Biochemistry S1 U2

water will form bonds with other polar mo;ecules in a solution and almost all the time act as this

a substance that can release hydrogen ions (protons) in a solution

a substanc hat can accept hydrogen ions in a solution

a mixture of an undissociated acid and its conjugate base (the form of the acid that has lost its proton)

when is a buffer most affective

what is the body's natural buffer mechanism (expiration)(excretion)

blood gass analysis: For oxygen, ________________ is used; oxygen diffuses through a membrane specific for oxygen permeability, and once oxygen passes through the membrane it diffuses to the cathode. When oxygen reaches the cathode, electrons are attracted from the anode, thereby reducing the oxygen to water

blood gas analysis: pCO2 is determined using a S_________________, which consists of an outer gas-permeable membrane, specific for CO2, and a bicarbonate buffer within the electrode. Once the CO2 crosses the membrane, the gas interacts with bicarbonate, altering the equilibrium among CO2, carbonic acid, and bicarbonate.

water: Its heat of fusion is (high/low), so a large drop in temperature is needed to convert liquid water to the solid state of ice.

a general term applied to bicarbonate and inorganic anions and cations.

water will move from a compartment with a ____________ concentration of solutes (lower osmolality) to one with a ____________ concentration to achieve an equal osmolality on both sides of the membrane.

pH equation with H+ ions

Acidic solutions have a __________ hydrogen ion concentration and a __________hydroxide ion concentration than pure water (pH < 7.0), and basic solutions have a ____________hydrogen ion concentration and a ____________ hydroxide ion concentration (pH > 7.0).

increased urine volume

The tendency of the acid (HA) to dissociate and donate a hydrogen ion to a solution is denoted by

the higher the ______- the reater is the tendency to dissacociate a proton

Ka equation

strong acid in the body

what are the major sources of sulfuirc acid in the body (H2SO4)

you can see that a weak acid is 50% dissociated at a pH equal to its __________

what is the henderson hasselbalch eq for wk acids

Buffers allow solutions to resist changes in _____ when hydrogen ions or hydroxide ions are added

a buffer can only compensate for an influx or removal of hydrogen ions within approximately __________ pH unit of its pKA

normal pH range of the body

intracelllar pH

major buffer systems of the body

major source of metabolic acid in the body

henderson hasselbalch for bicarbonate buffer system

Buffering systems of the body: CO2 produced from cellular metabolism is converted to ________________(x2) in the red blood cells. Within the red blood cells, the_______ is buffered by hemoglobin (Hb) and phosphate (HPO42−) (

occurs when salt and water intake are less than the combined rates of renal plus extrarenal volume loss

symptoms of moderate dehydration

symptoms of severe dehydration

ketone bodies symthesized in the liver (x2)

branched carbon chain prefix

another name for a ring group

loss of electrons and results in the loss of hydrogen atoms together with one or two electrons or the gain of an oxygen atom or hydroxyl group.

the gain of electrons and results in the gain of hydrogen atoms or the loss of an oxygen atom.

at physiological pH, many amines cary (+/-) charge

sugars assumed to be (D/L) unless specifically added to the name because glucose is this

have the same chemical formula but differ in the position of the hydroxyl group on one or more of their asymmetric carbons

sugars wit n asymetric centers have (____) stereoisomers unless it has a plane of symetry

stereoisomers that differ in the position of the hydroxyl group at only one of their asymmetric carbons

sugars can be oxidixed at the aldehyde carbon to form _______

if the carbon containing the treminal hydroyl group is oxidixed, the sugar is called...

glycosidic bonds found in nucleosides and nucleotides

glycosidic bondids found in lactose and other sugars that join one sugar to another

usually straight aliphatic chains with a methyl group at one end (called the ω-carbon) and a carboxyl group at the other end

usually straight aliphatic chains with a methyl group at one end (called the _-carbon) and a carboxyl group at the other end

fatty acids w have single bonds between the carbons in the chain

fatty acids with one or more double bonds in the chain

most common saturated fatty acids in the cell

Lipids with lower melting points are more __________ at body temperature and contribute to the fluidity of our cellular membranes.

a group of hormone-like compounds produced by many cells in the body. They are derived from polyunsaturated fatty acids such as arachidonic acid that contain 20 carbons (eicosa) and have 3, 4, or 5 double bonds.

comprises glycerol with one or more fatty acids (the acyl group) attached through ester linkages

contain fatty acids esterified to positions 1 and 2 of glycerol and a phosphate (alone or with a substituent) attached to carbon 3

precursor for the synthesis of the other phosphoacylglycerols.

a class of lipids in cell membranes that have a backbone of sphingosine and are crucial for structural integrity and cell signaling

are amides formed from sphingosine by attaching a fatty acid to the amino group.

which contains a phosphorylcholine group attached to ceramide, is a component of cell membranes and the myelin sheath around neurons.

the steroid precursor in human cells from which all of the steroid hormones are synthesized by modifications to the ring or C-20 side chain.

compounds that contain an amino group and a carboxylic acid group.

in prpteins, the amino acids are always _______ amino acids, (the amino group is attached to the α carbon in the L-configuration)

pyridines in the body

purpose of nitrogen containing ring stuctures

In many of the nitrogen-containing rings, the hydrogen can shift to produce a ________, a compound in which the hydrogen and double bonds have changed position

compounds that have a single electron, usually in an outer orbital. Free radicals are radicals that exist independently in a solution or a lipid environment.

are radicals that exist independently in a solution or a lipid environment.

normal value for anion gap

refers to the difference in concentration between routinely measured anions (chloride and bicarbonate) and cations (sodium and potassium) in the blood

what does exposiure to high levels of DDT cause in humans

what is a method to remove polychlorinated fderiities from the environment

lysosomes contain _____ enzymes that degrade proteins and other large molecules

peroxisomes contain enzymes that use or produce...

receptors that span the membrane and contain an ecxtracellular binding domain for the messenger

receptrors inside rge cell (cytoplasm or nucleus)

Uric acid levels in blood or urine can be determined enzymatically through use of the enzyme _________e, which converts uric acid (plus oxygen) to allantoin and hydrogen peroxide

an acquired autoimmune disease in which most patients have developed pathogenic antibodies against these receptors(acetylcholine nictoinic r)

The membrane layer facing the “inside” of the organelle or cell is termed the ________t; the other layer is the __________.

The principal phospholipids in the membrane are (4)

wat lipids are more concentrated in the outer leaflet

what lipids are more concentrated in the inner leaflet

family of proteins, which are bound to the intracellular membrane surface and provide mechanical support for the membrane

a covalently attached lipid that anchors proteins to the external surface of the membrane

The A, B, and O blood groups are determined by the carbohydrate composition of the _____________ on the surface of red blood cells.

Once acetylcholine secretion stops, the message is rapidly terminated by _____________, an enzyme located on the postsynaptic membrane that cleaves acetylcholine

Lipophilic hormones that use intracellular gene-specific transcription factors include

how are hydrophobic intracellular signals moved trough the blood

Stimulates adenylyl cyclase

inhibits adenylene cyclase

Stimulates cGMP phosphodiesterase

Activates phospholipase Cβ

Activate Rho-GEF (guanine nucleotide exchange factor)

arginine pka

asparic acid pka

cystine pkaa

glutamic acid pka

histidine pka

lysine pka

serine pka

threonine pka

tyrosine pka

what determines how a protein can fold and how it interacyts with other molecules in the cell

what makes up a basic amino acid

at physiological pH, the free amino acids exist as ________: ions in which the amino groip is positively charge and the carboxylate group is negatively charged

with chronic hemolusis, the amount of heme degraded to ________ is increased; this is a result of the chronic excretion of excessive amounts of ______- from the liber into the bile, leading to bilrubinate crystal depositions in the gallbladder lumen

crushing or compressive pain in the chest area often radiating to the neck or arms

(posititive/negative) hydropathic index, the greater is the tendency to cluster with other nonpolar molecules and exclude water in the hydrophobic effect

what amino acid, because of its side chain, causes the least amount if steric hinderence in a protein

glycine

alanine

valine

leucine

Methionine

Isoleucine

Serine

Threonine

Cysteine

Proline

Asparagine

Glutamine

Lysine

arginine

histidine

aspartate

glutamate

phenylalanine

tyrosine

tryptophan

The pH at which the net charge on the molecules in solution is zero is called the

pka COOH

pka NH3

If many different amino acid residues are tolerated at a position, the region is called

isoforms of a protein all have the same ______ wjile isoenzymes all ________

refers to the addition of carbohydrates to a molecule.

what does the mutation in sickle cell anemia affect? (structure)

protein: regions of structure that fold independently.

The affinity of a binding site for its ligand is characterized quantitatively by an association or affinity constant

dissociation constant

how do you solve the Kd from Ka?

enlarged tongue

proteins: usually soluble in aqueous medium and resemble irregular balls

proteins: geometrically linear, arranged around a single axis, and have a repeating unit structure.

proteins: consists of proteins that have one or more regions aligned to cross the lipid membrane

protein structure: has a rigid, stable conformation that maximizes hydrogen bonding while staying within the allowed rotation angles of the polypeptide backbone.

why cant proline make up an alpha helix

Parallel sheets tend to have hydrophobic residues on (both/one side) sides of the sheets; antiparallel sheets usually have a hydrophobic side and a hydrophilic side.

are hytdrogen bonds stronger in parallel or antiparallel beta sheets

structure of LDH domain

relatively small arrangements of secondary structure that are recognized in many different proteins.

relatively large patterns of three-dimensional structure that have been recognized in many proteins, including proteins from different branches of the phylogenetic tree.

characteristic of actin folds

trasmembrane domain: The amino terminus (residues 1 through 34) extends out of the membrane and has branched high-mannose oligosaccharides linked through N-glycosidic bonds to the amide of ___________

structure of insulin

pO2 is (high/low), as in the lungs, both myoglobin and hemoglobin are saturated with oxygen.

at the (low/high) levels of pO2 in oxygen-using tissues, hemoglobin cannot bind oxygen as well as myoglobin

passes into the urine (myoglobinuria) and turns the urine red because the heme (which is red) remains covalently attached to the protein.

tert structure og myoglobin

Organic ligands that are tightly bound to proteins, such as the heme of myoglobin, are called

protein with its attached prosthetic group is called

The conformational change of hemoglobin is usually described as changing from a _______ state with low affinity for O2 to a _______ state with a high affinity for O2.

fx 2,3-BPG

what do protons binding do to hemoglovin

As the pH (decreases/increases)(, the affinity of hemoglobin for oxygen decreases,

strucxture if immunoglobulins

antigens: The variable regions of the L and H chains (VL and VH, respectively) interact to produce

what is the kd for antigens?

AAs in Collagen (1)

Because the reaction is nonenzymatic, the rate of glycation is proportionate to the concentration of glucose present, and individuals with hyperglycemia have much (higher/lower) levels of glycated proteins than individuals with normal blood glucose levels.

end product of glycilation reacyions

an unstable high-energy complex with a strained electronic configuration that is intermediate between substrate and product.

a condition in which bonds in the substrate are maximally strained.

enzymes increase rate of reaction by decreasing

what are the nmost potent inhibitors if ebzymes

a functional group on the protein either donates a proton (acid catalysis) or accepts a proton (general base catalysis) during the course of the reaction.

the substrate is covalently linked during the course of the reaction to an amino acid side chain at the active site of the enzyme.

required cofactor for an enzyme usually forms a covalent bond with the substrate during the course of the reaction.

these AA can participate in covalent catalysis

aa that most often poarticipates in acid based catalysis

usually participate directly in catalysis by forming a covalent bond with a portion of the substrate; the tightly held substrate moiety is then activated for transfer, addition of water, or some other reaction.

nonprotein organic cofactors that participate in reactions.

involved in oxidation–reduction reactions catalyzed by enzymes categorized as oxidoreductases

oxidation–reduction coenzymes that can act as antioxidants and protect against oxygen free-radical injury.

transfer hydrogen (hydrogen atoms or hydride ions) from the substrate to an electron-accepting coenzyme, such as NAD+.

how do metal ion catalysts act in reactions

optimal human enzyme temp

inhibitors mimic or participate in an intermediate step of the catalytic reaction.
-irreversibly bind

inhbitrs form covalent or extremely tight bonds with functional groups in the active catalytic site. These functional groups are activated by their interactions with other amino acid residues and are therefore far more likely to be targeted by drugs and toxins than amino acid residues outside the active site.

how does DFP work?

extremely potent and specific inhibitors of enzymes because they bind so much more tightly to the enzyme than do substrates or products. Drugs cannot be designed that precisely mimic the transition state because of its highly unstable structure.

metabolized in the liver to a toxic derivative (malaoxon) that binds to the active-site serine in acetylcholinesterase and other enzymes, an action similar to that of DFP.

a drug used to treat gout, decreases urate production by inhibiting xanthine oxidase.

what causes heavy metal tox

reaction: at least one substrate gains electrons and becomes reduced, and another substrate loses electrons and becomes oxidized

catalyze group transfer reactions—the transfer of a functional group from one molecule to another.

nitrogen group from an amino acid is donated to an α-keto acid, forming a new amino acid and the α-keto acid corresponding to the donor amino acid.

C–O, C–N, or C–S bonds are cleaved by the addition of H2O in the form of OH– and H+ to the atoms forming the bond.

cleave C–C, C–O, and C–N bonds by means other than hydrolysis or oxidation.

simply rearrange the existing atoms of a molecule; that is, create isomers of the starting material

synthesize C–C, C–S, C–O, and C–N bonds in reactions coupled to the cleavage of a high-energy phosphate bond in ATP or another nucleotide.

blood clearance rate of etoh per hr

ethanol clearance equation

the concentration of substrate required to reach ½Vmax.

michelis menten equation

The approach to the finite limit of Vmax is

enzymes that do not fit michaelis meten model

MEOS makes a greater contribution to ethanol oxidation and clearance from the blood at (high/low) ethanol levels

“competes” with a substrate for binding at the enzyme’s substrate-recognition site and therefore is usually a close structural analog of the substrate

competitive inhibitors effect on Km and vmax

noncompetitive inhibitors Vmax and

activators of allosteric enzymes bind more tightly to the high-affinity _____ state of the enzyme than the ________ state

allosteric inhibitors bind more tightly to the __________ state, so either substrate concentration or activator concentration must be increased to overcome the effects of the allosteric inhibitor.

what causes the modulation by phosphorlation and dephosphorylation?

what type of kinase is protein kinase A

bind to other proteins and regulate their activity by causing a conformational change at the catalytic site or by blocking the catalytic site (steric hindrance).

increase the rate of GTP hydrolysis by the G-protein, and therefore the rate of dissociation of the G-protein–target protein complex

binds to a G-protein, it increases the rate of GTP exchange for a bound GDP, and therefore activates the G-protein

bind to the GDP–G-protein complex and inhibit dissociation of GDP, thereby keeping the G-protein inactive.

the regulatory enzyme, which catalyzes the ___________step in the pathway. This is the slowest step and is usually not readily reversible

refers to a situation in which the end product of a pathway controls its own rate of synthesis

may occur through an increased supply of substrate to an enzyme with a high Km, allosteric activation of a rate-limiting enzyme through a compound related to substrate supply, substrate-related induction of gene transcription (e.g., induction of cytochrome P450-2E1 by ethanol), or increased concentration of a hormone that stimulates a storage pathway by controlling enzyme phosphorylation state.

that is, the number of reactions the enzyme can catalyze per unit time

deficientr gactor in hemophilia A

The hydrostatic pressure in the arteriolar end of the capillaries (~37 mm Hg) exceeds the sum of the tissue pressure (~1 mm Hg) and the osmotic pressure of the plasma proteins (~25 mm Hg). Thus, water tends to _________ the capillaries and enter extravascular spaces.

At the venous end of the capillaries, the hydrostatic pressure falls to approximately 17 mm Hg while the osmotic pressure and the tissue pressure remain constant, resulting in movement of fluid _________ from the extravascular (interstitial) spaces and into the blood

individuals who lack albumin

liver: Binds free fatty acids, calcium, zinc, steroid hormones, copper, bilirubin

liver:
Binds copper; appears to be more important as a copper storage pool than as a transport protein; integrates iron and copper homeostasis

liver: binds cortisol

liver:
Binds extracorpuscular heme

liver: Transport cholesterol and fatty acids

liver: Binds vitamin A

liver: Binds estradiol and testosterone

liver: Transports iron

liver: Binds thyroxine (T4); also forms a complex with retinol-binding protein

what makes platelets

Binding to collagen by ______ (integrin α2β1) causes the platelet to change its shape from a flat disk to a spherical cell.

Binding of subendothelial vWF by _________ causes changes in the platelet membrane that expose GPIIb/IIIa (integrin αIIbβ3)-binding sites to fibrinogen and vWF.

Mutations in GPIb
-Platelet aggregation is affected because of the inability of GPIb to adhere to subendothelial vWF.

a disease characterized by the formation in the circulation of microclots (microthrombi) consisting of aggregated platelets

________ released from the platelets and from damaged red blood cells binds to a receptor on the platelet membrane, which leads to the further unmasking of GPIIb/IIIa-binding sites.

factors VII, XI, IX, X, and prothrombin) are _________- that, when activated by cleavage, cleave the next proenzyme in the cascade.

The cofactor proteins (tissue factor, factors V and VIII) serve as ______ for other factors.

how does warfarin work to compete with VKOR1

Upon binding to the factor Va–platelet complex, prothrombin undergoes a conformational change, rendering it more susceptible to_______

what reduces vitamin K (reaction type

Antithrombotic effects of thrombin result from its binding to an endothelial cell receptor called

Protein S anchors the activated protein C complex (APC) to the clot through...

The APC destroys the active blood coagulation cofactors factor VIIIa and Va by (rxn)

(serine protease inhibitors) are a group of naturally occurring inhibitory proteins that are present in the plasma at high concentration

Fibrinolysis involves the degradation of fibrin in a clot by ___, a serine protease that is formed from its zymogen, _________

a circulating serum protein that has a high affinity for fibrin, promoting the incorporation of ________ in the developing clot