BioChemistry I
Complete List of Terms and Definitions for BioChemistry I
| Terms | Definitions |
|---|---|
| anion | negative ion |
| Becker's syndrome | XR |
| RNA |
ribonucleic acid single helix adenine uracil guanine cytosine |
| Glycine, Gly, G | |
| Dry skinMelanoma | Mismatch repair |
| coenzymes | vitamins that assist enzymes |
|
Phospholipids |
constructed from four components -one or more fatty acids -a platform (usually glycerol) to which fatty acids attach -a phosphate attached to the last OH -an alcohol attached to the phosphate |
| Examples of movement proteins |
myosin actin troponin tropomyosin tubulin |
| Fabry's disease:inheritanceenzymeaccumulated substratefindings | XRa-galactosidase Aceremide trihexosideperipheral neuropathy of hands/feet, angiokeratomas, CV/renal disease |
| Glutathione | Purines (Glycine Aspartate Glutamine) |
| Resolvins (Rvs) promote | resolution of inflammation |
| dissacharides | C12H22O11. two monosacchaarides joinde by dehydration synthesis/condensation. |
|
Reaction 6 Glyceraldehyde-3-phosphate dehydrogenase G3PDH |
-oxidation reduction reaction -saves redox energy as reduced cofactor NADH -adds inorganic phosphate to make high energy intermediate Glyceraldehyde-3-phosphate + inorganic phosphate to 1,3-bisphosphoglycerate (NAD+ to NADH + H+) |
| Lysozyme | -site of general protein degradation-carries protein degradation via fusion with vesicles (internal) and endocytosis (external)-maintain a low pH-has its own complements of proteases |
| Percentage risk of transmitting multifactorial inherited disorder if two people have a child with that disorder, what is the chance the second child will have the disorder? | 1/4 |
| UDP-Glucuronyltransferase | catalyzes glucuronidation to make substances more water soluble/easier to absorb/excrete.Crigler-Najjar type I:enzyme is completely absent. Type II: <10% of normal |
| Chemical energy change during phosphorylation is reflected in what difference between the two sides? | pH |
| Proteinase | (hydrolyase) hydrolysis of peptide bond |
| They all end in "ine" | PhenylalanineIsoleucineTyrosineThreonine |
| ribose | a white, crystalline, water-soluble, slightly sweet solid, C5H10O5, a pentose sugar obtained by the hydrolysis of RNA. |
| disaccharide | two or more monosaccharides bonded together; examples include maltose, sucrose, and galactose |
| Essential Amino Acids |
1) Histidine 2) Isoleucine 3) Threonine 4) Leucine 5) Tryptophan 6) Lysine 7) Tyrosine 8) Mathionine 9) Valine 10) Phenylalanine |
| Acid | substance that increases the hydrogen ion concentration of a solution |
| unsaturated |
double bonds b/w some carbons liquid at room temp. |
| What gene product promotes the degradation of beta-catenin, which normally translocates to the nucleus to induce cellular proliferation? | APC |
| Hypo and Hypercalcemia |
Hypo: Tetany, osteoporosis; Hyper: Renal calculi, metastatic calcification, polyuria |
| DNA repair: double strandIf both strands are damaged, repair may proceed via _____ with undamaged homologous chromosome. | recombination |
| Only dehydrogenase for the AA's | glutamate dehydrogenase |
| Location in body where glycogenesis performed |
muscle liver |
| Homovanilic Acid | Dopamine is finally converted to? |
| Most cells are in which phase? | G0 |
| ionic bonds | an attraction between oppositely charged particles that are near each other |
| Under anaerobic conditions in a muscle cell, pyruvate is converted to:a. ethanolb. CO2 and HOHc. acetyl-CoAd. none of these | D |
| breaking covalent bonds by adding water | hydrolysis |
| 2 senses:*Hearing: Bilateral acoustic neuroma*Eyes: Juvenile cataracts | Tuberous Sclerosis |
| glycerol | a colorless, odorless, syrupy, sweet liquid, C3H8O3, usually obtained by the saponification of natural fats and oils: used for sweetening and preserving food, in the manufacture of cosmetics, perfumes, inks, and certain glues and cements, as a solvent and |
| cellulose | an inert carbohydrate, (C6H10O5)n, the chief constituent of the cell walls of plants and of wood, cotton, hemp, paper, etc. |
| first orbital | can hold up to 2 electrons |
| mucleic acid | very large and complex orgainc molecules that store and transfer important information in the cell |
| pH | a measure of the acidity and alkalinity in a solution. pH = -log[H+]. pH 7 = neutral <- similar to pH of most living cells, because even the slightest change is harmful. |
| colloid | stable suspension of fine particles in a liquid |
| CARBOHYDRATES | CHO in a 2:1 Hydrogen Oxygen ratio |
| Geometric isomers | differ only in spatial arrangement found around double bonds |
| What cofactor is required by delta-aminolevulinate? | vitamin B6 |
| Molecular motor proteins | transport cellular cargo toward opposite ends of microtubule tracksDynein = retrograde to microtubule (+ to -)Kinesin = anterograde to microtubule (- to +) |
| Elevated Creatine Kinase | MI (CK-MB), Duchenne MD (CK-MM) |
| This polymerase is responsible for mitochondrial DNA synthesis | polymerase gamma |
| What portion of NAD/NADP will bind within the active site of alcohol dehydrogenase? | nicotinamide |
| Function of oxaloacetate (OAA) in TCA | carrier molecule |
| puromycin action | cause premature chain termination by acting as an analog of aminoacyl-tRNA |
| ACTH | what stimulates the conversion in the first stage of steroid hormone synthesis |
| SGLT-1 | galactose and glucose get into the intestinal cells by using this; it is a Na+ dependent transporter and requires energy |
| hydrocarbon | a olecule that contains only carbon and hydrogen |
| galactose | the C4 epimer of glucosean important component of milk sugar |
| Which enzyme degrades chylomicrons and VLDL? | lipoprotein lipase |
| What is an affinity label? |
Irreversible inhibitor: structurally similar to substrate for enzyme -- covalently binds to active-site reside. More specific than group-specific reagents. |
| Not as efficient as malate-aspartate-shuttle | Used by muscle |
| protein | any of numerous, highly varied organic molecules constituting a large portion of the mass of every life form and necessary in the diet of all animals and other nonphotosynthesizing organisms, composed of 20 or more amino acids linked in a genetically cont |
| LOX converts arachidonate into | HPETE's, (precursor for Leukotrienes) or into Lipoxins (LX) |
| condensatoin reaction | monomers linking to form polymers (a water molecule is released) |
| radioactive iodine (use) | I-131, used to diagnose/treat diseases of thyroid gland |
| isotope | atoms of the same element that have different numbers of neutrons |
| catalyst | a molecule that helps to speed up chemical reactions |
| Alpha Helix | A delicate coil held together by hydrogen bonding between every fourth amino acid. Some fibrousp roteins, such as beta keratin, the structural protein of hair, have the alpha helix formation over most of their length. |
| What is WADR syndrome? | Wilms tumor, aniridia, genital anomalies, mental retardation (defect on chromosome 11) |
| X-linked dominant | transmitted through both parentsM or F offspring of affected motherAll F or affected fatherHypophosphatemic rickets - formerly known as Vit-D resistant rickets, inherited, increases phosphate wasting at proximal tubule and causes rickets like presentation |
| Start codon is:Stop codons are: | AUG(AUG inAUGerates protein synthesis)UGA, UAA, UAG(U Go Away, U Are Away, U Are Gone) |
| Types of interactions that stabilize the structure of a protein |
H bonds electrostatic interaction disulfide bonds (only covalent bond in the group) hydrophobic bonds |
| Three forms of vitamin A |
retinol (primary alcohol) retinal (aldehyde) retinoic acid (carboxylic acid) |
| Mode of inheritance of mutation of BRCA genes and tumor suppressor genes | autosomal dominant |
| PDH phosphotase | E1 which contains vitamin B is activated by? |
| grains | what type of food is High in methionine, low in lysine |
| Amino Acid | monomer of proteins, 20 within a protein, contain an amine and a carboxylate |
| 458. Cells are not islands and need to communicate. What fulfills the necessity of intercellular communication? | Hormones |
| Proton motive force is analogous to what in an electrical cell | electromotive force |
| Which 2 bacteria species commonly infect ppl with cystic fibrosis? | Pseudomonas, S. aureas |
| Sucrose is table sugar and is made from a polymer of two different sugars chemically bonded together. Sucrose is a ___________? | disaccaride |
| Problem w/Phe --> Tyrosine either:1. Phe hydroxylase defect2. THB defect (reduces Phe using Phe hydroxylase as catalyst) | Results:*Tyrosine becomes essential*Phe buildup --> Phenylketones in urine |
| organic | noting or pertaining to a class of chemical compounds that formerly comprised only those existing in or derived from plants or animals, but that now includes all other compounds of carbon. |
| Active Site | region on the surface of an enzyme where substrate molecules attach |
| covalent bond | sharing a pair of valence electrons by two atoms |
| Structure of protein | Made up of polypeptides with repeating units called amino acids which are bonded together by peptide bonds. |
| Primary structure of type II collagen | three alpha 1 (II) |
| Mechanisms of Thymidilate Synthesis Regulation | 1. inhibition of Thymidilate synthesisFluotouracil(suicide inhibitor) takes place of uracil to form FdUMP [recognized as a substrate by the enzyme]*fluorine can not be eliminated to add a CH3 group/enzyme is 'stuck'2. inhibition of DHFR*DHF, Methotrexate, Aminopterin (last two are DHF analogs)---all three bind as well as each other (competitive inhibitors--->prevent the synthesis of dTMP and replenishing of N,N-methylene-THF)3. inhibition of dTMP synthesis & thus DNA synthesis*FdUMP inhibits Thymidilate synthase and Methotrexate Aminopterin inhibits DHFR |
| What is the simplest glycerophospholipid? Describe it. | Phophatidic acidGlycerol molecule with an esterified phosphate at an alpha carbon |
| Define nutrients | raw materials and fuels of the diet which are required by the body |
| Definition of etiologic heterogeneity | even though firm diagnosis, several causes are possible (ex: deafness, mental retardation) |
| Structure of lipid rafts |
rich in saturated FA's much higher proportion of cholesterol in this region lot of semi crystalline phospholipids and sphingolipids many proteins (GF's, TF's) are found in these lipid raft regioins GF's want to bind here and they can become activated |
| pyrimidine phosphoribosyl transferase | Orotate + PRPP --> orotidylate is catalyzed by? |
| Once triple helix procollagen get outside fibroblast: | procollagen peptidases cleave terminal ends --> insoluble tropocollagen |
| pHpH scale | measure of acidity: 1/ log of H+ concentration1 - 6.9 acid, 7.1 - 14 basic |
| How are ELISA's sensitivity and specificity? | close to 100% (awesome) |
| Plants store glucose in the form of a polymer of glucose called___________? | Cellulose |
| Inhibited by statins | What happens to 2/3 of plasma cholesterol? |
| fleece | the coat of wool that covers a sheep or a similar animal. |
| Proteins | consist of elements S, P, C, O, H, & N |
| Beta pleated sheet | Two or more regions of the polypeptide chain lying side by side are connecte by hydrogen bonsd between parts o the two parallel polypeptide backbones. Usually make up the core of many globular proteins. |
| Primary structure of collagen molecule |
three polypeptide chain called alpha chains EACH TYPE OF COLLAGEN HAS UNIQUE ALPHA CHAINS (alpha 1 I or alpha 1 VIII) |
| What transcription factor binds to the TATA box region? | TATA Binding Protein (TBP) |
| Proces of producing tetrahydrofolate |
folate and NADPH produce NADP and dihydrofolate via FH2 reductase dihydrofolate and NADPH produce NADP and tetrahydrofolate via FH2 reductase |
| Rxns that free unsaturated FA's undergo |
reduction- add hydrogen to eliminate DB oxidation- form short chain aldehydes, as well as lipid peroxides and free radicals dialdehydes are volitale and cause rancid smell of fat |
| Information provided in genetic counseling |
medical diagnosis and its implications in term of prognosis and possible treatment mode of inheritance of disorder risk of developing and/or transmitting disorder choices/options available for dealing with the risks |
| LDL (major core lipids, apoproteins, mech. of lipid delivery) |
major core lipids- cholesterol esters apoproteins- B100 mechanism of lipid delivery receptor mediated endocytosis by liver and other tissues |
| Type 3 collagen found in: | skin, vessels, uterus, fetal tissue, granulation tissue (early wound repair) |
| 471. What interaction do water-soluble hormones stimulate?Two things... | 1. Production of second messenger molecules2. Kinase cascades |
| What is a second order reaction? | When there are two reactants.V=k[A]^2orV=k[A][B] |
| Where does trypsin cleave? | Hydrolyzes a peptide bond after lysine or arginine |
| AD mutation in LDL receptor(absent, defective) | Heterozygote (1/500): Cholesterol over 300 |
| numerical subscript on prostaglandins denotes: | number of Double Bonds in Hydrocarbon chains |
|
Which Hydoxylated amino acid residues are glycosylated with glucose and galactose? |
Hydroxylysine is the amino acid that is glycosylated w/ glucose & galactose. |
| Describe structure of beta pleted sheet |
segments held together by H bonding can be: parellel- polypeptide chain run in same direction antiparellel- polypeptide chain runs in the opposite directions |
| Fate of oxidation of ascorbic acid | form dehydroascorbic acid (remove H from enediol group) |
| Various eukaryotic promotor elements |
TATA box (-30- -50 nt) GC box (-40- -150 nt) CAAT box (-40- -150 nt) AP-1 and SP-1 sites |
| Type II DNA topoisomerases | These enzymes bind tightly to the DNA double helix and make transient breaks in both strands. The enzyme then causes a second stretch of the DNA double helix to pass through the break and, finally, reseals the break (Figure 29.13). As a result, both negative and positive supercoils can be relieved by this ATP-requiring process. |
| 468. What are cAMP and cGMP?Three things... | 1. Modified purine nucleotides2. Allosteric regulators3. Made by adenyly cyclase and guanyly cyclase respectively |
| How does ELISA indicate a positive test result? | peroxidase enzyme generates color change in solution |
| CARnitine = CARnage of fatty acids | Carnitine deficiency = Inability to utilize LCFAs + toxic accumulation |
| What disease is associated with smudge cells? | small lymphocytic lymphoma or chronic lymphocytic leukemia |
| In a fatty acid where is the site of carbon number 1? | Carboxylic acid carbon |
| What AA's are both ketogenic and glucogenic |
Ile Phe Tyr Trp Some C's go to glucose while others go to acetyl CoA. |
| Sequence of Rapoport Luebering Shunt |
1,3 BPG goes to 2,3 BPG via mutase 2,3 BPG goes to 3-PGA via phosphatase |
| 429. List all the cofactors we know and what they transfer.Eight total! | 1. Thiamin: active acetaldehyde2. CoA: acetyl3. Biotin: active carbon dioxide4. Folate: 1 carbon,various oxidation states5. S-adenosylmethionine: activated methyl6. Flavins: e-7. Nicatinamide: e-8. Pyridoxal phosphate: NH4 |
| What is the correct mechanism by which endonucleses cleave DNA? | Direct hydrolysis: attack by water molecule. * Determined by EcoRV: replacing oxygen with sulfer, saw no inversion of stereochemistry |
| AD mutation w/incomplete penetrance, variable penetration | White to green while in the CAR:*Ash leaf spots (depigmented skin)*Shagreen patch (orange peel skin)*Other skin lesions (facial adenoma sebaceum) |
| Explain how sickle cell anemia happens |
on the surface of beta subunit, you replace a Glu with a Val (replace hydrophilic AA with hydrophobic, changing solubility) there is a natural hydrophobic patch on the Hb valine will bind with another Hb at that hydrophobic patch when in the deoxygenated form |
| What is going on in the body after 16 hours-7 days of starvation? |
liver increase glyconeogenesis, cause increase glucose increase gluconeogenesis, cause increase glucose increase urea cycle increase Ala gluconeogenesis becomes the main way for maintaining blood glucose level increase ketogenesis (concentration of 3 mM) (ratio of 3:1 favoring beta HOB over acetoacetate), increase ketone bodies increase uptake of free fatty acids increase beta oxidation muscle (PROTEIN MAIN SOURCE OF ENERGY) increase proteolysis, cause increase in glucogenic AA's (esp. Ala, Gln) increase free FA uptake, increase in energy production adipose cells increase lipolysis, cause increase FA's and glycerol pancrease (closer to day 5)- slight increase in insulin to slow down lipolysis in muscle and drop blood glucose brain- adjust to metabolize ketone bodies decrease basal metabolic rate, so we can be more efficient in producing ATP turn off production of digestive enzymes |
| How many "packets" of energy released by oxidation of acetate to 2 CO2? | 4 hydride ions/4 packets of energy (remember, there are three C-H's bonds and one C-C bond) |
| Process of oxidative pathway of pentose phosphate pathway |
G6P and NADP form NADPH and 6PG lactone via G6P dehydrogenasereacts with glucose in ring form and oxidizes anomeric carbon 6PG lactone turned into linear form: 6PG via lactonase 6PG and NADP create NADPH, CO2, and ribulose 5-phosphate via 6PG DHcontrolled by cytosolic NADPH/NADP ratio |
| 526. What is the role of blood? | It's the main transport system for food and waste*Blood glucose levels must be tightly controlled |
| what is the function of an enzyme? | to speed up the cell's chemical reactions |
| RNA polymerase I requires what 2 factors to bind to DNA and transcribe rRNA genes?? | factor B and S factor(does anyone else think it's BS that we have to memorize factor B and S factor??) |
| Problem with doing glycolysis in the liver | ATP inhibits PK and PFK, and the ATP/ADP ratio does not change much in the liver |
| What is the role of magnesium in endonucleases? | Helps to position and activate water molecule for attack of phosphorous atom. |
| fate of free fatty acids in liver |
add a CoA to it use fatty acyl CoA carnitine transferase system undergo beta oxidation produces acetyl CoA |
| What are the five key features of an enzyme's active site? | 1. 3D cleft/crevice2. Takes up small % of total enzyme volume3. Unique microenvironment4. Binds to substrate by many weak bonds5. Specificity depends on arrangement of atoms |
| What determines if a carbohydrate is D or L? | the position of OH on C closest to the primary alcohol |
