BioChem Flashcards
What is the sterochemistry of all chiral carbons in Eukaryotes?
L-amino acid (S configuration)
What is the isoelectric point?
The pH when the molecule is electrically neurtral
How does proline behave in secondary structres?
It si rigid so it introduced kinks into the alpha-helices or creates turns in the Beta-pleated sheets
What is the difference between heat and solutes denaturing proteins?
heat: disrupts hydrophobic bonds
solutes: disrupt secondary, tertiary, and quaternary structures
Is polypeptide formation a condensation or hydration rxn?
condensation
What is a tightly bound cofactor or coenzyme that is necessary for enzyme function called?
prosthetic groups
What are the two differences between the Michaelis-Menten plot and the Lineweaver-Burk plot?
- Michaelis-Menten plot is v vs. [S] and has a hyperbolic shaped curve
- Lineweaver-Burk plot is (1/v) vs. (1/[S]), which is a straight line
What does a high kcat and a small Km mean?
high catalytic efficiency
What is the ideal temp for most enzymes in the body?
37 degrees celcius=98.6 degrees F” 310 K
What is the ideal pH for…
- Most enzymes
- Gastric enzymes
- Pancreatic enzymes
- 7.4
- 2
- 8.5
Where can mixed inhibitors bind and how does the difference in binding change the Km of enzyme? How does Vmax change?
Binds to allosteric site
- Bind to enzyme–> increase Km value
- Bind to enzyme-substrate complex –> lower Km
Vmax for both decreases
Where do uncompetitive inhibitors bind and how do they influence Km and Vmax?
They bind to an allosteric site. Bind to enzyme-substrate complex and lock the substrate in enzyme.
Km and Vmax both decrease
What are two possible methods for irreversible inhibition?
- active site is made unavailable
- enzyme is permanently altered
What are the two domains of zymogens and why do they have these domains?
They have a catalytic (active) and a regulatory domain
Zymogens are secreted in inactive form because dangerous and regulatory domain can be removed or alterd to expose active site
What are the 5 structural proteins?
- Collagen: provide strength/flexibility, makes up extracellar matrix of connective tissue
- Elastin: stretch and recoil, component of extracelluar matrix of connective tissue
- Keratin: intermediate filament proteins in epithelial cells/mechanical integrity of cell/regulatory proteins
- Actin: microfilaments and thin filaments in myofibrils. Is polar to allow motor proteins to travel undirectionally/most abundant protein in eukaryotes
- Tubulin: makes up microtubules, have polarity (negative end is near nucleus and positive end is in the periphery of cell)
What are three motor protons and their primary functions?
- Myosin: interact with actin/cellular transport/involved in thick filaments in myofibril
2/3. Kinesins and dyneins: vesicle transport
- Kinesin: align chromosoms during metaphase
- Dyneins: involved in sliding movement of cilia and flagella
-
What are two difference between cytoskeletal and motor proteins?
- Cytoskeletal tend to be fibrous with repeating domains (motifs)
- Motor proteins have ATPase activity and binding heads
What are the three major families of cell adhesion molecules?
- Cadherins: glycoproteins that mediate Ca-dependent cell adhesion
- Integrins: two membrane spanning proteins\play role in cell signaling (cell-cell adhesion)
- Selectins: bind to carbohydrates that project from cell surfaces/ play role in host defense
Define opsonization?
antibody marks pathogen for destruction
Define agglutinating?
clumbing together the antigen and antibody into a large insoluble protein complex that can be phagocytized
What two types of bonds hold the heavy and light chains of antibodies together?
disulfide bonds and noncovalent bonds
What are the two domains of an antibody? Function for each?
V-domain: bind to antigen
C-domain: activate complememt/phagocytosis
What are four steps in GPCR pathway?
- Ligand binding enages the G protein
- GDP–> GTP, alpha unit dissociates from beta and gamma
- activated alpha subunit alters the activity of adenylate cyclase or phospholipase C
- GTP is dephosphorylated to GDP, alpha subunit rebinds to gamma and beta
What are the three main types of G proteins?
- Gs=stimulates adenylate cyclase, increases cAMP in cell
- Gi=inhibits adenylate cyclase, decreases cAMP in cell
- Gq=activates phospholipase C, which cleaves a phospholipid from the membrane to form PIP2 –> cleaved inton DAG and IP3
What are two difference between a Native PAGE and SDS-PAGE?
- Native maintains shape of protein so complete protein can be recoved after analysis and more accurately determines globular size of protein
- SDS- denatures protein and masks charge to can compare size of protein
What is one important concept for Size exclusion chromatography?
larger molecules elute first bc small molecules are trapped in small pores of beads
What are two drawbacks to affinity chromatography?
- protein of interest may not elute because affinity is too high
- protein may be permanently bound to the free receptor in the elutent
What is the primary method of determining protein structure?
X-ray crystallography but NMR can be used as well
What are two ways amino acids that compose a protein can be determined?
- amino acids that compose a protein can be determined by protein hydrolyisis and then chromatographic analysis
- Use edman degradation: selectively and sequentially removes the N-terminal amino acids and then anaylze via mass spectroscopy
What are four ways protein concentration can be detemrined? Which one is most common?
- UV spectroscopy: bc proteins can have aromatic side chains so do not need any treatment, but sensitive to contaminants
- Colorimetric changes –> BCA assay, Lowry reagent assay, Bradford assay
What die does Bradford Assay use and how does it work?
- Coomassie Brilliant Blue dye (green-brown)
- Gives up protons when bind to amino acids and will turn blue
- more protein, stronger blue color
Equation for vmax?
vmax=[E]xkcat
What might be two plausible explainations if you detect a low activity with a high concentration of protein when using affinityn chromatography?
- protein is inactive
- Protein elutes off of an affinity collumn by binding free ligand. The binding might not have be reversed for the active site to be occupied for the free ligand so stayed on column
Name?
D-fructose
How do you find the number of steroisomers?
2^n
n=the number of chiral carbons
What is the difference between a diastereomers and epimers?
Epimers are diastereomers but epimers differ in configuration at exactly one chiral center
How can monosaccharides for cyclic hemiacetals or hemiketals?
the hydroxyl serves as a nucleophile and the carbonly group is the electrophile
What is the difference between and alpha-anomer and a beta-anomer?
Alpha: has the -OH of the C-1 trans to the CH2OH (axial)
Beta: has the -OH group of the C-1 cis to the -CH2OH (equitorial)
What is Mutarotation?
Hemiacetal rings ossilate btw either alpha or beta anomer
the alpha-anomer is less favored bc the hydroxyl of anomeric carbon is axial
What are oxidized aldehydes called? Are they strong reducing or oxidizing agents?
Aldonic acids –> strong reducing agents
What two reagents are used to detect reducing sugars?
- Tollens’ reagent: Tollen’s reagent is reduced to produce a silver mirror in the presence of aldehydes
- Benedict’s reagent: form a red ppt. This test is specific for glucose
Which one of the three most important disaccharides is this?
Sucrose (glucose alpha 1, 2 fructose)
Which one of the three most important disaccharides is this?
Lactose (galactose Beta 1,4 glucose)
Which one of the three most important disaccharides is this?
Maltose (glucose alpha 1,4 glucose)
What are three characteristics of cellulose?
- Beta D glucose linked by B 1,4 glycosidic bonds
- H-bonds holding polymer chains together for support–> very strong
- humans do not have cellulase
What are four characteristics of starch?
- alpha D glucose linked by alpha 1,4 glycosidic bonds
- plants store starch as amylose
- amylopectin is a starch but has branches bia alpha 1,6 glycosidic bonds
- Broken down by alpha and beta amylase
What are three characteristics of glycogen?
- Similar to starch but with more alpha 1,6 glycosidic bonds
- more branching –> decrease intermolecular bonding –> more soluble in water so more glucose to be stored in body
- Branching allows gylcogen phosphorylase to cleave at mutliple nonreducing ends and phosyphorylate them
What are three types of structural lipids?
- Phospholipids
- Glycerophospholipids
- Spingolipids
What are three components of Phospholipids?
- a phosphate
- alcohol which is joined to a 3)hydrophobic fatty acid by a phophodiester linkage
What are three components of Glycerophospholipids? How are they bonded together?
- phospholipid that contains a glycerol back bone bonded by ester linages to two fatty acids and by a phosphodiester bond to a polar head group
What are the three components of sphingolipids?
- sphingosine or sphingoid backbone instead of a glycerol one
- long chain, non-polar fatty acid tails
- polar head group
What are two traits of waxes?
- esters of long chain fatty acids with long chain alcohols
- help animals and plants prevent dehydration
What are four signaling lipids?
- Terpenes/Terpenoids
- Steroids
- Prostaglandins
- Fat-soluble vitamins
What are two traits of cholesterol?
- amphipathic
- a low temps keeps membrane from freezing and at high temps keeps memebrane intact
What is the defining structure of steroids?
three cyclohexane rings and one cyclopentane ring
What are 3 traits of prostaglandins?
- paracrine and autocrine signaling molecules (not endocrine)–> they affect regions close to where they are produced rather than affecting entire body
- regulate synthesis of cAMP
- affect smooth muscle contraction, body temp, fever, pain, sleepwake cycle
What are three main traits of vitamin A?
- important for vision, growth, immune function
- Vit A/carotene is metabolized to retinal
- Retinol is the storage form of vit A and is oxidized to retinoic acid which regulate gene expression in epithelial development
What are three main traits of vitamin D?
- can be consumed or formed in UV light driven rxn in skin
- Vit D/cholecalciferol: in liver and kidney is converted into calcitriol which increases Ca and phosphate uptake in intestines to promote bone production
- lack of vit D can result in rickets, which is curved long bones and impeded growth in children
What are three traits of vitamin E?
- also known as tocopherols
- act has biological antioxidants
- aromatic rings destroy free radicles, preventing oxidative damage (ex:cancer)
What are three traits of vitamin K?
- called phylloquinone and menaquinones
- allows for postranslational modification of prothrombin (clotting factor in blood)
- required to introduce Ca-binding sites on calcium dependent proteins
What are two lipids involved in energy storage?
- Triacylglycerols
- Free Fatty Acids
What are three traits of triacyglycerols?
- three fatty acids bonded by ester linkages to glycerol
- adipocytes store triaglycerides
- the carbon atoms in lipids are more reduced than carbohydrates so they release 2x as much energy
What are two traits of free fatty acids?
1) esterfied fatty acids with a free carboxylate group
2) circulate in the blood by noncovalently bonding to albumin
What is saponification?
ester hydrolysis of trycylglycerols using a strong base (lye–> NaOH/KOH)–> leaving glycerol and fatty acid salt (soap)
What is the function of soap and how does it work?
It is a surfactant and lowers the surface tension of the liquid surface (detergent and emulsiferi)
aggregates of soap with hydrophobic tails turn inward with hydrophilic tails outward (micelles) to dissolve lipid-soluble molecules, watch away water and the formation of a colloid, combo of two phases
What two susbtances in body allow the formation of micelees?
fatty acids and bile salts secreted from gallbladder
What are topoismerases? What is one example?
They are involved in DNA replication and mRNA synthesis
ex: negative supercoils into the DNA molecules. facilitate DNA replication by keeping the strands separated and untangled
What is the main function of flippases?
Responsible for the movement of phospholipids between the layers of the plasma membrane because it is otherwise energetically unfavorable
What are the two structures phospholipids spontaneously form into?
micelles (monolayer vessicles) and liposomes (bilayer vessicles)
What are desmosomes and Hemidesmosomes?
- Desmosomes: bind adjacent cells by anchoring to the cytoskeleton and are formed by interactions btw transmembrane proteins associated with intermediate filaments inside adjacent cells
- Hemisomes: main function is to attach epithelial cells to underlying structures
What is osmotic pressure? How does it relate to the direction of water flow?
- pressure applied to a pure solvent to prevent osmosis
- water will move towards area with highest osmotic pressure
What is pinocytosis?
endocytosis of fluid and disolved substances
What 4 lipids make up the plasma membrane?
- Triagylcerides and fatty acids–> precursor for phospholipids
- Glycerophospholipids: replace one fatty acid with phosphate group
- cholesterol
- wax
What is the difference between the inner mitochondrial membrane and other biological membranes? What is the pH gradient btw cytoplasm and intermembrane space?
- Innermembrane space lacks cholesterol
- no pH gradient bc the outer mitochondrial membrane has a high permeability for molecules
What is the Nernst Equation?
E=(61.5/z)log ([ion]out/[ion]in)
z=charge of ion
What are 4 difference/similarities between GLUT 2 and 4?
- GLUT 2 is in hepatocytes and pancreatic cells and GLUT4 is in adipose and muscle cells
- The Km for GLUT2 is higher (has first order kinetics) than for GLUT4 (zero order kinetics)
- GLUT4 is responsive to insulin bit GLUT2 is not (but it serves as a glucose sensor to cause release of insulin in pacreatic B-cells)
- GLUT4 is saturated when blood glucose levels are just a bit higher than normal (still only permit a constant flow of glucose so increase transport but increase number of transporters). GLUT2 cannot be saturated under normal conditions
What are the 2 difference between Hexokinase and Glucokinases?
- Hexokinase found in most tissue and glucokinases present in hepacytes and pacreatic B-iselt cells
- Hexokinase has low Km, glucokinase has high Km
What is the main function of lactate dehydrogenase?
- reduce pyruvate to lactate and make more NAD+, which replenishes the oxidized coenzyme for glyceraldehyde 3 phosphate
What are the three steps for fructose metabolism?
- liver phosphorylates fructose using furctokinase to trap inside cells.
- Fructose 1-phosphate is cleaved into glyceraldehyde(can be phosphorylated into G3P and DHAP by aldolase
- go to glycolysis, glycogenesis, glucoeogenesis
What are these called?
- thiamine
- pyrophosphate
- lipoic acid
- CoA
- FAD
- NAD+
cofactors
What are 4 traits of the Pyruvate dehydrogenase reaction?
- Pyruvate enter mitochondira and converted to acetyl-CoA for entry into the citric acid cycle
- pyruvate hydrolysis is inhibited by acetly-CoA and pyruvate is converted into oxaloacetate by pyruvate carboylase to enter gluconeogensis
- pyruvate dehydrogenase in liver is activated by insulin
- reactants are pyruvate, NAD+, CoA and products are NADH, CO2, and acetyl CoA
What is glycogenesis?
forming glycogen
What are 3 facts about glycogen synthase?
- rate-limiting enzyme of glycogen synthesis and forms the alpha-1,4 glycosidic bond found in linear glucose
- stimulated by G6P and insulin
- inhibited by epinephrine and glucagon
What are 2 facts about branching enzyme?
- introduces alpha 1-6 linked branches into the granile as it grows
- role in glycogensis
What are 3 facts about glycogenolysis?
- process of breaking down glycogen using glycogen phosphorylase
- glycogen phosphorylase is activated by glucagon in the liver and by AMP/Epinephrin in the skeletal muscles
- cannot break down alpha 1-6 bond so stops near the outmost branch points
What are 3 facts about debranching enzymes?
- two enzyme complex that deconstructs the branches in glycogen that have been exposed to glycogen phosphorylase
- breaks alpha 1,4 bonds adjacent to the branch points and moves the small oligo-glucose chains that is releases to exposed end of other chain, form new alpha 1,4 bond to a longer link.
- role in glycogenolysis
What is the difference btw glucogenic and ketogenic amino acids?
Glucogenic aa (all except leucine and lysine) can be converted into intermediates and feed into gluconeogenesis
ketogenic aa can be converted into ketone bodies which can be used as alternative fuel
Under what two conditions should the body carry out gluconeogensis?
- when a person is fasting for more than 12 hours
- hepatic and renal cells must have enough energy to drive the process of glucose creation, which require succificent fat stores and B oxidation
mostly in the liver
How does acetyl-CoA shift the metabolism of pyruvate?
- Acetly-CoA inhibits pyruvate dehyrogenase complex while activating pyruvate carboxylase. Shift from burning pyruvate in the citric acids cycle to creating new glucose molecules for the rest of the body. The acetle CoA from this regulations comes from B-oxidation (fatty acid oxidation)and not glycolysis (bc would just burn the glucose that is being generated)
What are the two main functions of the pentose phosphate pathway?
- producetion of NADPH
- source ofr ribose-5-phosphate for nucleotide synthesis
What is glutathione?
reducing agent that can help reverse radical formation before damage is done
What is the overall reaction of the pyruvate dehydrogenase complex?
Pyruvate +CoA-SH +NAD+–> Acetyl-CoA +CO2+NADH+H+
What is the main purpose of the citric acid cycle?
complete oxidation of carbons in intermediates to CO2 so can have reductions coupled with CO2 formation to form NADH and FADH2 for ETC
What are the three main sites of regulation for citric acid cycle? Which one is the rate limiting enzyme?
- Citrate synthase: Inhibitors are ATP, NADH, succinyl-CoA and citrate/ no activators
- Isocitrate dehydrogenase (rate limiting enzyme): Inhibitors are ATP and NADH, activators are ADP and NAD+
- Alpha-ketoglutarase complex: Inhibitors are ATP, NADH, succinyl-CoA/ activiators are ADP, Ca2+
What are the the 3 products yeilds from citric acid cycle? How many ATPs do they produce?
- 3 NADH–> 10 ATP
- 1FADH2–> 1.5 ATP
- 1 GTP–> 1ATP
(mutliple by two for one glucose molecule)
What are the 4 different complexes in the ETC?
- Complex I: transfer of electrons from NADH to CoQ. First site of proton pump (4 protons)
- Complex II: FADH2 reduced by iron-sulfate protein in CoQ. No hydrogen pumping here
- Complex III: transfers of electrons from CoQ to cytochrome c. proton pump here (4 protons)
- Complex IV: transfer of electron from cytochrome c to oxygen. proton pump here (two protons)
What are the two important subunits of CoQ out of the 20 subunits?
- proteins that has a iron-sulfer cluster
- Flavoprotein that oxidizes NADH. Flavoprotein has a coenzyme called FMN.
What are the 2 shuttle mechanisms that cause a range of 30-32 ATPs to be produced?
Shuttle mechanism: transfers high energy electrons of NADH to a carrier than can cross the inner mitochondrial membrane because NADH cannot cross inner mitchondrial membrane
Gylcerol 3-phosphate Shuttle: allow NADH produces in cytosol to be used in ETC. Created RADH2 to contributed to complex II
Malate-asparate shuttle: cystolic oxalacetate, cannot pass through inner mitochondrial membrane and is reduced into malate, which can. Once malate crosses into matrix, mitochondrial malate dehydrogenase reverse the reaction to form mitochondrial NADH and pass electrons to complex I.
What is the difference between chemiosmotic and conformational coupling?
- Chemiosmotic: H+ flow into F0 protions of ATP synthase and chemical energy of gradient is harnessed to convert ADP into ATP in F1 portion
- conformational: proton gradients and ATP synthesis is indirect. ATP releases by synthase as a result of conformational changes caused by gradient (turbine)
How is cystein different from other amino acids?
It is in the R configuration while the rest of amino acids are in the S
How are peptide bonds formed and cleaved?
Formed by condensation reactions and cleaved by strong acids and based
Why is the C-N bond in an amide planar?
it is a partial double bond character due to resonance
What are the two ways amino acids are synthesized?
- Strecker synthesis
- Gabriel Synthesis
What are two characteristics that make inorganic phosphates have so much energy?
- contain negative charge, so when bonded to other phosphate groups, this creates repulsion with adjacent phosphate groups
- can be resonance stabilized
What is an organic phosphate?
are carbon containing compounds that also have phosphate groups (ATP,GTP, DNA)
What are two traits of phosphoric acids?
- three acidic hydrogens with unique pKa
- wide variety of pKa act as a moderate buffer over a large range of pH values. can pick up or donate H+
What 4 substances contributes to chemical digestion of lipids in small intestine?
- bile
- pacreatice lipase
- colipase
- cholesterol esterase
What is one difference between how large and small fatty acid chains are absorbed?
- Small: absorbed across intesting into blood
- long: are absorbed as micelles and assembled into chylomicrons for releases in lymphatic system
What are 3 traits of hormone-sensitive lipase (HSL)?
- insulin activates it/ also epinephrine and cortisol can activate it
- hydrolyzes triacylgerols, yeilding fatty acids and glycerol –> releases glycerols can go to liver for glycolysis or glucogenesis
- effective within adipose tissue
What are the 5 different types of lipoproteins? Function?
- Chylomicrons: transport triacylglycerols, cholesterol, and cholesteryl esters from intestine to tissue
- VLDL: transports triaglycerols and fatty acids from liver to tissue/ produced and assembled in liver cells
- IDL: picks up cholesteryl esters from HDL to become LDL
- LDL: delivers cholesterol into cells
- HDL: picks up cholesterol accumulating in blood vessesl/delivers cholesterol to liver and steroidogenic tissues/transfers apoliproteins to other lipoproteins. synthesized in liver and intestines
What are apoproteins?
they are receptor molecules and are involved in signaling/control interactions between lipoproteins
What is the primary method of transporting free fatty acids in blood?
free fatty acids remain in blood, bonding to albumin and other carrier proteins. Much smaller amount will remain unbonded
Order the 5 lipoproteins from greated percentage to least?
HDL>LDL>IDL>VLDL>chylomicrons
where are lipoproteins primarly synthesized?
liver and intestine
Where does fatty acid synthesis take place?
cytosol, mostly in liver
How do fatty acids enter mitrochondria for beta oxidation?
Small and medium sized chains can freely diffuse. Long chains need carnitine acyltransferase I (rate-limiting enzyme of oxidation)
What what are three product generated by beta oxidation?
- FAD–> FADH2
- (NAD+–> NADH)
- acetyl-CoA
what does acetyl-CoA stimulate in the liver?
glucogensis by activating pyruvate carboxylase
How does Beta oxidation of unsaturated fatty acids differ from that of saturated fatty acids?
additional isomerase and reducatasewhich provide the sterochemistry necessary for futher oxidation
What is ketogenesis? What is the main enzyme?
occurs in the mitochondria of liver cells when there is excess acetyl-CoA acculating during fasting
HMG-CoA synthase main enzyme
What is ketolysis?
aim to regain energy via oxidation of ketone bodies, which takes place in mitochondria. stimulated by low energy states in muscle and brain tissue
What is ketolysis of brain?
during prelonged fast, the brain gets 2/3 of its energy from ketone bodies are metabilized in acetyl-CoA.
Why are fatty acids used to create ketone bodies instead of creating glucose?
fatty acid degradation results in large amounts of acetyl-CoA, which cannot enter the gluconeogenic pathway to reproduce glucose. only odd numbered fatty acids can act as a source of carbon for gluconeogenesis
fatty acid synthesis is used to store energy
Where does proteolysis occurs and what enzymes are involveed?
Stomach: pepsin
small intestine: trypsin, chymotrypsin, carboxypeptidases A and B