANY OTHER HOST CELLS IN BLOOD CONTAIN DAF WHICH ACCELERATES DESTRUCTION OF C3b BY H & I

PEOPLE WITH PAROXYSMAL NOCTURNAL HEMOGLOBINURIA OFTEN LACK DAF. URINE TURNS RED AT NIGHT DUE TO INCREASED DESTRUCTION OF ERYTHS

BEGINS WHEN BLOOD TOUCHES ABNORMAL SURFACE

TRIGGERED BY ELECTROSTATIC INTERACTIONS BETWEEN (-) SURFACE AND (+) LYSINE RESIDUES IN FXII

ENDS WHEN FX IS ACTIVATED

1) XII BINDS TO SURFACE

2) XIIa CLEAVES/ACTIVATES PREKALLIKREIN

3) KALLIKREIN CLEAVES/ACTIVATES XIIa TO FORM XIIb

4) XIIb CLEAVES AND ACTIVATES XI

5) XIa CLEAVES/ACTIVATES IX

6) IXa COMBINES WITH VIIIa, Ca, AND A MEMBRANE

7) THIS COMPLEX CLEAVES/ACTIVATES X

INITIATED BY TISSUE FACTOR (TF)

ENDS WHEN X IS ACTIVATED, WHICH IS LOCATED ON MEMBRANES OF ENDOTHELIAL CELLS.

WHEN MEMBRANES DAMAGED, TF CONFORMATIONALLY CHANGES AND ACTIVATES, BINDS TO VII

TF NOT AN ENZYME

1) TF ACTIVATED

2) TF BINDS TO VII AND PATIALLY ACTIVATES

3) VII CLEAVES/ACTIVATES X

4) Xa CLEAVES VII AND INCREASES ITS ACTIVITY

5) VIIa CLEAVES/ACTIVATES MORE X. VIIa ALSO CLEAVES/ACTIVATES IX WHICH CONNECTS INTRINSIC/EXTRINSIC PATHWAYS

1) Xa COMPLEXES WITH Va, Ca, AND A MEMBRANE

2) THIS COMPLEX CLEAVES/ACTIVATES PROTHROMBIN (II)

3) THROMBIN CLEAVES FIBRINOGEN (I) AND MAKES FIBRIN AND FIBRINOPEPTIDES A & B

4) FIBRIN AGGREGATES TO FROM SOFT CLOT

5) XIIIa CROSS-LINKS FIBRIN TO FORM HARD CLOT. XIIIa IS A TRANSGLUTAMINASE THAT CROSS-LINKS GLUTAMINE TO LYSINE

NOT AN ENZYME

ACTS TO MAKE CLEAVAGE OF THROMBIN FASTER

CLEAVED BY Xa AND THROMBIN (CLEAVAGE BY THROMBIN EXAMPLE OF FEED-FORWARD ACTIVATION)

SIMILAR TO V

CLEAVED BY IXa, Xa, AND THROMBIN

NOT AN ENZYME

ACCELERATES CLEAVAGE OF X

ZYMOGEN ACTIVATION

MADE BY CLEAVAGE OF INACTIVE PRECURSER BY THROMBIN

PRODUCT NOT PROTEOLYTIC ENZYME BUT TRANSGLUTAMINASE (CROSS-LINKING ENZYME)

1) DILUTION OF ACTIVATED COAGULATION FACTORS

• 2) REMOVAL BY LIVER CELLS OF ACTIVATED COAGULATION FACTORS
• IF PROTECTIVE OLIGOSACCHARIDE IS LOST THROUGH ACTIVATION, COAG FACTORS ARE DESTROYED THROUGH LIVER CELLS

• 3) INACTIVATION OF ACTIVATED COAG FACTORS
• a2-MACROGLOBULIN INACTIVATES SEVERAL PROTEOLYTIC ENZYMES GENERATED IN COAGULATION. ENZYME ACTS ON a2 CAUSING CONFORMATIONAL CHANGE THAT TRAPS IT. COVALENT BOND FORMED BETWEEN a2 AND EZYME (THIOESTER IN a2). ALSO a2 LOSES OLIGOSACCHARIDE AND THEN DESTROYED BY LIVER

ANTITHROMBIN III INHIBITS THROMBIN AND ALL PROTEOLYTIC ENZYMES. ENHANCED BY HEPARIN

a1-ANTITRYPSIN, TF INHIBITOR, SERPIN, AND PROTEIN Z

• 4) DESTRUCTION OF VIIIa AND Va
• ACTIVATED PROTEIN C (APC) CLEAVED BY THROMBIN (REQUIRES THROMBOMODULIN)

• 5) DISSOLUTION OF BLOOD CLOTS
• THROMBIN --> tPA --> PLASMIN = FIBRINOLYSIS = UROKINASE <-- KALLIKREIN

ALSO, PLASMINOGEN BINDS TO FIBRIN CLOT AND tPA OR UROKINASE BINDS TO FIBRIN AND CLEAVES/ACTIVATES PLASMINOGEN. PLASMIN LYSES CLOT

LIPOPROTEIN A (LpA) COMPETES WITH WITH PLASMINOGEN FOR BINDING FIBRIN (ENHANCES CLOTTING)

NEEDED TO MAKE g-CARBOXYGLUTAMATE POST-TRANSLATIONALLY

g-C IS UNUSUAL AA THAT Ca BINDS ON MEMBRANES

VII, IX, X, PROTHROMBIN, AND PROTEIN C NEED Ca FOR ACTION OR ACTIVATION

VK TARGET FOR ANTICOAG THERAPY. DICUMAROL AND WARFARIN ARE COMPETITIVE INHIBITORS OF CARBOXYLATION REACTION (RESEMBLE VK)

LARGE IMPORTANT PROTEIN IN COAGULATION

HELPS VIII AND PLATELETS INTERACT WITH EACH OTHER

FACILITATES INTERACTION BETWEEN PLATELETS AND DAMAGED ENDOTHELIAL CELLS AT WOUND SITE

MOST COMMON BLEEDING DISORDER

• POINT PUTATIONS
• 1) TRANSITION - SUBSTITUTION OF PURINE FOR PURINE OR PYRIMIDINE FOR PYRIMIDINE

2) TRANSVERSION - SUBSTITUTION OF PURINE FOR PYRIMIDINE OR PYRIMIDINE FOR PURINE

• READING FRAME SHIFTS
• 3) DELETION

4) INSERTION

1) DEAMINATION - A-->HX, G-->X, X-->U, CAUSES DIFFERENT BASE PAIRING PROPERTIES

• 2) COVALENT MODIFICATION
• ALKYLATION - ETHYLENE OXIDE AND BENZO MODIFY GUANINE

• 3) CROSS LINKING
• PSORALIN DERIVATIVES ACIVATED BY UV LIGHT
• MITOMYCIN C AND CISPLATIN AS CHEMOTHERAPY

• 4) RADIATION DAMAGE
• DNA FRAGMENTATION
• THYMIDINE DIMERIZATION

SILENT MUTATIONS - SUBSTITUTION, USUALLY IN WOBBLE ZONE RESULTING IN SAME AA

MISSENSE MUTATION - SUBSTITUTION OF DIFFERENT AA

NONSENSE MUTATION - STOP CODON

SUBSTITUTION CAUSES HEMI-METHYLATION

1) FINDING MIS-MATCH - LOOK FOR BULGES CAUSED BY MIS-MATCH

2) REMOVAL OF MIS-MATCH - METHYLATION ON PARENT GROUP DIRECTS EXPNUCLEASE

3) REPAIR - DNA POL B AND DNA LIGASE

UV LIGHT CAUSES COVALENT LINKING OF ADJACENT THYMINE BASES FORMING DIMERS WHICH INHIBIT REPLICATION AND TRANSCRIPTION

DNA PHOTOLYASE BREAKS LINKAGE

NUCLEOTIDE EXCISION REPAIR SCANS FOR BULKY DIMERS, NEW DNA SEG SYNTHED BY DNA POL I, THEN DNA LIGASE

REPAIRS MANY DIFFERENT MUTATIONS INCLUDING DEAMINATED BASES, OXIDIZED BASES, AND AP SITES

1) FINDING DAMAGE - GLYCOSYLASE CLEAVES BOND BETWEEN BASE AND SUGAR

2) REMOVAL - BASE REMOVED, THEN BACKBONE BY AP ENDONUCLEASE AND SUGAR REMOVED BY AP LYASE

3) REPAIR - DNA POL AND LIGASE

MUATION IN GENES OF NUCLEOTIDE EXCISION REPAIR PATHWAY

• SYMPTOMS:
• SENSITIVITY TO UV LIGHT, SUNBURN, ULTRA-DRY SKIN, BLISTERS, MULTIPLE SKIN TUMORS

• CAUSE:
• UV CAUSES THYMINE DIMERS WHICH ARE NOT REPAIRED
• DAMAGE PERSISTS LEADING TO MUTATIONS
• CARCINOGENESIS

• TREATMENT:
• AVOID UV, FREQUENT SKIN/EYE EXAMS, PROMPT REMOVAL OF TUMORS

AKA LYNCH SYNDROME

DEFICIENCY IN PROTEINS AND ENZYMES OF METHYL-DIRECTED MIS-MATCH REPAIR SYSTEM

• SYMPTOMS:
• INCREASED RISK COLON CANCER (80%) AND OTHER CANCERS

• CAUSES:
• DEFECT IN MIS-MATCH REPAIR SYSTEM DUE TO MUTATION IN GENES (hMSH2, hMLH)
• UN-REPAIRED MUTATIONS
• UNRESTRAINED CELL GROWTH

• TREATMENT:
• TARGETED CHEMO

ATAXIA-TELANGIECTASIA AND BLOOM'S SYMDROME

• SYMPTOMS:
• LOW WBC, RBC, PLATELETS, INCREASED GENOMIC INSTABILITY AND RISK FOR LEUKEMIA/LYMPHOMAS/CANCERS/CHROMO TRANSLOCATIONS AND RECOMBINATIONS

• CAUSES:
• ATAXIA-TELAGIECTASIA - DEFECT IN ENZYMES THAT REPAIR DOUBLE STRANDED DNA BREAKS (PHOSPHODIESTER)

BLOOM'S - DEFECT IN DNA LIGASE

• TREATMENT:
• AVOID INONIZING RADIATION, REGULAR CHECKUPS FOR TUMORS, ERYTHROPOIETIN, BONE MARROW TRANSPLANT

HEREDITARY AND AFFECTS PRODUCT WHICH PARTICIPATES IN DNA REPAIR

MUTATION FOUND IN THIS GENE INCLUDE ALTERED SPLICE SITE, NONSENSE AND FRAMESHIFT MUTATIONS

CAUSED BY MUTATION IN PROMOTER REGION

TRANSLOCATION BETWEEN 8 AND 14 CAUSES DEREGULATION OF C-MYC PROTEIN AND OVEREXPRESSION LEADING TO UNRESTRAINED CELL DIVISION

TERTIARY STRUCTURE MADE OF 8 ALPHA HELICES

WIDE VARIANCE IN GLOBIN SEQUENCES, BUT CONSERVED REGIONS (HYDROPHOBIC) ALLOWS FOR FOLDING INTO IDENTICAL STRUCTURE

HIS F8, ASP FG1, TYR HC2, AND HIS HC3 IMPORTANT FOR Hb BINDING TO 02

COMPOSED OF ORGANIC AROMATIC RING STRUCTURE CALLED PROTOPORPHYRIN (Fe-PROTO WHEN BOUND TO IRON).

PORPHYRIN RING COMPOSED OF 4 PYROLE RINGS BRIDGED BY METHINE BRIDGES. ATTACHED TO PYROLE RINGS ARE 2 PROPIONATE GROUPS, 4 METHYL GROUPS, AND 2 VINYL GROUPS

• STABILIZE HEME WITH Hb:
• 1) COVALENTLY LINKED Fe VIA PROXIMAL HIS F8

2) (+) RESIDUES IN POCKET STABILIZE (-) PROPIONIC GROUPS

3) HEME TIGHTLY PACKED IN HYDROPHOBIC BINDING POCKETS THAT A) CREATE VAN DER WAALS FORCES B) PREVENTS H20 EXPOSURE AND C) PREVENTS Fe(2+) OXIDATION TO Fe(3+)

• 6 LIGANDS CAN BE BOUND TO Fe(2+):
• 1-4 PYROLE RING NITROGENS
• 5TH PROXIMAL HIS F8
• 6TH 02, CO, NO, AND H2S

Hb WITH ONLY 5 LIGANDS CALLED DEOXYHEMOGLOBIN & 02 AS 6TH CALLED OXYHEMEOGLOBIN

02 BINDS CAUSING TRANSFER OF ELECTRONS FROM Fe AND RESONANCE STRUCTURE Fe2+/O2 AND Fe3+/O2-

DISTAL HIS E7 STABILIZES

Hb WITH Fe3+ (METHEMOGLOBIN) DOES NOT BIND O2

SIMILAR TO Mb, BUT Hb FUNCTIONS AS TETRAMER AND POSSESSES A HYDROPHOBIC PATCH (ABSENT IN Mb) TO MEDIATE A QUARTERNARY STRUCTURE.

FUNC TETRAMER COMPOSED OF PAIR OF ab DIMERS, OR DIMER OF DIMERS

• 1) FIXED INTERFACE BETWEEN a1 AND b1 & a2 AND b2
• 2) VARIABLE INTERFACE BETWEEN a1 AND b2 & a2 AND b1. LEADS TO CONFORMATIONAL CHANCE UPON 02 BINDING

Hb IS ALLOSTERIC AND BINDING OF O2 CHANGES a1b1 RELATIVE TO a2b2 (R STATE CALLED OXYHEMOGLOBIN

DURING T STATE, 2,3-BPG CAN BIND AND ACT AS NEGATIVE MODULATOR OF Hb

HIS F8, ASP FG1, TYR HC2, HIS HC3 CLOSE TOGETHER IN TERTIARY STRUCTURE AND INDUCE CONFORMATIONAL CHANCE DURING 02 BINDING

6 DIFFERENT CHAINS - b,g,d,&e ON CHROM 11 AND z,a ON 16

a,b, AND g HAVE 2 TYPES

VARIOUS COMBINATIONS OF CHAINS CREATE DIFFERENT FORMS OF Hb, BUT ONLY PRODUCTS ON SAME GENE ARE INTERCHANGEABLE

DIFFERENT EXPRESSION OF THESE CHAINS DURING DEVELOPMENT ALLOWS FOR VARYING 02 LEVELS. PREDOMINANT ADULT FORM IS HbA CONSISTING OF 2 a AND 2 b CHAINS

ASP FG1, TYR HC2, AND HIS HC3 ALL CONSERVED AMONG b ISOFORMS

• THALASEMIA CAUSED BY LACK OF EITHER a OR b CHAINS
• a-THAL LACKS a CHAIN, 4 b CHAINS CANNOT EFFICIENTLY RELEASE 02
• b-THAL LACKS b CHAIN, a CHAINS BY THEMSELVES ARE NOT SOLUABLE AND ARE NONFUNCTIONAL

SINGLE GLU6-->VAL6 MUTATION AT POSITION A3 ON SURFACE OF b-SUBUNIT

DECREASED SOLUBILITY esp DEOXY FORM

HYDROPHOBIC PATCH ON SURFACE OF T-STATE (DEOXY) b-SUBUNIT CAUSES ASSOCIATION WITH HYDROPHOBIC PATCH MADE BY PHE85 AND LEU88 ON OTHER b-SUB.

EFFECTS NOT SEEN IN R-STATE AS PHE85 AND LEU88 ARE BURIED

HYDROPHOBIC INTERACTIONS LEAD TO FIBERS WHICH CHANGE RBC SHAPE

HbS CELLS DO NOT STAY IN CIRCULATION AS LONG, CAUSING ANEMIA

OTHER Hb MUTATION METHEMOGLOBIN REFERS TO ANY MUTANT Hb THAT CAUSES OXIDATION OF Fe2+ TO Fe3+

CHANGE FROM T TO R STATE INVOLVES a1b2 AND a2b1 INTERACTION

T STATE STABILIZED BY APOLAR AND IONIC INTERACTIONS LOCATED MOSTLY? ON b-SUBUNIT

HIS F8 - PROXIMAL HIS BOUND TO Fe2+ IN BOTH T/R STATES

ASP FG1 - FORMS IONIC BOND WITHIN b-SUB WITH FULLY PROTONATED HIS HC3 SIDE CHAIN

TYR HC2 - SIDE CHAIN HYDROXYL GROUP FORMS HYDROGEN BOND TO BACKBONE CARBONYL OF VAL FG5

HIS HC3 - SIDE CHAIN FORMS IONIC BOND WITHIN b-SUB WITH ASP FG1. REQUIRES FULLY PROTONATED HIS. ITS TERMINAL COO- PARTICIPATES IN IONIC BOND BETWEEN SUBUNITS

REGULATION OF Hb O2 BINDING BY pH AND CO2.

OTHER THAN COOPERATIVITY, BOHR EFFECT IS MOST IMPORTANT FACTOR IN DETERMINING THE PERCENT OF O2 BOUND IN THE LUNGS THAT IS DELIVERED TO TISSUES

pH DECREASE CAUSES O2 AFFINITY DECREASE

CO2 INCREASE CAUSES O2 AFFINITY DECREASE

Mb NOT AFFECTED BY pH

HIS HC3 - TO UNLOAD O2 (R TO T STATE), MUST BE PROTONATED (LOW pH HELPS), THEN IONIC BOND FORMED WITH ASP FG1 WITHIN b-SUB.

• DIRECT ROLE (10-14% OF CO2 TRANSPORT)
• INVOLVES N-TERMINUS OF EACH OF 4 SUBUNITS.

EACH N-TER FORMS COVALENT CARBAMATE OR CARBAMINO COMPOUND WITH CO2 WHICH FAVORS O2 RELEASE IN 2 WAYS.

1) RELEASES PROTONS WITH REDUCES pH AND FAVORS T STATE AND 02 RELEASE

2) (-) CARBAMATE USES SALT BRIDGE INTERACTIONS THAT STABILIZE THE T STATE

• INDIRECT ROLE
• CO2 IN TISSUES DIFFUSES INTO RBCs AND REACTS WITH H2O FORMING CARBONIC ACID (H2CO3)

10^6 - 10^7 TIMES FASTER WITH CARBONIC ANHYDRASE

H2CO3 SPONT BREAKS DOWN TO H+ AND HCO3- (BICARB). H+ RELEASE STABILIZES T STATE

HCO3- LEAVES RBC THROUGH SPECIFIC MEM TRANS PROTEIN IN EXCHANGE FOR Cl- IN PLASMA

ALLOSTERIC MODULATOR OF Hb, ONE CAN BIND PER Hb

SYNTHED IN RBCs FROM GLUCOSE

(-) 2,3-BPG BINDS IN (+) POCKET BETWEEN b-SUBUNITS ONLY IN T STATE

MORE T STATE Hb CAUSES MORE UNLOADING OF 02 IN TISSUES

AFFINITY FOR CO IS 200 TIMES GREATER THAN 02

BINDING CAUSES LEFTWARD SHIFT IN OXYHEME DISSOCIATION CURVE, IMPEDING O2 DELIVERY TO TISSUES