BIOCHEMISTRY Flashcards by Trinitine Poblete

Amino acids cannot be synthesized by the human body

Essential Amino Acid

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Antibiotic that inhibits cell wall synthesis

Bacitracin

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Antibiotic that interupt DNA and protein function

Gramicidin A

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Dreaded side effect of bleomycin

Pulmonary fibrosis

Other drugs:
Busulfan
Amiodarone

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Cyanobacterial peptides lethal (hepatic tumors) in large doses

Microcystin and nodularin

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Neurodegenerative disease associated with chick pea and grass pea

Lathyrism

paraplegia, tremors and muscular weakness

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Seed contains neurotoxins risk factors for neurodegenerative diseases ALS and PD

Cycad seeds

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Neurotoxic found in cycad seed - natives of Guam

Beta Methylaminoalanine

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Potentially toxic L alpha amino acids

ODAP
BMAA
BAPN
Diaminobutyric acid
Homoarginine

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Naturally occuring amino acids in brain tissue

Serine and aspartate

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Naturally occuring amino acids in gram positive bacteria

Alanine and Glutamate

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Bacteria with poly D glutamate capsule

B. anthracis

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excretes D-methionine, D-tyrosine, D-leucine and D-trypttophan which triggers biofilm disassembly

B subtilis

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Bacteria incorporates leucine and methionine into the peptide component of its peptidoglycan layer

Vibrio cholerae

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Amino acid precursor of thyroid hormone

Tyrosine

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Precursor of Tyrosine

Phenylalanine

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Enzyme catalyzes phenylalanine to tyrosine

Phenylalanine hydroxylase

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Neurotransmitter precursor of GABA

Glutamate (excitatory)

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enzyme that catalyses glutamate to GABA

Glutamate decarboxylase

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Determine classification of amino acid

Side chain

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found at the center, attached to four different substituents. It confers optical activity

chiral carbon

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Amino acid without chiral carbon. No optical activity. Cannot rotate plane polarized light.

Glycine

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Stereoisomer

Enantiomers “mirror image”

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Posttranslational modification of amino acid where proline and lysine –> 4 hydroxyproline and 5-hydroxylysine

Collagen synthesis

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Posttranslational modification of amino acid where carboxylation of glutamyl residues to y- carboxyglutamyl residues

Blood coagulation cascade

vitamin or cofactor required for collagen synthesis

Vitamin C

Vitamin K dependent clotting factors

Factor 2, 7, 9, 10

Drug inhibits gamma carboxylation of vit K dependent clotting factors

Warfarin/ Coumadin

Warfarin inhibits what pathway?

Extrinsic pathway W (warfarin) e(extrinsic) Pt (protime)

condition with vitamin c deficiency

Scurvy

Triple helix structure with glycine-X-Y (proline or hydrodyproline)

Collagen

Molecules that contain an equal number of + and - charged groups bear no net change. Dipolar ion

Zwitterions

Amino acids contains both acidic and basic group. at physiological pH (~7)

Amphoteric

Used to express the strength of weak acids

pKa smaller pKa = stronger larger pKa = weaker

Property of amino acids reflects their ionic character

Solubility *tryptophan, tyrosine and phenylalanine (aromatic rings) absorb higher wavelenght ultraviolet light

Responsible for formation of esters, amides and acid anhydrides

Carboxylic acid groups

for acylation and esterification

Amino groups

smallest amino acid

glycine

Protein structure - peptide bond

Primary structure

Protein structure - Beta pleated sheets or Alpha helix

Secondary structure

Protein structure - Domains, salt bridges, myoglobin

tertiary structure

Protein structure - hemoglobin

Quaternary structure

Amino acids are linked together by?

Peptide bond

Presence of peptide test (violet in color)

Biuret test

Rate limiting enzyme of pentose phosphate pathway / HMP

Glucose 6 phosphate dehydrogenare

3 amino acids comprises structure of glutathione

glutamyl cysteinyl glycine

amino acids with alipathic side chains

Glycine (heme synthesis) Alanine Valine Isoleucine Leucine

Branched chain amino acid

Valine Isoleucine Leucine

congenital deficiency of branched chain amino acid

maple syrup disease

Hydroxyl group amino acid

Serine Threonine Tyrosine

amino acids with sulfur atoms

Cysteine Methionine

1st amino acid in genetic code

Methionine

Amino acids with acidic groups

Aspartic acid Asparagine Glutamic acid Glutamine

Basic amino acids

Histidine Arginine Lysine

Precursor of nitric oxide, urea cycle

Arginine

undergoes decarboxylation - Histamine

Histidine

Amino acid with aromatic ring

Phenylalanine Tryptophan Histidine Tyrosine

Precursor of cathecholamines

Tyrosine

Precursor of vit B3 or niacin

Tryptophan

Amino acid with Imino group

Proline -causes collagen kinks

Atypical amino acids

Pyrrolysine Selenocycteine

21st amino acid

Selenocysteine

3 stop codons

UAG UAA UGA

Mutation when a stop codon is involved

Nonsense mutation

Essential amino acids

Phenylalanine Valine Threonine Tryptophan Isoleucine Methionine Histidine Arginine Leucine Lysin Always ARGues , never TYRs

Purely ketogenic amino acids

Leucine Lysine "KiLL"

Biochemical pathways occur in the mitochondria

Fatty Acid Oxydation Acetyl CoA TCA (Krebs cycle) Oxydative Phosphorylation (Respiratory Chain/ ETC) ***Mito FATO***

Biochemical pathways occur in the Cytosol and Mitochondria

Heme Urea Gluconeogenesis ***give BOTH of you a HUG***

Where does glycolysis occur?

Cytosol

2 types of glycolysis?

Aerobic and anaerobic

End product of aerobic glycolysis

Pyruvate

End product of anaerobic glycolysis

Lactate

Rate limiting enzyme of glycolysis

Phosphofructokinase (PFK)

Glycogen storage disease with deficiency in Phosphofructokinase (PFK)

Type 7 - Tarui's disease

Enzyme inhibited by Flouride

Enolase

Other name of glycolysis

Embden Meyerhoff Parnas Pathway

Metabolism of glucose to pyruvate/lactate

Glycolysis

First step in utilization of sugars

Phosphorylation of glucose

Found in most tissue Low Km Low Vmax

Hexokinase H = Humble (low Km low Vmax)

What inhibits hexokinase

Glucose-6-phosphate

What inhibits glucokinase?

Fructose 6 phosphate

What stimulates glucokinase?

Glucose Insulin

The most potent activator of Phosphofructokinase

Fructose 2, 6 bisphosphate

Well fed or starvation? Dec glucagon Inc insulin Inc frictose 2,6 bisphosphate Inc glycolysis

Well fed state

Cleaves fructose 1, 6 bisphosphate Found in the liver and kidney

Aldolase B

Used in the liver and adipose tissue for triglyceride synthesis Isomerized to become glyceraldehyde 3 phosphate

DHAP - Dihydroxyacetone Phosphate

Deficiency in aldolase B presents

Hemolytic anemia

MOA: competing with inorganic phosphate as substrate for G3P DEHYDROGENASE --- complex that spontaneously hydrolyzes to form 3-phosphoglycerate

Arsenic poisoning

Mg or Mn dependent Inhibited by flouride

Enolase

2nd most common cause of enzymatic related HEMOLYTIC ANEMIA

Pyruvate Kinase Deficiency

Most common cause of enzymatic related hemolytic anemia

Glucose 6 phosphate dehydrogenase deficiency (G6PD deficiency)

What enzyme catalyzes the first substrate level phosphorylation in glycolysis?

Phosphoglycerate kinase

What enzyme catalyze the irreversible reactions of glycolysis?

Hexokinase Phosphofructokinase Pyruvate kinase

Other names of Pentose Phosphate Pathway

Hexose Monophosphate Pathway/ Shunt Phosphogluconate oxidative pathway Warburg- Dickens Pathway

Products of Pentose Phosphate Pathway

NADP (2 generated per glucose6-P) Ribose

Location of PPP

Cytosol

Rate limiting enzyme of PPP/ HMP

Glucose-6- Phosphate Dehydrogenase (G6PD)

Reactants of PPP

NADP Glucose-6-P

Phases of PPP

1. Oxidative - produce NADPH 2. Non oxidative - Pentose sugars produced for nuclei cholesterol acid synthesis

Tissues with active Pentose phosphate pathway

RBC Adrenal gland Testes Adipose tissue Mammary gland

Pathways in mitochondrial matrix (3)

Kreb’s cycle Urea cycle B-oxidation

The only thiamine enzyme in the RBC that is needed for interconversion of sugars

Transketolase

NADPH functions (4)

1. Biosynthesis of FA and steroids 2. Supply of Reduced Glutathione 3. Bactericidal (respiratory burst) 4. Liver microsomal cytP450

What immune deficiency arises with defective respiratory burst?

CGD Chronic Granulomatous Disease "Lacks respiratory/oxidative burst" Recurrent pyogenic infection + granuloma

NADH is important for

ATP Production

NADPH is important for

Reductive biosynthesis

Reduced form of NADP

NADPH

Deficiency of G6PD causes?

Favism Fava beans - mediterranean diet

Converts 6 phosphoglucono lactone to 6 phosphogluconate

Lactonase

Second half of PPP

Non oxidative Reversible Interconversion of sugars occur Produce ribose No key enzymes

PPP and Glycolysis overlaps with what intermediates?

Glucose 6 phosphate Glyceraldehyde e phosphate Fructose 6 phosphate

Cellular antioxidant Reduces Glutathione disulfide(GSSG) to sulfhydryl form GSH

Glutathione reductase / selenium

Thiamine (Vit B1) deficiency in alcoholics

Wernickes korsakoffs Deficient transketolase activity

Genetic deficiency of NADPH oxidase i. WBC Lacks respiratory burst Susceptible to catalase positive organism Negative nitroblue tetrazolium test

Chronic granulomatous disease

Inner mitochondrial membrane (3)

ETC Succinate Dehydrogenase ATP synthase

Final common pathway in aerobic cells by which electrons derived from various substrates are transferred to oxygen

Electron Transport chain Respiratory chain pathway Oxidative phosphorylation

Synthesis of ATP from ADP by phosphorylation coupled with the exergonic breakdown of a high energy organic substrate molecule

Substrate level phosphorylation

Enzymes with substrate level phosphorylation (3)

Pyruvate kinase Phosphoglycerate kinase Succinylcholine CoA Synthase

Phosphorylation of ADP is coupled with the oxidation of substrate in the ETC

Oxidative phosphorylation

Final acceptor of electrons along ETC

Oxygen

Iron containing component of ETC

Cytochromes

The only mobile, water soluble protein cytochrome

Cytochrome C

A non protein isoprenoid quinone Most abundant Shares structural homologous with Vit E and A

Ubiquinone (Coenzyme Q)

Associated with metalloflavoproteins and cytochrome B

Fe-sulfur complex

Complexes of ETC (4 - 5)

Complex 1 - NADH dehydrogenase Complex 2 - succinate dehydrogensase Complex 3 - cytochrome b-c1 complex Complex 4 - cytochrome oxidase Complex 5 - ATP synthase

2 domains of ATP synthase (complex 5)

Fo - inhibited by OLIGOMYCIN F1 domain

Inhibitors of complex 1 (NADH dehydrogenase)

A -Barbiturate Amytal R - RotenONE P - Pericidine These do not deplete ATP production because they do not block the complex II

Inhibitors of complex 2 (succinate dehydrogenase)

Malonate TTFA (Thenoyl trifluroacetone) Carboxin You still have ATP production via complex 1

A chelating agent that blocks complex II

TTFA (Thenoyl trifluoroacetone)

Inhibitors of complex 3 (Q cytochrome c oxidoreductase)

Antomycin A Dinercapror No ATP Produced!

Inhibitors of complex 4 cytochrome oxidase

Cyanide CO Na azide H2S

Used in treatment for arsenic, gold, mercury, peas and other toxic metals

Dimercaprol - blocks complex III

Compounds that allow oxidation to continue without corresponding ATP synthesis

Uncouplers Ex. Thermogenin and 2,4 dinitrophenol and aspirin

Known uncoupling protein 1 or UCP1 found in brown adipose tissues (newborns) Used to generate heat

Thermogenin

Transports protons across the membrane and destroy the pH gradient

Uncouplers

Fat soluble vitamins

Vit A D E K

Energy yield from lipids

9kcal/gram

Energy yield from protein or carbohydrates

4 kcal/gram

Major dietary fat

Triglycerides

Saturated FA mostly comes from

Animal fats (meat, poultry, butter) Increased incidence of coronary artery disease because of high LDL

Polyunsaturated FA (PUFA) mostly comes from

Plant Oils (corn, sesame, soybeans, tuna)

Group of fatty acid that's good for the heart

Omega 3 Fatty acids

Fatty acid in coconut oil

LAURIC ACID C12 Saturated FA coconut oil and soaps Monolaurin - antimicrobial for acne and psoriasia

Treatment of hypercholesterolemia

Diets that contain MUFA and PUFA

Treatment of hypertriglyceridemia and protection from thrombosis

Omega 3 class of PUFA

Organelle in the cell that is responsible for the metabolism of very long fatty acids

Peroxysomes Contains emzymes for B oxidation

Palmitic acid

16 carbons - Hexadecanoid acid Firat FA produced during lipogenesis Most common saturated FA in animals and plants Good for the skin

Stearic acid

18 carbons = octadecanoic acid "Stearing wheel = 18yo" Cosmetics Soaps

Myristic acid

14 carbons Palm and coxonut oil Butter Milk

Fatty acids treatment of autism

Body can synthesize needed fat except

Linoleic and alpha linolenic acid

The only absolute Essential Fatty Acid

Linoleic Acid Precursor of arachidonic acid

Precursot of EPA and DHA

LinoLENIC acid Lowers TAGs and increases cholesterol clearance from plasma

LinoLEIC acid (C18)

2 double bonds

LinoLENIC acid (C18)

3 double bands

Arachidonic acid (C20)

4 double bonds

A 20 Carbon Omega 6 Fatty acid with 4 double bonds Give rise to Eicosanoids

Arachidonic acid

Drug that inhibits thromboxane A2 Antiplatelet property

Aspirin

Leukotriene inhibitors treatment for asthma

Montelukast Zafirlukast

Black box warning for montelukast

Depression Hallucinations Singulair Hostility Sleep disturbances Adults: suicidal thought

Anti-inflammatory drug inhibits phospholipase A2

Steroids

COX 2 specific inhibitors

Celecoxib Rofecoxib (vioxx - CVS effects - MI, CAD) Parecoxib (IV) Etoricoxib

Side effects of blocking Cox-1 activity

Gastritis GI bleed

Used for prophylaxis for colon CA

Aspirin

Produced by endothelial cells of blood vessels Causes vasodilation Inhibits platelet aggregation Increase camp

Prostacyclin (PGI2)

Produced by platelets Promote platelet aggregation Decrease camp Vasoconstrict Contractuon of smooth muscles

Thromboxane A2 (TXA2)

Produced by most tussues especially kidneys Causes arteriolar vasodilation Increase cap permeability Evokes chemokinesis of T cells Enhance PAIN caused by histamine and bradykinin induce labor

Prostaglandin E2 (PGE 2)

PGE1 agonist used to treat peptic ulcer but the side effect is abortion

Misoprostol

PGE2 in obstetrics

Dinoprostone

Mast cell stabilizer used for tx of asthma

Cromolyn sodium

Largest amount of stored energy in the body

Triacylglycerol

Energy source reserved for strenuous muscular activity

Muscle glycogen

Primary source of carbon for maintaining blood glucose levels during an overnight fast

Liver glycogen

Major precursor of urea in urine

Protein

After a fast for a few days, ketone bodies become an important fuel

Brain

Ketone bodies are used as a fuel after an overnight fast

Skeletal muscle

Fatty acids are not a significant fuel source at any time

Red blood cell

During starvation, this tissue uses amino acids to maintain blood glucose levels

Liver

This tissue converts lactate from muscle to a fuel for other tissues

Liver

Major process for maintaining blood glucose levels after an overnight fast

Liver GLYCOGENOLYSIS

Major fuel store of the body

Adipose triacylglycerol

Non specific but considered as the standard for assessing overall protein malnutrition

Albumin

Bond formed when a carboxylic acid reacts with phosphoric acid releasing H2O

Anhydride bond

Bond formed when phosphoric acid reacts with an alcohol releasing water

Phosphate ester

Bond formed when a phosphate group contains two ester linkages as in structures of the nucleic acids

Phosphodiester

This phase of cell cycle, the cells prepare to duplicate their chromosomes

This phase of cell cycle is where the synthesis of DNA (replication) occurs

S phase

This phase of cell cycle where the cell prepares to divide

This phase of the cell cycle is where the cell division occurs

M phase

Clustering of receptors over clathrin-coated pits in the inner membrane and then invagination of the membrane to form an intracellular vesicle that contains the receptor-growth factor complex

Receptor mediated endocytosis

Endocytosis without the receptors -- vesicle formation

Pinocytosis

Receptor mediated entry into a cell through caveolae

Potocytosis

Formation of membrane around a particle and then the endocytosis of that membrane containing the particle

Phagocytosis

Results from the inability to appropriately target lysosomal proteins and it is a lysosomal storage disease

I cell disease

Chief inhibitory neurotransmitter

GABA

Contains the most triacylglycerol Least dense of the blood lipoproteins

Chylomicrons

Contains more protein than chylomicron Demser than Chylomicrons but less dense than LDL

VLDL

Produced by the degradation of the triacylglycerols of VLDL

LDL

Most dense of the blood lipoproteins Has the most protein and least triacylglycerol

HDL

Determining factor if a Beta oxidation will occur

Chain length <10-12 carbons = no need for carnitine

Strong indicator of fatty acid oxidation problem

Hypokinetic hypoglycemia

Neuro deficit Lactic acidosis Increase serum alanine starting infancy Build up of pyruvate that gets shunted to lactate and alanine Dx? Tx?

Pyruvate dehydrogenase complex deficiency Tx: ketogenic diet

Pentose phosphate pathway

HMP shunt

Aldolase B deficiency Hypoglycemia Jaundice Cirrhosis Vomiting ---- after eating fruit, juice or honey Dx?

Hereditary fructose intolerance

Glucogenic amino acids

Methionine Histidine Valine "Met His Val-entine"

Most common urea cycle disorder Interferes with body's ability to eliminate ammonia Increase orotic acid blood and urine Decrease BUN

Ornithine transcarbamylasr deficiency

pH at which an equivalent distribution of acid and conjugate base exist in solution

PKa

pH at which the molecule is electrically neutral

Isoelectric point

A solution or substance which resists changes in pH when small quantities of an acid or base are added to it

Buffering

More likely to be exposed to water than to be found in the interior of a folded protein

Polar amino acids

The greatest buffering capacity at physiological pH would be provided by a protein rich in which amino acid?

Histidine

Hallmark feature of Gaucher disease

Presence of lipid-engorged cells of the monocyte/macrophage lineage with a characteristic appearance in variety of tissues

Disease where ganglioside GM2 is NOT catabolized

Tay sachs disease Absent hexosaminidase A

The carbon about which the rotation occurs in ring structures of carbohydrates is the?

Anomeric carbon 2 forms = anomers

Deficiency of hepatic enzyme ALDOLASE B would result in a reduced ability to metabolize which carbohydrates?

Fructose

Backbone of glycosphingolilids

Ceramide

Globotriaosylceramide Disorder characterized by lysosomal accumulation of glycosphingolipud with terminal a-galactosyl residues

Fabry disease

Class of lipid involved in the resolution of inflammatory responses

Resolvins Class D - DHA Class E - EPA

In patient with Severe Combined Immunodeficiency (SCID), what compound is expected to be elevated in the blood?

Adenosine and DEOXYADENOSINE Adenosine deaminase deficiency (ADA)

In patient with Lesch-Nyhan syndrome, what compound is expected to be elevated in the urine? In serum?

Urine --- Uric acid Serum --- xanthine Deficiency of hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

Protein structure resulting from interaction at least 2 protein subunits in the functional protein

Quaternary structure

BIOCHEMISTRY Flashcards

(221 cards)