Biochemistry Carbohydrates - by MHashi, Biochem ch 8, Ch. 9 Lehninger biochem, Chapter 10 multiple choice, Chapter 7 Biochemistry, Biochem ch 6, Old Test 3; June 2010, My Test 2, Quiz 1, Cell Components, Quiz 2, Quiz 3, Quiz 4, Quiz 5, Old Test 1, Ma...

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S+E<-> (step 1)

ES->P+E

Turnover number

[PL]/[P][L]

Kassociation

Kcat

1/Kassociation

Kdissociation

Hemiketal

Ketone+alcohol

lowers

Kink makes harder to pack and _____ melting point in fatty acid.

Km is equal to the concentration ([S]) that gives half the maximum velocity

Km= (In words)

discontinuous

Lagging-strand synthesis is ________.

shorter

Larger molecules cannot get into pores (excluded), spend more time in solvent surrounding beads, travel faster through the column and have a _____ elution time in Gel Filtration.

Zymogen

Larger precursor molecule for an active enzyme

w (omega) carbon

Last carbon is referred to as the ___ carbon in a fatty acid

collagen

Left-handed helix; forms triple-stranded fibers wrapped in a right-handed fashion

Like dissolves _____.

1/Vo=(Km/Vmax)(1/[S])+(1/Vmax)

Lineweaver Burk Equation

Glycoconjugates

Linked to other structures

B. The condensation of non polar substances into liquids

London forces are the main force responsible for: A. The formation of clathrates B. The condensation of non polar substances into liquids C. The dissolving of salts in water D. The high heat of vaporization of water

acid

Lowry-Bronsted: proton (H+) donor

base

Lowry-Bronsted: proton acceptor

store energy (adipose tissue, body fat)

Main function of Triacylglycerol

Blood buffering system

Main one --> bicarbonate/carbonic acid system (HCO3-/H2CO3)

DNA amplification

Make more from a little

Polysaccharides

Many monosaccharides joined

2^n

Max number of stereoisomers

-measure of enzyme efficiency -measure of enzyme's affinity for the substrate -measure of the [S] needed for effective catalysis

Meaning of Km?

Nucleus

Membrane bounded structure in eukaryotic cells which contains the genome

Lysosome

Membrane-bounded organelle in eukaryotes that acts as a recycling center and contains many degradative enzymes

Golgi apparatus

Membranous organelle in eukaryotes which modifies proteins after transcription

A. Instantaneous dipoles due to the constant motion of electrons allow for attraction between pentanes

Methane, ehtane, propane and butane are gases at room temperature. Pentane is a liquid at room temp. Why? A. Instantaneous dipoles due to the constant motion of electrons allow for attraction between pentanes B. Pentane has enough hydrogens to have enough hydrogen bonding to be a liquid C. The pentane molecules aggregate into a liquid due to hydrophobic interactions D. Ion pairing between pentane molecules make is a liquid

Step 1: S+E<->ES Step 2: ES->P+E

Michaelis Menton minimal mechanism

Vo=K2[S][E]total/Km+[S]

Michaelis-Menton Equation

Km=K-1+K2/K1

Michaelis-Menton constant

Initial Rate Method

Mix S and E, measure rate quickly, it will be in steady state by the time measurement is made, repeat with varying [S], keep [E] total constant

Affinity chromatography

Mobile phase = liquid solvent; Stationary phase = resing beads that have aligned for the molecule of interest covalently attached Saves many steps with good ligand

Ion-exchange chromatography

Mobile phase = liquid solvent; stationary phase = resin beads w/ covalently attached charged groups

Paper chromatography

Mobile phase = solvent; stationary phase = paper

Cation exchange column

Mobile phase @ low pH (<pKa) Gradually increase the pH (pH gradient) Initially all in protonated form (most positively charged) Adhere to column Deprotonated as titration increase Elutes @ pI (zwitterion) No charge so it detaches from column

the speed of migration per unit field strength during electrophoresis

Mobility is defined as.....

The speed of migration per unit field strength during electrophoresis

Mobility is defined as:

Regulatory site

Modulator binding site (not the active site)

chaperones

Molecular that assist in protein folding are called ______.

chaperones

Molecules that assist in protein folding are called ___________.

Carbohydrate

Most abundant bio molecule on earth

Glucose

Most abundant monosaccharide

Allosteric regulation

Most common for pathway control

Ethidium bromide

Most common stain for visualization (when working with agarose)

Coomassie blue

Most common stain for visualization (when working with polyacrylamide)

unbranched

Most fatty acids are ______.

Regulatory This avoids unnecessary buildup of intermediates

Most often the enzyme for the first step in the pathway is the _________ enzyme

anomers

Mutarotation refers to the interconversion of _____.

anomers

Mutarotation refers to the interconversion of ______

Phi

N-alpha carbon

still

N-terminus and C-terminus ______ ionizable.

Tertiary

NRR'R''

Cytosol

Name for the aqueous phase outside the nucleus that do not include the organelles.

Cytosol

Name for the aqueous phase outside the nucleus that does not include the organelles

dipole-dipole Ionic interaction Val der Wall's Hydrophobic

Name the 4 main types of weak interactions

C H O N S P

Name the 6 most common elements in living organisms.

Negatively charged

Name the class of amino acids that are acidic.

Positively charged

Name the class of amino acids that are basic.

Nonpolar, aliphatic

Name the class of amino acids that are non-aromatic groups.

Polar

Name the class of amino acids that are uncharged.

Aromatic

Name the class of amino acids that contains one or more benzene-type rings.

- Triacylglycerides - Phopholipids - Sphingolipids - Archaebacterial ether lipids - Steroids

Name the five major classes of lipids

- Vapor pressure (lowering) - Boiling point (elevation) - Freezing point (melting point) (depression) - Osmotic pressure (raising)

Name the four colligative properties.

1. solvent 2. reactant 3. structural component 4. thermal regulation

Name the four roles of water.

Centrifugation, Chromotography, Electrophoresis, Dialysis

Name the four techniques for purification and separation.

- Storage of energy - Insulation from environment - Water repellant - Buoyancy control and acoustics in marine mammals - Membrane structure - Cofactors for enzymes - Signaling molecules - Piments - Antioxidants

Name the functions of lipids (Hint: there are 9)

Microcentrifuge, table top, ultracentrifuge

Name the three models of centrifuges.

A. Ion-ion B. Ion-dipole

Name the types of ionic interactions

Non-polar tail (R group)

"cage" of ordered water molecules surround it (no hydrogen bonding possible between water and non-polar tail)

ligases

"joining" and requires ATP for energy

lactose

"milk sugar"

Hydrophobic

"water hating" - non polar, unable to favorably attract water

Hydrophilic

"water loving" - polar or ionic species able to attract water

%T=T x 100

% Transmittance

Endoplasmic reticulum

(Smooth and rough) double membranes extending throughout the cytoplasm in eukaryotic cells; encloses secretory channels

Ionic interactions

(charge-charge interactions) - electrostatic attraction between charged particles (full or partial charges)

Network polymer

(gels) - 3D interconnections (web)

oxidoreductase

(redox reactions) include dehydrogenase, peroxidases, oxygenases etc

Ellute

(v.) to come out

endergonic, nonspontaneous

+ deltaG

Carbon

- Light element that forms relatively strong covalent bonds - Great capacity to bond to itself and strongly to others - Number of ways to bond is great (isomerism) - Tetrahedral bonding pattern of C allows for many types of shapes

N and O-glycosides

- O-glycosides results from monosaccharide attached to OH group of another sugar or aglycone. - N-glycosides results from monosaccharide attached to NH2 of aglycone. NOTE: -All sugar-sugar glycosidic bonds are O type linkage.

exergonic, spontaneous

- deltaG

Amylopectin

-Amylopectin is the outer layer of starch -Constitutes 80-85% of the granule -Amylopectin is formed of branched chain, each chain is composed of 24-30 glucose units -Has α 1-4 glycosidic bond and α 1-6 glycosidic bond at the branching points

Amylose

-Amylose is the inner layer of starch -Constitutes 15-20% of the granule -Amylose is formed of non-branching helical structure of glucose unit -Has the glycosidic bond α 1-4

Sugar acids

-Are produced by oxidation of carbonyl carbon, last hydroxyl carbon or both.

Asymmetric carbon atoms

-Asymmetric carbon atom is the carbon atom to which 4 different groups or atoms are attached. -Any substance containing asymmetric carbon atom shows 2 properties, optical activity and optical isomerism

What is the definition of Carbohydrates?

-Carbohydrates are aldehyde or ketone derivatives of polyhydric alcohols or any substance derived from them.

Importance of carbohydrates:

-Energy production e.g. glucose -Formation of structural elements in animal and plant cells -Formation of Glycolipids and glycoproteins that enter in the structure of cell membrane and for the ground substances between tissues -Participates in biological transportation, cell-cell recognition

Epimeric carbon and epimers

-Epimeric carbon is the asymmetric carbon atom other than caron of adehyde or ketone group e.g. carbons number 2,3 and 4 of glucose -Epimers are isomers resulting from the change of position of groups around the epimeric carbons.

N.B

-Fibronectin binds to membrane receptor proteins called integrins. -In addition to to integrins, fibronectin also binds to extracellular matrix components such as: 1) collagen 2) Fibrin 3) Heparan sulfate proteoglycans

Glucose in solution

-Glucose in solution is present mainly 99% as glucopyranose and 1% as glucofuranose. Of the 99% of glucopyranose, 36% are present as α-D form and 63% as β-D form.

Role of Hyaluronic acid in disease

-Hyaluronic acid facilitates cell migration -It is produced in increased amounts by tumor cells. This facilitates migration of these cells through the extracellular matrix and spread of the tumor

Mutarotation

-It is a gradual change of specific rotation of any optical active substance having free aldehyde (-CHO) or ketose (C=O) groups i.e. having anomeric carbons

Inositol = cyclitol

-It is a sugar derived from glucose Function: 1)inositol enters in the structure of lipositol (a phospholipid) which is present in cell membrane 2)Acts as precursor of second messenger (inositol triphosphate) mediating hormonal action inside cells

Optical isomerism

-It is the ability of substance to present in more than one form (isomer) -> a substance containing one asymmetric carbon has 2 isomers ->a substance containing 2 or more asymmetric carbon atoms can exist in a number of isomer = 2n. Where n is the number of asymmetric carbon atoms. E.g. Glucose has 4 asymmetric carbon atoms, 2^4 = 2x2x2x2 = 16 isomers

Optical activity

-It is the ability of substance to rotate plane-polarized light either to the right or to the left. -If the substance rotates the plane polarized light to the right it is called dextrorotatory or d or + -If the substance rotates the plane polarized light to the left it is called levorotatory or L or - -Glucose contains 4 asymmetric carbon atoms, it is dextrorotatory so its sometimed called dextrose. -Fructose contains 3 asymmetric carbon atoms, it is levorotatory so it is sometimes called Levulose

Specific rotation

-It is the angle of rotation specific for each optically active substance when: a)The concentration of substance is 100 g/dl b)The length of measuring tube is 10 cm e.g. specific rotation of glucose is +52.5° and fructose is -91°

Racemic mixture

-It is the mixture containing equal number of molecules of 2 optically active sugars, one is dextrorotatory and the other is levorotatory. Thus it shows no optical activity as the angle of rotation is equal in both sides

Resolution

-It is the separation of optically inactive racemic mixture into its optically active substances

Glycogen

-Its some times called animal starch Structure: -glycogen is homopolysaccharide formed of α-D glucose units (α 1,4 and α 1,6) -Main glycosidic bond is α 1-4 linkage. -only at the branching point, the chain is attached by α 1-6 linkage -Each branch is made of 12-14 glucose units.

Functions of Laminin

-Laminin is glycoprotein found in extracellular matrix -Forms the basement membrane of all internal organs -Laminin is vital to making sure that the overall body structures are held together

Laminin in the renal glomerulus

-Laminin is the major protein component of renal glomerulus. It is one component of basal lamina -Primary components of the basal lamina are four proteins: 1) Laminin 2)Collagen 3) Entactin 4) Proteoglycans -The thick basal lamina in the renal glomerulus has an important role in glomerular filtration.

Trioses

-Monosaccharides containing 3 carbon atoms a) Aldotrioses : Glyceraldehyde b)Ketotrioses: Dihydroxyacetone

Tetroses

-Monosaccharides containing 4 carbon atoms a) Aldotetroses: Erythrose b) Ketotetroses: Erythulose (Note the suffix -ulose means keto group)

Pentoses

-Monosaccharides containing 5 carbon atoms a)Aldopentoses: Ribose, Deoxyribose, Arabinose, Xylose, Lyxose b)Ketopentoses: Ribulose, Xylulose

Hexoses

-Monosaccharides containing 6 carbon atoms a)Aldohexoses: Glucose Mannose Galactose b)Ketohexoses: Fructose

Classification of carbohydrates

-Monosaccharides: contain one sugar unit -Disaccharides: contain two sugar units -Oligosaccharides: contain 3-10 sugar units -Polysaccharides: contain more than 10 sugar units

Aldonic acids

-Oxidation of carbonyl carbon to carboxylic group gives aldonic acid. e.g. glucose is oxidized to gluconic acid.

Uronic acids

-Oxidation of last hydroxyl carbon gives uronic acid e.g. glucose is oxidized to glucuronic acid.

Homopolysaccharides

-The contain repeated same sugar units -They include: a) starch b) dextrins c) glycogen d) cellulose e) inulin f) dextrans

Amino sugar acids

-These are a condensation of amino sugars and some acids -They are occurring in glycoproteins Q) Draw: 1)Mannosamine + pyruvic acid 2)Neuraminic acid (NANA) 3)Sialic acid which is N-acetyl neuraminic acid

Polysaccharide

-These are carbohydrates, formed of more than 10 sugar units. -They are classified into: 1) Homopolysaccharides 2) Heteropolysaccharides

Proteoglycans

-These are chains of GAGs attached to protein molecule -They serve as a ground substance and associated with structure elements of tissues as bone, elastin and cartilage. -The carbohydrate part is presented in very long un-branched chains (more than 50 monosaccharides) attached to protein core.

Aldaric acids

-These are dicarboxylic acids produced by oxidation of both carbonyl carbon and last hydroxyl carbon. e.g. glucose is oxidized to glucaric acid (saccharic acid)

Disaccharides

-These are formed by condensation of 2 molecules of monosaccharides bound together by glycosidic bond. -General formula Cn(H20)n-1 Important disaccharides are: 1-Maltose 2-Isomaltose 3-Lactose 4-Sucrose 5-Cellobiose 6-Trehalose

Dextrins

-These are hydrolytic products of starch -They are formed of α- glucose units but simpler than starch -They include amylodextrin, erythrodextrin and achrodextrin -They give red color with iodine

Anomers

-These are isomers obtained from the change of position of hydroxyl group (-OH) attached to the anomeric carbon. e.g. α and β glucose are 2 anomers.

nucleotide functions

-energy for metabolism -enzyme cofactors -signal transduction -monomers of DNA and RNA

nucleic acid functions

-genetic material -transmission of genetic info - processing of genetic info - protein synthesis

amylopectin

-homopolymer -branched -main chain is alpha (1->4) -branched points are alpha (1->6) links -branches- spacing about 24-30 units, length about 15-25 units

Amino sugars

-in these sugars, the hydroxyl group attached to carbon number 2 is replaced by an amino or an acetylamino group. -Amino sugars are constituents glycoproteins, gangliosides, glycosaminoglycans Q) Draw: Glucosamine Galactosamine Mannosamines

Anomeric carbon

-is the asymmetric carbon atom obtained from carbonyl sugar group: carbon number 1 in aldoses and carbon number 2 in ketoses.

Glycosidic bond

-it is the bond between a carbohydrate and another compound to form a complex carbohydrate -This bond is between the hydroxyl group of anomeric carbon of monosaccharide (Carbon 1 of aldoses and Carbon 2 of ketoses) and another compound such as: a) another carbohydrates to form disaccharide b)Aglycone i.e. non-carbohydrate to form glycoside.

glycogen

-larger -more frequent branching from main chain (every 8-12 units) -branches are shorter -more compact

cellulose

-linear -homopolymer -beta (1->4) linkage -straight fibers can H-bond, form layers -very strong

amylose

-linear polymer -homopolymer -helical -alpha(1->4)linkage

y-intercept

-log Kd=

Sugar alcohols

-monosaccharides, both aldoses and ketoses may be reduced at carbonyl carbon to the corresponding alcohol. ->Glucose reduced to sorbitol (Glucitol) ->galactose reduced to galacticol (dulcitol) ->mannose reduced to mannitol ->fructose reduced to sorbitol and mannitol ->Ribose reduced to ribitol, a constituent of vitamin B2(riboflavin) and coenzyme FAD

Monosaccharides (glycoses)

-they are the simplest units of carbohydrates -they have the general formula Cn(H2O)n

Importance of Hexoses

1) Glucose is the most important sugar of carbohydrate: ->Glucose is the main sugar in the blood. ->Glucose is one of the major sources of energy in the body ->In the liver and other tissues, glucose is converted to all carbohydrates in the body 2)Fructose "fruit sugar": -> It can be converted into glucose in the liver ->It is the main sugar of semen 3)Galactose: -> It can be converted into glucose in the liver ->It is synthesized in the mammary gland to make the lactose of milk 4)Mannose: a constituent of many glycoproteins

Importance of cellulose

1) Increases the bulk of stool. This stimulates intestinal movement and prevents constipation 2) Cellulose is a constituent of dietary fibers. These fibers help in decreasing absorption of toxic compounds and reduce the incidence of cancer colon. 3) Cellulose can be utilized and serve as a source of energy in herbivores because their guts contains bacterial enzyme that can attack β-linkage

Nomenclature of monosaccharides

1)Named according to the present of aldehyde or ketone group: ->Aldoses (-CHO) has the suffix -ose meaning sugar ->Ketoses are monosaccharides that contain ketone group (-C=O) 2)Named according to number of carbon ->Trioses -> Contains 3 carbons ->Tetroses -> Contains 4 carbons ->Pentoses -> Contains 5 carbons ->Hexoses -> Contains 6 carbons

Importance (functions) of pentoses

1)Ribose and deoxyribose enter in the structure of nucleic acids RNA and DNA 2)Ribose enters om the structure of ATP, GTP and other high energy phosphate compounds 3)Ribose enters in the structure of coenzymes NAD, NADP and flavoproteins 4)Ribose phosphate and ribulose phosphate are the intermediates in pentose phosphate pathway (a minor pathway for glucose oxidation) 5)Arabinose and Xylose are constituents of glycoproteins in plants and animals 6)Lyxose is a constituent of a lyxoflavin isolated from human heart muscle 7)Xylulose is an intermediate in uronic acid pathway (a minor pathway for glucose oxidation)

Glycosaminoglycans include:

1- Hyaluronic acid 2- Chondroitin 4- and 6 sulfate 3- Keratan sulfate 4- Dermatan sulfate 5- Heparin and heparan sulfate

Ring (cyclic) structure of sugars:

1- Hydration of aldehyde group to form aldenol group 2-Intra-molecular reactions occur by subsequent condensation between one of the -OH of aldenol group and the -OH group of C4 or C5 to from ring structure (hemiacetal structure) 3- If the remaining -OH is on the right side, it is α- sugar. If the remaining -OH is on the left side, it is β- sugar.

Physical properties of monosaccharides

1-All monosaccharides are soluble in water 2-All monosaccharides show the property of optical activity 3-All monosaccharides can exist in α and β forms 4-All monosaccharides can undergo mutarotation

Deoxysugars

1-Are sugars in which one of the hydroxyl group has been replaced by a hydrogen atom i.e. one oxygen is replaced 2-Deoxyribose 3- L-fucose (6-deoxygalactose) occurring in glycoproteins

Examples of glycosides

1-Disaccharides 2-Sugar nucleotide as ATP, GTP and other nucleotides: aglycone here is purines and pyrimidines 3-Glycolipids: as cerebrosides 4-Glycoproteins 5-Cardiac glycosides: a)Aglycone here is steroid b)cardiac glycosides such as digitalis are important in medicine because of their action on heart

Chemical properties of monosaccharides

1-Oxidation (oxidation of sugar gives acids) 2-Reduction (reduction of carbonyl group gives the corresponding alcohol) 3-Reducing sugars (Sugars containing free aldehyde or ketone group can reduce other reagents)

Modifications for longer chains

1. Break all disulfide bonds 2. Cut chain into pieces <50 3. Separate pieces 4. Repeat using different enzymes 5. Use electrophoresis to locate disulfide bond

Life in molecular terms

1. Chemical structures 2. Physical and chemical properties 3. Reactions, interactions and organization 4. Energy considerations

Sequencing chains >50

1. Cleave chain into <50 residues 2. Break disulfide bonds 3. Desperate fragments by electrophoresis or chromatography 4. Sequence each fragment by roman degradation 5. Repeat with different protease 6. Determine S-S bond location with electrophoresis

Sequencing chains <50 amino acids

1. Derivatize N-terminal (PITC) 2. Cleave that N-terminal 3. Seperate the N-terminal 4. Detect identity of N-terminal (HPLC) 5. Repeat to each amino acid in the chain

Competitive

1/Vmax (y-int) doesn't change with this inhibitor (lines crossover at y-int)

Turnover time

1/k2

a. mutarotation

11b. The interconversion between anomeric forms is called _____. a. mutarotation b. racemization c. anomerization d. impossible

b. [ES] is constant

13b. The steady state assumption, as applied to enzyme kinetics, specifically implies: a. Vo=V max b. [ES] is constant c. this equilibrium is established quickly: E + S (>>><<<< (in equilibrium) ES d. rate = k2 [ES]

b. K1[S][E]free=k-1[ES]+k2[ES]

14. The steady state assumption, as applied to enzyme kinetics, implies: a. Km=Ks b. K1[S][E]free=k-1[ES]+k2[ES] c. Rate=k2[ES] d. K1[ES]=k-1[ES]

b. Deactivates glycogen phosphorylase by removing phosphate groups.

14b. What does phosphorylase phosphatase do? a. is a feedback inhibitor for glycogen phosphorylase b. Deactivates glycogen phosphorylase by removing phosphate groups. c. Reacts with phosphorylase kinase to activate glycogen d. activates glycogen phosphorylase by removing disulfide bonds.

b. 0.03125 s

15. Calculate the turnover time of an enzyme-catalyzed reaction that has a maximum velocity of 800 nM/s at a total enzyme concentrated of 25 nM. a. 32s b. 0.03125 s c. 20,000 s d.Cannot be determined without more information about the substrate concentration

alpha (1>>>4)

15b. What kind of link joins the monosaccharide units? Beta (1>>>4) Alpha (1>>>>3) (alpha 1 >>> Beta 3) alpha (1>>>4)

b. Zero; first

17. Initial rate measurements are made that vary the substrate concentration at a fixed concentration of enzyme. For an enzyme that obeys Michaelis-Menton type kinetics, it is observed that at high concentrations of substrate the reaction is ______ order while at low concentrations of substrate the reaction is _____ order a. Zero; second b. Zero; first c. Second; first d. First; second e. First; zero

b. Zero; first *

d. the Beta anomer predominates

18b. In an aqueous solution what will be true for D-glucose? a. a furanose form is present in greatest amounts b. it forms a racemic mixture of D and L forms c. There are equal amounts of two anomers in equilibrium d. the Beta anomer predominates

d. The pentoses are always in the B-furanoses forms

19. Which of the following is true of the pentoses found in nucleic acids? a. C-5' and C-1' of the pentose are joined to phosphate groups b. C-5' of the pentose is joined to a nitrogenous base, and C-1' to a phosphate group c. The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond d. The pentoses are always in the B-furanoses forms

a. glycogen & amylopectin

19b. Which are chemically identical? a. glycogen & amylopectin b. glycogen & amylose c. amylose and cellulose d. cellulose and glycogen

disaccharides

2 linked monosaccharides

heteroglycan

2 or more types of monomer units

Heteropolymer

2 or more types of monomers are present

Osmosis

2 solutions separated by a semi-permeable membrane will have solvent (water) move from low concentration of solute to high concentration of solute

from 12 Torr to 26 Torr

2,3 BPG raises P50 from __ to __

c. Oxidoreductases

20. A particular enzyme causes the conversion of a hydroxyl group to a carbonyl group on a carbohydrate. To what class of enzymes does this one belong? a. Hydrolases b. Ligases c. Oxidoreductases d. Lyases e. Transferases

c. Glycoconjugates

21. Glycolipids and glycoproteins are examples of ____. a. Glycosaminoglycans b. Heteropolymeric carbohydrates c. Glycoconjugates d. Heterotropic modulators

d. they have an absorbance peak at 280 nm

21b. Which of the following is false about the nitrogenous bases found in nucleic acids? a. the purines join to the sugars by N-9 b. they are atomatic c. they are flat d. they have an absorbance peak at 280 nm

b. B-D-galactopyranose and B-D-glucopyranose

22. What are the monomers of lactose? a. Alpha-D-galactopyranose and B-D-glucopyranose b. B-D-galactopyranose and B-D-glucopyranose c. B-D-fructofuranose and alpha-D-glucopyranose d. B-D-galactofuranose and B-D-glucopyranose

d. Trypsin loses all activity due to inactivation of one of the catalytic triad amino acids

23. What happens if a trypsin is exposed to diisopropylfluorophosphate? a. It is converted from its zymogen into active trypsin b. Phosphate groups are transferred to trypsin to activate it c. Trypsin's activity is inhibited by competitive inhibition d. Trypsin loses all activity due to inactivation of one of the catalytic triad amino acids e. Nothing happens. Trypsin is not affected by diisopropylfluorophosphate

a. sucrose can have mutarotation

23b. Which statement (a-d) is false? If all are true, select e. a. sucrose can have mutarotation b. the most stable forms of fructose in solution are furanoses c. cellulose is stabilized by many intrachain and interchain hydrogen bonds d. amylopectin is a branched homoglycan e. all of the above are true.

a. Activates glycogen phosphorylase by putting phosphate group on serine

24. What does phosphorylase kinase do? a. Activates glycogen phosphorylase by putting phosphate group on serine b. Cleaves trypsinogen to form tyrpsin c. Cleaves glucose units from glycogen d. Is a feedback inhibitor for enzymes in the glycolysis pathway

c. 2 x 10^8 mM/s Vmax=(1/2.5x10^-8)(5)=2x10^8

24b. Calculate the maximum velocity of an enzyme-catalyzed reaction that has a turnover time of 2.5 x 10 ^-8 s at a total enzyme concentration of 5 mM. a. 5 x 10^-9 mM/s b. 1.25 x 10^-7 mM/s c. 2 x 10^8 mM/s d. cannot be calculated without more information about the substrate concentration.

d. Binds tightly to the active site of an enzyme and prevents it from reacting with the normal substrate

26. A transition-state analog: a. Is an unstable compound that quickly reform the substrate b. Is often used to stabilize the substrate's transition state and enhance the reaction state c. Is a synthetic co-substrate that reduces the entropy of the normal substrate d. Binds tightly to the active site of an enzyme and prevents it from reacting with the normal substrate

c. V o = Vmax/K m times [S]

26b. Which equation applies to Michaelis-Menton kinetics at very low [S]? a. V o = V max b. K m equals approximately [S] c. V o = Vmax/K m times [S] d. Vo= Km [S]^2

b. Six amino acids are cleaved from trypsinogen's N-terminal to release trypsin

27. How is trypsin activated? a. The trypsinogen dimer is phosphorylated by phosphorylase kinase. b. Six amino acids are cleaved from trypsinogen's N-terminal to release trypsin c. DTT is used to form four disulfide bonds which converts trypsin into its active form d. Enteropeptidase forms a covalently bound dimer with trypsinogen to form active trypsin

b. Zymogen

29. When enzymes are activated by proteolytic cleavage, they are initially produced as a/an____. a. Apoenzyme b. Zymogen c. Holoenzyme d. Ribozyme

a. pppA

29b. What is another abbreviation for ATP? a. pppA b. pppdA c. Appp d. dAppp

d. Measure the rate of many samples each with a different [S], but the same [E]

2b. Which of the following describes how the initial rate method is conducted to collect kinetic data? a. Measure the rates of samples shortly after mixing before [E] changes much. b. measure the rates of many samples during the steady state and varying both [E] and [S]. c. Measure the rates of all samples in the pre-steady state. d. Measure the rate of many samples each with a different [S], but the same [E]

Triose

3 carbons

d. All of the above

30b. Two enzymes catalyze the same reaction. Which one would be more efficient? a. The one with the higher turnover number b. the one with the higher specificity constant c. the one with the lower K m d. All of the above

b. The solution changes from blue to brick red

32. What is observed if you mix the Benedict's reagent with fructose in a test tube? a. The solution stays blue the whole time b. The solution changes from blue to brick red c. The solution forms a silver mirror inside the test tube d. The solution goes from clear to pink

d. 300 mM/min *

33. Calculate the velocity (rate) of a reaction that has a maximum velocity of 500 mM/min, a substrate concentration of 75mM and a Km of 50mM? a.0.153 mM/min b. 4.6 mM/min c. 10mM/min d. 300 mM/min

c. the solution forms a silver mirror inside the test tube.

33b. What is observed if you mix the Tollen's reagent with the molecule shown? a. the solution stays blue the whole time b. the solution changes from blue to brick red c. the solution forms a silver mirror inside the test tube. d. no reaction

a. to see if serine residues are important for an enzyme's catalytic activity

34b. What can diisopropylfluorophosphate be used for? a. to see if serine residues are important for an enzyme's catalytic activity b. to convert an enzyme into its active form from its zymogen c. to phosphorylate an enzyme and activate it by covalent modification d. to determine if an inhibitor is competitive or not

c. The lactam form predominates at neutral pH

35. Which of the following statements concerning the tautomeric forms of bases such as uracil is correct? a. The all-lactim form contains a ketone group b. The lactam form contains an alcohol group c. The lactam form predominates at neutral pH d. The lactam and lactim forms are in an approximately equal molar equilibrium

d. pathways often allow the buildup of intermediates to store for use when demand for product is high

35b. Which statement is false about the regulation of a reaction pathway? a. enzymes early in the pathway are often regulatory enzymes b. in feedback inhibition of a pathway, the product is a negative modulator of enzyme for an early step in the pathway c. the most common method of pathway regulation is allosteric regulation. d. pathways often allow the buildup of intermediates to store for use when demand for product is high

b. Deoxyguanosine-5'-diphosphate

36. What is the name of the nucleotide with the abbreviation ppdG? a. Deoxyguanosine-3'-diphosphate b. Deoxyguanosine-5'-diphosphate c. 5'-diphosphate deoxyguanine d. Guanylate

a. stores energy in plant starch

37b. Which is a main function of amylopectin? a. stores energy in plant starch b. stores energy in mammalian liver and muscle c. is the main component of plant cell walls d. provides adhesion between plant cells

a.N^6-Methyladenosine....marking its own DNA to prevent degradation by enzymes that degrade foreign DNA

38. ________ can serve as an epigenic marker in bacteria for the purpose of _______. a.N^6-Methyladenosine....marking its own DNA to prevent degradation by enzymes that degrade foreign DNA b. 5-Ethylcytidine....marking a gene for activation c. Deoxyadenosine-2', 3' cyclic monophosphate....block DNA replication d. 5-hydroxymethylcytidine......preventing a gene from being activated

d. Phosphodiester

39. The bonds that connect the backbone of DNA are ______ bonds. a. Alpha (1à4) b. Peptide c. N-glycosidic d. Phosphodiester

d. the C-terminal ends of trypsin and trypsinogen are different

39b. Which is not a different between trypsin and trypsinogen? a. trypsin is an active protease; trypsinogen is not b. trypsin is smaller than trypsinogen c. trypsin is formed in the small intestine; trypsinogen is made in the pancreas d. the C-terminal ends of trypsin and trypsinogen are different

Turns (bends)

4 amino acids, H-bonding stabilizes, high percent of glycine and proline

Tetrose

4 carbons

porphyrin ring

4 pyrrole rings linked by methylene bridges

structure of Hb

4 subunits arranged tetrahedrally, 2 pairs (2 alpha and 2 beta chains) do not touch, 27 invariant residues and 40 conservative substitutions, and each chain has its own heme group

b. phosphate is the most common group that can be attached or removed by this method

40b. Which statement applies to covalent modification to regulate enzyme activity? a. since it involves covalent bonding, it is an irreversible process b. phosphate is the most common group that can be attached or removed by this method c. a covalent bond in the backbone of the enzyme is broken to release the active enzyme c. The most important feature is the formation of extensive hydrogen bonding to activate the enzyme

a. Regulatory enzyme

41. An enzyme whose activity is controlled by reversible modulation is called a/an? a. Regulatory enzyme b. Feedback enzyme c. Allosteric enzyme d. Zymogen

a. 38.5 mM/min

41b. Calculate the velocity (rate) of a reaction that has a maximum velocity of 100 mM/min, a substrate concentration of 50 mM and a K m of 80 mM? a. 38.5 mM/min b. 1.15 mM/min c. 0.0375 mM/min d. 0.77 mM/min

d. The effect of the inhibitor is reversed by high [S]

42. Which is not true for mixed inhibition? a. The inhibitor has its own binding site that is not the active site b. Vmax is lowered c. Km is either unaffected or changed only slightly d. The effect of the inhibitor is reversed by high [S]

b. At very high [S], the velocity curve becomes a horizontal line and the y-value is equal to 2Km.

42b. Which of the following statements about a plot of Vo vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false? a. As [S] increases, the initial velocity of reaction, Vo, also increases b. At very high [S], the velocity curve becomes a horizontal line and the y-value is equal to 2Km. c. Km is the [S] at which Vo=½ V max d. the shape of the curve is a hyperbola e. the y-axis is a rate term with units of delta concentration/delta time

43. T/F the simplest ketose is the achiral molecule dihydroxyacetone.

43b. Monosaccharide ketoses are alpha-hydroxyketones, which is why they are reducing sugars.

44. T/F The rate-determining step in the Michaelis-Menton model of enzyme catalysis is the formation of the enzyme-substrate complex.

44b. The alpha anomer of pyranoses is more reactive with mild oxidizing agents than the Beta anomer.

45. T/F Plant cell walls are primarily composed of cellulose which is stabilized by many intrachain and interchain hydrogen bonds.

F (I think that's only in competitive inhibition)

45b. In mixed inhibition the inhibitor is an analog of the substrate.

46. T/F Thymine is a pyrimidine

46b. The rate-determining step in the Michaelis-Menton kinetics is the formation of the product.

47. T/F In competitive inhibition the inhibitor is an analog of the substrate.

47b. Inosine is a major nucleoside frequently found in the tRNA.

48. T/F Pseudouridine is a minor nucleoside frequently found in tRNA and rRNA.

48b. Cellulase is an enzyme that can break alpha(1>>>4) bonds in polysaccharides.

49. T/F Amylase is an enzyme that can break both alpha (1à4) and alpha (1à6) bonds in polysaccharides.

49b. the simplest ketose and aldose are both trioses.

b. uncompetitive

4b. The data shown on the graph were obtained for a kinetic experiment. What type of inhibition is it? (it's a graph with parallel lines) a. competitive b. uncompetitive c. noncompetitive d. feedback

Pentose

5 carbons

50. T/F Glycogen and amylopectin are chemically identical and only differ in branching frequency and length.

50b. Comparing monosaccharides with the same number of carbons, ketoses have more possible stereoisomers.

Hexose

6 carbons

oxidoreductase, transferases, hydrolases, lyases, isomerases, and ligases

6 classes of enzymes

c. Beta-D-fructofuranose & alpha-D-glucopyranose

8b. Which are the monomers of sucrose? a. alpha-D-galactopyranose & Beta-D-glucopyranose b. Beta-D-galactopyranose & Beta-D-glucopyranose c. Beta-D-fructofuranose & alpha-D-glucopyranose d. Beta-D-galactofuranose & Beta-D-glucopyranose

Osmolarity

=ic Where i is the van't Hoff factor (i=1 for non-electrolyte) And c=solute's molar concentration

A small molecule that decreases the activity of an enzyme by binding to a site other than the catalytic site is termed a(n): A) allosteric inhibitor. B) alternative inhibitor. C) competitive inhibitor. D) stereospecific agent. E) transition-state analog

Based on Chargaff's rules, which of the following are possible base compositions for double-stranded DNA? %A %G %C %T %U A) 5 45 45 5 0 B) 20 20 20 20 20 C) 35 15 35 15 0 D) All of the above E) None of the above

In the Watson-Crick model for the DNA double helix (B form) the A-T and G-C base pairs share which one of the following properties? A) The distance between the two glycosidic (base-sugar) bonds is the same in both base pairs, within a few tenths of an angstrom. B) The molecular weights of the two base pairs are identical. C) The number of hydrogen bonds formed between the two bases of the base pair is the same. D) The plane of neither base pair is perpendicular to the axis of the helix. E) The proton-binding groups in both base pairs are in their charged or ionized form

In the Watson-Crick structure of DNA, the: A) absence of 2'-hydroxyl groups allows bases to lie perpendicular to the helical axis. B) adenine content of one strand must equal the thymine content of the same strand. C) nucleotides are arranged in the A-form. D) purine content (fraction of bases that are purines) must be the same in both strands. E) two strands are parallel

One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the: A) apoenzyme. B) coenzyme. C) holoenzyme. D) prosthetic group. E) substrate.

Phenyl-methane-sulfonyl-fluoride (PMSF) inactivates serine proteases by binding covalently to the catalytic serine residue at the active site; this enzyme-inhibitor bond is not cleaved by the enzyme. This is an example of what kind of inhibition? A) Irreversible B) Competitive C) Non-competitive D) Mixed E) pH inhibition

Sphingosine is not a component of: A) cardiolipin. B) ceramide. C) cerebrosides. D) gangliosides. E) sphingomyelin.

Tay-Sachs disease is the result of a genetic defect in the metabolism of: A) gangliosides. B) phosphatidyl ethanolamine. C) sterols. D) triacylglycerols. E) vitamin D.

The difference between a ribonucleotide and a deoxyribonucleotide is: A) a deoxyribonucleotide has an —H instead of an —OH at C-2. B) a deoxyribonucleotide has an —H instead of an —OH at C-3. C) a ribonucleotide has an extra —OH at C-4. D) a ribonucleotide has more structural flexibility than deoxyribonucleotide. E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose

The double-reciprocal transformation of the Michaelis-Menten equation, also called the Lineweaver-Burk plot, is given by 1/V0 = Km /(Vmax[S]) + 1/Vmax To determine Km from a double-reciprocal plot, you would: A) multiply the reciprocal of the x-axis intercept by −1. B) multiply the reciprocal of the y-axis intercept by −1. C) take the reciprocal of the x-axis intercept. D) take the reciprocal of the y-axis intercept. E) take the x-axis intercept, where V0 = 1/2 Vmax.

The phosphodiester bond that joins adjacent nucleotides in DNA: A) associates ionically with metal ions, polyamines, and proteins. B) is positively charged. C) is susceptible to alkaline hydrolysis. D) Links C-2 of one base to C-3 of the next. E) links C-3 of deoxyribose to N-1 of thymine or cytosine

Which of the following best describes the cholesterol molecule? A) Amphipathic B) Nonpolar, charged C) Nonpolar, uncharged D) Polar, charged E) Polar, uncharged

Which of the following has not been shown to play a role in determining the specificity of protein kinases? A) Disulfide bonds near the phosphorylation site B) Primary sequence at phosphorylation site C) Protein quaternary structure D) Protein tertiary structure E) Residues near the phosphorylation site

Which of the following is true of sphingolipids? A) Cerebrosides and gangliosides are sphingolipids. B) Phosphatidylcholine is a typical sphingolipid. C) They always contain glycerol and fatty acids. D) They contain two esterified fatty acids. E) They may be charged, but are never amphipathic.

Which of the following statements about sterols is true? A) All sterols share a fused-ring structure with four rings. B) Sterols are found in the membranes of all living cells. C) Sterols are soluble in water, but less so in organic solvents such as chloroform. D) Stigmasterol is the principal sterol in fungi. E) The principal sterol of animal cells is ergosterol.

Which of the following statements concerning fatty acids is correct? A) One is the precursor of prostaglandins. B) Phosphatidic acid is a common one. C) They all contain one or more double bonds. D) They are a constituent of sterols. E) They are strongly hydrophilic.

A & T are complementary with ___ hydrogen bonds.

RNA

A & U are complementary in ____.

5 Units/mg 50/2=25 25/5=5

A 1 mL sample of enzyme is used to catalyze a reaction. It is found by absorbance measurements that 50 micro moles of substrate were consumed by the reaction in 2 minutes at 25C. The concentration of total protein in the enzyme solution was found in a separate experiment to be 5 ug/mL. Calculate the specific activity of the enzyme solution.

Amino acid

A DNA nucleotide sequence that codes for a single protein

b. the cooperatively between ligand biding sites.......a slope >1

A Hill plot is used to determine ______ by observing ______. a. the cooperatively between ligand binding sites......slope=1 b. the cooperatively between ligand biding sites.......a slope >1 c. pH dependence........ shift in sigmoidal shape d. pH dependence...... change in Vmax

displaying information about secondary structure

A Ramachandran plot is useful for:

secondary

A Ramachandran plot shows different ______ structures.

peptide

A _____ bond is an amide bond between two amino acids where water is lost.

clathrate

A ______ is an ordered cage of water molecules

transition-state analog

A ______ resembles the transition-state structure of the normal substrate.

micelle

A ______'s formation in an aqueous environment is caused by a large gain in entropy for water.

conservative

A _______ residue is when there are two amino acids in the same group but they are not the same amino acids.

sigmoidal; positive

A _______ shaped curve is found for the binding of oxygen to hemoglobin. This is an illustration of the phenomenon of ________ cooperativity.

signature sequence

A ________ is unique to a given taxonomic unit like a species or genus, etc.

Ramachandran plot

A ________ is useful for displaying information about secondary structures.

hyperbolic.......the law of mass action

A _________ shaped curve is found for the binding of oxygen to myoglobin. This shape is a result of __________.

Sigmoidal; positive cooperativity

A __________ shaped curve is found for the binding of oxygen to hemoglobin. This is an illustration of the phenomenon of_________.

hyperbolic; the law of mass action

A ________________ shaped curve is found for the binding of oxygen to myoglobin. This shape is a result of ______________.

6 units

A certain substrate has a strong absorbance at 450 nm. Enzyme is added to the substrate and as the substate is being converted to product, a drop of 0.10 absorbance units per minute is observed. The sample had a column of 3 mL (0.003 L) and the absorbance was measure using a standard 1 cm cuvette. The molar absorptivity constant (molar extinction coefficient, E) of the substrate is 50 M-1 cm-1. How many units of activity of the enzyme are in the sample?

D. depends only on the number of solute particles dissolved

A colligative property ____. A. involves the aggregation of non polar species B. measures a molecule's hydrophobicity C. measures how soluble a substance is D. depends only on the number of solute particles dissolved

solute particles

A colligative property depends only on the number of _______ ________ dissolved.

Oligosaccharides

A few monosaccharides joined

carbohydrate

A glycoprotein contains ______.

D. has a carbohydrate unit attached

A glycoprotein is one that: A. Has quarternary structure B. Can act as either an acid or a base C. Has multiple disulfide bonds D. Has a carbohydrate unit attached

phosphorylase kinase

A high concentration of ____ will increase the activity of glycogen phosphorylase.

lipids

A lipoprotein containts ______.

C. The last product, W, is likely to be a negative modulator of X, leading to feedback inhibition.

A metabolic pathway proceeds according to the scheme, R-S-T-U-V-W. A regulatory enzymes, X, catalyzes the first reaction in the pathway. Which of the following is most likely correct for this pathway? A. Either metabolite U or V is likely to be a positive modulator, increasing the activity of X. B. The first product S is probably the primary negative modulator of X, leading to feedback inhibition. C. The last product, W, is likely to be a negative modulator of X, leading to feedback inhibition. D. The last product, W, is likely to be a positive modulator, increasing the activity of X. E. The last reaction will be catalyzed by a second regulatory enzyme.

Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe-His

A nonapeptide was determined to have the following amino acid composition two Lys, two Gly, two Phe, one each of His, Leu, and Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed. Analysis by HPLC detected 2,4-dinitrophenylglycine. When the native peptide was exposed to cyanogen bromide, a heptapeptide and dipeptide were recovered. Incubation of the native peptide with trypsin gave a pentapeptide and a tetrapeptide. Incubation of the pentapeptide with FDNB and hydrolysis yielded 2,4-dinitrophenyllysine. Are any of the sequences shown below consistent with this data? If so, select one. If there is not enough information for you to determine if one of the sequences is consistent with the data, select E.

Oxidoreductases

A particular enzyme causes the conversion of a hydroxyl group to a carbonyl group on a carbohydrate. To what class of enzymes does this one belong?

aromatic

A protein must have some _____ amino acids to have a significant absorbance at 280 nm.

quarternary

A protein that performs its natural biological function as a single polypeptide lacks ______ structure.

performic acid

A reaction of disulfide bonds with ______ will cause the formation of R-CH2-SO3-

exergonic

A reaction that liberates free energy is ______.

non-repetitive region

A region of a protein's tertiary structure that appears to be a random coil is also called a/an ________.

collagen helix

A repeating sequence of amino acid in a certain protein is found to be -Gly-Pro-Hyp-. The sequence is most probably part of a(n) ______.

signature

A sequence in homologous proteins that only occurs in a particular group (species, genus, etc) is called a ______ sequence

signature

A sequence in homologous proteins that only occurs in a particular group (species, genus, etc.) is called a/an________ sequence.

beta turn

A sequence of amino acids in a certain protein is found to be Ala-Gly-Pro-Gly. The sequence is most probably part of a ______.

beta-turn

A sequence of amino acids in a certain protein is found to be Ser-Gly-Pro-Gly. The sequence is most probably part of a(n):

is unique to a given taxonomic unit like a species or genus, etc.

A signature sequence __________.

4.82 5=pKa+log(0.150/0.100)

A solution with a butyric acid concentration of 0.100 M and a potassium butyrate concentration of 0.150 M has a pH equal to 5.00. What is the value of pKa of butyric acid?

d. Binds tightly to the active site of an enzyme and prevents it from reacting with the normal substate.

A transition-state analog: a. Is an unstable compound that quickly reforms the substates. b. Is often used to stabilize the substrate's transition state and enhance the reaction rate. c. Is asynthetic co-substrate that reduces the entropy of the normal substrate. d. Binds tightly to the active site of an enzyme and prevents it from reacting with the normal substate.

From the abbreviated name of the compound Gal(beta1 --> 4)Glc, we know that: A) C-4 of glucose is joined to C-1 of galactose by a glycosidic bond. B) the compound is a D-enantiomer. C) the galactose residue is at the reducing end. D) the glucose is in its pyranose form. E) the glucose residue is the beta anomer.

A) C-4 of glucose is joined to C-1 of galactose by a glycosidic bond.

Glycogen location, properties and functions

A) Location: glycogen is present mainly in liver and muscles B) Property: -It gives reddish violet color with iodine. C)Functions: ---> Liver glycogen : it maintains normal blood glucose concentration especially during the early stage of fast. After 12-18 hours fasting, liver glycogen is depleted ---> Muscle glycogen: It acts as a source of energy within the muscle itself especially during muscle contraction

In glycoproteins, the carbohydrate moiety is always attached through the amino acid residues: A) asparagine, serine, or threonine. B) aspartate or glutamate. C) glutamine or arginine. D) glycine, alanine, or aspartate. E) tryptophan, aspartate, or cysteine.

A) asparagine, serine, or threonine.

conjugated

A/an _______ protein contains non-amino acid parts to function properly.

About ___ base pairs per turn in DNA helix

A = -logT = log(1/T)

Absorbance

According to the method discussed in class, small peptides are synthesized from the C-terminal amino acids to the N-terminal amino acid.

DCC

Activates amino acids for the reaction that synthesizes proteins

fractions

Add higher concentrations of ammonium sulfate and centrifuge longer @ higher speeds to obtain ______.

covalent modification

Addition and deletion of methyl groups that change an enzyme's activity is an example of ______.

sequencing

After composition comparison, _______ is the next step.

quantification

After detection, separate amino acids for ________.

known

After quantification, compare to _____ % comp.

Hemiacetal

Aldehyde+alcohol->

ampholytic

All amino acids are _______ (can act as an acid or base)

Micelles

All hydrophobic groups are sequestered from water; ordered shell of H2O molecules is minimized, and entropy is further increased.

can, reducing

All monosaccharides aldoses are aldehydes and ______ react with the oxidizing agents. They are ________ sugars.

reducing sugars

All monosaccharides are also __________ ________.

glycine

All of the amino acids except ______ are chiral.

weak

All organic acids are ____ acids.

weak

All organic bases are ____ bases.

K.5

Allosteric enzymes use ___ instead of Km

Non

Allosteric enzymes usually show ___-Michaelis-Menton kinetics

Secondary structures

Alpha helices, beta sheets, and bends

loss of function

Alteration of 3D shape of proteins can cause loss of function; shows importance of structure <-> function

percent composition

Amino acid analysis determines __________.

amphoteric

Amino acids and water are _________, can be either an acid or base.

purple

Amino acids appear _____ after the addition of ninhydrin except proline, which turns yellow.

monomers of proteins

Amino acids are __________ __ _______.

acid or a base

Amino acids are ampholytes because they can function as either a(n):

Primary

Amino acids are classified as ______ amines.

ionize

Amino acids can _____.

amide

Amino acids can covalently link to each other by ____ bonds. This is a CONDENSATION REACTION.

Amino acids occur naturally as the ___-enantiomer form.

non-repetitive region

An apparently random region of a protein's structure that connects secondary structures is called a ______.

non-repetitive rgion

An apparently random region of a protein's structure that connects secondary structures is called a/an ______.

Non-repetitive

An apparently random region of a protein's structure that connects secondary structures is called a/an____.

iodoacetic acid

An average protein will not be denatured by:

Protease

An enzyme that cleaves peptide bonds is called a/an ________.

two functional domains

An enzyme that consists of a single polypeptide chain but has two sections, each of which has its own specialized function has....

Regulatory enzyme

An enzyme whose activity is controlled by reversible modulation is called a/an _______.

The protein consists of two chains of amino acids joined by a disulfide bond

An explanation most likely about a pure protein if treated with the Sanger reagent (FDNB) is found to derivative both Ala and Leu, in roughly equal amounts is....

28 pitch / rise = 3.6 100 aa / 3.6 = 28

An ideal alpha-helix has a pitch of 0.54 nm and a rise of 0.15 nm. Approximately how many turns are in a helix that contains 100 amino acids?

56 .54/.15=3.6 200/3.6=55.6

An ideal alpha-helix has a pitch of 0.54 nm and a rise of 0.15 nm. Approximately how many turns are in a helix that contains 200 amino acids?

15 nm (length/rise)=AA length=AA x rise

An ideal alpha-helix has a pitch of 0.54 nm and a rise of 0.15 nm. What is the length along the helix axis for a segment of an ideal alpha-helix that contains 100 amino acids?

6.0 nm

An ideal alpha-helix has a pitch of 0.54 nm and a rise of 0.15 nm. What is the length along the helix axis for a segment of an ideal alpha-helix that contains 40 amino acids?

6.0 nm (# of amino acids)(rise)

An ideal alpha-helix has a pitch of 0.54 nm and a rise of 0.15nm. What is the length along the helix axis segment of an ideal alpha-helix that contains 40 amino acids

28 .54/2=.27 .27 x 100

An ideal alpha-helix has a pitch of 0.54 nm. Appx how many turns are in a helix that contains 100 amino acids?

glycyl......alanyl

An octapeptide composed of four repeating glycylalanyl units has one free amino group on the ____ residue and one free carboxyl group on an ____ residue.

Nucleosome

An overall structure that consists of a single chromatin fiber composed of a DNA strand wrapped around histones; form the fundamental repeating units of chromatin

glycerophopholipids

Another name for Phospholipids

Inflection point

Another term for equilibrium point

Size-exclusion chromatography

Another word for Gel Filtration

colligative

Any property that depends only on the number of dissolved particles and not the nature of the particles is called a/an ________ property.

Affinity chromatography technique

Apply mixture to column. Only molecule that binds to ligand will pass. All others pass through. Release molecules by adding more ligands. Molecules elute w/ the ligand Ligand must not bind molecule too tightly. molecule+ligand <> molecule-ligand complex

Ultrafiltration

Apply pressure to force through a semi-permeable membrane

glycine and proline

Are common in β turns

Increases

As efficiency _________ K2-increases 1/k2-decreases Km-decreases K2/Km-increases

entropy

As the randomness of a system increases, the ______ increases.

+0.5

Aspartate has the following pKa's: carboxylate group = 1.88............amino group = 9.60.............R group = 3.65. Calculate the average charge at a pH of 1.88

glyceraldehyde

Assignment of L and D is based on comparison to __________, a convention originated by Emil Fischer.

Val and Phe

Assume the sequence below is part of an alpha helix. There will be a hydrogen bond between which amino acids? Ile-Val-Met-Leu-Ala-Phe-Asn-Val-Leu

Met & Asn......val & Phe ....etc.

Assume the sequence below is part of an alpha helix. There will be a hydrogen bond between which amino acids? Ile-Val-Met-Leu-Ala-Phe-Asn-Val-Leu

Met and Asn

Assume the sequence below is part of an alpha-helix. There will be a hydrogen bond between which two amino acids? Ile-Val-Met-Leu-Ala-Phe-Asn-Val-Leu

40 units (200/5=40)

At 25 degrees C, 200 micromoles of a substrate are consumed in 5 minutes by enzyme catalysis. How many units of enzyme are present?

40 units

At 25C 200 micro moles of a substrate are consume in 5 minutes by enzyme catalysis. How many units of enzyme are presents?

half

At Tm ribonuclease will exhibit ____ the activity of a sample in its native conformation.

ionized; histidine

At biological pH (near 7) all ionizable groups will be _____, except for the side-chain of ______. (pKa=60)

pKa=pH

At half-titration, Ka = [H3O+] and ____ __ ____.

above; deprotonated

At pH's ____ a given group's pKa, the group will be _________.

below; protonated

At pH's _____ a given group's pKa the group will be _________.

conservative

At position #10 in a particular set of homologous proteins, it is found that the amino acid may be Val, Ile or Met. How would you classify residue #10?

equal; 50%; protonated; 50% deprotonated

At the pH ____ to the pKa of a given functional group, statistically ___ will be _________ and ___ __________.

A compound containing N-acetylneuraminic acid (sialic acid) is: A) cardiolipin. B) ganglioside GM2. C) phosphatidylcholine. D) platelet-activating factor. E) sphingomyelin.

A good transition-state analog: A) binds covalently to the enzyme. B) binds to the enzyme more tightly than the substrate. C) binds very weakly to the enzyme. D) is too unstable to isolate. E) must be almost identical to the substrate

Both water and glucose share an —OH that can serve as a substrate for a reaction with the terminal phosphate of ATP catalyzed by hexokinase. Glucose, however, is about a million times more reactive as a substrate than water. The best explanation is that: A) glucose has more —OH groups per molecule than does water. B) the larger glucose binds better to the enzyme; it induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis. C) the —OH group of water is attached to an inhibitory H atom, while the glucose —OH group is attached to C. D) water and the second substrate, ATP, compete for the active site resulting in a competitive inhibition of the enzyme. E) water normally will not reach the active site because it is hydrophobic

Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA molecules by: A) breakage of phosphodiester bonds. B) deamination of bases. C) depurination. D) formation of thymine dimers. E) transformation of A → T.

Double stranded regions of RNA typically take on a(n): A) A-form left-handed helix. B) A-form right-handed helix. C) B-form left-handed helix. D) B-form right-handed helix. E) Z-form left-handed helix.

Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that: A) a Glu residue on the enzyme is involved in the reaction. B) a His residue on the enzyme is involved in the reaction. C) the enzyme has a metallic cofactor. D) the enzyme is found in gastric secretions. E) the reaction relies on specific acid-base catalysis

Enzymes differ from other catalysts in that only enzymes: A) are not consumed in the reaction. B) display specificity toward a single reactant. C) fail to influence the equilibrium point of the reaction. D) form an activated complex with the reactants. E) lower the activation energy of the reaction catalyzed.

Fatty acids are a component of: A) carotenes. B) cerebrosides. C) sterols. D) vitamin D. E) vitamin K.

In a double-stranded nucleic acid, cytosine typically base-pairs with: A) adenosine. B) guanine. C) inosine. D) thymine. E) uracil.

In a plot of l/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the: A) curvature of the plot. B) intercept on the l/[S] axis. C) intercept on the l/V axis. D) pK of the plot. E) Vmax.

The DNA oligonucleotide abbreviated pATCGAC: A) has seven phosphate groups. B) has a hydroxyl at its 3' end. C) has a phosphate on its 3' end. D) has an A at its 3' end. E) violates Chargaff's rules

The allosteric enzyme ATCase is regulated by CTP, which binds to the T-state of ATCase. CTP is a: A) positive regulator. B) negative regulator. C) co-factor. D) competitive inhibitor. E) coenzyme.

The benefit of measuring the initial rate of a reaction V0 is that at the beginning of a reaction: A) [ES] can be measured accurately. B) changes in [S] are negligible, so [S] can be treated as a constant. C) changes in Km are negligible, so Km can be treated as a constant. D) V0 = Vmax. E) varying [S] has no effect on V0

The difference between thymine and uracil is: A) one methylene group on the pyrimidine ring. B) one methyl group on the pyrimidine ring. C) one hydroxyl group on the ribose ring. D) one amine group on the pyrimidine ring. E) one methyl group on the purine ring

The experiment of Avery, MacLeod, and McCarty in which nonvirulent bacteria were made virulent by transformation was significant because it showed that: A) bacteria can undergo transformation. B) genes are composed of DNA only. C) mice are more susceptible to pneumonia than are humans. D) pneumonia can be cured by transformation. E) virulence is determine genetically

When double-stranded DNA is heated at neutral pH, which change does not occur? A) The absorption of ultraviolet (260 nm) light increases. B) The covalent N-glycosidic bond between the base and the pentose breaks. C) The helical structure unwinds. D) The hydrogen bonds between A and T break. E) The viscosity of the solution decreases

Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence (5')AGACTGGTC(3')? A) (5')CTCATTGAG(3') B) (5')GACCAGTCT(3') C) (5')GAGTCAACT(3') D) (5')TCTGACCAG(3') E) (5')TCTGGATCT(3')

Which of the following is not a fat-soluble vitamin? A) A B) C C) D D) E E) K

Which of the following is not true of sterols? A) Cholesterol is a sterol that is commonly found in mammals. B) They are commonly found in bacterial membranes. C) They are more common in plasma membranes than in intracellular membranes (mitochondria, lysosomes, etc.). D) They are precursors of steroid hormones. E) They have a structure that includes four fused rings.

Which of the following is true of the binding energy derived from enzyme-substrate interactions? A) It cannot provide enough energy to explain the large rate accelerations brought about by enzymes. B) It is sometimes used to hold two substrates in the optimal orientation for reaction. C) It is the result of covalent bonds formed between enzyme and substrate. D) Most of it is derived from covalent bonds between enzyme and substrate. E) Most of it is used up simply binding the substrate to the enzyme

Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false? A) As [S] increases, the initial velocity of reaction V0 also increases. B) At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km. C) Km is the [S] at which V0 = 1/2 Vmax. D) The shape of the curve is a hyperbola. E) The y-axis is a rate term with units of μm/min

Which of the following statements is true of lipids? A) Many contain fatty acids in ester or amide linkage. B) Most are simply polymers of isoprene. C) Testosterone is an important sphingolipid found in myelin. D) They are more soluble in water than in chloroform. E) They play only passive roles as energy-storage molecules.

D-Glucose is called a reducing sugar because it undergoes an oxidation-reduction reaction at the anomeric carbon. One of the products of this reaction is: A) D-galactose. B) D-gluconate. C) D-glucuronate. D) D-ribose. E) muramic acid.

B) D-gluconate.

Which of the following is an epimeric pair? A) D-glucose and D-glucosamine B) D-glucose and D-mannose C) D-glucose and L-glucose D) D-lactose and D-sucrose E) L-mannose and L-fructose

B) D-glucose and D-mannose

Which of the following monosaccharides is not an aldose? A) erythrose B) fructose C) glucose D) glyceraldehyde E) ribose

B) fructose

The basic structure of a proteoglycan consists of a core protein and a: A) glycolipid. B) glycosaminoglycan. C) lectin. D) lipopolysaccharide. E) peptidoglycan.

B) glycosaminoglycan.

alcohols

Based on intermolecular forces and their relative strengths, for which class of compound do you expect the highest boiling point? Assume you are comparing molecules of equal size (molecular weight). A. alkanes B. aldehydes C. alcohols D. esters

A=(el)(c)

Beer's Law

linear

Beer's law is a _____ relationship.

O, H, S, P, N

Besides carbon, what are the net five more prevalent elements in living systems?

Organic chemistry

Biochemistry is a subclass of _______ ________.

non-amino acid

Biologically active proteins often have __________ components.

B. The larger glucose binds better to the enzyme; it induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis.

Both water and glucose share an -OH that can serve as a substrate for a reaction with the terminal phosphate of ATP catalyzed by hexokinase. Glucose, however, is about a million times more reactive as a substrate than water. The best explanation is that: A. Glucose has more -OH groups per molecule than does water. B. The larger glucose binds better to the enzyme; it induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis. C. The -OH group of water is attached to an inhibitory H atom, while the glucose -OH group os attached to C. D. Water and the second substrate, ATP, compete for the active site resulting in a competitive inhibition of the enzyme. E. Water normally will not reach the active site because it is hydrophobic .

sucrose

Buffers used in labs often contain about 0.2 M ______ to protect cells from osmotic lysis.

5' to 3'

By convention, the sequence is given in the _____ direction.

A transition-state analog: A) is less stable when binding to an enzyme than the normal substrate. B) resembles the active site of general acid-base enzymes. C) resembles the transition-state structure of the normal enzyme-substrate complex. D) stabilizes the transition state for the normal enzyme-substrate complex. E) typically reacts more rapidly with an enzyme than the normal substrate

Allosteric enzymes: A) are regulated primarily by covalent modification. B) usually catalyze several different reactions within a metabolic pathway. C) usually have more than one polypeptide chain. D) usually have only one active site. E) usually show strict Michaelis-Menten kinetics

An enzyme-catalyzed reaction was carried out with the substrate concentration initially a thousand times greater than the Km for that substrate. After 9 minutes, 1% of the substrate had been converted to product, and the amount of product formed in the reaction mixture was 12 μmol. If, in a separate experiment, one-third as much enzyme and twice as much substrate had been combined, how long would it take for the same amount (12 μmol) of product to be formed? A) 1.5 min B) 13.5 min C) 27 min D) 3 min E) 6 min

An example of a glycerophospholipid that is involved in cell signaling is: A) arachidonic acid. B) ceramide. C) phosphatidylinositol. D) testosterone. E) vitamin A (retinol).

Double-stranded regions of RNA: A) are less stable than double-stranded regions of DNA. B) can be observed in the laboratory, but probably have no biological relevance. C) can form between two self-complementary regions of the same single strand of RNA. D) do not occur. E) have the two strands arranged in parallel (unlike those of DNA, which are antiparallel).

For enzymes in which the slowest (rate-limiting) step is the reaction k2 ES → P Km becomes equivalent to: A) kcat. B) the [S], where V0 = Vmax. C) the dissociation constant, Kd, for the ES complex. D) the maximal velocity. E) the turnover number.

For the helix in double-stranded B-form DNA, the majority of the stability can be attributed to: A) base-pairing interactions via H-bonds. B) interactions along the phosphate backbone. C) base-stacking interactions via van-der-Waals interactions. D) covalent bonds between adjacent bases in one strand. E) ionic interactions with metal ions.

How is trypsinogen converted to trypsin? A) A protein kinase-catalyzed phosphorylation converts trypsinogen to trypsin. B) An increase in Ca2+ concentration promotes the conversion. C) Proteolysis of trypsinogen forms trypsin. D) Trypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into active trypsin monomers. E) Two inactive trypsinogen dimers pair to form an active trypsin tetramer.

In nucleotides and nucleic acids, syn and anti conformations relate to: A) base stereoisomers. B) rotation around the phosphodiester bond. C) rotation around the sugar-base bond. D) sugar pucker. E) sugar stereoisomers

Penicillin and related drugs inhibit the enzyme ; this enzyme is produced by . A) β-lacamase; bacteria B) transpeptidase; human cells C) transpeptidase; bacteria D) lysozyme; human cells E) aldolase; bacteria

The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: V0 Substrate added (μmol/min) (mmol/L) ————————————— 217 0.8 325 2 433 4 488 6 647 1,000 ————————————— The Km for this enzyme is approximately: A) 1 mM. B) 1000 mM. C) 2 mM. D) 4 mM. E) 6 mM

The steady state assumption, as applied to enzyme kinetics, implies: A) Km = Ks. B) the enzyme is regulated. C) the ES complex is formed and broken down at equivalent rates. D) the Km is equivalent to the cellular substrate concentration. E) the maximum velocity occurs when the enzyme is saturated.

Which of the following is not true of all naturally occurring DNA? A) Deoxyribose units are connected by 3',5'-phosphodiester bonds. B) The amount of A always equals the amount of T. C) The ratio A+T/G+C is constant for all natural DNAs. D) The two complementary strands are antiparallel. E) Two hydrogen bonds form between A and T.

Which of the following statements concerning the tautomeric forms of bases such as uracil is correct? A) The double-lactim form contains a ketone group. B) The lactam form contains an alcohol group. C) The lactam form predominates at neutral pH. D) Formation of the lactim from the lactam is irreversible. E) The lactim and double-lactim forms are stabilized at high pH

Which of the following statements is false? A) A reaction may not occur at a detectable rate even though it has a favorable equilibrium. B) After a reaction, the enzyme involved becomes available to catalyze the reaction again. C) For S → P, a catalyst shifts the reaction equilibrium to the right. D) Lowering the temperature of a reaction will lower the reaction rate. E) Substrate binds to an enzyme's active site.

Which vitamin is derived from cholesterol? A) A B) B12 C) D D) E E) K

C & G are complementary with ___ hydrogen bonds.

almost the same

C and H electronegativities are ______ ___ ____.

Which of the following statements about starch and glycogen is false? A) Amylose is unbranched; amylopectin and glycogen contain many (alpha1--> 6) branches. B) Both are homopolymers of glucose. C) Both serve primarily as structural elements in cell walls. D) Both starch and glycogen are stored intracellularly as insoluble granules. E) Glycogen is more extensively branched than starch.

C) Both serve primarily as structural elements in cell walls.

To possess optical activity, a compound must be: A) a carbohydrate. B) a hexose. C) asymmetric. D) colored. E) D-glucose.

C) asymmetric.

Which of the following monosaccharides is not a carboxylic acid? A) 6-phospho-gluconate B) gluconate C) glucose D) glucuronate E) muramic acid

C) glucose

Hemoglobin glycation is a process where_______ is _________ attached to hemoglobin. A) glycerol; covalently B) glucose; enzymatically C) glucose; non-enzymatically D) N-acetyl-galactosamine; enzymatically E) galactose; non-enzymatically

C) glucose; non-enzymatically

The reference compound for naming D and L isomers of sugars is: A) fructose. B) glucose. C) glyceraldehyde. D) ribose. E) sucrose.

C) glyceraldehyde.

When the linear form of glucose cyclizes, the product is a(n): A) anhydride. B) glycoside. C) hemiacetal. D) lactone. E) oligosaccharide.

C) hemiacetal.

Psi

C-alpha carbon

Oxidation-Reduction Reactions

C6H12O6 + 6O2 -> 6CO2 + 6H2O CO2 + H2O -> (HCO3-) + (H+)

a. left b. left c. right d. right

CH3COOH + H2O <> H3O+ + CH3COO- Which way will this equilibrium for acetic acid shift when: a. pH is lowered (e.g. adding HCl) _____ b. add sodium acetate (NaCH3COO) ______ c. increase concentration of acetic acid _____ d. dilute with water _____

aerobic metabolism

CO2 and H+ and Bohr Effcet are products of...

0.2M

Calculate the osmolarity of 0.1M potassium chloride solution.

0.4 M

Calculate the osmolarity of a 0.1 M sodium phosphate solution.

0.8M

Calculate the osmolarity of a 0.2M sodium phosphate solution.

1.50

Calculate the osmolarity of a 0.50M magnesium hydroxide solution.

20 s^-1

Calculate the turnover number of an enzyme catalyzed reaction that has a maximum velocity of 60 mM/s at a total enzyme concentration of 3 mM.

0.1 min

Calculate the turnover time for a reaction that follows Michaelis-Menton kinetics when the maximum velocity is 100 micro molar/min at an enzyme concentration of 10 micro molar.

0.03125 s

Calculate the turnover time of an enzyme-catalyzes reaction that has a maximum velocity of 800 mM/s at a total enzyme concentration of 25 mM.

300 mM/min

Calculate the velocity (rate) of a reaction that has a maximum velocity of 500 mM/min, a substrate concentration of 75 mM and a Km of 50 mM.

Ramachanron Plot

Can completely identify secondary structure by specifying all angles of phi and psi

Glycolipid

Carbohydrate + lipid

Glycoproteins

Carbohydrate + protein

Multiple OH's, C=O as aldehyde (aldose) or ketone (ketose)

Carbohydrate functional groups

hydrogen bonding

Cellulose can form very strong fibers mostly due to ______.

strong acids, proteases, strong bases

Chains can be hydrolyzed by _______, ________ & ________.

Function

Change of structure often changes _______. (e.g. sickle cell anemia)

Watson-Crick base-pairing

Charger's rule lead to _______________.

Chloroplasts

Chlorophyll-containing organelles in plant cells; produce ATP

are not

Cis and trans isomers are configurations that ____ interconvertible by rotation about bonds.

Primary

Classification of amines: NH2-R

Secondary

Classification of amines: NHRR'

Proteolytic cleavage (irreversible)

Cleavage of larger precursor molecule to form the active enzyme

Reduction with 2-mercaptoethanol (DTT or Cleland's reagent)

Cleave S-S bond to give 2 -SH groups

prosthetic group

Cofactors distinguished by being tightly bound to their proteins are called

prosthetic groups

Cofactors distinguished by being tightly bound to their proteins are called _______.

vitamin C

Collagen requires ______ for synthesis.

Cytoplasm

Collective name for the material that is not in the cell's nucleus but is within the plasma membrane which includes organelles

Dabsyl chloride

Colored (used for N-terminus detection)

Monosaccharides

Colorless, crystalline, water soluble, sweet, optically active (chiral)

S+E<->ES->P+E

Combined Michaelis Menton minimal mechanism

Matrix

Concentrated aqueous phase inside mitochondria

interconvertible

Conformation are _____________ by rotation about bonds

interconvertible by rotation around bonds

Conformation are:

Lipoproteins

Conjugated proteins that have lipids

Metalloproteins

Conjugated proteins that have metal (mostly ions)

Glycoproteins

Conjugated proteins that have sugar groups

remains constant

Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the pH ____.

cardiovascular disease

Consuming trans fats increases risk of _______ ______.

10^9 A

Convert 10cm to Angstroms

10^9 Angstroms

Convert 10cm to Angstroms.

Fehling's and Benedict's reagents

Cupric(blue) + sugar -----> Cuprous(red) + oxidized sugar a)These tests are one of the earliest tests for sugar detection in urine of diabetics b)These tests are nonspecific, because these reagents can be reduced also by other hexoses or other reducing compounds as vitamin C

a substance that cleaves peptide bonds

Cyanogen bromide is an example of:

oxidized

Cystine forms when two CH3-SH groups are ______ to form a CH2-S-S-CH2 group.

oxidation

Cystine is formed by the _______ of two cysteines.

B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a rise of ____ Å per base pair. A) left; 20; 3.9 B) right; 18; 3.4 C) right; 18; 3.6 D) right; 20; 3.4 E) right; 23; 2.6

For the oligoribonucleotide pACGUAC: A) the nucleotide at the 3' end has a phosphate at its 3' hydroxyl. B) the nucleotide at the 3' end is a purine. C) the nucleotide at the 5' end has a 5' hydroxyl. D) the nucleotide at the 5' end has a phosphate on its 5' hydroxyl. E) the nucleotide at the 5' end is a pyrimidine

For the simplified representation of an enzyme-catalyzed reaction shown below, the statement "ES is in steady-state" means that: k1 k2 E + S ES E + P k-1 k-2 A) k2 is very slow. B) k1= k2. C) k1= k-1. D) k1[E][S] = k-1[ES] + k2[ES]. E) k1[E][S] = k-1[ES].

In DNA sequencing by the Sanger (dideoxy) method: A) radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic synthesis of complementary strands. B) specific enzymes are used to cut the newly synthesized DNA into small pieces, which are then separated by electrophoresis. C) the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence. D) the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs occur in the template strands. E) the template DNA strand is radioactive

In competitive inhibition, an inhibitor: A) binds at several different sites on an enzyme. B) binds covalently to the enzyme. C) binds only to the ES complex. D) binds reversibly at the active site. E) lowers the characteristic Vmax of the enzyme.

In the Watson-Crick model for the DNA double helix, which of the following is not true? A) The two strands run anti-parallel to one another. B) The base-pairing occurs on the inside of the double helix. C) The double helix is right-handed. D) There are two equally sized grooves that run up the sides of the helix. F) The two strands have complementary sequences.

In the chemical synthesis of DNA: A) the dimethoxytrityl (DMT) group catalyzes formation of the phosphodiester bond. B) the direction of synthesis is 5' to 3'. C) the maximum length of oligonucleotide that can be synthesized is 8-10 nucleotides. D) the nucleotide initially attached to the silica gel support will become the 3' end of the finished product. E) the protecting cyanoethyl groups are removed after each step.

Michaelis and Menten assumed that the overall reaction for an enzyme-catalyzed reaction could be written as k1 k2 E + S ES → E + P k-1 Using this reaction, the rate of breakdown of the enzyme-substrate complex can be described by the expression: A) k1 ([Et] − [ES]). B) k1 ([Et] − [ES])[S]. C) k2 [ES]. D) k-1 [ES] + k2 [ES]. E) k-1 [ES].

The Lineweaver-Burk plot is used to: A) determine the equilibrium constant for an enzymatic reaction. B) extrapolate for the value of reaction rate at infinite enzyme concentration. C) illustrate the effect of temperature on an enzymatic reaction. D) solve, graphically, for the rate of an enzymatic reaction at infinite substrate concentration. E) solve, graphically, for the ratio of products to reactants for any starting substrate concentration

The alkaline hydrolysis of RNA does not produce: A) 2'- AMP. B) 2',3'-cGMP. C) 2'-CMP. D) 3',5'-cAMP. E) 3'-UMP

The concept of "induced fit" refers to the fact that: A) enzyme specificity is induced by enzyme-substrate binding. B) enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction. C) enzyme-substrate binding induces movement along the reaction coordinate to the transition state. D) substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation. E) when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate

The double helix of DNA in the B-form is stabilized by: A) covalent bonds between the 3' end of one strand and the 5' end of the other. B) hydrogen bonding between the phosphate groups of two side-by-side strands. C) hydrogen bonds between the riboses of each strand. D) nonspecific base-stacking interaction between two adjacent bases in the same strand. E) ribose interactions with the planar base pairs.

The nucleic acid bases: A) absorb ultraviolet light maximally at 280 nm. B) are all about the same size. C) are relatively hydrophilic. D) are roughly planar. E) can all stably base-pair with one another

The ribonucleotide polymer (5')GTGATCAAGC(3') could only form a double-stranded structure with: A) (5')CACTAGTTCG(3'). B) (5')CACUAGUUCG(3'). C) (5')CACUTTCGCCC(3'). D) (5')GCTTGATCAC(3'). E) (5')GCCTAGTTUG(3').

The role of an enzyme in an enzyme-catalyzed reaction is to: A) bind a transition state intermediate, such that it cannot be converted back to substrate. B) ensure that all of the substrate is converted to product. C) ensure that the product is more stable than the substrate. D) increase the rate at which substrate is converted into product. E) make the free-energy change for the reaction more favorable

The role of the metal ion (Mg2+) in catalysis by enolase is to: A) act as a general acid catalyst. B) act as a general base catalyst. C) facilitate general acid catalysis. D) facilitate general base catalysis. E) stabilize protein conformation

Triple-helical DNA structures can result from Hoogsteen (non Watson-Crick) interactions. These interactions are primarily: A) covalent bonds involving deoxyribose. B) covalent bonds involving the bases. C) hydrogen bonds involving deoxyribose. D) hydrogen bonds involving the bases. E) hydrophobic interactions involving the bases

Vmax for an enzyme-catalyzed reaction: A) generally increases when pH increases. B) increases in the presence of a competitive inhibitor. C) is limited only by the amount of substrate supplied. D) is twice the rate observed when the concentration of substrate is equal to the Km. E) is unchanged in the presence of a uncompetitive inhibitor.

Which of the following are possible base compositions for single-stranded RNA? %A %G %C %T %U A) 5 45 45 0 5 B) 25 25 25 0 25 C) 35 10 30 0 25 D) All of the above E) None of the above

Which of the following contains an ether-linked alkyl group? A) Cerebrosides B) Gangliosides C) Phosphatidyl serine D) Platelet-activating factor E) Sphingomyelin

Which of the following is a palindromic sequence? A) AGGTCC TCCAGG B) CCTTCC GCAAGG C) GAATCC CTTAGG D) GGATCC CCTAGG E) GTATCC CATAGG

Which of the following statements about membrane lipids is true? A) Glycerophospholipids are found only in the membranes of plant cells. B) Glycerophospholipids contain fatty acids linked to glycerol through amide bonds. C) Lecithin (phosphatidylcholine), which is used as an emulsifier in margarine and chocolate, is a sphingolipid. D) Some sphingolipids include oligosaccharides in their structure. E) Triacylglycerols are the principal components of erythrocyte membranes.

Which of these statements about enzyme-catalyzed reactions is false? A) At saturating levels of substrate, the rate of an enzyme-catalyzed reaction is proportional to the enzyme concentration. B) If enough substrate is added, the normal Vmax of a reaction can be attained even in the presence of a competitive inhibitor. C) The rate of a reaction decreases steadily with time as substrate is depleted. D) The activation energy for the catalyzed reaction is the same as for the uncatalyzed reaction, but the equilibrium constant is more favorable in the enzyme-catalyzed reaction. E) The Michaelis-Menten constant Km equals the [S] at which V = 1/2 Vmax.

Which one of the following is not among the six internationally accepted classes of enzymes? A) Hydrolases B) Ligases C) Oxidoreductases D) Polymerases E) Transferases

Which one of the following is true of the pentoses found in nucleic acids? A) C-5 and C-1 of the pentose are joined to phosphate groups. B) The pentoses are in a planar configuration. C) The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond. D) The pentoses are always in the β-furanose forms. E) The straight-chain and ring forms undergo constant interconversion

Which one of the following statements is true of enzyme catalysts? A) Their catalytic activity is independent of pH. B) They are generally equally active on D and L isomers of a given substrate. C) They can increase the equilibrium constant for a given reaction by a thousand fold or more. D) They can increase the reaction rate for a given reaction by a thousand-fold or more. E) To be effective, they must be present at the same concentration as their substrate

Which one of the following statements is true of enzyme catalysts? A) They bind to substrates but are never covalently attached to substrate or product. B) They increase the equilibrium constant for a reaction, thus favoring product formation. C) They increase the stability of the product of a desired reaction by allowing ionizations, resonance, and isomerizations not normally available to substrates. D) They lower the activation energy for the conversion of substrate to product. E) To be effective, they must be present at the same concentration as their substrates.

Which of the following does not contain a glucosamine? A) Syndecans B) Glypicans C) Chitin D) Amylopectin E) Chondrotin

D) Amylopectin

Which of the following is a heteropolysaccharide? A) Cellulose B) Chitin C) Glycogen D) Hyaluronate E) Starch

D) Hyaluronate

Which of the following is a dominant feature of the outer membrane of the cell wall of gram negative bacteria? A) Amylose B) Cellulose C) Glycoproteins D) Lipopolysaccharides E) Lipoproteins

D) Lipopolysaccharides

Which of following is an anomeric pair? A) D-glucose and D-fructose B) D-glucose and L-fructose C) D-glucose and L-glucose D) alpha-D-glucose and beta-D-glucose E) alpha-D-glucose and beta-L-glucose

D) alpha-D-glucose and beta-D-glucose

Starch and glycogen are both polymers of: A) fructose. B) glucose1-phosphate. C) sucrose. D) alpha-D-glucose. E) beta-D-glucose.

D) alpha-D-glucose.

Why is it surprising that the side chains of tryptophan residues in proteins can interact with lectins? A) because the side chain of tryptophan is hydrophilic and lectins are hydrophobic. B) because the side chain of tryptophan is (-) charged and lectins are generally (+) charged or neutral. C) because the side chain of tryptophan can make hydrogen bonds and lectins cannot. D) because the side chain of tryptophan is hydrophobic and lectins are generally hydrophilic. E) none of the above.

D) because the side chain of tryptophan is hydrophobic and lectins are generally hydrophilic.

The biochemical property of lectins that is the basis for most of their biological effects is their ability to bind to: A) amphipathic molecules. B) hydrophobic molecules. C) specific lipids. D) specific oligosaccharides. E) specific peptides.

D) specific oligosaccharides.

When two carbohydrates are epimers: A) one is a pyranose, the other a furanose. B) one is an aldose, the other a ketose. C) they differ in length by one carbon. D) they differ only in the configuration around one carbon atom. E) they rotate plane-polarized light in the same direction.

D) they differ only in the configuration around one carbon atom.

ligase

DNA ____ joins the Okazaki fragments in lagging-strand synthesis.

stable

DNA backbone is fairly _____ and hydrolysis is accelerated by enzymes (DNAse).

supercoiling

DNA can also be circular and may twist upon itself by ________.

right

DNA helix is _____-handed.

conservative

DNA is semi-_______.

annealing

DNA may be reversible: ________

DNA polymerase __ removes RNA primers from the lagging strand.

III

DNA polymerase ___ requires short stretch of RNA as a primer before it can add new nucleotides.

primary

DNA sequencing also determines ______ structure.

Regulations of gene expression

DNA-binding proteins

Depends on the number of solute particles dissolved Vapor pressure, boiling point, melting point, Osmolarity

Define a colligative property and name them

high temp, change in pH and chaotropic agents (urea)

Denaturation can be induced by ______, ________, and _________.

12% to 40%

Denatured DNA absorbs ______ more than dsDNA

SDS Page

Denaturing gel

right

Deprotonated forms are on the ____ of the equilibrium expression.

N:M^delta x,y,z... N = number of carbons in the chain M = number of carbon-carbon double bonds x,y,z.. = locations of double bonds by carbon number

Describe the fatty acid nomenclature

Like charges, steric hindrance (proline and glycine)

Destabilizes helices

Benzedrine is a racemic mixture and Dexedrine is a single pure stereoisomer.

Dexadrine and Benzedrine have the same chemical formula and the same physical properties such as melting point, solubility, etc and were used for the same treatment. Benzedrine (no longer available) was prescribed at twice the dosage of Dexedrine to yield the same physical response. Which is a likely explanation? A. The two drugs are cis-trans isomers. B. Benzedrine is a racemic mixture and Dexedrine is a single pure stereoisomer. C. Dexadrine and Benzedine are enantiomers of each other. D. The drugs are structural isomers of each other that just happen to have the same medicinal activity.

elongation

Dideoxies block _______.

Variable residues

Different among homologs

Domain

Distinct structural units

Higher

Does a pure sample have a higher or lower specific activity?

cis

Double bonds are usually in ___ configuration in fatty acids. They form kinks in the chain.

double helix

Double-stranded structure of DNA is twisted into a _______.

A. They will breathe out a greater carbon dioxide content

Due to its buffering system, what will happen if a person develops a metabolic condition that decreases the pH of the blood? A. They will breathe out a greater carbon dioxide content B. They will have an increase in bicarbonate ion concentration in the blood C. They will have a decreased concentration of hydrogen phosphate in the blood. D. All of the above

A major component of RNA but not of DNA is: A) adenine. B) cytosine. C) guanine. D) thymine. E) uracil

Blood coagulation involves: A) a kinase cascade. B) zymogen activation. C) serine proteases. D) A and B. E) B and C

Chargaff's rules state that in typical DNA: A) A = G. B) A = C. C) A = U. D) A + T = G + C. E) A + G = T + C.

Enzymes are potent catalysts because they: A) are consumed in the reactions they catalyze. B) are very specific and can prevent the conversion of products back to substrates. C) drive reactions to completion while other catalysts drive reactions to equilibrium. D) increase the equilibrium constants for the reactions they catalyze. E) lower the activation energy for the reactions they catalyze

Identify the molecule(s) derived from sterols. A) Arachidonic acid B) Gangliosides C) Phosphatidylglycerol D) Prostaglandins E) Vitamin D

In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is: A) DNA-DNA > DNA-RNA > RNA-RNA. B) DNA-DNA > RNA-RNA > DNA-RNA. C) RNA-DNA > RNA-RNA > DNA-DNA. D) RNA-RNA > DNA-DNA > DNA-RNA. E) RNA-RNA > DNA-RNA > DNA-DNA.

In living cells, nucleotides and their derivatives can serve as: A) carriers of metabolic energy. B) enzyme cofactors. C) intracellular signals. D) precursors for nucleic acid synthesis. E) all of the above.

In the Watson-Crick model of DNA structure (now called B-form DNA): A) a purine in one strand always hydrogen bonds with a purine in the other strand. B) A-T pairs share three hydrogen bonds. C) G-C pairs share two hydrogen bonds. D) the 5' ends of both strands are at one end of the helix. E) the bases occupy the interior of the helix

In the Watson-Crick model of DNA structure: A) both strands run in the same direction, 3' → 5'; they are parallel. B) phosphate groups project toward the middle of the helix, where they are protected from interaction with water. C) T can form three hydrogen bonds with either G or C in the opposite strand. D) the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines. E) the distance between two adjacent bases in one strand is about 3.4 Å.

In the laboratory, several factors are known to cause alteration of the chemical structure of DNA. The factor(s) likely to be important in a living cell is (are): A) heat. B) low pH. C) oxygen. D) UV light. E) both C and D.

Purines have ____ ring(s), (each) containing _____ nitrogen(s), whereas pyrimidines have _____ ring(s), (each) containing _____ nitrogens. A) 1; 1; 1; 1 B) 1; 2; 1; 2 C) 2; 1; 1; 2 D) 2; 2; 1; 1 E) 2; 2; 1; 2

The "energy carrier" ATP is an example of a(n): A) deoxyribonucleoside triphosphate B) di-nucleotide C) peptide D) ribonucleotide E) ribonucleoside triphosphate

The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is: A) a deoxyribonucleoside. B) a purine nucleotide. C) a pyrimidine nucleotide. D) adenosine monophosphate. E) adenosine

The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the: A) dissociation constant. B) half-saturation constant. C) maximum velocity. D) Michaelis-Menten number. E) turnover number.

The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA: A) always link A with T and G with C. B) are susceptible to alkaline hydrolysis. C) are uncharged at neutral pH. D) form between the planar rings of adjacent bases. E) join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next

To calculate the turnover number of an enzyme, you need to know: A) the enzyme concentration. B) the initial velocity of the catalyzed reaction at [S] >> Km. C) the initial velocity of the catalyzed reaction at low [S]. D) the Km for the substrate. E) both A and B.

Which of the following molecules or substances contain, or are derived from, fatty acids? A) Beeswax B) Prostaglandins C) Sphingolipids D) Triacylglycerols E) All of the above contain or are derived from fatty acids.

Which of the following statements about allosteric control of enzymatic activity is false? A) Allosteric effectors give rise to sigmoidal V0 vs. [S] kinetic plots. B) Allosteric proteins are generally composed of several subunits. C) An effector may either inhibit or activate an enzyme. D) Binding of the effector changes the conformation of the enzyme molecule. E) Heterotropic allosteric effectors compete with substrate for binding sites

Which of the following is not a reducing sugar? A) Fructose B) Glucose C) Glyceraldehyde D) Ribose E) Sucrose

E) Sucrose

Which of the following pairs is interconverted in the process of mutarotation? A) D-glucose and D-fructose B) D-glucose and D-galactose C) D-glucose and D-glucosamine D) D-glucose and L-glucose E) alpha-D-glucose and beta-D-glucose

E) alpha-D-glucose and beta-D-glucose

three

E.coli contains ____ DNA polymerases

template

Each strand of DNA acts as a _______ for synthesis of a new strand in DNA replication.

template

Each strand serves as a ________ for the synthesis of a new strand.

interior

Endonucleases cleave _______ sequence of nucleic acids.

Regulatory enzyme

Enzymes whose activity is controlled by reversible modulation

established quickly

Equilibrium for S+E<->ES is __________ ________ (MM assumption)

Equivalence point is ___ for weak acid titrations with a strong base.

Equivalence point is ____ for weak base titrations with a strong acid.

Equivalence point is at __ for strong acid titration with a strong base.

Ethanol must act as a competitive inhibitor for the alcohol dehydrogenase and therefore slows the formation of formaldehyde.

Ethanol (CH3CH2OH) is the alcohol found in beverages. It is oxidized in the body to acetaldehyde by the enzyme alcohol dehydrogenase. Methanol (CH3OH), also known as wood alcohol, is converted to formaldehyde by the same enzyme. Acetaldehyde is toxic, but formaldehyde is far more toxic to humans, which is why the ingestion of relatively small amounts of methanol can cause blindness or death. One treatment for mild methanol poisoning is the administration of ethanol. Why might a doctor choose this treatment?

Mitochondria

Eukaryotic organelle which are principle producers of ATP; "engines of the cell"

glycine

Example of a zwitterion

Ion-dipole

Examples: Solvation (surrounding of a solute by the solvent) - Hydration (salvation with water as the solvent) -Dissolving of NaCl (note the gain in entropy)

from the end

Exonucleases cleave nucleotides ____ __ ___ of nucleic acids.

the primary sequence of RNAse is sufficient to determine its specific secondary and tertiary structure and the protein folding is not random

Experiements on denaturation and renaturation of the enzyme ribonuclease (RNAse) have shown that:

Cell/plasma membrane

Exterior membrane surrounding the cytoplasm of the cell; provides a barrier (physical) from the surroundings and also facilitates exchange of material

long

Fats are for ____-term needs (good storage, slow delivery)

more; less

Fats have an advantage over polysaccharides because they store ____ energy per gram and carry ___ H2O along because they are non polar

4-36

Fatty acids have chains from _____ carbons long but are usually even number of carbons

Fermentation

Fermentation is the action of bacterial or yeast enzymes on carbohydrate. a)fermentation of sugars give ethyl alcohol and CO2 b)All D-monosaccharides are fermentable C6H12O6 -> 2 CH3-CH2-OH + 2CO2

(CH2O)n

First carbohydrates studied had empirical formula ____

toward

Fischer projections: Horizontal bonds project _____ the viewer.

HPLC

Follow % comp with detection techniques such as _____.

closest

For AA with ionizable R-groups, take the average of the two ______ pKas.

3.5

For a hypothetical amino acid, the pKa's of a alpha-carboxyl group, alpha-amino group and side chain are 2.5, 9.0 and 4.5 respectively. Calculate the isoelectric point.

Heterotrophic

For allosteric enzymes, modulators are usually ________

Non-covalently

For allosteric enzymes, modulators bind _________

Large, multi subunit

For allosteric enzymes, most are ____, ___________ enzymes

first; zero

For an enzyme that obey Michaelis-Menton type kinetics, it is observe that at low concentrations of substrates the reaction is ____ order while at high concentrations of substrate the reaction is _____ order.

1. contain one or more polar bonds 2. the bonds can't cancel each other out

For any molecule to be polar, it must meet two requirements. Name them.

A-DNA

Form of DNA that is: -dehydrated -right-handed helix -planes of bases not perpendicular to helix axis -smaller pitch than B-DNA -wider than B-DNA

B-DNA

Form of DNA that is: -hydrated -right-handed helix -predominant in living cells -planes of bases appx perpendicular to helix axis

Z-DNA

Form of DNA that is: -rare, some sequences have it -left-handed helix -narrower than B-DNA -No grooves

Trans fatty acid

Formed by partial dehydrogenation of unsaturated fatty acids and allows for a more extended conformation than cis.

Conformation

Forms of the same molecule that are interconvertible by rotation about bonds

Drag force

Friction from the surrounding medium

stationary phase of porous resin beads....... size

Gel filtration chromatography is based on _____ and separates molecules based on their ____. A. a protein-ligand attraction......charge B. a stationary phase of porous resin beads......size C. ionic attraction for the stationary phase.....pI D. sedimentation of particles..........density

a stationary phase of porous resin beads.......size

Gel filtration chromatrography is based on ______ and separates molecules based on their _____.

-OOCR R is long

General structure of a fatty acid

alpha

General structure of amino acid: The carbon with the R-group attached is called the ______-carbon.

Prosthetic group

General term for non-amino acid group

Organelle

Generic term for membrane-bounded structures in eukaryotic cells (ex: mitochondria)

Configurations

Geometric isomers that are not interconvertible by rotation about bonds

- membranes - proteins - enzyme-substrate interactions

Give examples of things that maintain structure

2.2

Given the pKa values for phosphoric acid of 2.14, 6.86 and 12.4, what is the ratio of (HPO4)^-2/)H2PO4)- in a typical muscle cell where the pH is 7.2?

short

Glucose and glycogen are for ____-term needs (quick delivery)

Glucose has __ chiral carbons

3.2

Glutamic acid contains two carboxylic acid groups (pKa values of 2.2 and 4.2) and an amine group (pKa=9.7). What is the pI for glutamic acid?

Ampholytic and achiral

Glycine is ______ and _____.

-ose

Glycoconjugates suffix

to store energy in mammalian liver

Glycogen's main biological function is:

glycoconjugates

Glycolipids and glycoproteins are examples of _________.

Proteoglycan

Glycosaminoglycan + core protein

no longer

Groups in amide bond ______ ionizable.

Covalent modification (reversible)

Groups taken off or put on to activate/deactivate

H+ protonates groups on Hb which stabilizes deoxy Hb and increases the efficiency of O2 delivery

H+ protonates groups on Hb which ______deoxy Hb and ______ the efficiency of O2 delivery

cannot

Hemiacetals and hemiketals _______ react directly with oxidizing agents

two

Hemoglobin has ___ matching pairs of protein chains.

Peptidoglycan

Heteroglycan + peptide

London forces

Hexane, C6H14, is a liquid at room temperature. What forces are responsible for hexane not being a gas at room temperature?

HPLC

High Pressure/ Performace Liquid Chromatography

Dansyl chloride

Highly fluorescent (used for N-terminus detection)

nlog[L]-logKd

Hill equation

Orthologs

Homologous proteins from different species

Paralogs

Homologous proteins in the same species

c. Proteolytic cleavage of trypsinogen forms trypsin

How are trypsinogen and trypsin related? a. A protein kinase-catalyzed phosphorylation converts trypsinogen to trypsin b. Trypsinogen is the apoenzyme; trypsin contains cofactors. c. Proteolytic cleavage of trypsinogen forms trypsin d. Trypsinogen is a monomer; trypsin is a dimer of trypsinogen formed by a disulfide bond. e. Two inactive trypsinogen dimers pair to form an active trypsin tetramer.

look where Vo=1/2Vmax

How do we get Km in the lab?

2^n where n = # of chiral centers

How do you figure out how many stereoisomers you can have?

>80,000 rpm

How fast does an ultracentrifuge spin?

Add HF

How is a completed protein released from a protein synthesis column?

addition of HF

How is a protein released from protein synthesis column?

Addition of HF

How is protein released from protein synthesis column?

d. Take the reciprocal of the M-M equation and rearrange

How is the Lineweaver-Burk equation derived from the Michaelis-Menton (M-M) equation? a. Take the log of the M-M equation and rearrange b. Divide the M-M equation by Vmax and rearrange c. Substitue [E]tot - [ES] for [E]free in the M-M equation and rearrange d. Take the reciprocal of the M-M equation and rearrange

b. Six amino acids are cleaved from trypsinogen's N-terminal to release trypsinogen.

How is trypsin activated? a. The trypsinogen dimer is phosphorylated by phosphorylase kinase. b. Six amino acids are cleaved from trypsinogen's N-terminal to release trypsinogen. c. DTT is used to form four disulfide bonds which converts trypsin into its active form. d. Enteropeptidase forms a covalently bound dimer with trypsinogen to form active trypsin.

How many atoms are in a furanose ring?

How many atoms are in a pyranose ring?

How many carbon atoms are found in the smallest molecules that are classified as carbohydrates?

How many linear stereoisomers are possible for a monosaccharide with 3 chiral centers?

oxidoreductase

How would you classify an enzyme that changed a structure from an alcohol to a carbonyl or vise versa?

weaker

Hydrogen bonds are typically ______ than ionic or covalent bonds.

C=O and N-H

Hydrogen bonds between amino acids in a polypeptide occur between which chemical groups?

ice, water

Hydrogen bonds give ___ an open structure and give _____ its unusually high heat of vaporization and heat capacity.

optimum; biological activity

Ideal pH is called the _______; pH of greatest _______ ______.

Invariant residues

Identical among homologs

ester

Identify the function group RCOOR

carbonyl

Identify the organic function group. RCOR'

amido

Identify the organic functional group.. RCONH2

less than 1

If a buffer is made with the pH below the pKa of the weak acid, the ratio of [base]/[acid] will be:

hypotonic

If a cell bursts when placed in a buffer solution, the buffer is ________.

polymorphic

If a protein is _________, there are variation in the sequence that have no effect on the function of the protein.

there are variations in the sequence that have no effect on the function of the protein

If a protein is polymorphic this means:

exothermic........decreasing

If a reaction gives off heat it is ______ and has _______ enthalpy.

The reaction is first order with respect to [A]

If a reaction's rate is doubled when the concentration of reactant A is doubled, then...

the reaction is first order with respect to [A].

If a reaction's rate is doubled when the concentration of reactant A is doubled, which statement applies?

If a sample contains 20 unites of enzyme and 10.0 mg of total protein, what is the numerical value (without the units) of the specific activity?

If a sample contains 20 units of enzyme and 10.0 mg of total protein, what is the numerical value (without the units) of the specific activity?

oxidoreductase

If an enzyme catalyzes the conversion of an aldehyde group to a carboxylate group, to what class does the enzyme belong?

isomerase

If an enzyme could cover D-glucose into D-galactose, how would you classify the enzyme?

Concerted

If an oligomeric enzyme makes a transition from tense to relaxed with all subunits converting simultaneously, we say the conversion is by a _______ mechanism.

endothermic

If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be ______.

If higher priority is on right, the chiral center is assigned the letter ___.

If higher priority is on the left, the chiral center is assigned the letter ___.

at equilibrium

If the free energy change (delta G) for a reaction is zero kj/mol, the reaction is:

affinity chromotography

If you are attempting to decrease the number of procedures needed to purify a protein, what technique would be the best to use, if available?

HCO3- (aq) + H+ (aq) <> H2CO3 (aq)

If you breathe repeatedly into a paper bag, in the blood this equilibrium will shift to the left.

hydrolyze the protein with 6M HCL, then analyze with HPLC

If you wanted to know what percent of a protein consisted of glutamate, what would you do?

Watson and Crick

In 1953, _____ and ______ proposed the DNA structure we use now.

separate; increases

In DNA denaturation, two strands _____ (ds DNA to ss DNA), base stacking is lost and UV absorbance ______.

termination site

In DNA replication, complex stuff happens at the ________ site and finishes the replication to release two new DNAs

smallest

In SDS, the ______ molecules travel faster in the second step using MW.

beta sheets

In ______, hydrogen bonds form between C=O and N-H groups on neighboring chain segments.

DNA denaturation

In _________, covalent bonds and genetic code remain in tact but hydrogen bonds are broken.

In a Hill plot, if the slope is ___ 1 it is an indication of interaction between binding sites.

C(alpha)-C bond

In a _____ bond, it is free to rotate for all amino acids except as limited by steric hindrance.

Hill plot

In a ______, if the slope=1 then there is no interaction between binding sites.

in order from lowest pI to highest pI acidic to basic

In a cation exchange chromatography column, how will proteins elute from the column (first to last)?

glutamate; glutamine; lysine

In a cation ion exchange chromatography experiment, in what order (first to last) will glutamate, lysine and glutamine elute?

covalently

In a hydrogen bond, the hydrogen atom involved must be ________ bonded to a very electronegative atom.

largest

In a size-exclusion gel (gel-filtration), the ______ MW elutes first.

5.5 cm

In an SDS-PAGE experiement, two markers of known molecular weights of 10,000 g/mol and 1000 g/mol traveled 4 cm and 9 cm, respectively. What is the approximate distance travels by a protein whose molecular weight is 5000 g/mol?

3200 g/mol

In an SDS-PAGE experiment, two markers of known molecular weights of 10,000 g/mol and 1000 g/mol traveled 4 cm and 9 cm, respectively. What is the approximate molecular weight of an unknown that travels 6.5 cm in the gel?

are found on the outside of the helix spiral

In an alpha helix, the R groups on the amino acid residues:

outside

In an alpha-helix, the R groups on the amino acid residues are found on the _____ of the helix.

are found on the outside of the helix spiral

In an alpha-helix, the R groups on the amino acid residues:

number 7

In an alpha-helix, the carbonyl group of the third amino acid will form a hydrogen bond with the group on which amino acid?

large gain in entropy for water

In an aqueous environment, what drives the formation of a bilayer structure?

C. It forms an equilibrium mixture of anomers and a linear form

In an aqueous solution, what will be true to D-glucose? A. It forms a racemic mixture of enantiomers B. It polymerizes to form a glycogen-like structure. C. It forms an equilibrium mixture of anomers and a linear form. D. D-glucose is insoluble in water.

Elluent / effluent

In column chromatography, the liquid that comes out of the bottom of the column is called the ______.

synthesize ATP

In eukaryotes, what is the main function of the mitochondria?

decreases

In fatty acids, melting point ______ as the chain length increases.

decreases

In fatty acids, solubility ______ as the chain length increases.

in order from highest molecular weight to lowest molecular weight

In gel filtration chromatography, how will proteins elute from the column (first to last)?

pH...........pI

In isoelectric focusing a ____ gradient is established across a gel and particles migrate according to their ____.

pH.......pI

In isoelectric focusing a ________ gradient is established across a gel and particles migrate s according to their______.

one to a histidine

In myoglobin the iron ion in the heme group has coordinate bond(s) to which amino acid(s) in the protein?

4.........1 HAS 1 OTHER COORDINATE BOND TO O2.......SO 6 IN TOTAL

In myoglobin, the iron in the heme group forms_____coordinate bonds to the porphyrin ring and _____ coordinate bonds to amino acids in the protein chains.

4.........1

In myoglobin, the iron ion in the heme group forms ____ coordinate bonds to the porphyrin ring and ___ coordinate bonds to amino acids in the protein chain.

one to a histidine

In myoglobin, the iron ion in the heme group has coordinate bonds to which amino acids in the protein?

In naming fatty acids, carboxylate carbon is number __.

In nature __-enantiomers predominate (>90%)

In nature, the ___-enantiomer predominates.

d. the inhibitor binds to a site other than the active site either before or after the substrate binds

In noncompetitive (mixed) inhibition, which of the following best explains how the inhibitor binds to the enzyme? a. the inhibitor binds to the active site only after the substrate binds b. the inhibitor binds to a site other than the active site only before the substrate binds c. the inhibitor binds to a site other than the active site only after the substrate binds d. the inhibitor binds to a site other than the active site either before or after the substrate binds e. none of the above

phosphodiester

In polynucleotides, covalent bonds form via _______ linkages in a negatively charged backbone.

form an equilibrium mixture

In solution a-D-glucose and B-D-glucose ______.

interconvert by mutarotation

In solution, a-D-glucopyranose and B-D-glucopyranose _____.

cyclic

In solution, monosaccharides are predominately in their _______ forms.

F3CCOOH

In the Edman degradation, which substance is used to cleave a peptide bond?

e. the bases occupy the interior of the helix

In the Watson-Crick model of DNA structure (now called B-form DNA): a. a purine in one strand always hydrogen bonds with a purine in the other strand b. A-T pairs share three hydrogen bonds c. G-C pairs share two hydrogen bonds d. the 5' ends of both strands are at one end of the helix e. the bases occupy the interior of the helix

down

In the alpha form of D-glucose, -OH points ____

C-N

In the backbone of a protein, which bond's rotation is most restricted?

deprotonated as pH passed pKa

Increasing pH

protomers or subunits

Individual chains in quarternary structure

Chromatography

Inherent differences in affinity for mobile vs. stationary phase effects separation

More sigmoidal

Inhibitor (negative modulator) has what shape on graph?

Mixed (reversible inhibitor)

Inhibitor binds either to free enzyme or ES (rare)

Uncompetitive (reversible inhibitor)

Inhibitor binds only to ES at site other than active site

Hyperbolic

Initial rate data for enzyme reaction is what shape?

zero; first

Initial rate measurements are made that vary the substrate concentration at a fixed concentration of enzyme. For an enzyme that obeys Michaelis-Menton type kinetics, it is observed that at high concentrations of substrate the reaction is ____ order while at low concentrations of substates the reaction is _____ order.

first; zero

Initial rate measurements are made that vary the substrate concentrations at a fixed concentration of enzyme. For an enzyme that obeys Michaelis-Menton type kinetics, it is observed that at low concentration of substrate the reaction is ____ order while at high concentrations of substrate the reaction is _____ order.

Cristae

Inner-membrane folds inside mitochondria

I knot

Intensity of incident light (before the cuvette)

Intensity of transmitted light (after the cuvette)

all alpha

Into which folding pattern class would you assign myoglobin?

Accelerating force

Ions attracted to oppositely charged poles

-covalent bonding -Inactivators or deactivators -destroy important functional groups

Irreversible inhibitor

Nonpolar

Is carbon dioxide polar or non polar?

Yes, anomeric carbon of the glucose unit is still in equilibrium with the reactive form.

Is lactose a reducing sugar?

Nonpolar

Is methane polar or non polar?

No, the glycosidic bond joins the anomeric carbon atoms from both monomers. Neither monomer is in equilibrium with the reactive linear form.

Is sucrose a reducing sugar?

It has more than one possible sequence that can function normally

It a protein is polymorphic this means:

the Vmax is an asymptotic value

It can be difficult to determine either Km or Vmax from a graph of velocity vs substrate concentration because:

Bidirectional DNA

New strands of DNA are synthesized at the two replication forks where replisomes are located

one daughter strand and one parent strand

Newly made DNA molecule has:

saturated

No double bond between carbons in the chain of a fatty acid

Reversible inhibitor

Non covalent association

Native gels

Non-denaturing gel

Nucleoid

Non-membrane bound structure in prokaryotic cells that contains the cell's genome

lipid; water-soluble

Nonpolar R groups are often on surfaces of ____ structure and interior on ____-______ proteins.

phosphate ester

Nucleotide monomers link by _______ _____ (phosphodiester) bonds.

Number of chiral carbons

Turnover number

Number of substrate to product conversions per unit time

derivatives the N-terminal of a polypeptide during sequencing

Of what use is phenyisothiocyanate (PITC)?

it derivitizes the N-terminal of a polypeptide during synthesis

Of what use is pheyisothiocyanate (PITC)?

polar (hydrophilic)

Often on surface of water soluble proteins and interior of lipid soluble proteins

nonpolar (hydrophobic)

Often on surfaces of lipid soluble proteins and interior on water soluble proteins

There is no cooperativity among binding sites

On a Hill plot, what does a slope=1 indicate?

acidic to basic

On a cation exchange column, amino acids elute from the most _____ to most _____.

3200 g/mol

On an SDS-PAGE gel proteins with molecular weights of 10,000, 1000 and 100 g/mol, respectively migrated 2, 4 and 6 cm from the starting wells. What is the approximate molecular weight of an unknown that migrates 3 cm?

3200 g/mol

On an SDS-PAGE gel proteins with molecular weights of 10,000, 1000 and 100g/mol, respectively migrated 2,4, and 6 cm from the starting wells. What is the approximate molecular weight of an unknown that migrates 3 cm?

3200 g/mol

On an SDS-PAGE gel, proteins with molecular weights of 10,000, 1000 and 100 g/mol, respectively migrated 2, 4 and 6 cm from the starting wells. What is the approximate molecular weight of an unknown that migrates 3 cm?

On the titration curve for glycine, at what point is glycine fully protonated?

On the titration curve for glycine, at what point is the charge on glycine -1?

On the titration curve for glycine, which point is glycine's isoelectric point if the pKa values are 2.34, 5.97, 9.60 and 11.3 respectively?

10^-10 m

One Angstrom is equal to ____.

react with performed acid

One method to preven disulfide bond interference with protein sequencing procedures is:

acetyl

One method used to prevent disulfide bond interference with protein sequencing procedures is by protecting the sulfhydryl groups with an _____ group.

acetylation

One method used to prevent disulfide bond interference with protein sequencing procedures is by reducing disulfide bonds and preventing their reformation by ______>

Lipids

One of the 4 main classes of biochemicals that is composed of fats, oils, membranes and steroids. Used for energy storage, forms cell membranes, lubrication and protection, waxes, hormones and vitamins of their precursors

Carbohydrates

One of the 4 main classes of biochemicals that is made of "sugars" (mono-, oligo-, and polysaccharides). Used for energy storage (glucose; blood sugar), structure (cellulose)

Nucleic acids

One of the 4 main classes of biochemicals which is composed of DNA and RNA (polymers of nucleotides) Used for information transfer, direction of protein synthesis, storage and release of energy (ATP to ADP)

apoenzyme

One of the enzymes involved in glycolysis is aldolase, which requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme lacks zinc, the form of aldolase would be referred to as the:

Proteins

One of the main classes of biochemicals which are composed of amino acids and produce muscles, collagen, hair, enzymes, transport, ect.

strong acid

One substance that can be used to hydrolyze peptide bonds.

oligomers (multiple parts)

Only ________ have quaternary structures

homologous proteins in different species

Orthologs are ________________.

Osazone formation

Osazones are characteristic crystals resulting from the reaction of sugars with phenylhydrazine. All sugars having free carbonyl group can form osazone crystals

Antibodies

Other specialized functions

Quarternary

Overall 3D structure of a multisubunit protein is called the _______ structure.

where theta =.5

P50 is the pressure where theta=__

Template DNA

PCR needs DNA to be copied:

RNA primer

PCR needs ______ for polymerase to start making DNA.

Thermocycler

PCR needs a buffer and _______ to alternate the temperature.

Taq polymerase

PCR needs a heat stable DNA polymerase

Nucleotides

PCR needs the monomers needed to make the DNA polymer

denature RNA primers replication 2

PCR procedure: 1. Mix all together 2. Heat to ______ DNA - separate strands 3. Cool to allow __________ to attach 4. Adjust temperature to optimum for ________ 5. Repeat - increase number of DNA molecules by a factor of ___ for each cycle

5' to 3'

Palindrome for DNA-sequences on both strands are the same in the _____ direction.

endonucleases

Palindromes can be recognition sequences for _________ (enzymes) such as DNAse or RNAse.

hairpins and cruciforms

Palindromic sequences can form _______ and _______.

proteins from one species with the same function

Paralogs are:

Homologous protein in the same species

Paralogs are_____.

Delta

Partial charge

Motifs

Patterns in families of proteins

280 nm

Peak at _____ for proteins (tyrosine and tryptophan)

C.......N

Peptides are synthesized from __-terminal to ___-terminal.

Peptides have their own ___.

Activation

Phosphorylase kinase

Deactivation

Phosphorylase phosphatase

antibiotic-resistant genes

Plasmids are often carriers of _______.

conjugation

Plasmids can be passed between bacteria by _________. This is why you need to take all of you antibiotics.

novel genes

Plasmids can be used in the lab to introduce ______ _____.

PAGE

Polyacrylamide Gel Electrophoresis

Aldose (carbohydrate)

Polyhydroxyl aldehydes

Ketose (carbohydrate)

Polyhydroxyl ketones

Polyacrylamide

Polymer of acrylamide

Branched polymer

Polymer with side chains (like tree branch)

Proteins, carbohydrates and nucleic acids

Polymeric forms are important for:

linear

Polynucleotides are _______ polymers with no branching or cross-links.

Agarose

Polysaccharide derived from seaweed

collagen

Proline residues are likely to occur most frequently in what protein? a. hair b. collagen c. silk d. myoglobin

Coligative Properties

Properties of a solution that depend on the NUMBER of solute molecules dissolved.

non-amino acid groups needed by a protein

Prosthetic groups are ________________.

b. the rotation about the peptide bond

Protein folding to a native conformation is highly dependent upon all of the following except: a. rotation about the alpha-carbon-----carbon bond in the backbone b. the rotation about the peptide bond c. the relative size of amino acid R groups d. the rotation about the alpha-carbon ------ nitrogen bond

Ribosomes

Protein/RNA complex that is the site of protein synthesis

linear heteropolymers

Proteins are _____ ________.

conjugated

Proteins that have non-amino acid groups attached are called _____ proteins.

Polymorphic

Proteins with normal variations in sequence within family

left

Protonated forms are on the ____ of the equilibrium expression.

base pair (bp)

Purine pairs with pyrimidine = _______

oligomeric

Quarternary protein with 4prime structure is called _______.

Acid hydrolysis

RCONHR' + (H+) ---------> RCOO- + NH2R

unstable

RNA backbone is ______. In water, RNA lasts for a few years. In cells, mRNA is degraded in a few hours.

single

RNA is _____-stranded but can have helical sections.

Ribosomal (rRNA)

RNA that makes up most of the ribosome

uracil; ribose

RNA uses _____ instead of thymine and _____ instead of deoxyribose.

ES->P+E

Rate determining step (MM assumption)

Vdepletion=K-1[ES] + K2[ES]

Rate of depletion of ES (steady state assumption)

Vformation=K1[S][E]free

Rate of formation of ES (steady state assumption)

K2=[ES]

Rate=Vo=

Controlling the first step prevents the buildup of unneeded intermediates

Regulatory enzymes in metabolic pathways are often found in the first step of the pathway. Why?

"nick"

Relaxed DNA (no extra twisting) can be induced by a break, _____, in just one of the DNA strands.

Sugar-phosphate backbone

Repeating structure in DNA

Oxidation by performic acid (HCOOOH)

Replaces S-S with 2 SO3-

semiconservative

Replication of DNA is best considered ___________.

nonpolar.........polar

Reverse phase HPLC refers to the column packing being _______ and a _____ solvent is used.

The column packing is nonpolar and a polar solvent is used.

Reverse phase HPLC refers to which of the following application?

Cell wall

Rigid structure outside the plasma membrane in plant cells; composition mostly polysaccharides

0.33 nm

Rise per base pair in DNA helix

Strong acid titration with a strong base

S-shaped curve

denatures......equal......molecular weight

SDS in SDS-PAGE ______ proteins, gives all proteins ____ charge/mass ratio, and makes the separation based only on molecular weight.

2',3'-dideoxynucleoside triphosphates (ddNTPs)

Sangar method useds ____________ which are incorporated at the 3' end of a growing chain in place of a dNTP

FDNB

Sangar's reagent

chain terminators or dideoxynucleotides

Sanger used special bases called _______ or _______ (two places where there will be no oxygen) to sequence DNA.

ester + NaOH -----> salt + alcohol fat + NaOH (lye) ------> soap + glycerol

Saponification structure formation (Triacylglycerol formation backwards)

mostly straight

Saturated chains extend _____ _____.

Isoelectric focusing

Separate by PI

Fractionation

Separate by charge, size, etc.

Gel electrophoresis

Separation and characterization of a charged species

Centrifugation

Separation based on density

Gel electrophoresis

Separation depends on: net charge on particle, molecular weight (size), and shape

Gel Filtration

Seperation due to penetration into pores in beads. Mobile phase = liquid solvent; stationary phase = small, porous resin beads

Pathway

Sequence of reactions leading to an overall product

Less active

Serines are de-phosphorylated

Active

Serines are phosphorylated

still

Side chains (R groups) _____ ionizable.

Monosaccharides

Simple sugars, single monomers

Glyceraldehyde (chiral)

Simplest aldose

Dihydroxyacetone (achiral)

Simplest ketone

cannot

Since ddNTPs lack a 3' hydroxyl group, subsequent nucleotide addition _______ take place.

terminate

Small amounts of ddNTPs _______ replication at some chains at each step, leaving a set of fragments of different lengths.

metabolites

Small molecules formed by the degradation of larger molecules by metabolic reactions are called:

Pyruvate

Small organic molecules that are metabolic pathway intermediates

Plasmid

Small, circular DNA often found in bacteria. Not a necessary part of the genome and often contain genes that confer antibacterial resistance.

plasmids

Small, circular extrachromosomal DNAs in bacterioa (not part of the regular, necessary genetic material

longer

Smaller molecules get into pores more easily, spend more time in the beads, and have a _____ elution time in Gel Filtration.

SDS Page

Sodium Dodecyl Sulfate

C. Solution A's is 100 times greater than in B

Solution A has pH=4 and solution B has pH=6. Which statement is true when comparing the [H+] between the two solutions? A. Solution A's is 10 times greater than in B B. Solution A's is 2 times greater than in B C. Solution A's is 100 times greater than in B D. Solution A's is 10 times lower than in B E. Solution A's is 1000 times lower than in B

capillary action

Solvent wicks up the paper by _____ _____ in paper chromatography.

Conservative residues

Some difference among homologs, but substitutions are always with similar residues

Sphingolipids

Some of these lipids may also be phospholipids.

- Micelle - Monolayers at air-water interface - Bilayers - Liposomes

Some structures whose formation is caused by hydrophobic interactions when amphipathic molecules are in contact with water:

zymogen

Sometimes enzymes are initially produced in a large inactive form and later cut to yield the active form. The larger inactive form is called a/an ________.

Starch

Source: -Cereals, potatoes, legumes, and other vegetables Function: -Starch is the main carbohydrate content in our diet -It constitutes about 60% of our daily ingested food Properties: 1) Reducing agent : starch gives blue color with iodine. Amylopectin gives red color with iodine. 2) Partial hydrolysis (digestion) by amylase enzyme gives various forms of dextrins

Opposite charges and aromatic rings

Stabilizes helices

Super secondary structure

Stable clustering of secondary structures

a-D-glucopyranose

Starch and glycogen are both polymers of:

Enantiomers

Stereoisomers that are nonsuperimposable mirror images of each other are ______.

complementary

Strands are _______ (not same sequence).

Lipids

Structurally diverse class that has low solubility in water, can be non polar or amphipathic, and has good solubility in non polar solvents.

Dextrans

Structure: -It is branched chain homopolysaccharide. -Each branch is composed of glucose units -The glucose units are linked together by a α 1-3 glycosidic bond and α 1-6 glycosidic bond at branching point Source: -Dextrans is synthesized from sucrose by certain bacteria ( lactic acid bacteria, the best-known being Leuconostoc mesenteroides and Streptococcus mutans) Functions: -Dextrans is used as plasma substitute and prevents thrombosis

Inulin

Structure: -It is fructosan i.e. formed of repeated units of fructose -Has β 1-2 glycosidic bonds. Source: -Root of artichokes and other plants Medical importance: -Inulin clearance is one of diagnostic tests for investigation of glomerular filtration rate.

Laminin

Structure: -Laminin (about 850 kDa, 70 nm long) consists of three distinct elongated polypeptide chains. ( A, B1 and B2) -Has three binding sites for: 1) Proteoglycans 2) Collagen 3) Entactin --> major cell attachment factor -It has four arms that can bind to four other molecules. -Three shorter arms are particularly good at binding to other laminin molecules. -Longer arm binds to cells, which helps anchor the actual organs to the membrane.

Chondroitin 4- and 6 sulfate

Structure: -Present in association with protein to form proteoglycan aggregates. -The repeated dissacharide units consists of glucuronic acid, N-acetylgalactosamine with sulfate on either Carbon 4 or Carbon 6. NOTE: Chondroitin 4- and 6 sulfate is the most abundant GAGs in the body. Site: 1) cartilage, tendons, ligaments and bones 2) Aorta, skin, cornea, umbilical cord and in certain neurons Functions: 1) in cartilage, it binds collagen and hold fibers in strong network 2) it makes cartilage compressible 3) Help to maintain the shape of skeletal system

Hyaluronic acid

Structure: -Repeated disaccharide units of glucuronic acid and N-acetylglucosamine Note: hyaluronic acid is the only GAGs which contains no sulfate group Site: -Cartilage, Connective tissue, Synovial fluid, Vitreous humor of the eye and embryonic tissue Function: -Acts as lubricant in the joints -It makes cartilage compressible -It makes extracellular matrix loose because of its ability to attract water. -It permits cell migration during wound repair -It permits cell migration during morphogenesis i.e. differentiation of cells in the form of organs and tissue in the early embyo.

Starch (glucosan or glucan)

Structure: -Starch granule is formed of inner (amylose) and outer (amylopectin) layers

Heparin

Structure: -The repeated disaccharide unit consists of Induronic acid with sulfate on C2, and glucosamine with sulfate on C2 and C6 Site: -Present in mast cells -Mast cells are located along the wall of blood vessels of liver, lungs, skin, heart, kidney and spleen. Function: -It acts as anticoagulant Heparan sulfate (which has the same structure as heparin) has the following functions: --> it acts as cell membrane receptors --> it participates in cell adhesion and cell-cell interaction --> it is present in basement membrane of the kidney and plays a role in the glomerular filtration

Dermatan sulfate

Structure: -The repeated disaccharide unit consists of L-induronic acid and N-acetylgalactosamine with sulfate on Carbon 6 Site: 1) Cornea 2) Sclera 3) skin, blood vessels and heart valves Functions: -In cornea, it plays an important role in corneal transparency -Its presence in sclera may play a role in maintaining the overall shape of the eye

Keratan sulfate

Structure: -The repeated disaccharide unit consists of galactose with sulfate on Carbon 6 and N-acetylglucosamine with sulfate on Carbon 6 Site: 1) Cornea 2) Cartilage Function: ---> it plays an important role in corneal transparency

Glycosaminoglycans (GAGs, mucopolysaccharides)

Structure: -They are formed of repeating disaccharide units (acidic sugar - amino sugar)n -The acidic sugar is either D-glucuronic acid or its epimer, L-induronic acid -The amino sugar is either D-glucosamine or D-galactosamine in which the amino group is usually acetylated. -GAGs often contain sulfate group -GAGs are un-branched -Most GAGs are present extracellularly except heparin -Most GAGs form structural components of connective tissues such as bone, elastin and collagen -GAGs act as lubricants and cushion for other tissues because they have the property of holding large quantities of water. -When a solution of glycosaminoglycans is compressed, the water is squeezed out and the glycosaminoglycans are forced to occupy a smaller volume. -When the compression is released, the GAGs return to their original, hydrated volume because of the repulsion of their negative charges.

Fibronectin

Structure: 1) it is a high-molecular weight (~440kDa) extracellular matrix glycoprotein 2)Fibronectin exists as a dimer, consisting of two nearly identical monomers linked by a pair of disulfide bond. 3) Two types of fibronectin are present: a) soluble plasma fibronectin -> produce in the liver b) insoluble cellular fibronectin -> a major component of extracellular matrix. it is secreted by various cells primarily fibroblast. Function: -Cell adhesion -Cell Growth -Cell migration and differentiation -Would healing and embryonic development

Glycoproteins (mucoproteins)

Structure: a) protein core b) carbohydrate chain which are branched short chain (from 2-15 monosaccharide units) i.e. oligosaccharide chains. They include: 1) Hexoses: Galactose and mannose 2) Acetylhexosamines: N-acetylglucosamine 3) Pentoses: Arabinose and xylose 4) Methylpentose: L-fucose 5) Sialic acid 6) They contain no uronic acids or sulfate group

Cellulose

Structure: -It is long straight non-branching chains of β-glucose units -It is linked together by β 1-4 glycosidic bond Source: -Cellulose is the chief constituent of the framework of plant, leafy vegetables, fruits, wood, cotton ect Properties: 1) Gives no color with iodine 2) insoluble in water 3) Many mammals cannot digest cellulose because of the absence of digestive hydrolase enzyme that attacks β linkage.

Invert sugar

Structure: It is a sugar that contains equal number of both glucose and fructose molecules Source: a) Been honey b) By hydrolysis of sucrose by sucrase Properties: -Invert sugar contains free carbonyl groups, so it has the same properties as lactose and maltose.

Cellobiose

Structure: It is formed of 2 units of β-D glucopyranose Glycosidic bond: β 1-4 Source: -It is obtained by partial hydrolysis of cellulose present in plants

Trehalose

Structure: It is non-reducing sugar, formed by 2 units of α-D glucopyranose Glycosidic bond: α 1 - 1 Source: -present in fungi and yeast Importance: -Used as a sweetener and preservation of foods. -It can be used in organ and tissue preservation solutions that provide improved viability of an organ such as heart or lung.

Isomaltose

Structure: it is formed by 2 molecules of α glucopyranose Glycosidic bond : α 1-6 glycosidic bond Source: -isomaltose is produced during digestion of starch and glycogen by amylase properties: Same as maltose

Maltose

Structure: it is formed by 2 molecules of α-D glucopyranose Glycosidic bond: α 1-4 glycosidic bond Source: a)malt b)Maltose is produced during digestion of starch by amylase enzyme Property: -Maltose contains free carbonyl (aldehyde) group a-it is reducing agent b-can be present in α and β forms c-it can show mutarotation d-it can form characteristic osazone crystals

Lactose

Structure: it is formed by 2 molecules of β-D glucopyranose and β-D glucopyranose Glycosidic bond: β 1-4 glycosidic bond Source: -It is the sugar present in milk Properties: a) it is reducing agent b) it can be presented in a α and β forms c) it can show mutarotation d) it can form characteristic osazone crystals e)lactose is digested by intestinal enzyme, lactase. This enzyme breaks lactose into galactose and glucose.

Sucrose

Structure: it is formed of 2 molecules α-D glucopyranose and β-D fructofuranose. Glycosidic bond: α 1- β 2 glycosidic bond Source: -cane and beet sugars. -it is also present in pineapple and carrot Properties: -Sucrose doesn't contain free carbonyl group a) It is NOT a reducing agent b) it CANNOT be present in α and β forms c) it CANNOT show mutarotation d) it CANNOT form osazone crystals e) sucrose is dextrorotatory. It is hydrolyzed by invertase (sucrase) enzyme to give a mixture of equal number of glucose and fructose. This mixture is called invert sugar and it is lavorotatory

Inhibitor

Substance that reduces an enzymes activity

oxidizing agent

Substance which causes the oxidation of another substance. During a redox reaction this itself is reduced.

reducing agent

Substance which causes the reduction of another substance. During a redox reaction this itself is oxidized.

Competitive (reversible inhibitor)

Substrate and inhibitor compete for the active site on the enzyme

-ogen -gen

Suffix (Zymogen)

Genome

Sum of all genetic material (DNA) contained in the cell (in the nucleus in eukaryotes)

Overall order

Sum of orders for all reactants

Tryacylglycerides

Synonyms: simple lipids, neutral fats, storage lipids

DNA polymerases

Synthesis is catalyzed by enzymes known as _________.

5' to 3'

Synthesis of the new strand of DNA from DNA polymerase is always ______.

minimize

Systems seek to _______ the loss of entropy because they prefer to gain entropy.

T / F A lysine just outside the C-terminal end of an alpha helix will help to stabilize the helix's dipole.

T / F An isoelectric focusing gel has different pH's at either end. (gradient)

T / F DTT oxidizes disulfide bonds.

T / F Since enzymes are catalysts, they do not change in any way during the course of a reaction.

T / F The most common stain for DNA in agarose gel electrophoresis is coomassie blue.

T/F According to the method discussed in class, small peptides are synthesized from the C-terminal amino acid to the N-terminal amino acid.

T/F Disulfide bonds can be removed by oxidation or reduction by proteases.

T/F Enzymes lower both the free energy and the energy of activation of a reaction.

T/F Holoenzymes contain protein and all cofactors.

T/F In affinity chromatography the protein may be released from the column by adding excess free ligand.

T/F The alpha helix has a dipole due to the consistent orientation of the N-H and C=O bonds.

T/F The most common stain for proteins in gel electrophoresis is coomassie blue.

T/F Usually four amino acids make up a B-turn and all four amino acids are in the cis configuration

T/F: A lysine just outside the C-terminal end of an alpha helix will help to stabilize the helix's dipole.

T/F: A solution with a pH=7 has one hundred times the H3O+ as a solution with a pH=9.

T/F: ATP is an example of a small peptide.

T/F: According to the method discussed in class, small peptides are synthesized beginning from the C-terminal amino acid and extending to the N-terminal amino acid.

T/F: According to the method discussed in class, small peptides are synthesized from the C-terminal aid to the N-terminal amino acid.

T/F: Affinity chromatography can save many steps in purifying a protein if it's available.

T/F: All amino acids are in their zwitterion forms at pH=7.

T/F: All molecules that contain one or more polar bonds are polar.

T/F: All proteins have tertiary structure, but not all have quaternary structure.

T/F: All sulfur containing amino acids can form disulfide bonds.

T/F: Allosteric modulators bind non-covalently to the regulatory site of an enzyme and change its conformation.

T/F: Ammonium sulfate can cause proteins to precipitate from solution

T/F: Amylase is an enzyme that can break both a(1 to 4) and a(1 to 6) bonds in polysaccharides.

T/F: An isoelectric focusing gel has different pH's at either end.

T/F: At sufficiently high substrate concentration all types of reversible inhibition can be overwhelmed. At high substrate concentration the enzyme will be saturated and the reaction will proceed at the same maximum velocity as in the absence of inhibitor.

T/F: At sufficiently high substrate concentration all types of reversible inhibition can be overwhelmed. At high substrate concentration, the enzyme will be saturated and the reaction will proceed at the same maximum velocity as in the absence of inhibitor.

T/F: At the equivalence point, pH=7.

T/F: At the equivalence point, stoichiometric amount of acid and base are present.

T/F: Carbon dioxide is non-polar because it contains no polar bonds.

F Because of geometry, it is non-polar but it does have polar bonds.

T/F: Carbon dioxide is non-polar because it contains no polar bonds.

T/F: Collagen is required for the synthesis of vitamin C.

T/F: Conjugated proteins are ones that are connected to form a network polymer.

T/F: Cysteine is the only amino acid that contains sulfur.

F DTT actually reduces disulfide bonds

T/F: DTT oxidizes disulfide bonds

T/F: Differential centrifugation involves successive spins that are faster and longer each time.

T/F: Disulfide bonds can be removed by oxidation or reduction by proteases.

T/F: During oxygen binding, the iron ion in heme is oxidized from +2 to +3.

T/F: Enteropeptidase is the zymogen of trypsin.

T/F: Enzymes lower both the free energy and the energy of activation of a reaction.

T/F: Enzymes lowers both the free energy and the energy of activation of a reaction.

T/F: Enzymes make reactions go faster by lowering the delta G for the reaction.

T/F: Globular proteins often have the same secondary structure nearly throughout their entire length.

T/F: Glycogen and amylopectin are chemically identical and only differ in branching frequency and length.

T/F: Group transfer from one substrate to another is often achieved via covalent catalysis.

T/F: Hemoglobin helps increase the concentration of oxygen in blood to a level nearly equal to the concentration of oxygen in air.

T/F: Holoenzymes contain protein and all cofactors

T/F: In affinity chromatography, the protein can be released from the column by adding excess ligand.

T/F: In affinity chromatography, the protein may be release from the column by adding excess free ligand.

T/F: In competitive inhibition, the inhibitor is an analog of the substrate.

T/F: In nature, L-glycine is more prevalent than D-glycine.

T/F: In the Merrifield method, peptide chains are synthesized in the C to N direction.

T/F: Keratins in hair are classified as all alpha.

T/F: Most genomes are composed of DNA.

T/F: Myoglobin is present in muscle tissue to store oxygen.

T/F: Not all proteins have quaternary structures.

T/F: Phe residues are particularly abundant in B-sheets

T/F: Plant cell walls are primarily composed of cellulose which is stabilized by many intrachain and interchain hydrogen bonds.

T/F: Proline is usually in the cis configuration in turns

T/F: Pseudoridine is a minor nucleoside frequently found in tRNA and rRNA.

T/F: Since enzymes are catalysts, they do not change in any way during the course of a reaction

T/F: Since it's a ketone, dihydroxyacetone will not react with Tollen's reagent.

T/F: Since it's a ketose, dihydroxyacetone will not react with Tollen's reagent.

T/F: Tautomers differ only in the positioning of double bonds and hydrogen atoms.

T/F: The alpha helix has a dipole due to the consistent orientation of the N-H and C=O bonds

T/F: The alpha helix has a dipole oriented from the N-terminal (+) to the C-terminal (-).

T/F: The conversion of Hb from R to T is by a concerted mechanism.

T/F: The heme iron converts for +2 to +3 when oxygen is bound.

T/F: The higher the specificity constant, the more effective the catalysis.

T/F: The lower the specificity constant, the less effective the catalyst.

T/F: The major difference between prokaryotes and eukaryotes in the absence or presence, respectively, of a nuclear membrane.

T/F: The major difference between prokaryotes and eukaryotes is the absence or presence, respectively, of a nuclear membrane.

T/F: The mitochondria are the principle cellular site of protein production.

T/F: The most common stain for DNA in agarose gel electrophoresis is coomassie blue.

T/F: The most common stain for proteins in gel electrophoresis is coomassie blue.

T/F: The proximity effect involves increasing the degrees of freedom for a substrate by its being in the active site.

T/F: The rate-determining step in the Michaelis-Menton model of enzyme catalysis is the formation of the enzyme-substrate couplex.

T/F: The reaction where cysteine converts into cystine is an oxidation reaction.

T/F: The ribosomes are the principle cellular site of protein production.

T/F: The simplest aldose is glucose.

T/F: The simplest aldose is the chiral molecule glyceraldehyde.

T/F: The simplest ketose is the achiral molecule dihydroxyacetone.

T/F: The stronger the weak base, he large the Kb

T/F: The stronger the weak base, the larger the pKb.

T/F: The vital theory was proven untrue by the laboratory synthesis of urea.

T/F: Thyrine is a pyrimidine.

T/F: Usually four amino acids make up a beta-turn and all four amino acids are in the cis configuration

Transmittance

T=(I/I0) Fraction of light that gets through sample

top

TS is at ___ of energy curve (goes easily to product)

Eukaryote

Term defined as a type of organism whose cells have a true nucleus (ex: mammals, plants)

b. has a hydroxyl at its 3' end

The DNA oligonucleotide abbreviated pATCGAC: a. has 7 phosphate groups b. has a hydroxyl at its 3' end c. has a phosphate on its 3' end d. has an A at its 3' end e. violates Chargaff's rule

d. Easily find the rate of an enzymatic reaction at infinite substrate concentration from a linear graph

The Lineweaver-Burk plot is used to: a. determine the effect on the activation energy for an enzymatic reaction b. See if there is cooperatively between enzyme subunits c. illustrate the effect of temperature on enzymatic reaction d. Easily find the rate of an enzymatic reaction at infinite substrate concentration from a linear graph

psi

The ___ angle for each amino acid represents the relative orientation of groups on Ca and C.

initial rate method

The _____ is conducted by measuring the rate of many samples, each with a different [S] but the same [E].

turnover number

The _____ of an enzyme is a measure of the number of product molecules forms per unit time.

linear

The ______ form is the reactive form

Lower, greater

The ______ the Km the _______ the efficiency

lock-and-key

The _______ model is really an energetic trap with an intermediate formed that has lower energy than the substrate.

Induced fit

The ________ model proposes that a protein and its ligand change shape as they bind.

induced fit

The ________ model proposes that a protein and its ligand change shape as they bind.

0.100

The absorbance of a 0.30M aqueous solution at 550 nm is 0.200. What is the absorbance of this solution if water is added to dilute the solution to 0.15M?

0.020 1cm=10mm .200/10=0.020

The absorbance of a 1.0M solution at 300nm is 0.200 in a 1 cm cuvette. What is the absorbance of this solution if the absorbance is measure with a 1 mm cuvette?

0.175

The absorbance of a 1.0M solution of compound A is 0.350. What is the absorbance if the solution is diluted to a concentration of 0.5M?

reactant and transition state

The activation energy is the different between the energy of the ____ and ____.

The amino acid form present depends on the ___.

a phosphate and a sugar

The backbone of a strand of nucleic acid is formed by linkages between ________ of adjacent monomer units.

glycosaminoglycan

The basic structure of a proteoglycan consists of a core protein and a:

a. [S] is assumed to change little in the time it takes to make a measurement

The benefit of measuring the initial rate of a reaction Vo is that at the beginning of a reaction: a. [S] is assumed to change little in the time it takes to make a measurement b. [ES] can be measured accurately c. The back reaction ES > E +S has not had time to occur appreciably d. Vo = Vmax d. Vo is linearly dependent on [S]

super-secondary structure

The beta-alpha-beta pattern is often found in a larger protein structure. These regions are called:

hemoglobin

The binding of one molecule of O2 to one subunit of ______ enhances the affinity of other subunits for O2.

polarity

The bonding of atoms of very different electronegativities is the source of ______.

phosphodiester

The bonds that connect the backbone of DNA are _____ bonds.

5' end

The end where the 5' carbon of the sugar does not lead to another nucleotide

activation

The energy needed to go from the reactants to the transition state is called the ______ energy.

D. both A and B

The equivalence point of a titration curve occurs when ________. A. stoichiometric amounts of acid and base are present B. the slope is the greatest and it's an inflection point C. pH=pKa D. Both A and B E. All of the above

polymorphic

The fact that there are many human variants of normally functioning hemoglobin indicates the protein is :

bioinformatics

The field of science that uses computers for the collection and analysis of genomic data

bioinformatics

The field of science that uses computers for the collection and analysis of genomic data.

proteins with similar isoelectric points become further separated according to their molecular weights

The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, place on another gel containing SDS and electric current is again applied. In the second step:

Proteins with similar isoelectric points become further separated according to their molecular weight

The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:

hydrophobic interactions

The forces causing the aggregation are called _______ _______.

zwitterion

The form of amino acids that has charges, but has no net charge is called the _______.

condensation

The formation of a peptide bond between two amino acids is an example of a(n) _________ reaction.

condensation

The formation of a peptide bond is classified as a/an ________ reaction.

tetrahedral

The four covalent bonds in methane (CH4) are arranged around carbon to give what geometry?

strengthened

The hydrogen bond is ______ when three atoms align.

stronger

The larger the Ka, the _______ the weak acid.

stronger

The larger the Kb, the _______ the weak base.

weaker

The larger the pKa, the _______ the weak acid.

weaker

The larger the pKb, the ________ the weak base.

nucleic acids

The macromolecules that serve in the storage and transmission of genetic information are ______.

carbonate/bicarbonate

The main buffering system of the blood is:

Adenosine triphosphate (ATP)

The major carrier of chemical energy in all cells is ______.

6.7 mM/s

The maximum velocity of an enzyme-catalyzed reaction is 20 mM/s and Km is 200 mM. What is the velocity of this reaction when the substrate concentration is 100 mM?

high CG increases Tm

The midpoint of melting (Tm) depends on base composition:

C=O and N-H

The most common kind of hydrogen bonds that stabilize secondary structures occur between which chemical groups?

protein synthesis

The most important function for most RNA's is their involvement in:

d. are roughly planar

The nucleic acid bases: a. absorb ultraviolet light maximally at 280 nm b. are all about the same size c. are relatively hydrophilic d. are roughly planar e. can all stably base-pair with one another

Spermaceti organ

The organ made of lipids in the head of a whale that controls buoyancy

The osmolarity of a 1M solution of aluminum nitrate, Al(NO3)3 is ____.

-1.08

The pH of a 12M concentrated HCl is:

logarithmic

The pH scale is a __________ scale.

10.00 14-4=10

The pKa for a weak acid, HA, is 4.00. What is the pKb for A-?

9.90

The pKa's of tyrosine's alpha-carboxyl group, alpha-amino group and side chain are 2.2, 9.11 and 10.7 respectively. Calculate the isoelectric point.

four peptide bonds

The peptide alanylglutamylglycylalanylleucine has:

amplifying

The polymerase chain reaction (PCR) is used for _______ a small amount of DNA.

a. a large loss of entropy by bringing reactive groups closer to one another

The proximity effect of speeding an enzyme-catalyzed reaction is explained by: a. a large loss of entropy by bringing reactive groups closer to one another b. a large gain in entropy by binding the substrate to the enzyme c. a conversion of a reaction from endergonic to exergonic d. increasing the flexibility of the substrate by increasing its degrees of rotational freedom about bonds

Separate proteins exclusively on the basis of molecular weight

The purpose of adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, is to make it possible to:

condensation..................amide

The reaction between amino acids that results in a peptide bond is classified as a/an _____ reaction and it forms the _____ functional group.

condensation..........amide

The reaction between amino acids that results in a peptide bond is classified as a/an _______ reaction and it forms the _____ functional group.

amide

The reaction between amino acids that results in a peptide bond is classified as a/an condensation reactions and it forms the ____ functional group.

glucose

The reference compound for naming D and L isomers of sugars is:

Primary structure of a protein

The sequence of amino acids in the protein chain from the N-terminal to the C-terminal

c. states that the formation of ES is equal to its breakdown

The steady state assumption in enzyme kinetics: a. insures that the product of an enzymatic reaction will always be formed b. explains why enzymes are effective catalysts c. states that the formation of ES is equal to its breakdown d. is based upon the fact that the maximum velocity of an enzyme is very high e. none of the above

[ES] is constant

The steady state assumption, as applied to enzyme kinetics means:

k1[S][E]free = k-1[ES] + k2[ES]

The steady state assumption, as applied to enzyme kinetics, implies:

b. The ES complex is formed and broken down at equivalent rates

The steady state assumption, at applied to enzyme kinetics, implies: a. The enzyme is saturated with substrate b. The ES complex is formed and broken down at equivalent rates c. The rate does not change with [S] d. The equilibrium S + E <> ES forms slowly.

ammonium sulfate........increased

The substance _____ is used to precipitate proteins by "salting out", which means the solution has a(n) ________ ionic strength.

Urea

The synthesis of which molecule is considered by many to be the root of biochemistry since it was the first biological molecule synthesized from non-biological precursors and disproved the vital theory.

turnover

The time to produce one product molecule from one substrate molecule is called the ______ time.

negative

The titration curve is _____ for a weak base.

product molecules formed per unit time

The turnover number of an enzyme isa measure of the number of _____.

Carbohydrate

Their oxidation is the central energy-wielding pathway in non-photosynthetic cells

There are __ standard amino acids which are ubiquitous throughout living systems.

polymorphic

There are many variations in the primary sequence of hemoglobin among humans. Usually these variants still function normally. Because of this, we say that hemoglobin is a/an ______ protein.

polymorphic

There are many variations in the primary sequence of hemoglobin among humans. Usually these variants still function normally. Because of this, we say that hemoglobin is a/an_______ protein.

260 nm

Thermal DNA denaturation is monitored by UV spectrophotometry at ______ nm.

Heteropolysaccharides

They contain repeated different sugar units and include glycosaminoglycans

Conjugated carbohydrates

They include: 1- Glycolipids 2- Proteoglycans and glycoproteins 3- Fibronectin 4- Laminin

Uncompetitive

This inhibitor has parallel lines on its graph

Turnover time

Time for one substrate to product conversion

b. greater than 7...............hydrolysis of the acid's conjugate base

Titration of a weak acid with a strong base has an equivalence point ____ due to __________. a. equal to 7.........complete neutralization b. greater than 7...............hydrolysis of the acid's conjugate base c. less than 7.........some weak acid always staying unreacted d. that could be greater, less than or equal to 7......variations in weak acids

>7.......hydrolysis

Titrations of a weak acid with a strong base has an equivalence point ____ due to _______ of the acid's conjugate base.

longer DNA has higher Tm

Tm depends on DNA length:

high salt increases Tm

Tm depends on pH and ionic strength:

large

To be a good buffer, concentrations of components should be relatively ____ compared to expected possible added acid or base.

equal

To be a good buffer, concentrations of conjugate pairs should be approximately _____.

ultrafiltration

To concentrate a protein sample which technique would you choose?

Ultrafiltration

To concentrate a protein sample which technique would you choose? A. isoelectric focusing B. ultrafiltration C. dialysis D. SDS-PAGE

cation; NaOH

To make a buffer for pH greater than 7, make a solution of the salt of the ____ of a weak base and adjust to desired pH with _____. Example: ammonium chloride; NaOH

Weak base; cation; weak base

To make a buffer for pH greater than 7, mix a ____ ___ with a salt of the ____ of the _____ ____. Example: ammonia; ammonium chloride

salt of anion; HCl

To make a buffer for pH less than 7, make a solution of the ____ __ ____ of weak acid and adjust to desired pH with ___. Example: sodium acetate; HCl

weak acid; salt; weak acid

To make a buffer for pH less than 7, mix a ____ ____ with a ___ of the anion of the ____ ____. Example: acetic acid; sodium acetate

nonpolar

To which classification group does the amino acid methionine belong?

Activity

Total number of units in a sample

higher

Trans fatty acids pack more regularly so they have a ______ melting point than cis forms.

Iodoacetate

Treatment with this prevents disulfide bonds from oxidizing in air

oils

Triacylglycerol liquid = ____

fats

Triacylglycerol solid = ___

carboxylic acid + alcohol -----> ester + water

Triacylglycerol structure formation

less; less

Triacylglycerols are _____ soluble in water than fatty acids and ____ dense than water (fats and oil float)

proteolytic cleavage

Trypsinogen is converted to trypsin by ______.

Rotor

Tube holder in centrifuge

threonine and serine

Two amino acids of the standard 20 have alcohol groups in their side chains. They are:

epimers

Two carbohydrates are ______ when they differ only in the configuration around one chiral carbon atom.

hybridize

Two near-complementary DNA strands can _______.

Prokaryote

Type of organism whose cells have no true nucleus (ex: bacteria)

concentrate

Ultrafiltration is typically used to ______ the protein.

Specific activity

Units of enzyme per mg total protein

1/time

Units of k2

Ethidium bromide

Used as a stain for DNA

Polyacrylamide

Used for proteins and small DNA's and RNA's

Ammonium sulfate

Used to "salt out" proteins in differential centrifugation

Dialysis

Used to exchange buffers or purify large molecules from small

SDS

Used to give proteins the same charge-to-mass ratio

Dansyl chloride

Used to identify only the N-terminal of a protein

Sucrose

Used to increase the osmolarity of solutions to make them isotonic

Fmoc

Used to protect the N-terminal of an amino acid from reaction

Spectrophotometer

Used to take absorbance measurements

Ninhydrin

Used to visualize amino acids/proteins on thin layer or paper chromatography

k-1 [ES] + k2 [ES]

Using the enzyme-catalyzed reaction assumption Michaelis and Menton created, the rate of depletion of the enzyme-substrate complex can be described by the expression:

Rate

Velocity

away from

Vertical bonds project _____ the viewer or are in the plane of the drawing.

Vformation=Vdepletion

Vformation__Vdepletion (steady state assumption)

ninhydrin

Visualize amino acids with ______.

Vo=(Vmax/Km)([S])

Vo= (M-M equation when [S]<<<[Km])

Vo=Vmax[S]/Km+[S]

Vo= (M-M equation when [S]>>>[Km])

Self-ionize

Water has the ability to _______.

Product

Water in reactions: ______- in condensation reactions ADP + P1 (inorganic phosphate) -> ATP + H2O

Reactant

Water in reactions: ______- in hydrolysis reactions Pyrophosphate + H2O -> 2 Phosphates

acidic

Water is _____ in the presence of something more basic than itself.

Polar

Water is very _____.

entropy

Water loses ______ when it's in a clathrate.

Hydrogen bonds

Water molecules attract each other by ________ _____.

decrease..........increase

We would expect the total protein amount to ______ and specific activity to ______ when comparing crude extract to the same sample after successful enzyme purification.

Vmax does not change, Km appears to increase

What are the expected changes in kinetics in the presence of a competitive inhibitor?

phosphorus and sulfur

What are the fifth and sixth most common elements in living organisms? (That means there are four other elements more common than these two)

Amino group, carboxylic acid group and variable group

What are the parts of the general structure of an amino acid?

reaction of disulfide bond with performic acid

What can cause the formation of the structure shown? O II the figure pictured is R-CH2-S- O - II O

decrease blood pH

What can happen if a person breathes continuously into a paper bag?

visualize amino acids in paper chromatography

What can ninhydrin be used for?

strong acid, strong base, proteases

What can you use to treat a protein so that you could find the percent composition of amino acids?

d. the covalent bonding of atoms of different electronegativity

What causes a molecule to have a permanent dipole (be polar)? a. the constant motion of electrons b. having either a bent or trigonal planar geometry c. the presence of lone pairs of electrons d. the covalent bonding of atoms of different electronegativity

What charge would you expect for valine at pH=7?

Performic acid ?? MIGHT NOT BE CORRECT

What chemical reagent will cause the formation of the chemical structure shown on the side chains of some amino acids when it is used to treat a protein?

performic acid

What chemical reagent will cause the formation of the chemical structure shown on the side chains of some amino acids when it is used to treat a protein? R-CH2-SO3-

nonpolar

What classification group does the amino acid methionine belong?

collagen

What consists of protein chains that are cross-linked?

Binds in the central pocket of hemoglobin and act as a negative modulator

What does 2,3-BPG do?

binds in the central pocket of hemoglobin and act as a negative modulator

What does 2,3BPG do?

decreases a protein's activity when it binds

What does a negative regulator do?

increases a protein's activity when it binds

What does a positive regulator do?

a. Activates glycogen phosphorylase by putting phosphate groups on series

What does phosphorylase kinase do? a. Activates glycogen phosphorylase by putting phosphate groups on series b. Cleaves trypsinogen to form trypsin. c. Cleaves glucose units from glycogen. d. Is a feedback inhibitor for enzymes in the glycolysis pathway.

That the native protein has at least one disulfide bond

What does the electrophoresis gel show?

It will destabilize the helix by hydrogen bonding to the amino acids in the helix

What effect will water have on a alpha helix

it will destabilize the helix by hydrogen bonding to the amino acids in the helix

What effect will water have on an alpha helix?

Shape and charge per unit mass also affect the migration of the proteins

What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of SDS?

d. Trypsin loses all activity due to inactivation of one of the catalytic triad amino acids

What happens if a trypsin is exposed to diisopropyl fluorophosphate? a. It is converted from its zymogen into active trypsin. b. Phosphate groups are transferred to trypsin to activate it. c. Trypsin's activity is inhibited by competitive inhibition. d. Trypsin loses all activity due to inactivation of one of the catalytic triad amino acids e. Nothing happens. Trypsin is not affected by diisopropylfluorophosphate

collagen

What has a left-handed helix for individual protein chains, that combine to form triple-stranded fibers wrapped in a right-handed fashion?

chloroplast

What has a main purpose of synthesizing ATP in plants?

-To determine evolutionary relationships and relatedness of species -To determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins -To predict similarity in protein folding

What information can be gained by comparing the sequences of proteins that have the same or similar function in different species?

D. All of the above

What information can be gained by comparing the sequences of proteins that have the same or similar function in different species? A. To determine evolutionary relationships and relatedness of species. B; To determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins C. To predict similarity in protein folding D. all of the above

If the slope>1 it is an indicator of interaction between binding sites if the slope=1 there is no interaction between binding sites

What information can be gained from a Hill plot?

The protein consists of two chains of amino acids joined by a disulfide bond

What is a likely explanation for a pure protein if treatment with the Sanger reagent (FDNB) is found to derivative both Ala and Leu, in roughly equal amounts?

hemoglobin

What is a tetramer with two pairs of identical chains and four heme prosthetic groups?

protein

What is an example of a linear polymer?

D-glucose and D-galactose

What is an example of a pair of epimers?

Carboxylate end

What is easily solvated when a soap anion is dissolved in water?

b. The solution changes from blue to brick red

What is observed if you mix the Benedict's reagent with fructose in a test tube? a. The solution states blue the whole time. b. The solution changes from blue to brick red. c. The solution forms a silver mirror inside the test tube. d. The solution goes from clear to pink.

It allows hemoglobin to shift between low and high affinities for oxygen

What is the biological advantage to the sigmoidal binding curve of hemoglobin for oxygen?

H2CO3

What is the conjugate acid of HCO3-

H2PO4-

What is the conjugate acid or HPO4^-2

(PO4)^-3

What is the conjugate base of (HPO4)^-2)

(CO3)^-2

What is the conjugate base of bicarbonate ion, HCO3-?

5' to 3'

What is the convention for writing the sequence of a strand of DNA (from left to right)?

rate=k[A]^2[B}^2

What is the correct rate equilibrium for the mechanistic step 2A + 2B ----> C + D

It's the normal number of bonds that element forms with other atoms. Sulfur has a covalence of 2.

What is the covalence of an element? What is it for sulfur?

c. a general term for a polysaccharide

What is the definition of a glycan? a. a disaccharide b. an energy storing molecule in plants c. a general term for a polysaccharide d. an enzyme used in the conversion of glycogen

pyramidal

What is the geometry of ammonia, NH3?

c. lowers the entropy of the reactants

What is the main result of the proximity effect in catalysis? a. increases the entropy of water in the active site of the enzyme b. stabilizes the transition state of the substrate during catalysis c. lowers the entropy of the reactants d. substrates are pushed into their transition states by induced fit

600 M-1 cm-1 0.600=(0.001)(1)E

What is the molar absorptivity constant for a substance that has an absorbance of 0.600 when its concentration is 0.001 M and a 1 cm cuvette is used to determine the absorbance?

the carbon in carbon dioxide

What is the most oxidized form of carbon?

deoxyguanosine-5'-diphosphate

What is the name of the nucleotide with the abbreviation ppdG?

-2

What is the net charge on alanylaspartylthreonine at a pH above th pKa's of all ionizable groups?

-2

What is the net charge on glutamylisoleucine at a very high pH (above the pKa's of all ionizable groups)?

-2

What is the net charge on the tripeptide valyllysylglutamate at a pH above the pKa's of all ionizable groups?

What is the one-letter abbreviation for Asparagine?

What is the one-letter abbreviation for tryptophan?

+0.7

What is the pH of a 0.1M H2SO4 solution?

-1 -log(10)=(-1)

What is the pH of a 10M HCl solution?

4.58

What is the pH of a solution that is 0.2M in acetate and 0.3M in acetic acid? (pKa acetic acid = 4.76)

9.24

What is the pH of a solution with a hydroxide ion concentration of 1.75x10^-5?

3.40 nm or 34 A

What is the pitch of the DNA helix?

Lys, Ile, Glu

What is the proper order of elution of the following amino acids from an anion exchange column? Glutamate Lysine Isoleucine

To stabilize the pH gradient

What is the purpose of adding polyampholytes to an isoelectric focusing gel?

C. The covalent bonding of atoms with different electronegativities

What is the root cause of dipole-dipole interactions? A. The constant motion of electrons and transient dipoles B. Magnetic attractions between particles C. The covalent bonding of atoms with different electronegativities D. The increase in entropy due to the attractions

gamma-carboxyglutamate

What is the uncommon amino acid found in the blood-clotting protein thrombin?

The bonding of atoms of very different electronegativities

What is the underlying cause of molecules having a permanent dipole?

4 are to porphyrin rings, 1 is to a histidine and 1 is to O2

What is true about a single iron ion's coordinate bonds in Hb?

D-isomers predominate

What is true about naturally occurring monosaccharides?

Water can compete with the hydrogen bonds in a helix and will destabilize it

What is true about the interaction of water and alpha helixes?

Water can compete with the hydrogen bonds in a helix and will destabilize it.

What is true about the interaction of water and alpha-helixes?

Trifluoroacetic acid

What is used to break peptide bonds in the Edman degradation?

lipids

What kind of molecules have a main purpose of making up cell membranes?

amphipathic

What kind of molecules might form a micelle?

S + E <> ES > P + E

What mechanism did Michaelis and Menton finally use in their kinetic analysis?

S + E <> ES > P + E

What mechanism did Michaelis and Menton use in their kinetic analysis?

amphipathic

What property of fatty acids and SDS allow them to form micelles in water? They are _______.

iodoacetate

What reagent helps prevent the reformation of disulfide bonds after they have been removed?

slope of the line

What remains constant for a plot of 1/Vo against 1/[S] for an enzyme-catalyzed reaction in the presence of an uncompetitive inhibitor?

isoelectric focusing

What technique relies on a pH gradient stabilized by polyampholytes?

zymogen

What term describes an inactive precursor of an enzyme such as the precursors to protease enzymes produced by the pancreas?

has to have dipole moment and O, N or F

What to you need to form a hydrogen bond?

Uncompetitive inhibitor

What type of inhibitor would give parallel lines on a Lineweaver-Burk plot?

It will burst

What will happen to a cell immersed in a hypotonic solution?

Total number of units decreases and specific activity increases

What would you expect when comparing a crude cellular extract before purification to the sample obtained after successful purification of an enzyme from the extract?

ammonium sulfate

When "salting out" increase concentrations of _____ to precipitate proteins during centrifugation.

Le Chatelier's Principle

When a system at equilibrium is disturbed, the system adjusts to a new equilibrium in a way that partially counteracts the disturbance.

the native protein has at least one disulfide bond

When an electrophoresis gel shows three points in the first row with Protein + trypsin + DTT but combines two of those point in the second row with protein + trypsin, .....

zymogen

When enzymes are activated by proteolytic cleavage, they are initially produced as a/an _______.

crude extract

When in purification and separation, break cells to obtain ____ ____.

equal

When pH=pKa, the weak acid and salt concentrations in a buffer are _____.

antiparallel beta sheet

When the hydrogen bonds in a protein are perpendicular to the direction of the protein, it is:

a. The reaction is first order reaction with respect to each substrate

When there are two reactants in a reaction, the reaction is said to be second order overall if: a. The reaction is first order reaction with respect to each substrate b. the substrate concentrations are known c. the substrate concentration are equal d. doubling the concentrations of both substrate doubles the rate

- polymerase chain reaction - site-directed mutagenesis

When two near-complementary DNA strands hybridize, amplification of a specific DNA is performed by:

- radioactive detection - fluorescent DNA chips

When two near-complementary DNA strands hybridize, detection of a specific DNA molecule in complex mixture is done by:

evolutionary

When two near-complementary DNA strands hybridize, it eventually forms ______ relationships.

That the two largest fragments are joined by a disulfide bond

When you start with three lines on you gel and end with two, SDS-PAGE gel shows:

on the outer surface

Where would isoleucine residues most likely be found in a lipid-soluble protein?

On the outer surface

Where would serine residues most likely be found in a water-soluble protein?

proline

Which amino acid adds the most rigidity when it is part of an amino acid chain?

cysteine

Which amino acid can dimerize?

c. isoleucine

Which amino acid is least likely to be found on the surface (exterior) of a water-soluble protein? a. threonine b. asparagine c. isoleucine d. lysine

Met

Which amino acid will hydrogen bond with Ile if the following segment is in an alpha-helix? Ile-Gly-Trp-Val-Met-Leu-Ala

glycine

Which amino acid will tend to make a protein chain very flexible where it occurs?

lysine

Which amino acid would best help to stabilize an alpha helix when positioned one amino acid beyond the C-terminal end of the helix?

B. valine

Which amino acid would you most expect to occur on the interior of a water soluble protein? A. serine B. valine C. aspartate D. glutamine

cysteine

Which amino acid(s) monomers can form dimers that help stabilize protein structure?

b. lysine and glutamate

Which amino acids could form an ion-pair between their R groups at pH 7? a. asparatate and serine b. lysine and glutamate c. threonine and alanine d. asparagine and proline

2 and 3

Which are classified as chemical modes of catalysis? 1. Transition state stabilization 2. Acid-base catalysis 3. Covalent catalysis 5. Proximity effect

b. B-D-galactopyranose and B-D-glucopyranose

Which are the monomers of lactose? a. a-D-galactopyranose and B-D-glucopyranose b. B-D-galactopyranose and B-D-glucopyranose c. B-D-fructofuranose and a-D-glucopyranose d. B-D-galactofuranose and B-D-glucopyranose

lipids

Which class of biochemicals does not generally have polymeric forms?

d. Interconversion between alpha and beta forms of cyclic carbohydrates

Which defines mutarotation? a. Interconversion between conformations of a molecule by rotation about bonds. b. Interconversion of cis/trans isomeric forms. c. Interconversion between sun and anti forms of nucleotides. d. Interconversion between alpha and beta forms of cyclic carbohydrates

d. Interconversion between alpha and beta forms of cyclic carbohydrates

Which defines mutarotation? a. Interconversion between conformations of a molecule by rotation about bonds. b. Interconversion of cis/trans isomeric forms. c. Interconversion between syn and anti forms of nucleotides d. Interconversion between alpha and beta forms of cyclic carbohydrates

it has a unique quaternary structure

Which does not apply to myoglobin?

D. It has a unique quaternary structure

Which does not apply to myoglobin? A. It is a metalloprotein B. Its prosthetic group is the heme group C. It stores oxygen in muscle tissue D. It has a unique quaternary structure

K Not sure why Na is listed as a most common element here... (C,N,O,H,S,P are more common)

Which does not belong in the six most common elements in living organisms? A. K B. S C. Na D. None. All belong

collagen

Which has a left-handed helix for individual protein chains, that combine to form triple-stranded fibers wrapped in a right-handed fashion?

D. none of the above

Which has a positive charge at pH=14? A. glycine B. aspartate C. lysine D. none of the above E. all of the above

leucine

Which has the higher hydropathy index? Choice one: Arginine or leucine

bacteria

Which have a nucleoid? a. viruses b. eukaryotes c. bacteria d. autotrophs e. all living cells

nucleic acids

Which have information transfer, direction of protein synthesis, and storage and release of energy as their main functions? A. Nucleic acids B. amino acids C. proteins D. mitochondria

Protein

Which is a heteropolymer? A. cellulose B. protein C. lipid D. ribosome

D. Mitochondria, ER, peroxisomes

Which is a list of organelles? A. Mitochondria, chromatin, ER B. Peroxisomes, lysosomes, plasma membrane C. Proteasomes, peroxisomes, lysosomes D. Mitochondria, ER, peroxisomes E. All of the above

c. Glycogen

Which is a main storage molecule for energy in mammalian liver and muscle? a. Amylopectin b. Myoglobin c. Glycogen d. Fibronectin e. Trypsinogen

domain

Which is a secondary structure? a. motif b. a-helix c. domain d. signature sequence

A. Micelle's of SDS in water

Which is caused by hydrophobic interactions? A. Micelle's of SDS in water B. The dissolving of NaCl in water C. The primary structure of proteins D. The stabilization of the structure of ice

A. They often are at the ends of contiguous sections of a parallel beta-sheet

Which is false about beta-turns? A. they often are at the ends of contiguous sections of a parallel beta-sheet B. They frequently contain cis-proline C. They are stabilized by hydrogen bonding D. None are false, they are all true

Arginine

Which is most likely a zwitterion at a pH above pH 7? A. Arginine B. Proline C. Cysteine D. Tryptophan E. None of the above

E. all of them

Which is most likely a zwitterion near pH=7? A. isoleucine B. glycine C. proline D. valine E. all of the above

a. An enhanced ability to adopt psi and phi angles outside the common ranges

Which is not associated with the formation of oligomers? a. An enhanced ability to adopt psi and phi angles outside the common ranges b. Increased stability compared to the dissociated subunits c. The formation of active sites between adjacent subunits d. Increased efficiency by synthesizing smaller subunits rather than a single chain the same size as the oligomer

D. All the above are true

Which is not true about histidine? A. It's side chain is aromatic B. It is classified as basic but the pKa of the side chain is less than 7 C. It contains nitrogen in the side chain D. All the above are true

d. the effect of the inhibitor is reversed by high [S]

Which is not true for mixed inhibition? a. The inhibitor has its own binding site that is not the active site. b. Vmax is lowered. c. Km is either unaffected or changed only slightly d. The effect of the inhibitor is reversed by high [S]

a. They catalyze an early reaction in the pathway for efficiency

Which is often true about regulatory enzymes in metabolic pathways? a. They catalyze an early reaction in the pathway for efficiency b. they usually are activated by increase in pH c. they act as modulators for other enzymes in the pathway d. they rarely are oligomers

H2CO3

Which is the conjugate acid of the hydrogen carbonate ion, HCO3-?

it interacts with proteins to give them the same charge per unit length

Which is true about SDS (sodium dodecyl sulfate)?

C. It has two matching pairs of protein chains

Which is true about hemoglobin? A. Its protein chains are identical to myoglobin except for one amino acid difference B. It has four protein chains that are all completely different in sequence C. It has two matching pairs of protein chains D. About 70% of the amino acids are in a beta-strand conformation

At Tm ribonuclease will exhibit half the activity of a sample in its native conformation

Which is true about the melting temperature, Tm, for ribonuclease?

b. The L form predominates

Which is true about the naturally occurring amino acids? A. 19 of 20 amino acids are achiral B. the L form predominates C. the enantiomers occur equally as frequently d. most are meso compounds

C. the L forms predominate

Which is true about the naturally occurring amino acids? A. Each amino acid has multiple diasteromers B. 19 of 20 amino acids are achiral C. The L forms predominate D. Enantiomeric forms occur in equal propertions

SDS

Which is/are amphipathic? A. amino acids B. water C. SDS D. Both A and B E. All three (A,B,C)

B. Prokaryotes

Which lack a nuclear envelope? A. eukaryotes B. prokaryotes C. autotrophs D. heterotrophs E. Both B and C

b. log(ab) = log(a) + log(b)

Which log expression is true? a. log(ab) = log(a)log(b) b. log(ab) = log(a) + log(b) c. log(ab) = alog(b) + blog(a) d. log(ab) = 10^a+b

dodecanoic acid

Which of the following could likely form micelles in an aqueous solution? A. hexane B. glucose C. DNA D. dodecanoic acid E. none of the above

Which of the following elements is *not* among the top four most abundant elements in living systems, but it still required for life in all organisms? A. H B. N C. P D. C E. O

E. none of the above

Which of the following is a major difference between B-DNA and A-DNA? a. B-DNA has a right-handed helix, A-DNA has a left handed helix b. B-DNA has 10 residues per helix turn while A-DNA has 9 c. B-DNA base pairs are stacked almost parallel to one another while A-DNA base pairs are significantly tilted with respect to each other d. The major groove of A-DNA is much larger than that in B-DNA e. None of the above

a. Measure the rate shortly after mixing S and E before [S] changes much

Which of the following is most important when using the initial rate method to obtain kinetic data? a. Measure the rate shortly after mixing S and E before [S] changes much b. Measure the rate shortly after mixing S and E to be sure the sample is still in the pre-steady state. c. Make sure you have lots of samples with different [S] and [E] d. The reaction must be known to be first or second order with respect to [S]] to use this method.

Sucrose

Which of the following is not a reducing sugar? A. Fructose B. Glucose C. Glyceraldehyde D. Sucrose E. None of the above, they are all reducing sugars

Polymerases

Which of the following is not among the six internationally accepted classes of enzymes? a. Hydrolases b. Ligases c. Oxidoreductases d. Polymerases e. Transferases

b. It is likely to involve amino acids such as asp or lys

Which of the following is true about general acid-base catalysis? a. It involves a transient covalent bond between the enzyme and the substrate. b. It is likely to involve amino acids such as asp or lys c. It is the method primarily responsible for the loss of entropy in enzyme-catalyzed reactions. d. It is not seen in the catalytic mechanism for the serine proteases.

D. aspartic acid and arginine

Which of the following pairs of amino acids could interact via ion-paring of their R-groups? A. methionine and histidine B. glutamine and lysine C. serine and glutamic acid D. aspartic acid and arginine E. threonine and asparagine

B. At very high [S], the velocity curve becomes a horizontal line and the y-value is equal to 2Km

Which of the following statements about a plot of Vo vs. [S] for an enzyme that follows Michaelis-Menton kinetics is false? A. At [S] increases, the initial velocity of reaction, Vo, also increases B. At very high [S], the velocity curve becomes a horizontal line and the y-value is equal to 2Km C. Km is the [S] at which Vo = 1/2 Vmax D. The shape of the curve is a hyperbola E. The y-axis is a rate term with units of delta concentration/delta time

b. Km = 1/2 Vmax

Which of the following statements about a plot of Vo vs. [S] for an enzyme that follows Michaelis-Menton kinetics is false? a. At very high [S] saturation is reached b. Km = 1/2 Vmax c. The shape of the curve is a hyperbola d. The velocity has units of delta concentration / delta time

E. Heterotropic allosteric effectors compete with the soubrette for binding sites

Which of the following statements about allosteric control of enzymatic activity is false? A. Allosteric modulators give rise to sigmoidal V0 vs. [S] kinetic plots. B. Alloseric proteins are generally composed of several subunits C. A modulator may either inhibit or activate an enzyme. D. Binding of the modulator may change the conformation of the enzyme molecule. E. Heterotropic allosteric effectors compete with the soubrette for binding sites

e. Heterotropic allosteric modulators compete with substrate for the same binding sites.

Which of the following statements about allosteric control of enzymatic activity is false? a. Allosteric modulators give rise to sigmoidal Vo vs. [S] kinetic plots b. Allosteric proteins are generally composed of several subunits c. A modulator may either inhibit or activate an enzyme d. Binding of the modulator changes the conformation of the enzyme molecule e. Heterotropic allosteric modulators compete with substrate for the same binding sites.

B. Good buffers have approximately equal concentrations of a weak acid-conjugate base pair

Which of the following statements about buffers is true? A. Buffers are best at pH=7 B. Good buffers have approximately equal concentrations of a weak acid-conjugate base pair C. The pH of a buffered solution remains constant no matter how much acid or base is added to the solution. D. The stronger buffers are those composed of strong acids and strong bases

c. Both serve primarily as structural elements in cell walls

Which of the following statements about starch and glycogen is false? a. Amylose is unbranched; amylopectin and glycogen contain many (a1-6) branches. b. Both are homopolymers of glucose c. Both serve primarily as structural elements in cell walls d. Both can be broken down by amylase e. Glycogen is more extensively branched than starch

c. The lactam form predominates at neutral pH

Which of the following statements concerning the tautomeric forms of bases such as uracil is correct? a. The all-lactim form contains a ketone group. b. The lactam form contains an alcohol group. c. The lactam form predominates at neutral pH. d. The lactam and lactim forms are in an approximately equal molar equilibrium.

A. carbon-carbon bond

Which one of the following is not considered a noncovalent interaction? A. carbon-carbon bond B. hydrogen bond C. hydrophobic interaction D. ionic interaction E. van der Waals interaction

d. The pentoses are always in the beta-furanose forms

Which one of the following is true of the pentoses found in nucleic acids? a. C-5' and C-1' of the pentose are joined to phosphate groups. b. C-5' of the pentose is joined to a nitrogenous base, and C-1' to a phosphate group. c. The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond. d. The pentoses are always in the beta-furganose forms.

a. collagen; carbohydrate

Which pair is incorrectly matched? a. collagen; carbohydrate b. waxes;lipids c. ATP; nucleotide d. enzymes; proteins

Gly to Ile or Asp to Glu

Which possible variation at a particular amino acid among homologous proteins classifies that amino acid as a conservative residue?

Asp to Glu

Which possible variations at a particular amino acid among homologous proteins classifies that amino acid as a conservative residue? A. Gly to Ser B. Met to Cys C. Asp to Glu D. Phe to His

c. It helps tell if serine is involved in the catalytic mechanism

Which refers to diisopropylfluorophosphate? a. it produces active enzyme from a zymogen b. it detects the amino acid at the N-terminal c. it helps tell if serine is involved in the catalytic mechanism d. it is a negative modulator of hemoglobin

GVLIAGGI

Which sequence is most likely to form an alpha helix? A. GVLIAGGI B. RDEKSTPP C. CRESNPFG D. RRPPNGSS

GVILA (glycine....alanine)

Which sequence will be more likely to form an alpha helix?

A. GVILA

Which sequence will be more likely to form an alpha helix? A. GVILA B. DPGGF C. SCTEE D. PYRQD

D. Hydrophobic interactions are generally much stronger than hydrogen bonds.

Which statement about hydrogen bonds is NOT true? A. Hydrogen bonds account for the anomalously high boiling point of water. B. In ice, the average water molecule forms four hydrogen bonds with other water molecules. C. Individual hydrogen bonds are weaker than covalent bonds. D. Hydrophobic interactions are generally much stronger than hydrogen bonds. E. The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond.

A. The deoxy form of Hb is stabilized by increase [H+]

Which statement best describes the Bohr effect? A. The deoxy form of Hb is stabilized by increase [H+] B. The P50 of Hb is increase by 2,3BPG C. Positive cooperatively is exhibited by the subunits of Hb D. The energy of activation of oxygen binding to Hb is increased by temperature

Increasing the p50 of Hb by decreasing the pH

Which statement describes the Bohr effect?

B. Increasing P50 of Hb by decreasing the pH

Which statement describes the Bohr effect? A. The dependence of a alpha-helix formation by changing the pH B. Increasing P50 of Hb by decreasing the pH C. Unfolding a protein and loss of biological activity by changing the ionic strength D. Elimination of positive cooperatively of ligand binding by changing the temperature

the deoxy form of Hb is stabilized by increasing [H+]

Which statement describes the bohr effect?

It binds at the heme group of Hb

Which statement is false about 2,3-BPG?

B. It binds at the heme group of Hb

Which statement is false about 2,3BPG? A. At biological pH, it has a charge of -5 B. It binds at the heme group of Hb C. It is a negative heterotropic modulator D. In red blood cells, its concentration is about the same as the concentration of Hb

b. Desmosine is a secondary cross-linker between collagen fibers

Which statement is false about collagen? a. The collagen helix is tighter and narrower than an alpha-helix b. Desmosine is a secondary cross-linker between collagen fibers c. Cross-linking increases with age and makes collagen more brittle d. Virtually no other proteins have the same secondary structure as collagen

d. it contains a tertiary amine

Which statement is false about histidine? a. It has an aromatic ring structure. b. It would more likely be toward the exterior of a water-soluble protein. c. It is one of the "basic" amino acids. d. It contains a tertiary amine.

b. it helps to stabilize alpha-helices

Which statement is false about proline?

A. It has an aromatic ring structure

Which statement is false about proline? A. It has an aromatic ring structure B. Of all the amino acids, it has the most restricted rotations about the N-C(alpha) bond C. It would more likely be toward the interior of a water-soluble protein. D. It contains a secondary amine.

B. It helps to stabilize a-helixes

Which statement is false about proline? A. It is one of the most common amino acids in B-turns B. It helps to stabilize a-helixes C. It has restricted rotation about the N-Ca bond D. It adopts the cis configuration more than any other aa

C. In two myoglobin molecular from the same source, they will be in very different configurations

Which statement is false about random coil regions? A. They are also called non-repetitive regions B. They link secondary structures to each other C. In two myoglobin molecular from the same source, they will be in very different configurations D. The backbone bond angles are about the same as those in an alpha helix E. none

C. Amylopectin has one reducing end and as many non-reducing ends as it has branches.

Which statement is true about amylopectin? A. Amylopectin has no reducing ends and one non-reducing end. B. It has one reducing end and one non-reducing end C. Amylopectin has one reducing end and as many non-reducing ends as it has branches. D. Amylopectin has as many reducing ends as it has branches and one non-reducing end.

c. Amylopectin has one reducing end and as many non-reducing ends as it has branches*

Which statement is true about amylopectin? a. Amylopectin has no reducing ends and one non-reducing end b. Amylopectin has one reducing end and one non-reducing end c. Amylopectin has one reducing end and as many non-reducing ends as it has branches d. Amylopectin has as many reducing ends as it has branches and one non-reducing end.

b. one is branched, the other linear

Which statement is true about amylose and amylopectin? a. they are composed of different monomers b. one is branched, the other linear c. they have different biological functions d. all of the above

C. It is polar and has some polar bonds

Which statement is true about dichloromethane, CH2Cl2? A. It is polar and has all polar bonds B. It is non polar and has all non polar bonds C. It is polar and has some polar bonds D. It is non polar because the polar bonds are canceled by geometry

C. It can hydrogen bond with water, but not to other formaldehyde molecules

Which statement is true about formaldehyde (methanol; CH2O)? A. It can hydrogen bond with water and with other formaldehyde molecules. B. It cannot hydrogen bond with anything C. It can hydrogen bond with water but not to other formaldehyde molecules D. It cannot hydrogen bond with water but it can hydrogen bond with other formaldehyde molecules

A. They are not driven by inherent attractions, but by the entropy gain for the surrounding solvent.

Which statement is true about hydrophobic interactions? A. They are not driven by inherent attractions, but by the entropy gain for the surrounding solvent. B. They are about as strong as hydrogen bonds. C. They involved the ability of water to denature proteins. D. They primarily involve the effect of polar solutes on the entropy of aqueous systems.

b. Water gains entropy with the aggregation of the fatty acids

Which statement is true about micelle formation of fatty acids in an aqueous environment? a. the most important stabilizing forces are hydrogen bonding of polar head groups with each other b. Water gains entropy with the aggregation of the fatty acids c. Micelles are more stable than isolated fatty acids because of the increase in clathrate formation for the micelles d. All of the above

Anitparellel B-sheet

Which structure has hydrogen bonds approximately perpendicular to the protein chain?

Antiparallel beta-sheet

Which structure has hydrogen bonds approximately perpendicular to the protein chains?

affinity chromatography

Which technique, if usable, might save many purification steps due to its high specificity for a particular protein?

DDP (negative/negative/nonpolar) 2-

Which tripeptide would you expect to elute first from a cation exchange column where a buffer of changing pH is used during the chromatography?

DDP

Which tripeptide would you expect to elute first from a cation exchange column where a buffer of changing pH is used during the chromatography? a. GVR b. DDO c. EAR d. KHR

tyrosine and tryptophan

Which two amino acids have a strong absorbance at 280 nm?

Lys

Which will most help to stabilize an alpha helix if it occurs close to or just beyond the C-terminal end of the helix? A. Lys B. Asp C. Gly D. Pro

b. Ser to Thr

Which would be considered a conservative substitution among homologous proteins? a. Ala to Asp b. Ser to Thr c. Gln to Glu d. Cys to His

B. Arginine

Which would have the lower hydropathy index? A. cysteine B. arginine C. phenylalanine D. isoleucine E. asparagine

Alanine

Which would you expect to have the highest hydropathy index? A. Arginine B. Aspartate C. Asparagine D. Alanine E. Adenine

proline

Which would you expect to have the highest hydropathy index? a. histidine b. serine c. aspartate d. proline

Glutamate

Which would you expect to have the lowest hydropathy index? A. Valine B. Phenylalanine C. Methionine D. Isoleucine E. Glutamate

b. glutamate

Which would you expect to have the lowest hydropathy index? a. tryptophan b. glutamate c. cysteine d. proline

C. enantiomers

Which, by definition, are chiral? A. diasteromers B. enantiomers C. structural isomers D. mesocompounds

Diffusion from air is too slow and solubility of O2 in blood plasma is low

Why is an O2 carrier needed?

the lock-and-key model is really an energetic trap with an intermediate formed that has lower energy than the substrate

Why is the induced fit model of the interaction between an enzyme and its substrate better than the lock-and-key model?

2.47 nm

Width of DNA helix

Order of reaction

With respect to a particular reactant- its the power on that reactant's concentration in the rate equation

Protein Data Bank, NCBI, Bioinformatics

Worldwide data banks

No, myoglobin cannot release O2 well to the tissues

Would you expect myoglobin that is injected intravenously to perform the same function as hemoglobin?

Wilkins and Franklin

X-ray crystallographic data was obtained by _______ and _______ concerning Watson and Crick's DNA structure.

Mixed

Y-int does change with this inhibitor, there's very little space between x-int (three lines crossover the y axis)

Your purified sample has a higher specific activity than the crude extract

You are purifying an enzyme from a crude cell extract. When you are done, which would tell you that you were successful in purging your enzyme?

Your purified sample has a higher specific activity than the crude extract

You are purifying an enzyme from a crude cell extract. When you are done, which would tell you that you were successful in purifying your enzyme?

Do not include SDS in the electrophoresis

You have an enzyme that you wish to verify by electrophoresis, but you want to preserve the enzymatic activity. What do you do?

d. You cannot distinguish these two by this test alone

You have two white crystalline samples whose labels have fallen off. You know one is fructose and one is lactose and you try to test them to see which is which. What would you see if you reacted each with Benedict's reagent? a. Fructose would cause a change from blue to red, lactose would not. b. Neither reacts because they are both reducing sugars c. A silver mirror will form only for lactose d. You cannot distinguish these two by this test alone

reverse phase HPLC

You wish to separate threonine and valine from one another. Their molecular weights are 119 g/mol and 117 g/mol, respectively. Which technique would be best?

Reverse phase HPLC

You wish to separate threonine and valine from one another. Their molecular weights are very close at 119g/mol and 117g/mol, respectively. What technique would be best?

[E]free+[ES]

[E]total= (MM assumption)

[PL]=Kassociation[P][L]

[PL]= ?

Buffering region

[weak acid] = [conjugate base]

[S]>>[E]

__ >> __ when taking kinetic data (MM assumption)

__ O2 can bind per unit of hemoglobin

__% of mass of living organisms comes from C,O,H,N with S and P next most important.

Two grooves

___ _______ run along the helix -good sites for protein binding - access to base sequence. -major -minor

10%, 2%

___ of the liver is glycogen, ___ in the muscle

Acid hydrolysis

____ _______ cleaves all peptide bonds to leave free amino acids.

weak acids

____ acids ionize incompletely (<100%) in water Reach equilibrium

PCR

____ can also increase the proportion of a particular DNA sequence in a mixed DNA population.

SDS

____ interacts with proteins to give them the same charge per unit length.

Hair

____ is a protein in which the polypeptides are mainly in the alpha-helix conformation.

Water

____ is often very important in maintaining structure. Inside proteins Associated with DNA and RNA Can detect by x-ray crystallography, NMR, etc.

Amino acids

_____ ____ are colorless.

Cross Linking

_____ _______ between chains involves Lys or HyLys and increases with age.

Strand seperation

_____ ________ occurs first in replication of genetic code.

strong acids

_____ acids ionize completely (100%) in water - HCl, HNO3, H2SO4

alpha-helixes

_____ are stabilized by exposure to water, which will compete for hydrogen bonding.

Fmoc.........N

_____ is used as a protective group on the ___-terminal of amino acids during the laboratory synthesis of peptides.

Fibrous proteins

______ _____ have a single secondary structure encompassing nearly all of the protein.

Leading strand

______ _____ is synthesized as one continuous polynucleotide (beginning at origin and ending at the termination site)

Conjugated proteins

______ ______ contain tightly associated non-amino parts to function.

Glycine and proline

______ and _______ are common in turns.

Paralogs

______ are homologous proteins from the same species.

Orthologs

______ are homologous proteins in different species.

Proteins

______ are often considered the most important class for biochemicals.

strong

______ bases ionize completely (100%) in water NaOH, other soluble metal hydroxides

Weak

______ bases ionize incompletely (<100%) in water Reach equilibrium

Transfer (tRNA)

______ carries amino acids to ribosome.

collagen

______ is a left-handed helix that forms triple-stranded fibers wrapped in a right-handed direction.

Spider web

______ is a protein in which the polypeptide is almost entirely in the beta conformation.

linear

______ is always intermediate in mutarotation

Mobility

______ is defined as the speed of migration per unit field strength during electrophoresis.

Daughter

_______ DNA contains one parental and one newly synthesized strand.

Signature sequence

_______ _____ are sequences that are unique to a particular taxonomic group like a species, genus, etc.

Paralogs

_______ are homologous proteins in the same species.

Compostions

_______ can help determine if you have a new protein or an already known one. [NOT DEFINITIVE]

Polar

_______ gases dissolve easily in water NH3, H2S

Nonpolar

_______ gases dissolve poorly in water. O2, N2, CO2

Chirality

_______ is important for the amino acids and their polymers, the proteins.

iodoacetate

_______ is used to prevent the reformation of disulfide bonds due to air oxidation after the disulfide bonds have been removed by reduction.

Acidosis

_______ occurs when blood pH is too low. Treatment for mild cases: breathe pure O2

Primary

_______ structure is the order of the nitrogenous bases.

Lagging strand

________ _____ is synthesized discontinuously in short pieces called Okazaki fragments.

Polymerization

________ continues bidirectionally in DNA replication until the replisomes approach the terminal site.

Glycogen

________ is the main storage molecule for energy in mammalian liver and muscle.

Primary

________ structure ultimately confers the overall 3D structure and is tightly linked to the function.

Conjugated proteins

_________ _______ have non-amino acid groups.

London forces

_________ are intermolecular attractions caused by the constant motion of electrons that lead to transient dipoles.

Ribonuclease A

_________ can spontaneously regain its conformation when denaturing agents are removed.

a. N6-Methyladenosine.........marking its own DNA to prevent degradation by enzymes that grade foreign DNA

__________ can serve as an epigenic marker in bacteria for the purpose of ____________. a. N6-Methyladenosine.........marking its own DNA to prevent degradation by enzymes that grade foreign DNA b. 5-Ethylcytidine.......marking a gene for activation c. Deoxyadenosine-2', 2'-cyclic monophosphate......blocking DNA replication d. 5-Hydroxymethylcytidine............preventing a gene from being activated

Thermal DNA Denaturation (Melting)

__________ is the basis for the polymerase chain reaction (PCR). -dsDNA at normal temperatures -two strands dissociate at elevated temps -reanneal when temp is lowered

iodoacetate

__________ is used to prevent the reformation of disulfide bonds due air oxidation after the disulfide bonds have been removed by reduction.

Chargaff's Rule %purines=%pyrimidines

__________- studied base composition of DNA's from many organisms. Written as a sum: ________=_________ or %A +%G=%T+%C

The size of the DNA region specifically recognized by type II restriction enzymes is typically: A) 4 to 6 base pairs. B) 10 to 15 base pairs. C) 50 to 60 base pairs. D) 200 to 300 base pairs. E) about the size of an average gene.

Which of the following is not needed to build a cDNA library? A) Genomic DNA B) mRNA C) Reverse transcriptase D) dNTPs E) DNA polymerase

Which of the following is not used as a heterologous host for the expression of recombinant proteins? A) Retroviruses B) Bacteria such as E. coli C) Eukaryotes such as S. cerevisiae D) Insect cells E) Mammalian cells

Hydrogen bonds

a particularly strong type of dipole-dipole interaction found when H is covalently bonded to O,N,F.

allosteric protein

a protein whose activity is regulated by a modulator

reducing sugar (there are also non reducing sugars which don't react)

a sugar that will react with oxidizing agent

Pyranose and furanose

a) The 1-5 ring form is called pyranose as it resembles an organic compound called pyran b) The 1-4 ring form is called furanose as it resembles an organic compound called furan

Reactions of phosphoric and sulfuric acids

a)Reaction with phosphoric acid with monosaccharide gives phosphate esters. b)Reaction with sulfuric acids: This acid is a dehydrating agent, removing 3 molecules of H2O from the sugar giving a compound called furfural.

Functions of glycoproteins

a-Glycoproteins are components of extracellular matrix b-They are components of mucins of gastrointestinal and urogental tract, where they act as protective biologic lubricants c- Glycoproteins are components of cell membrane as: 1) Blood group antigens (A, B, AB) 2) Cell surface receptors: e.g. for hormones 3)Glycophorin: It is glycoprotein present in human red cell membrane, it prolonged the life span of lipid membrane. d- Plasma proteins: present in plasma e) Most enzymes and protein hormones glycoprotein

Electronegativity

ability of atoms of an element to attract electrons in a covalent bond

Neutralization reaction

acid + base > a salt (ionic compound) + water (usually)

lyases

addition of groups to double-bonds or the formation of double-bonds

Amphipathic

adjective for molecules that contain both polar and non polar parts (e.g. soap)

Ampholytic/Amphoteric

adjective which describes any molecule that can act as either an acid or a base

HbA

adult hemoglobin

Non-polar

aggregate to minimize clathrate formation

Hydrophobic interactions

aggregation of non-polar species or parts driven by entropy increase in surrounding solvent

metalions

aid substrate binding via their charge or by redox reactions

motifs (know pics)

all alpha, all beta, or both

Homopolymer

all monomers identical (one type of monomer)

N-terminus

amino-terminus on left

epimers

anomers are a subset of ________

chaperones

assist in the folding process

x: course of reaction y: free energy (G)

axis for graph that displays energy of reaction

Current estimates indicate that ________ % of the human genome is translated into protein. A) less than 0.5% B) roughly 1.5% C) roughly 10% D) roughly 25% E) more than 50%

The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering experiments. pBR322 has all of the following features except: A) a number of conveniently located recognition sites for restriction enzymes. B) a number of palindromic sequences near the EcoRI site, which permit the plasmid to assume a conformation that protects newly inserted DNA from nuclease degradation. C) a replication origin, which permits it to replicate autonomously. D) resistance to two different antibiotics, which permits rapid screening for recombinant plasmids containing foreign DNA. E) small overall size, which facilitates entry of the plasmid into host cells.

The biological role of restriction enzymes is to: A) aid recombinant DNA research. B) degrade foreign DNA that enters a bacterium. C) make bacteria resistant to antibiotics. D) restrict the damage to DNA by ultraviolet light. E) restrict the size of DNA in certain bacteria.

Which of the following does not apply to the construction or use of a DNA library? A) Determining the location of a particular DNA sequence in a DNA library requires a suitable hybridization probe. B) Genomic libraries are better for expressing gene products than cDNA libraries. C) Many segments of DNA from a cellular genome are cloned. D) Specialized DNA libraries can be made by cloning DNA copies of mRNAs. E) The DNA copies of mRNA found in a cDNA library are made by reverse transcriptase.

Which of the following statements about the polymerase chain reaction (PCR) is false? A) DNA amplified by PCR can be cloned. B) DNA amplification is linear in magnitude. C) Newly synthesized DNA must be heat-denatured before the next round of DNA synthesis begins. D) The boundaries of the amplified DNA segment are determined by the synthetic oligonucleotides used to prime DNA synthesis. E) The technique is sufficiently sensitive that DNA sequences can be amplified from a single animal or human hair.

Which of the following tags is not used to study protein function? A) Green fluorescent protein (GFP) B) Synteny tag C) Tandem affinity purification (TAP) D) Gal4p DNA binding domain E) Gal4p activation domain

Cation exchangers

beads have negatively charged groups (e.g. sulfate)

Anion exchangers

beads have positively charged groups (e.g. ammonium)

Cu2 + -> Cu2 0 reduced --->

benedict's or fehling's reagents

Fe2+ of the heme group

binding site for Mb and Hb

active site (catalytic site)

binding site for substrate

Enzymes

biological catalysts

gamma-carboxyglutamate

blood-clotting protein (thrombin)

2-mercaptoethanol

breaks disulfide bonds when added (ribonuclease)

urea

breaks hydrogen bonds when added (ribonuclease)

A convenient cloning vector with which to introduce foreign DNA into E. coli is a(n): A) E. coli chromosome. B) messenger RNA. C) plasmid. D) yeast "ARS" sequence. E) yeast transposable element.

Certain restriction enzymes produce cohesive (sticky) ends. This means that they: A) cut both DNA strands at the same base pair. B) cut in regions of high GC content, leaving ends that can form more hydrogen bonds than ends of high AT content. C) make a staggered double-strand cut, leaving ends with a few nucleotides of single-stranded DNA protruding. D) make ends that can anneal to cohesive ends generated by any other restriction enzyme. E) stick tightly to the ends of the DNA they have cut.

Current estimates indicate that humans have about ________ genes. A) 3,000 B) 10,000 C) 30,000 D) 100,000 E) 300,000

Rank the following organisms in order from smallest genome (number of base pairs of DNA) to largest genome. A) Human, fruit fly, E. coli bacterium B) E. coli bacterium, human, fruit fly C) E. coli bacterium, fruit fly, human D) Fruit fly, E. coli bacterium, human E) Fruit fly, human, E. coli bacterium

Restriction enzymes: A) act at the membrane to restrict the passage of certain molecules into the cell. B) are highly specialized ribonucleases that degrade mRNA soon after its synthesis. C) are sequence-specific DNA endonucleases. D) are very specific proteases that cleave peptides at only certain sequences. E) catalyze the addition of a certain amino acid to a specific tRNA.

The PCR reaction mixture does not include: A) all four deoxynucleoside triphosphates. B) DNA containing the sequence to be amplified. C) DNA ligase. D) heat-stable DNA polymerase. E) oligonucleotide primer(s).

Which of the following is not a commonly used tag for affinity purification of cloned proteins? A) Glutathione-S-transferase B) Maltose binding protein C) Nickel D) Protein A E) Chitin-binding domain

Which one of the following analytical techniques does not help illuminate a gene's cellular function? A) DNA microarray analysis B) Protein chip analysis C) Southern blotting D) Two-dimensional gel electrophoresis E) Two-hybrid analysis

Which type of DNA sequence is not found in the human genome? A) Long repetitive repeats B) Introns C) Retro-palindromes D) Simple sequence repeats E) Transposons

glycogen

carbohydrate storage in animal liver

starch

carbohydrate storage in plants

anomeric carbon

carbon in the cyclic structure that was the carbonyl carbon in the linear structure

oxidoreductase

carbonyl --> alcohol (reduction) carbonyl<-- alcohol (oxidation)

C-terminus

carboxy-terminus on right

hydrolases

catalyze hydrolysis reactions (special class of transferase), water is the acceptor of the group

cellulase

cellulose is hydrolyzed by the enzyme _________. Humans don't have this, so don't eat grass!

Peptide

chains of linear polymer linked amino acids

rate

change in concentration/change in time

5-hydroxylysine

collagen

Hydropathy index

comparison of AA to each other; numerical scale to indicate relative hydrophobicity and hydrophilicity; helps predict folding of protein chain

induced fit

complementary to transition state in this model

Equivalence point

complete neutralization; stoichiometric amounts of acid and base are present

isomerases

convert isomers

>1 ligand binding sites per unit protein

cooperative binding takes place when...

loosley (so they can come and go)

cosubstrates on enzymes are _______ bound

furanoses

cyclic monosaccharides with 5-attom ring

pyranoses

cyclic monosaccharides with 6-atom ring

Which of the following is not needed in 454 pyrosequencing of DNA? A) dNTPs B) Sulfurylase C) Luciferase D) ddNTPs E) Apyrase

Which of the following methods is not used in linkage analysis? A) Compare densely spaced polymorphisms. B) Collect DNA from a family affected by the disease of interest. C) Sequence selected parts of the genome. D) Introduce retroviruses at the mutated locus. E) Look for SNP variants.

Which of the following statements about type II restriction enzymes is false? A) Many make staggered (off-center) cuts within their recognition sequences. B) Some cut DNA to generate blunt ends. C) They are part of a bacterial defense system in which foreign DNA is cleaved. D) They cleave and ligate DNA. E) They cleave DNA only at recognition sequences specific to a given restriction enzyme.

n (which is also slope)

degree of interaction between binding sites is represented by what letter?

residue

denotes amino acid that is part of amino acid chain because it lacks water which is split out during formation.

initial pH

determined by concentration and pKa or pKb

amylase

digestive enzyme breaks alpha (1->4) links

Polar

dipole moment

CO2

dissolves as bicarbonate ion (HCO3-)

max 260 nm

dsDNA (pH 7.0), absorbance max _____.

Common features found in a cloning plasmid used for protein expression include all except which of the following? A) Polylinker B) Origin of replication. C) Antibiotic resistance marker(s) D) Ribosome binding site E) Telomeric ends

In the laboratory, recombinant plasmids are commonly introduced into bacterial cells by: A) electrophoresis—a gentle low-voltage gradient draws the DNA into the cell. B) infection with a bacteriophage that carries the plasmid. C) microinjection. D) mixing plasmids with an extract of broken cells. E) transformation—heat shock of the cells incubated with plasmid DNA in the presence of CaCl2.

The technique known as two hybrid analysis for detecting interacting gene products depend on: A) activation of DNA polymerase by the nearby binding of hybridizing protein complexes. B) direct binding of a Gal4p activation domain to a DNA sequence in the promoter region. C) having a promoter that responds directly to one of the two proteins whose interactions is being measured. D) hybridization of DNA segments corresponding to the two genes being examined. E) stimulation of transcription by interaction of two Gal4p domains via fused protein sequences.

Which of the following statements regarding plasmid-cloning vectors is correct? A) Circular plasmids do not require an origin of replication to be propagated in E. coli. B) Foreign DNA fragments up to 45,000 base pairs can be cloned in a typical plasmid. C) Plasmids do not need to contain genes that confer resistance to antibiotics. D) Plasmid vectors must carry promoters for inserted gene fragments. E) The copy number of plasmids may vary from a few to several hundred.

Structural

e.g. hair, nails

Storage & transport

e.g. hemoglobin carries oxygen

Desmosine

elastin

Dipole-dipole attractions

electrostatic attractions between polar molecules

1.0 unit= amount of enzyme needed to consume 1 umole of substrate per min at 25 C

enzyme activity 1.0 unit= ?

lock and key mechanism

enzyme and substrate are complementary in this model

x.y.z.a

enzyme numbering system

Intramolecular forces

exist between "distant" parts of the same molecule

Intermolecular forces

exist between different molecules

chitin

exoskeleton of insects

Binding of the first O2 causes a conformational change, which induces a conformational change on the other 3 attachment sites, making it easier for O2 to attach to those sites.

explain sigmoidal curve

proteoglycan

extracellular matrix of animal tissues

HbF

fetal hemoglobin

oligopeptide

few (2-20 residues)

fibrous proteins (tertiary structure)

fibers where a single secondary structure encompasses the whole protein chain

Virtual Theory

first discredited in 1828 by Friedrich Wohler, who synthesized urea (organic) from ammonium cyanate (inorganic)

cooperative folding

first few interactions aid subsequent folding steps

positive cooperativity

first oxygen is hardest to bind to hemoglobin, subsequent ones are easier to bind

Motility

flagella, muscles

globular proteins (tertiary structure)

folded, compact, like a "glob", has more than one type of secondary structure in the chain

glycogen

found in animals, primarily in the liver in mammals, stores energy, regulates blood glucose levels

heme group

found in myoglobin, hemoglobin, cytochromes, etc

theta

fraction of binding sites occupied with ligand

Differential centrifugation

fractionation technique performed by adding ammonium sulfate and centrifuging

oxidation

gain of O, loss of H (loss of e-)

Tm graph

graph x: temperature y: percent unfolded

Polyprotic acid

has 2 or more H+ to donate (H3PO4)

Selenocysteine

has Se instead of S (rare); vitamins

w-3 fatty acid

has a double bond between 3rd and 4th carbons from the end of a fatty acid chain

Hypertonic solution

has higher osmolarity than cytosol

Hypotonic solution

has lower osmolarity than cytosol

Monoprotic acid

has only 1 H+ to donate (HCl, HAc)

has soluble protein carriers (hemoglobin & myoglobin)

causes of denaturation

heat, pH, urea, solvents, detergents (SDS)

release of O2 to tissues that need it

high CO2 and H+ levels (active tissues) favors...

fully deprotonated

high pH

Clathrate

highly ordered water molecules surrounding non-polar molecule(s)

hydrophobic

highly positive values

homoglycan

identical monomer units

mutarotation

interconversion between anomers

Messenger (mRA)

intermediate that takes code for protein sequences from DNA to RNA.

transferases

involved in group transfer (moving a chemical group)

RNA

involved in protein production

Ion-ion

ions with full charges attract each other Ex. carboxylate ion and ammonium ion

apoenzyme (apoprotein)

just the protein part of the enzyme

Vmax

k2[E]total=

collagen helix

left handed helix, 3 residues per turn, repeating tripeptide (Gly-X-Y)

substrate (reactant)

ligand

substrate

ligand and is a reactant of the reaction catalyzed by the enzyme

ligand for Mb and Hb

O-glycosidic bond Beta(1->4) link

link between monomers in lactose

alpha1 -> beta2 link

link between monomers in sucrose

supernatant

liquid

Secondary

local region of organized structure

nlog(a)

log(a^n)=

reduction

loss of O, gain of H (gain of e-)

denaturation

loss of native conformation by loss of levels of structure other than primary structure and sufficient to cause loss of function

O2 binding

low CO2 levels (lungs) favors....

fully protonated

low pH

polypeptide

many (>20 residues)

melting point when helf-denatured

Ornithine/Citrulline

metabolite involved in arginine biosynthesis

Half-titration point

midpoint of the buffering region

starch

mixture of amylose and amylopectin

HPLC

mobile phase: solvent (nonpolar) stationary phase: column packing (beads with polar group)

heterotrophic

modulator that is not the same as the protein's ligand

homotrophic

modulator that is the same as the protein's ligand

random coil regions

molecules in this region have the same phi and psi as the alpha helix

Amylose

monomer is alpha-D-glucopyranose

amylopectin

monomer is alpha-D-glucopyranose

cellulose

monomer is beta-D-glucopyranose

Linear polymer

monomers joined sequentially (train cars)

features of oligomers

more stable than separated monomers, active sites formed by association, synthesis efficiency (lower probability of error)

Polyunsaturated

more than one double bond in the alkyl chain of a fatty acid

cellulose

most abundant polysaccharide, main component of plant cell walls

NH4

most common functional group in proteins

mobile phase

moving phase of chromatography

6-N-methyllysine

myosin (muscle)

slope

no association

nH=1 means...

indicates positive cooperativity

nH>1 means...

2,3 BPG

negative modulator, stabilizes the deoxy form of Hb, allows Hb to release its O2 at the pressures in the tissues

T, U

nitrogenous base that is only in DNA is ___ and the base that is only in RNA is ___

cofactors

non-amino groups required by certain enzymes

random coil regions

non-replicative regions

stationary phase

not moving phase of chromatography

phosphate + ribose or deoxyribose + nitrogenous base

nucleotide structure

Turns (bends)

occur at the ends of antiparallel B-sheets at the surfaces of proteins or in the interior where the chain make a sharp turn.

allosteric interactions

occurs when a modulator molecule binds to a protein at a site other than the normal binding site and regulates its activity

Alkalosis

occurs when blood pH is too high Treatment for mild cases: breathe in bag

asymptotically

on theta vs [L] graph, maximum value is approached ________

Monounsaturated

one double bond between carbons in the alkyl chain of a fatty acid

negative cooperativity

opposite of positive cooperativity

Primary

order (sequence) or amino acids from the N-terminal to the C-terminal

coenzymes

organic or organometallic cofactors

Tertiary

overall 3D structure of a single polypeptide chain

tertiary structure

overall 3d conformation of 1 polypeptide chain

quaternary structure

overall 3d structure of a multi-chain protein

pH ___ 7 acidic

pH ___ 7 basic

pH ___ 7 neutral

Cytosol buffering system

pH of cytoplasm is near 7; H2PO4- + H2O <-> HPO4(2-) + H3O+

-log[H3O+]

pH=______

+/- 1

pKa (or pKb) of weak acid (or base) should be ___ from pH desired

Proteins

peptide with MW > 10,000

4-hydroxyproline

plant cell walls/collagen

polysaccharides

polymers of monosaccharides

branched or linear

polysaccharides can be either ________ or _______ polymers

oligomer, therefore it cannot have a quaternary structure

positive cooperativity cannot occur in myoglobin because myoglobin is not an _______.

experiment

powers a and b in rate equation must be determined by __________

pellet

precipitant

tightly

prosthetic groups on enzymes are _______ bound

holoenzyme

protein + all cofactors (whole active unit)

lectins

proteins that bind to specific oligosaccharides

rate constant

review notes!!

rate equation derivation

rate= k[A]^a[B]^b

rate= ?

Henderson-Hasselbach equation

rearrangement of the expression for Ka; pH=pKa+log[A-][HA]

Isotonic

refers to solutions of equal osmolarity often compared to osmolarity of the cytosol of cells

renaturation

regain of native conformation after denaturation

Hormones

regulate activities in target cells

R, binds easily to ligand (circle in example)

relaxed state

DNA polymerase I

repairs DNA and participates in DNA synthesis of one strand

DNA polymerase II

role in DNA repair

sigmoidal

s-shaped curve on graph (oxygen binding on hemoglobin)

Saponification

same process as making ole-fashioned soap

sigmoidal

shape of hemoglobin on graph

hyperbolic

shape of myoglobin on graph

HbS

sickle hemoglobin

parts of myoglobin

single polypeptide chain (153 amino acids) + prosthetic group (heme) + metalloprotein (Fe2+)

rate determining step

slowest step in the mechanism

a detergent

sodium dodecyl sulfate (SDS)

a soap

sodium oleate

Buffers

solutions which resist pH change upon addition of acid or base; important for maintaining homeostasis; even relatively small changes in pH can have dramatic effects

tertiary structure

stabilized by disulfide bonds, H-bonds between R groups, ionic interactions, hydrophobic interactions, and van der waals forces

reaction mechanism

step by step sequence of elementary reactions by which overall (net) chemical change occurs

anomers

stereoisomers that differ only about the anomeric carbon in the linear structure (alpha and beta forms)

epimers

steroisomers that differ in configuration about one chiral carbon (D-glucose and D-galactose)

functions of myoglobin

stores O2 in tissues for use when deprived and shuttles O2 from the blood into the tissues

induced fit

structural adaptations (conformational changes) when protein and ligand bind

peptidoglycan

structural component of bacterial cell wall

cellulose

structural component of plant cell walls

glycogen

structure is almost identical to amylopectin

catalyst

substance which speeds a reaction, usually by lowering activation energy (Ea)

sequential theory (like example with circles and squares?)

subunit may have R->T conversion induced by others. Different orders for subunit conversion from R->T.

concerted theory

subunits all change simultaneously between R and T states

-ase

suffix for enzymes

lyases

syntases

collagen helix

synthesis requires vitamin c

ligases

synthetases

sucrose

table sugar

T, does not easily bind ligand (square in example)

tense state

3' end

the end where the 3' carbon of the sugar does not lead to another nucleotide

DNA polymerase III

the major DNA replication enzyme, responsible for chain elongation

slowest

the rate equation of the _______ step is the rate equation for the net equation

Biochemistry

the study of living systems at the molecular level; the study of the chemistry of life processes

hyperbola (this shows it's just a regular equilibrium)

theta vs [L] is a _______

theta= binding sites occupied/total # binding sites

theta= ? (equation in words)

theta=[PL]/[PL]+[P]= [L]/[L]+(1/Kassoc)=[L]/[L]+Kdissoc

theta= ? (equation, not in words)

AG + -> Ag 0 reduced --->

tollen's reagent

trehalose

transport/storage in insects

Hb function

transports O2 from the lungs to the tissues via the blood

Polymer

very large molecule consisting of smaller similar subunits (monomers) which are joined covalently

hydrophilic

very negative values

hyaluronate

viscosity, lubrication of extracellular secretions

Weak interactions

weaker than covalent bonds that can exist between different or distant molecules

myoglobin

when hemoglobin has 0 BPG, its curve looks like that of _______

Isoelectric point (pI)

where zwitterion predominates; the AA is neutral here; the average of the pKa's of the amino and carboxylic groups

Palindromes

words or phrases hat are the same when read backwards or forward.

collagen helix

wraps right handed into triple strand

x: log(theta/1-theta) Y: log[L]

x and y axis on Hill plot

class

x= ____ of enzyme

subclasses

y, z, a= __________

See all study sets

Biochemistry Carbohydrates - by MHashi, Biochem ch 8, Ch. 9 Lehninger biochem, Chapter 10 multiple choice, Chapter 7 Biochemistry, Biochem ch 6, Old Test 3; June 2010, My Test 2, Quiz 1, Cell Components, Quiz 2, Quiz 3, Quiz 4, Quiz 5, Old Test 1, Ma...

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