Tips Chapter 12- biochemistry Carbohydrate biochemistry Catabolism- breaking down of molecules- it is anerobic and requires energy- examples are glycoylsis when glucose or pyruvate from glycolysis is converted to carbon dioxide and water Annabolism- formation of molecules- it doesn’t require energy for example formation of the porphyrin ring in heme- Fermentation is a reaction in which ethanol or lactate are fromed from glucose. It is anaerobic Carboydrate metabolism include- glycogenesis, glycogenolysis, gylcolysis, glucogenesis. Glycogenesis- formation of glycogen Glycolysis- break down of glucose Glucogenesois- formation of glucose Glycogenolysis – break down of glycogen In anaerobic conditions glycolysis occurs in cells without mitochondria- and glucose is converted to lactic acid Citric acid cycle is the krebs cycle and is break down or synthetic purposes – occurs in the mitochondria In aerobic conditions = pyruvate from glycolysis enters the krebs cycle and then it is oxidized to water and carbon dioxide – if there is not enough 02 pyruvate is converted to lactate Protein biochemistry Amino acids are building blocks of proteins. Proteins are formed from a polymerization reaction between two amino acids and cause a bonding (peptide bond) Essential amino acids are those that can not be synthesized in the body and need to be gotten from the diet- (PVT TIMHALL) Essential Aminoacds Phenylalanine Valine Trypthophan Theorine
Transcript
Tips
Chapter 12- biochemistry
Carbohydrate biochemistry
Catabolism- breaking down of molecules- it is anerobic and requires energy- examples are glycoylsis when glucose or pyruvate from glycolysis is converted to carbon dioxide and water
Annabolism- formation of molecules- it doesn’t require energy for example formation of the porphyrin ring in heme-
Fermentation is a reaction in which ethanol or lactate are fromed from glucose. It is anaerobic Carboydrate metabolism include- glycogenesis, glycogenolysis, gylcolysis, glucogenesis. Glycogenesis- formation of glycogen Glycolysis- break down of glucose Glucogenesois- formation of glucose Glycogenolysis – break down of glycogen In anaerobic conditions glycolysis occurs in cells without mitochondria- and glucose is converted
to lactic acid Citric acid cycle is the krebs cycle and is break down or synthetic purposes – occurs in the
mitochondria In aerobic conditions = pyruvate from glycolysis enters the krebs cycle and then it is oxidized to
water and carbon dioxide – if there is not enough 02 pyruvate is converted to lactate
Protein biochemistry
Amino acids are building blocks of proteins. Proteins are formed from a polymerization reaction between two amino acids and cause a
bonding (peptide bond) Essential amino acids are those that can not be synthesized in the body and need to be
gotten from the diet- (PVT TIMHALL) Essential Aminoacds Phenylalanine Valine Trypthophan Theorine Isoleucine Methionine Histidine (infants) Argenine (infants) Leucine Lysine
Amino acid derivatives
PhenylalanineTyrosine dopadopamine norepherine ephedrineEnzymes-> Tyrosine hydroxylase dopa decarboxylasedopamine b hydorxylase phenlethanolamine n methyl transferase
Amino acids- acidic side chain- aspartic acid and glutamic acidAmino Acids –basic side chain- argine. Lysine, histadineAmino Acids- Polar and non ionic- Glycine, serine cystineAmino Acids non polar and hydrophobic- Alanine, Valine, Leucine, Methionine, Trypthophan, Phenylamine, Leucine, Isoleucin
Amino acids are zwitterions- this means that they have no net charge as they are made up of +ve and –Ve ions. 50% is dissociated and they have 2 titration curves. Isoelectric point (pl) is the point in which there is no net charge
pH>pl (-ve charge)PH<pl (+ve charge)
There are four structures-primary structure: sequence of amino acids- location of disulfide bondsSecondary structure- arrangement of proteins in an alpha helix or beta sheathTertirary- 3d structureQuatanery- arrangement of individual subunit chains into a complex molecue
Simple proteins- are naturally occurring proteins and hydrolysis yields only alpha amino acds
eg albumin, prolamine glutelinConjugated proteins- classified on the nature of their prosthetic groups- Derived proteins- are formed from primary or conjucated proteins by the actions of an acid- alkali- heat –water-alcohol or an enzyme. They differ in chemical and physical properties of the primary or secondary derived protein.
Protein DenaturationWhen the structure of the protein is unfolded and the structure gets disorganized due to the base pairs being broken. Proteins not denatured by hydrolysis but denatured by heat, ph, alcohol or enzymes. The process is usually irreversaible
Globular and Fibrous proteinsGlobular proteins- Heme protens are specialized proteins- and they contain tightly bound prosthetic groups- Haemoglobin and myoglobin are the most common heme proteins in humans. They bind to oxygen reversaibly and they have a high affinity to carbon monoxide
Haemoglobin- is a complex ring- of porphyrin and of ferrous ion (fe2+) It transports oxygen in the blood- and CO and CO2 bind reversailby with haemoglobin
Myoglobin- is a complex of prorpyrin ring and Fe2+- transports oxygen in the tissues and the muscles and skeletal muscles
Hemoglobinopathies- eg for thalsemia and for sickle cell anemia
4 pyrol rings make this porphyrin ring in Haemoblobin and myoglobin
Methamoglobin (fe3+) can not bind to oxygen and is converted to haemoglobin by methamoglobin reductase.
Fats and lipids
In fatty acid synthesis- the end product is Palmitate It is associated with Hexose monophosphate shunt,
Lipids are divded into 5 classes due to their structure
Glycolipids-known as cerbrosides-Isolated from the brain-in hydrolysis they yield fatty acid, galactose and sphingosine-Known as galactolipids due to presence of galactose- such as phrenosin and kerasin
- Sphingolipids- formed from palmitoyl CoA and serine- Sphingosine forms a ceramic backbone
when joined to fatty acids- Sphingosine + (sugars, choline phosphate, sialic acid)= cerborsides or shingomyelin found in nerve tissues and membrane.
Phospholipids- known as phosphatides- they are esters that consist of fatty acid and phosphoric acid eg lethicin- form part of membranes
Sterols (steroids)the sterols are alcohols and structurally related to steroidsThey have 3 cyclohexane ring and 1 cyclopentane ringThe steroids are converted to compounds such as bile, vitamin D and are not broken down completely
WaxesHigh molecular weight estersMade up of monohydric alcohol and fatty acids eg spermaceti
Fixed oils and fats- Esters of glycerol and fatty acids fixed oil solid at room temperature is called fat
Essential Fatty acids-Linoleic acid, arachiondinc acid, and these are broken down by acetyl co a and enter the krebs cycle- very rapid break down causes ketoacidosis in diabetes
Fatty acid synthesis is cytosolic and the end product is palamitic acid. Acetly co A is the substrate-
Cholesterol synthesis- the RLS is 3 hydroxy- 3 methylglutaryl co A reductaseAcetyl co A 3 hydoxy 3 melthyl glutraly co A HMG Co A - melvanonatemelvanoate isoprene6 xIsoprene squaleneSqualene lanosterolLanosterol cholesterol
Iron-most abundant metal in the body-microcytic/hyopchonic anemia is deficiency-Hemochromatosis- in high doses
ZincChildren- poor growthAdults – sexual defiecincy
Selinium- Deficincy causes cardiomyopathy
Chromium- impaired glucose tolerance
Molybendum- present in xanthine oxidase – needed to convert purine to uric acid
Iodine- deficiency can cause goiter disease (diffuse toxic goiture , toxic non glodular goiter)
TIPS
Nitric oxide is derived from arginine - Arginine also gives creatinine and urea
Serotonin is produced by tryptophanTryptohan- 5-hydoxy trypophan—5 hydroxy triptamine (serotonin)
Phenylketanuria- is excessive phenylalanine in the urine
Carbon monoxide has affinity Haemoglobin, myoglobin and cytochrome oxidase
Carboxyhaemoglobin- Carbon monoxide and oxy haemoglyobin
Iron in haemoglobin is in the ferrous state
Rate limiting step in cholesterol synthesis is HMG CO A reductase
Essential fatty acids- lineloic and linelonic (omega 3 and omega 6)
Eiconosaids are prostaglanids
Basic amino acid is arginine – also is histamine and lycine
Amino acid with a negative and positive charge- zwitter ion
They have 2 tituration curves
Ph>pl - -ve charge
Ph <pl- positive charge
Energy stored in the body in glycogen
Starch made up of glucose
Leithicins are phospholipids
Sphingolipids contain sphinogsne and are glycolipids
End product of anaerobic glycoyisi- lactate – lactic acid
End product of aerobic glycosis is pyruvic acid
Krebs cycle in the mitochondria
Gylcolysis occurs in the cycoplasm
End product or purine is uric acid
Interstitial fluid surrounds the cells – so the ion that is most extracellular is sodium, calcium and chloride- if inside the cell most abundant is potassium, magnesium and phosphate
Lineloic acid (omega 6-) above is lineloic acid as the c=c is on 6 carbon atom! Linolic acid (omega 3)
13- Clinical Biochemistry
Renal Function test- Crcl and BUN(blood urea nitrogen) Liver function test- LDH, AST, ALT, ALP Cardiac enzymes- TROPIONINS, CREATINE KINASE Urine analysis- KETONE BODIES, PH , SPECIFIC GRAVITY Blood works- CBC, Anticoagulants- INR- WARFARIN (2-3 INR), HEPARIN (APTT), LMWH Thyroid test: SERUM TSH (0.5-5MU/L) TT4, FT4, TT3, FT3 Blood urea nitrogen is an end product of protein metabolism- it is produced In the liver and
excreted by the kidneys- in normal conditions the urea clearance is 60% GFR. BUN increase indicates renal disease.
Normal values for BUN- 8mg/dL to 18mg/dL (3 to 6.5mmol/L) the concentration of the BUN reflects renal function- because the urea nitrogen in the blood is filtered completely at the glomeruli of the kidney. Then it is absorbed and tubuar secreted within the nephron.
Increase in BUN indicated acute renal failure. The BUN decrease may indicate a terminal liver disease- as the liver only produces BUN. Increase in BUN is due to azetomia.
Serum creatinine- the creatinine is a metabolic product of muscle creatine phosphate- it is a more sensitive indicator for renal damage than BUN indicators.
Normal values are 50-120mmol/l or 0.6-1.2mg/dl Serum creatinine will double by 50% with decrease in GFR. A decrease in GFR leads to an increase in CrCl so renal failure is indicated Serum creatinine decreases in the elderly Crcl is the rate at which creatinine is removed from the blood by the kidney. Normal is 80-120
and if and if its less than 50- it indicates renal disease
Liver function test- LDH- ALP- AST- ALTLDH- lactate dehydrogenase- LDH1 and LDH2- heartLDH 3 –lungsLDH4 and LDH5 – liver and skeletal muscle
ALP- alkaline phosphate
AST- Aspartate aminotransferase
ALT Alanine aminotransferase
LDH- this is a glycocyitc enzyme – catalyeses interconversion of lactate and pyruvate in most tissues. LDH present in high concentration in the liver, heart, kidney, lung and skeletal muscles- LDH is quickly liberated by the liver when diagnosed by trauma, infection or ischemia. So it is useful for MI, hepatic disease and Lung disease
ALP- Alkaline phosphate- produced from the liver and the bones – sensitive to partial to moderate bile obstruction
AST- Aspartate aminotransferase- also known as SGPT- found in the heart, liver tissues, skeletal muscles and renal tissues. ALT sensitive to cell damage and less sensitive than AST.
Cardiac Enzymes Cardiac Troponins (Tn)
Troponin C T and I are compex proteins that mediate the calcium mediated interactions of actin and myosinTroponin T is in cardiac and skeletal musclesTroponin I is only in cardiac muscleTroponin C is present in two isoforms in cardiac and skeletal muscleTroponin T and I are more careful indicators in myocardial injuryThey are used to assist in the diagnosis of acute MI
Troponin is a primary diagnostic test for MI
Serum bilirubin (bile)
Breakdown product of rbc and is formed in the reticulocytes and then transported into the bloodBile is bound to serum albuminWhen bilirubin arrives in the liver at the sinusoidal surface of the liver cells the free fraction is rapidly taken up by the liver and converted to bilirubin diglucorinde and monoglucorinide (conjugated bilirubin)- This is then released into the intestine.
Most is destroyed in the freaces but some is absorbed in the blood and the liver.
Increase of bilirubin indicates jaundice.
Causes of increased bilirubin :-increase hemolysis – urine colour not changed-biliary obstruction- bile in urine and kidney stones and dark urine, chlorpromazine gives intra hepatic cholestatsis-liver cell necrosis- viral hepatitis- dark urine colour and bile in the urine
Serum proteins (blood proteins)These are albumins and globulins (alpha beta and gamma)Albumin is the major glycoprotein in the blood- it binds to acidic drugsit is produced by the liverlevels are decreased in liver disease eAlbumin contributes of 80% colloidal osmotic pressure and hence hypoalbumineia is associated with edema and ECF.
Hypoalbumineadecrease in essential amino acids due to malnutrition can lead to hypoalbumineaIt can be lost directy from the blood because of haemorrge and burns
HyperalbuminemiaIncrease in this can cause shock or volume depletion
They are the same as Igopposite effect to albuminBind to basic drugs
Urinalysisprovides basic information regarding renal infection and function and UTI
Normal urine- clear, pale yellow or golden yellow Red- usually indicates blood in the urine- or can be drugs such as -phenolphtalein- laxative Brownish yellow- bile- jaundice Orange red- rifampicin Dark urine- metrondiazole and metformine Blue urine- triamterine Pyuria and bacteruia are UTI and are normally symptomless.
Drugs that discolour urine Rifampicin- red/orange and alos body fluids Metronidazole (dark) Tetracycline Riboflavin Pyrinzinamide Trimaterin Nitrofuration Phenolphatin Pyrivium pamoate
Specific gravity increase- indicated excessive blood sugar or protein in the urinedecreased SG indicates – diabetes insipidusFixed SG- kidney loses ability to dilute or concentrate the urine
Protein in the urine –proteinurea- can be caused by UTI, renal infection, venous congestion
Albuminurea- indicates glomerular permeabilitymicroalbimurea- - albumin the the urine that is higher than normal but lower than the set standards- sign of renal nephritis
Glycosuria- indicates diabetes
Ketones
They do NOT normally appear in the urine- and if there are no glucose stores then the fat stores start to metabolise to form ketones.
Ketonuria is uncontrolled DM or starvation or zero or low carbohydrate diets Three types of ketone bodies:
Urine Ph- 4.5-9Specific gravity- 1.010-1.025Protein levels -50-80mgGlucose levels 180Ketone – do not appear in urine
Common serum enzymesCK or CPK is found in the heart and skeletal muscleCK transfers the high energy phosphate group in tissues that use a lot of energyTotal CK- increases with excersise and IM injections of drugs irritating to tissues like diazepam
Ck isoenzyme-Deep IM jnection can increase CK levelscan use to diagnose MI or skeletal muscle damage
-CK-MM in skeletal muscleCK-BB- brain tissueCK MB – in the heart for MI
Blood workCBCHaemoglobinHct or PCV- this is the % of the RBC per volume of bloodWBC
RBCMCHCPlatelet count, reticulocyte count and LDC do not usually need to be included in a CBC
Hct- this sit he percentage of the RBC per the volume of blood. Decrease in HCt is results from anaemia or bleeding or bone marrow depression. Chronic anaemia or hemolysis
-Bacterial infections indicate increase in neutrophil and drcrease in lymphocytes-Viral infection increase lymphocytesAllergic reaction- increase basophils (asthma)COPD- neutrophils increaseAIDS- T cell decrease (lymphocytes decrease)TB- increase monocytes
Warfarin and anticoagulants
Warfarin Heparin LMWHOral Iv or SC ScINR and PT apTT Not monitored due to
predictable reactions but monitor rash and bleeding and heparin assay
Normal INR 2-3 Heparin- apTT, heparin assay and PT
PT- prothrombin is syntheisied in the liver and then is converted into thrombin during the blood clotting process. -Thrombin is critical in the homeostatic process because it creates the fibrin monomers that
form the mesh over the wound and activates the platelets-Clotting time is measured-PT- measures 2,7,9,10 factors-Normal value is 10-13 seconds
Increase in PT (INR)can occur due to inadequate vitamin K in the diet or drugs that incrase PT- warfarin, heparin, LMWH, high dose of salicycates, and antibiotics.Higher the INR- more bleeding- thinner blood
Decrase in PT (INR)due to increase in vitamin K- vegetables and supplements and can cause an increase in blood clots
IF not bleeding and increase in INR- stop warfarin
aPTTthis measures the intrinsic clotting system which depends on the facors 2 7 9 10measures the other clotting factors- 8,9,10,12,13monitored for heparin therapynormal values are 21-45 seconds
Increase in aPTT-liver dysfunction-inadequate vitamin K intake-poor or inadequate nutrition-increase in aPTT increases the risk of bleeding
INR>3- overdose of blood thinners – warfarin, NSAIDSINR<2 oral contraceptives , vitamin K
Normal lipoprotein level-Low density- (LDL) <2.2-TCG<3.6-HDL >0.9-C.HDL – 5mmol/L
Thyroid function tests (serum)
Normal hypothyroidism hyperthryroidsm
Serum TSH 0.5-5 >5 <0.5Serum TSH elevated Serum TSH, Free T4 and T3
Thyroid disease test free T4 and serum TSH
Free T3 and T4Replacement therapy for hypothyroidism is serum TSH, Free thyroxin index, resin TII uptake (Rt3U) and TT4
Free T3 and T4
FT4 is the mist reliable test for hyopthyroidsm and hyperthyroidism in contrast to:FT3 is expensiveTotal tt3 and tt4TT3 and TT4 measure free and bound total serum t3 and t4TT3 is useful in Graves disease TT3- not good for hypothyroidsm
DehydrationBUN normal in mildModerate increase BUNSever increase BUN, increase Hb and low sucrose
TIPS
Normal K level range is 3.5-5mmol/L Precursor of plasma cells B lymphocytes Leukopenia- reduced lycocytes Normal CrCL- 80-120ml/min Bilirubin is icnrased in jaundice and AST and ALT – AST>ALT and AST more sensitive Alcholic hepitisi- AST >ALT (both elevated) INR is normal test for warfarin INR in warfarin patient should be between 2-3 LMWH- not monitored- monitor for rash bleeding and heparin assay INR >5 bleeding talk to dr stop warfarin aptT and PTt is heparin in MB- CK MB and LDH and Ti Troponin I is elevated after an MI Calcitionin opposes action of parathyroid hormone Hypothyroidism measured by TSH Hyperthyroidism TT3 and TT4 (free)
14- Nutrition
Canada Health Food Guide-Carbohydrate 55%-Proteins 30%Fats <5% Fibre 30g/dayMinerals and vitaminsWater 8-10 glasses a day Salt <2g /day
Contains a sulphur atom Made from pryrimidine and a thiazole and couple by the methylene bridge Rapidly converted to Thiamine pyrophosphate ad thiamine diphophosporansferase Usually in the diet – but if not need to take thiamine Deficiency: Reduced capacity for the cells to release energy Can cause beri beri Wernicke korskaoff syndrome Found in chronic alcoholics so vit b1 supplement is needed
Vitamin B2- Riboflavin
-Precursor for co enzyme FMN and FAD-It decomposes when exposed to light -Can cause deficiencies in new born-Found in eggs, meat, cereal and milk-1.2-1.7 daySeen in alcoholics due to poor diet-Glossitis, stmatisis, photobhobia and sehorrhea is deficiency
NiacIn Vitamin B3Nicotinic acid and nicotinamide can serve the source for thisNiacin is required for the synthesis of active form of vitamin B3NAD and NADP are co factors for dehydrogenasesNiacin can be derived from tryptophan and is not a true vitaminNicotinic acid can be used in the diet but is not recommended in patients with gout or diabetesGlossitis, depression dementia, are the deficiencyCan cause PELLAGRA- depression, diarrhea, Hartnup disease causes it toodecrease in niacin can be caused by isonazid therapy for TB
Vitamin B5- Pathothenic Acid
- It is formed from Beta alanine and panthtenci acid- can be gained from wholemeal grains, legumes and meat\
- -Extremely rare
Vitamin B6- Pyridoxine- pyridoXAL
Used as a supplement for nausea and vomiting in pregnant women0.6mg/dayDrugs can reduce it like anti tb – isonazaid, penicillamine for RA , avoid with levodopa- as vitamin b6 causes the conversion of levodopa to dopamine and can give nausea and vomiting
Biotinthis is co factor that is required by enzymes involved in carboxylation reactions- eg acetyl coA carboxylase and pyruvate carboxylase-Found in foods and synthesized in the bacteria-Can be got from excessive consumption of raw eggs--Antiboitics can cause decrease in biotin in the long run
Cyanocobalamin- Vitamin B12
Has a corrin ring and a tetrapyrolle ring structrehas a cobalt ion in the center
It is absorbed in the ileumit is a co factor used in catabolism of fatty acids- and amino acids valine isoleucine and transcobalaminMegoblastic or pernicious anaemia can occur from the defficeicny due to the lack of the intrinsic factor that is produced to help it to be absorbedShould be given parentally- oral supplements are not effectiveOral contraceptives, trifluperazine, KI metformin should not be taken at the same time Use in the elderly
Folic AcidCOnjucated molecule and has a pteridine structure|it is linked to PABAAnimals cant synthezise paba so it mst be got from folic or folate in the dietYeast and leafy vegetables- are a good sourceMegoblastic anaemia and in preg can cause neural tube defectConc decreased by- anticonvulsants, oral contraceptives, metformin, dapsone, 5-FU, sulfonamides
Vitamin C – Ascorbic Acid
Wound healing- used in collagen synthesisFruits and vegdeficiency causes scurvy – smokers are vit C deficient
Vitamin A
Has 3 active moleculesBeta carotene retinol retinal retinoic acidRetinol, retina and retinoic acidBeta carotene is precursor of vitamin A Rhodopsin is inactive form of vit A in visionB-carotene is two molecules than of retinal that are linked at their aldehyde ends also called pro vitamin A Good anti oxidantsod vit A is toxiccan cause bone pain- nausea – diarrhea and hepatosplegenomy (enlarged liver and spleen)Def- xeroplhtalmiaNight blindness- Early symptoms- increased suspectivity to infection, cancer anaemaiaprolonged- deterioration of the eye tissue- and progressive keratinzation of the corneaAccutaine- cis retinoic acid- oral onlyTTT Retin A – trans retinoic acid- creamov >2500IU
Retinol
Retinoia acid
Vitamin D
Steroid hormone1,25 dihyoxycolecalcferol is the active formderoved from ergosterol and prodced in the skinChronic renal failure is a deficiency of vitamin D3Milk- fish – eggs – liver oilrickets in children and oesteomalacia in adultsNewborn should get vitamin D drops (oral)
Vitamin EAlpha tocopherol 0 is the strongest antioxidantVitamin $E is a natural antioxidantStorage site is the adipose tissuesIncreased intake is needed in premature infants and persons with fat dietcause increase in blood cell fragility
Vitamin K (Quinolone structre)
K1(phylloquninone) green vegetablesk2(menaquinone) interstinal bacteriaK3 synthetic mendione- When administed it is alyklated to V2maintain clotting 2 7 9 10 antidote for warfarin
Essential fatty acidsThese include lineloic acid (omega 3), arachdionic acid, eicosopentanoic acid, EFA- need to be gained from the diet- Omega 3 and omega 6 is from vegetable oil and fish oil provide eicosapentanoic acid- some EFA can be made from other EFA like araciondonic acid
TIPS Vitamin B12- commonly found in animal products PABA is a precursor of folic acid Vitamin D deficiency is common in Canada and USA D3 1,25 dihydroxycolecalciferol is the active form of vitamin D Supplement of folic acid in pregnancy reduces neural tube defect Storage form of vitamin D is D2 Skin exposed vitamin D is cholecalciferol ADEK absorption occurs in the small intestine All B compex washout except vitamin B12 Folic acid is used for DNA and RNA synthesis Vit A overdose causes toxicity Alcoholic patients deficient in vitamin B12 Chronic renal disease need vitamin D Deficincy in newborn treateted for hyperbilurimea by photo therapy riboflavin Niacin is not a true vitamin Pellagra is due to def of vitamin d3 Pteridine ring is in folic acid Scurvy is in vitamin C def B carotene is the precursor of Vitamin A Omega 6- lineloic acid Omega 3 linelonic acid – act like aspirtin – antiplatlet Vit E toxicity prevents vit C from working Vit B1 is beriberi and Wrnick Korsaff syndrome Vitamin D in chronic renal disease Vit b12 has cobalt center- cycobalamin Vitamin b2 riboflavin- pellagra
Chapter 15Microbiology
Bacteria: Contain cell membrane and cell organs Bacterial shape- round(coccus) rod like (bacillus) spiral (spirochete) Bacterial nucleus is not surrounded by a cell membrane Bacterial ribosomes are 30s 50s and 70s Cell membrane consist of cytochrome, lipids and enzymes Mesosomes are invaginations of bacteria Plamid- circular piece of dna Endospore- is a inactive cell External layer is a capsule and is resistant to phagocytosis Cell wall- resistant to osmotic pressure Peptidoglycan cell wall present in gram positive and gram negative cells Mucopeptide is presnt in peptidoglycan Techoic acid- water soluble polymer- present in gram positive only Periplasmic space – gram positive bacteria – between cell memembrane and outer cell Outer membrane- grame nevative- phospholipid layer embedded proteins and prions Lipopolysaccharide- gram –ve and consist of lipid A an endotoxin Glyocalyx is the external layer- slime layer and is adhesive Appendages- flagella/pilli/ ordinally pillae or sex pillae Bacteria growth cuvre- lag- increase in size and exponential is increase in numbers Decline is death phase Obligate aerobe- generate h202 are a bactericidal Superoxide dismustase- enzyme released to neturalise h202 Obligate anaerobe- has no superoxide dimusterase Facultative anerobe- most pathogenic- can switch from fermentative to respiratory metabolism Aero tolerant anerobes- similar to facultative and remain fementative Canophilic anaerobe- similar to facultative
Oxygen requirement
Facultative anerobe- most pathogenic – can shift from fermanetative to respiratory Obligate aerobe – has superoxide dismustase enzyme and releases h202 Obligage aerobe – killed by 02 Aerotoelarnt anaerobe –femain fermentative
VirusNo cell structures Made of DNA RNA and proteinAll are harmful
Fungicell membrane contain ergosterol layermade up of thread like structures called chitin
Protozoaeg amoebaunicellular or single cell organisms- based on flagelletes-
Atypical bacteriaMycoplasma: have no cell wallRickettsia- can be transported by ticks and mitesChlymaida- lack ATP synthesis
MycobacteriaCell membrane contain a mycolic layeracid fast test can detect it
Gram –ve has more layers than gram +ve
Gram +ve Gram –veStain blue or purple Stain pink or redTechoic acid LPs in the outer membranePeptidoglycan layer is thick Peptidoglycan layer is thinExotoxin is a metabolic product Endotoxin is metabolic productExotoxin is thermoliable- and destroyed at high temperature. It is a high molecular weight protein
Endotoxin is complex and made of phospholipid- polysaccharide and protein
HSV1 and HSV2 can cause oral and genital lesions. HSV 1 is cold sores and kertaoconjunctivitisHSV 2 is genital
VZV can cause chicken pox- shingles glandular fever rosella infantum (6th disease)
AciclovirFamciclovirFoscarnet Ganciclovir
Hepandavirus Hepatits B Transmitted via sexual or bodily fluids
Interferon Alpha
Papilliovirus
Polyomaviurs
Warts and cervical cancer
Hamaerogic cysts
Garadsil used for cervical cancer
Poxovirus SmallpoxOrthyomyxoviruses- Influenza A and B
Influenza (flu) AmatadineNeurominidase inhibitiosOsetlamavir ZanamavirRimantidine (influenza A )
Flavivirus- yellow fever- hepititis
Yellow fever – chronic hepititis
Paramyxoviruses- Enterovirus- RSv measles mumps
Resp infections Croup Can be severe in infacnts
Reterovirus Rhinorrhea- hepatitis common cold
Rhino- runny nose
Rotavirus gastroenteritisReterovirus HIV HTLV Aids T cell leukaimea NRTI NNRTI protease
inhibitors
Rhabdovirus- rabies rabies Zoonotic infection
Togavirus – Rubella Alpha virus
German measlesEncephilitis
Bacterial infections
Stye- external hordeulu or internal hordelum
Causes- S aurus Site of infection- edge of the eyelid- and head ruptures within a few days
TreatmentWarm compress and cloxacillin or flucloxacillin
Inclusion and drainage are indicated and patient should be referred if they do not respond to the treatment
Conjuncitivits Pink eye or red eyeViral- bacterial- chlyamidialNon infectious- foreign or allergy
TreamtnetOral tetracycline – doxyclineErythromycin – safe in pregnancyAzithromycn 1g as a single doseAmoxiciilin safe in pregnancyCeftraixone- 1g IM single dose – Genococcal conjuncitivits in adults
Purleunt or mucopurleunt discharge is bacterialViral non mucouperulent discharge
Watery discharge can be due ti URTI or adenovirus
Viral conjunctivitis is follicular reaction and prerucicula lympadenothpy
Viral conjunctivitis Treatment is supportive- topical corticosteroid therapy is controversial
Children kept out of school for 2 weeks following onset of infection
Bacterial conjuncitivitsStaphylococcus and strepoloccus H influenza in children
Gentamicin or tobramcyin eye drops Fusicidic acid eye drops
New born conjunctivitisc.trachomitis or n gonnorheachylamidia trachomonitis- erythromcycinn gonnherea- ceftriaxone
2.5% povidone iodine is best for the propylaxis
CannilcuitisActimces
Mechanical expression of exudative or granular material from the canculi and penicillin GRefer the patient for a definitive treatment
DarocystitisStreptococci or s pneumonaieInfection of nasoscrlimal sacAcute- amoxicillin Chronic irrigation nd penicillin G
KeratitisBacteria fungi herpes simplex acanthameobeaSight threatening and so an emergencyHerpes simplex keratitisHSV 1Topical disease- acyclovir 5 times a day and continued 3 days after healingTrifluridine and hifluridine drops Stromal disease- antiviral and corticosteroids
Ear nose and thoratCommon cold Rhinovirus
Sinusitis Bacteria s pneumoniaPharngitis sore throat Virus adenovirus
Bacteir s pyogneesPneumonia H pneuomina Bronchitis H influenzaOtitis media S pnenonia h influenza m catrrahlis
Skin and soft tissuesCellulitisS pyrogens or s aureusDermisPenicillin and flucolaxcillin
Acute spreading of the dermis- lesion is hot and red and swollen
ImpetigoS aureus and S pyogenesBullous crusted pustular eruption of the skinDue to invasion of local causative agentPenicillin or amox and flucloxFolliculitis (boil)S aureusPenicillin or amoxicillinErysipelas- rapidly spreagind infection fo the skin
S pyrgiens or s aureus Dermis of the facePenicillin or amoxic with or without fluclox Neroctising fasicitsInflammatory response of tissue below the dermis and spread along the facial planes and disrupt the blood supply and cause necrosis and gangreneS pyogenes (B haemolytic group)Benzyl penicillin and clinamycin with or without metrondizaoleGangreneColiform or sterptococco (group A)Penicillin and celhaliposin – beta lactam and qunilones can be used Pai fever systemic toxicity VirusesPapillonoma virusMolluscum contagiosum (pox virus)Pox virus from sheeps or goats
Common wartFleshy papulePapovascular lesions with systemic spread like herpes simplex
FungiDermatophyte Ring worm or skine lesions (keratin loving
CNS infectionsNeonatal (6 weeks) group B strep E coli and other
Ampicillin + gentamicin or ampicillin and cefrtiaxone
Children > 3 months and adults S pneumonia N meningitis H influenza type B
Cefrtoixone or ampicillin and vancomycin
Eldery alcoholics immunocomprimesd E cloli S pneumonia
Cefrtixione or ampicillin or vancomycin
Meningococcal infection N menignigitis Respiratory route
Haemophilus influenza type B Affects 6 month to 5 year old children Hib vaccine spreadBlood-> meninges
encepelitis Viral infection of the brain –cns and cellsHSV 1 is most common CMV rabies mumps
polio Enterovirus
TB meningitis Meningococcus Pneumoccus H influenzaCNS Benzyp penicillin – menicoccoisBezyl penicillin/cefotaxime or vancomycin if resistant for pneumoccusH influenza – cefotaxime Prop meng rifampicin or ciprofloxacin whole family or close contacts
Respiratory infectionsCAP Causative agent: S pneumonia (most common)
Requiring hospital administrationS pneumonia (17%)M pneumonia(14%)Chylamidia pneumonia (10%)H influenza (7%)L pneumophilia (1%)Emergency treatment is penicillin VS pneumonia – amoxicillin, penicillin G or macrolideH infleuzna 2nd or 3rd gen cephalosporin + clauvnateS aureus- Methicillin susceptible- CloxacillinMethicillin resistant – Vancomycin M pneumonia and C pneumonia- Doxycylcine or macrolideLegionella- Fluroquinolones- marcolide rifampicinE coli- aerobic gram –ve bacilli- 2nd or 3rd gen cephalosporins- initial therapy should be with cefoxitin pipercillin or tazobactum
Brochitis Based on age group<1 year- RSV , parainfuenza , corona virus1-10 years- parainfluzna , enterovirus rsv>10 years- influenza RSV adenovirus
Treatment Routine antibitict not recommended Atipyrectci or angalestic – aciteomenophenAntiussive- dextromethorphanBeta agonist salbutamol`
Urinary Tract infectionLower UTI Cystitis – and urethritisUpper UTI Polynephritis and uretitis
UTI most common agent is E coliCystitis Cotrimoxazole, or amoxicillin or ciprofloxacinUrethritis Urea plasma and chlymidia infection-
doxycylcine – during pregnancy use erythromycin
Pyleonephritis Bacterial infection of kidney subustances Amoxicillin cephalosporins cortimoxazole or aminoglycosides
Sexually transmitted infectionsCausative agentsNisseria gonorrheaChylamidiaLymphogranulomaBacterial vaginosis AIDSHepititis B and C Chancroid (syphilis)Genital herpes Genital Warts Candidia or yeast are not STI
Candidia is not STI so no treatment and if the symptoms recur within two months then the partner would need treatment
Infectious Arthiritis Lyme dieaseOseteomyleitis are all bone and joint infections
Infectious arthiritis
The gonococcus bacteria can cause different symptoms in males and females
Women develop red sores on the hands and feet and severe pain in the wrist and ankles
In men gonococcus only affects a single joint and most often the knee is affected.
Arthiritis is due to gonococcus and oral ampicillin is the treatment
Surgery doesn’t really help
Lyme disease Is tick bourne and can cause arithirits and in severe cases heart and cns complications
Spirochete (Boreli bergodorferi) Is transmitted to humans via deer tick and prevelant during summer months
Tetracycline is the drug of choice
Oesteomylitis Bone infection of the marrow and caused by S aureus
G I infectionsStomach H pylori is the common infection and is
associated with peptic ulcer disease – and gastric cancerLarge intesting 99% anaerobesBactersisides- Bifidobacterium clostridium anerobic cocci and anaerobesAnerobes – enterobacaea- e coli enterococci proteus
Food poisoningShigella Dysentry travelers diaorrheaC jejuni Travelers diahrea Salmonella Eggs meat poultry and travelers diarrheaC difficile P colitisE coli Meat poisingig and travelers diarrheaS aureus Meat mayonnaise custardc. perfigines Actue gastroenteritis and reheated dishesNorwalk virus Diarrhea in hospitalized patients Entomebea AmeobiasisB cerus Reheated rice
V parahemolyticus Contaminated sea foodListeria Meat
TIPS Beta haemolytic bacteria- Sterp. Pyogenes ( Group A strep_ Toxic shock syndrome- S aureus Lyme disease is borrelia burgodorferi Techoic acid- is in gram positive bacteria – S pneumonaia, S aureus Encephelitis is a brain infection caused by:
-Viral – alpha viruses- the ones that cause rubella or rabies virus HSV virus-bacterial- N meningitis
Chylamidia in new more is C trachomitis- Non gonococcal infections that cause UTI is E coli and chylamidia Diphtheria- Corynebacterium diphteriae, URTI Sypiliis- Treponema palladium Anthrax- bacillus anthraics E coli- gram negative anaerobic cocci The bacteria that degrades h202 is obligate anaerobe S aureus- s epidermis does not Live vaccines- MMR, sabine, small pox, VZ, yellow fever Killed vaccine- polio, influzna rabies Viral diarrhea- rota virus CAP- S pneumonia – ambulatory patients M pneumonia. And Hospital admission is S
pneumonia Sub acute endocaritis- s aureas and s viridians Syphillis Tropenem Pallidum Gram +ve bacilli= B diarrhea- C jejuni, E colli shigella Otitis externa- pseudomonas Aspiration of ear is in middle ear infection Encephalitis HSV Gram +ve bacilli C diptheri Sinusitis H pneumonia, H inflenze M carttharalis Nocosomial infections S aureus and Pseudomonas Shingles herpes zoster Herpes- HSV 1 HSV 2 VZV CMV Epistein barr Tuberculosis:
caused by – Menigicococcus, Pneumoccocus, H influenzaMenigcoccus- benzyl penicillinPneumococcus- benzyl penicillin/ cefotaxime/ vancomycin if resistantH influanzae- Cefotaxime (start with penicillin + cefotaxime)Propylaxsis- Rifampicin or ciprofloxacin
Pneumoniaemergency treatment- Penicillin V
S pneumonia- Penicillin G- amox or macrolide High level resistant- quinolines and 3rd gen cephalosporins H influenza- 2nd 3rd generation cephalosporins or amoxicillin and clavanate S aureus- Methicillin Susceptible- Cloxacillin and meth resistant vancomycin M pneunonae or C pneumonia- Doxycycline or macrolide Legionella – florquniolines macrolide and rifampicin Ecoli- 2nd nd 3rd cephalosporins- initial therapy- cefoxtin or piperacollin and
tazobactum
16 - Cell and molecular Biology
DNA replicationThis first occurs by separating the double stranded DNA molecules and then each new strand then serves as a template onto which new bases are paired upon in complementary base pairing. The same thing is done in transcription from DNA t RNA. The RNA is the intermediate between the DNA and the protein.
Cell organelles
ER – membranes that extend throughout the cytoplasm . only in eukaryotic cells. Cytochrome P450 is present in ERRER- helps in protein synthesisSER- helps in lipid synthesis
Golgi bodies contain sacs – help in protein and lipid synthesislysosomes – help in digestion
Genome- complete set of DNA in the organismGene expression- gene is DNA sequence that encodes a protein or RNA molecules
Nucleotide- Base+sugar+phosphatepentose sugar- ribose or deoxyribisephosphate 5’ carbonnirotgenous base
cDNA- complementary DNA – that is syntheisezed from RNA rather than from DNA templateused in cloning or to locate specific probes\
RNA differences has Uracil instead of Thiamine, single stranded, has ribose instead of deoxyribose
RNA polymerases- enzymes help in the synthesis of rRNA tRNA and mRNA
3 types of RNA based on their functions:
rRNA- ribosomal = 80% is syntheisie in ribosome in cellstRNA- 15% of tota- tRNA amino acid carries the specific amino acid to the site of protein synthesis and it contains an anticodon that recongnizes al codons on mRNAmRNA- 5% carries the genetic information from DNA to cytosol in protein synthesis
Codonpresent in MRNA – nd is have a set of 3 bases- there are 64 combinations but 20 common amino acids
UAG UAA UGA- don’t code for anthing
When UA UGA UAG is reahed its nonsense codon and it stops
Step 1-> transcription
Step 2 -> translation
DNa mrnatrna rrna protein
Transcription – 1st process of protein synthesis and DNA is copied into mRNAfrom mrna to dna s reverse transcriptase
Translation- mrna is brought to the ribosme by the trna and then under goes complimentary base pairing – catalysed by amino acyl trna synthase- and then it keeps going until a stop codon is reached. After which there is post translational modification – glycoslyation sulfation etc – splicing of exons
Intron and exons
Coding reigon of a eukaryotcyte gene is introns and exons- intron is a segment of a gene that is suited between exons.
It is not responsible for the coding of a protein- so they wud be spliced out of the mRNA- the exon is a nucleotide seuqnece in DNA that carries the code for the final mRNA molecule- and so defines the amino acid sequence
Remoiving introns is called splicing-
DNA recombinant technology
CloningDuplicating DNA and it is identical using a vector
Insert the DNA into a plasmid vector- it is usually an antibiotic resistant getna and recombinant molecule is formed. Plasmids and DNA fragments must have compatible RE ends for ligation by DNA ligase- The ends are joined together to form the circular DNA product .
Once the Recombinnt (circular DNA ) is formed- it is then inserted into a host cell like E coli and allowed to replicate –and then the memebrane of the cells are made permeable with shock treatment of calcium ions to allow the cells to take up the DNA pieces –
So the cells are grown in an antibiotic medium and only the resistant cells will grow
Select the cells with the DNA x and the antibiotic resistant cell – use beta galactosidase to get cells with the DNA x and not the vector due to unsuccessful ligation.
Kill the cells and extract the DNA X
Eg Cystic fibrosis etc
DNA recombinant technology
Plasmid circular piece of DNA used in recominbation and cloning
Endonuclease enzymes- Restriction enzymes are a set of enzymes that are bacterial and they cut the DNA at specific sites – called the restriction sites- by breaking the phospohidester bonds- between the nucleotides- to form the single stranded DNA – they are isolated from bacterial species- and break foreign DNA
Lyase and lygase are the enzymes
Lyase- splits DNA on specific sitesLygase- joins the DNA on specific sites
TIPS Nucleic acid- DNA and RNA Building blocks are nucleotides Purine bases are adenine and guanine Pyrimidine bases are thiamine cytocine and uracil Base only in RNA uracil All genetic information in an organism is called as genome DNA sequence that encodes a protein or a DNA is a gene Fist step in protein synthesis is transcription Segment of gene between exons is intron Split DNA on specific sigte DNA lyase Join DNA DNA ligase Small circular chromosome of DNA is plasmid Genetic disease with chromosome X is haemophilia Geneome all the genes etc Microtubule in cell division- centrosomes Prokaryotes- have cell membrane Eukaroycte- have cell wall Nucleotide is sugar phosbate and base DNA- A G C T RNA A G C U Complementary- A—T C—G A—U Transcription is DNa to mRNA Translation is mRNA to tRNa Andicodon on tRNA cDNA is complementart DNA syntheisized fromm RNA rather than DNA rRNA- 80% virus have single stranded DNA RNA polymerase is in transcription – mRNA DNA transferase cataylses moving of specific functional grouos such as phosphate DNA isomerase- isomeraisation DNA lyase- cutting apart DNA ligase joining together Reverse transcriptase is used to make DNa from rna it is a RNA dependent DNA
polymerase NNRTI- reverse transcriptase inhibitiors and it is a virus DNA synthesis by reverse ranscriptase- inhibits by AZT Hapten is a low MW compound that act as an immunogen by chemically complexing to
a large molecue at the cell surface PCR is used to make a bigger DNA chain or to amplify it- can be used in finger printing 1st step is denaturation and the DNA heated o 96 0C to break it up – done for 9 minutes
and oly used in DNa that need heat activation
Denaturation is then used heating to 96-98 degrees for 20 -30 mins so DNA double strand is broken and – as hydrogen bonds are broken
Annealing step- lower the temp to 50-60 degrees to allow the bonds to reform between the base pairs
Elongation – depends on the tem and Taq polymerase is used-
Extension/elongation step: The temperature at this step depends on the DNA polymerase used; Taq polymerase has its optimum activity temperature at 75–80 °C,[12][13] and commonly a temperature of 72 °C is used with this enzyme. At this step the DNA polymerase synthesizes a new DNA strand complementary to the DNA template strand by adding dNTPs that are complementary to the template in 5' to 3' direction, condensing the 5'-phosphate group of the dNTPs with the 3'-hydroxyl group at the end of the nascent (extending) DNA strand. The extension time depends both on the DNA polymerase used and on the length of the DNA fragment to be amplified. As a rule-of-thumb, at its optimum temperature, the DNA polymerase will polymerize a thousand bases per minute. Under optimum conditions, i.e., if there are no limitations due to limiting substrates or reagents, at each extension step, the amount of DNA target is doubled, leading to exponential (geometric) amplification of the specific DNA fragment.
Final elongation- is the single step and performed at the end to ensure the last DNA is fully extended – done at 70-74oC for 15 mins
Final hold: This step at 4–15 °C for an indefinite time may be employed for short-term storage of the reaction
This is when genetic differences in individuals can affect the way that the drugs work or are metabolized in their bodies and the drug response
This allows drugs to be made that are customized to each persons genetic mark up and they used for cytochrome enzymes that are responsible for drug interactions.
The first step is a detailed analysis of teach of the genes un a single nucleotide polymorphism
SNP- single nucleotide polymorphism- is used when one base pair on a nucleotide replaces another- A single base differences exist between individuals- this is the most commogenetic variation In DNA.
Defective splicing- is which an internal polypeptide segment is abnormally removed and the ends are then joined.
Gene therapy
This is the use of genes to cure diseases by altering a single defective gene like in cystic fibrosis
Eg drugs used are HER2 receptor genes and traszumatab used for breast cancer-
HER2 Rna inhibitor
Immunology
In organ transplant rejection due to infiltration of T cells Most common antibody is IgG Munorab ad Monoclonal antibody attack CD4 igM first produced when exposed to an antigen igE activated in asthma patients acute graft rejection is type 2 tuberculin test is type 4 infliximab is for RA and chrons disease hapten is low molecular weight molecule that covalently binds to a larger molecule infliximab is iv hashimoto is hypothyroidism and is type 2- organ specific autoimmune diease acute graft rejection is type 2 igE mediates type 1 poison ivy is type 4 neutrophil- respond to bacterial and fungal infection monocytes hightest cell in the body basophils not mast cells penicillin hypersensitivity type 1 lupus drugs HIPP MCQ- hydralazine- isonazid- procanamide- penicillamine- methyldopa-
chlorpromazine qunidine SLE is type 3 non organ specific autoimmune Steven Johnson- od of pshycotics or TCA- rash- photosensitivity feverer – 3rd degree burns SASPAN- sulphonamides phenytoin allopurinol – nsaids –sulfoxazole Red man syndrome – vancomycin Gluten in wheat and rye ____________________________________________________________________________
Immunization
High risk for flu jab- 6month- 2 year kids, egg allergy, asthma, cvd, pregnancy and seniors
Who should not take- < 6 month- egg allergy and flu symptoms
Live vaccines – not given to pregnant and immunocompromisedLive vaccine eg – MMR, varciella, yellow fever, small pox- sabine polioFlu vaccine is killed vaccine and effective against influenza a and bKilled vaccine- flu, hepatitis A and B, thypoid, choleraTravellers should take Hep A and BHep C is chronic hepatitisHep B vaccine protects against Hep DDukoral oral vaccine is for E coli and cholera- - two doses one week apart and the last one a week before you travel- High risk latin America- south east asia and Africa ( basically poor countries)Giadardisil is used for papilloma virus
Biotechnology-Anameia with chemotherapy- chronic renal disease- erythropoietin-anaemia for cancer chemotherapy and chronic dialyisis and AZT- epoeitn alph and darpoeitn-Neutropenia associated with chemotherapy- filgristim-TNF alpha and beta- enterecept-Graft rejection- muromonab-Chrons and ra is infliximab-haemophilia A def of clotting factor 8-muromonab attacks CD4 cells
VaccnesAscorbic acid can detoxify the urineConjcation reaction is the one that causes acetominphen toxicity
