Biochemistry - Year 2

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D-ribose (Figure 1) is treated with a mild oxidizing agent. Edit the structure for D-ribose to show the product of this reaction.

D-galactose (Figure 2) reacts with methanol. Edit the structure of D-galactose drawn below to create the glycoside formed.

Identify the chiral carbon atoms by selecting each atom and assigning it a map number of 1 until all atoms are mapped. To do this, right-click on an atom and choose Atom Properties.

How many chiral carbon atoms does the monosaccharide galactose have?

4

Ignoring chirality, draw the Haworth structure of allose. The open-chain Fischer projection for the monosaccharide is given here. (Figure 2) Include only the hydrogen atoms attached to the oxygen atoms in the OHOH groups when drawing the cyclic form.

Pentoses and hexoses can form stable ring structures by internal ________ formation.

* Hemiketal
* Hemianionic
* Hemiacetal
* Hemicationic

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Hemiacetal

Maltose has a (1→4) α linkage between glucose and ________.

* Xylulose
* Galactose
* Glucose
* Mannose

Glucose

A saccharide is a ________.

* Carbohydrate
* Nucleic acid
* Lipid
* Protein

Carbohydrate

Assign the name of each sugar to its corresponding aldose or ketose.

1) D-erythrose A) aldohexose

2) D-glucose B) ketopentose

3) D-ribose C) aldopentose

4) D-xylulose D) aldotetrose

* 1D; 2A; 3C; 4B
* 1A; 2D; 3C; 4B
* 1D; 2C; 3A; 4B
* 1D; 2A; 3B; 4C

1D; 2A; 3C; 4B

Which of the following molecules of psicose, a ketohexose, has the chiral carbon furthest from the carbonyl group marked with a 1?

a

In the following Fischer projection, the hydroxyl group on the chiral carbon furthest from the carbonyl group points _____, meaning that this is the _____ isomer of tagatose.

* right / D
* right / L
* left / D
* left / L

right / D

In the following Fischer projection, the hydroxyl group on the chiral carbon furthest from the carbonyl group points _____, meaning that this is the _____ isomer of mannose.

* right / D
* right / L
* left / D
* left / L

left / L

Sort the following monosaccharides as D or L isomers.

In a Haworth projection for D-glucose, what would be the position (above or below the ring) for the hydroxyl groups at C-2, C-3, and C-4?

* C-2: below; C-3: above; C-4: above
* C-2: above; C-3: below; C-4: above
* C-2: below; C-3: above; C-4: below
* C-2: above; C-3: above; C-4: below

C-2: below; C-3: above; C-4: below

Choose Haworth projections for the following:

in α-furanose form.

a

Name the sugar.

* α-D-Fructopyranose
* α-D-Fructofuranose
* α-D-Ribopyranose
* α-D-Ribofuranose
* α-D-Xylofuranose

α-D-Ribofuranose

Choose Haworth projections for the following:

The L isomer of

E

Choose Haworth projections for the following:

α-D-GlcNAc

B

Choose Haworth projections for the following:

α-D-Fructofuranose

C

Which structure is NOT a carbohydrate?

B

Which of the following sugars would yield a positive Fehling's test (red color change)?

* maltose
* lactose
* All of the listed responses would yield a positive result.
* glucose

All of the listed responses would yield a positive result.

What type of bond links the monomers of a polysaccharide?

* Phosphate ester bond
* Glucosidic bond
* Peptide bond
* Glycosidic bond

Glycosidic bond

Polysaccharide structure can be varied by differences in ________.

* The presence of branching
* Chain length (number of sugars in each polysaccharide)
* The kind(s) of sugars in each polysaccharides
* All of the above

All of the above

Cellulose is NOT highly branched because it ________.

* Does not have β (1→4) linkages
* Does not have a polysaccharide backbone
* Is insoluble in water
* Does not have α (1→6) linkages

Does not have α (1→6) linkages

Select the statement that is *incorrect*.

* Polysaccharides are carbohydrates.
* All carbohydrates have the general formula Cn(H2O)n.
* Simple sugars are carbohydrates.
* Simple sugars, disaccharides, and polysaccharides contain only carbon, oxygen, and hydrogen atoms.

All carbohydrates have the general formula Cn(H2O)n.

Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.

Amylose and amylopectin are the principle storage polysaccharides of ________.

* Bacteria
* Plants
* Animals
* Mollusks

Plants

Which is NOT a similarity between glycogen and amylopectin?

* Each is highly branched.
* Each has one reducing end and many nonreducing ends.
* They each contain about 6000 glucose residues.
* Each has branches of similar chain length.

Each has branches of similar chain length.

Chitin is all of the following EXCEPT ________.

* Composed of linear fibrils like cellulose
* Found in plant cell walls
* Found in insect and crustacean shells
* Composed of N-acetylglucosamine subunits

Found in plant cell walls

Which of the following polysaccharide is a predominant constituents of the fibrous parts of plants?

* amylose
* glycogen
* hyaluronic acid
* xylans

xylans

N-linked glycans are attached to proteins through N-acetylglucosamine or N-acetyl galactosamine to the amide side chain of ________.

* Glutamine
* Histidine
* Asparagine
* Arginine

Asparagine

Explain how oseltamivir (Tamiflu) interferes with influenza virus replication.

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The main reasons that glycoproteins are so diverse when compared to other proteoglycans are ________.

* They may contain the same sugars in different combinations and chain lengths
* They are found in both bacterial, plant and animal cells
* They use a single type of glycosidic linkages
* β or α-glycosidic linkages may join various carbon atoms in the sugars

β or α-glycosidic linkages may join various carbon atoms in the sugars

In a DNA double helix an adenine of one strand always pairs with a(n) _____ of the complementary strand, and a guanine of one strand always pairs with a(n) _____ of the complementary strand.

* cytosine ... uracil
* guanine ... adenine
* thymine ... cytosine
* cytosine ... thymine
* uracil ... cytosine

thymine ... cytosine

Which of the following statement about RNA is true?

* Ribozymes are RNA molecules capable of catalyzing chemical reactions.
* All answers are correct.
* Ribose is the five-carbon sugar in RNA.
* RNA contains uracil instead of thymine.

All answers are correct

Purines which are found mainly in both deoxyribonucleotides and ribonucleotides are ________.

* Adenine and guanine
* Thymine and cytosine
* Thymine, cytosine and uracil
* Adenine and thymine

Adenine and guanine

The difference between a nucleoside and a nucleotide is:

* methylated cytosine.
* a 2' —H group.
* a phosphodiester bond.
* the presence of uracil.
* a phosphate group.

a phosphate group.

________ different bases are found in most DNA and RNA molecules.

* 2
* 3
* 4
* 5

5

Uracil is found in most RNA, while ________ is found in most DNA.

* 5-methyluracil
* 3-methyluracil
* 3-methylguanosine
* 5-methylguanosine

5-methyluracil

"Five prime to three prime" description of a DNA strand refers to ________.

* The phosphorylated 5' carbon on one sugar and the 3' carbon on the next sugar
* The location of the hydroxyl groups
* The phosphodiester backbone of DNA
* The phosphorylated 5' carbon at one end, the 3' at the other end

The phosphorylated 5' carbon at one end, the 3' at the other end

In proteins, amino acids are linked by peptide bonds; in polynucleotides, nucleotides are linked by ________.

* 3'-5'phosphodiester bonds
* Phosphoanhydride bonds
* 5'-3'phosphodiester bonds
* Phosphoester bonds

3'-5'phosphodiester bonds

Identify three possible components of a DNA nucleotide.

* cytosine, phosphate group, ribose
* 2-deoxyribose, phosphate group, uracil
* 2-deoxyribose, phosphate group, thymine
* guanine, phosphate group, ribose
* cytidine, phosphate group, ribose
* adenine, phosphate group, ribose

2-deoxyribose, phosphate group, thymine

Which is NOT a difference between RNA and DNA?

* RNA cannot form helices.
* RNA is usually single-stranded; DNA is double-stranded.


* The sugar ring of RNA is more oxidized than that in DNA.
* RNA contains uracil; DNA usually does not.

RNA cannot form helices.

Classify the following molecules as lipids (or lipid components), carbohydrates, or nucleic acids.

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Identify the hydrophobic fatty acid tail region(s) and the phosphate group of the phospholipid shown. Leave labels that do not correspond to either region blank.

Select the hydrophobic region(s) of the glycerophospholipid shown.

Which of the following are characteristics of cholesterol?


1. It is a weakly amphipathic, rigid substance.
2. It is the precursor for all steroidal hormones.
3. It packs neatly with the fatty acid tails of membrane bilayers.
4. It is part of the lipid family of biomolecules.

* Only statements 1, 2, and 4 are characteristics of cholesterol.
* All of the listed statements are characteristics of cholesterol.
* Only statements 1, 3, and 4 are characteristics of cholesterol.
* Only statements 1, 2, and 3 are characteristics of cholesterol.

Only statements 1, 2, and 4 are characteristics of cholesterol.

Glycerophospholipids have ________ heads and long ________ fatty acid tails.

* Polar; hydrophobic
* Hydrophobic; hydrophobic
* Hydrophobic; polar
* Polar; polar

Polar; hydrophobic

Sphingomyelin contains a fatty acid linked by ________ bond and phosphocholine linked via the C-3 hydroxyl group of sphingosine.

* Amide
* Hydrogen
* Sulfhydryl
* Hydroxyl

Amide

Which of the following statements about biological membranes is FALSE?

* Phospholipids often require a specialized enzyme to facilitate movement across (flipping) the membrane.
* The faces of biological membranes are distinct and usually different in both composition and structure.
* Lipids and proteins move laterally at approximately the same rate within the membrane.
* They are composed of a mixture of lipids and proteins in which lateral diffusion of components is possible.

Lipids and proteins move laterally at approximately the same rate within the membrane

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Which two are present in each category?

Please complete the following sentence. \n Membrane rafts are..

* depleted in cholesterol, sphingolipids, and GPI-linked proteins. The bilayer is thinner in the raft domains than in the surrounding membrane.
* depleted in cholesterol, sphingolipids, and GPI-linked proteins. The bilayer is thicker in the raft domains than in the surrounding membrane.
* rich in cholesterol, sphingolipids, and GPI-linked proteins. The bilayer is thinner in the raft domains than in the surrounding membrane.
* rich in cholesterol, sphingolipids, and GPI-linked proteins. The bilayer is thicker in the raft domains than in the surrounding membrane.

rich in cholesterol, sphingolipids, and GPI-linked proteins. The bilayer is thicker in the raft domains than in the surrounding membrane.

Which type of membrane protein might be dissociated from the membrane by changing the pH or the ionic strength?

* Peripheral membrane protein
* Integral membrane protein
* Lipid-anchored membrane protein
* All of the above

Peripheral membrane protein

Biological membranes are most functional when they are in the liquid crystalline state. What is the relationship between the body temperature and the melting temperature of a biological membrane?

* The melting temperature of a membrane is different for every cell type and has nothing to do with the body temperature.
* The melting temperature of a membrane is below the body temperature.
* The melting temperature of a membrane is at exactly the body temperature.
* The melting temperature of a membrane is above the body temperature.

The melting temperature of a membrane is below the body temperature.

Phospholipids can move to different places in the same bilayer by ________.

* Biosynthesis
* Increased diffusion
* Lateral diffusion
* Flippases and floppases

Lateral diffusion

Determination of the tertiary structure of a membrane protein finds that the outer surface is composed primarily of hydrophobic residues. Which conclusion is most likely from this observation?

* The protein must be involved in passive transport.
* The protein can undergo transverse diffusion.
* It is a lipid-anchored membrane protein.
* It is an integral protein.

It is an integral protein.

Which of the following is unlikely to be a characteristic of a membrane protein?

* Largely hydrophobic transmembrane segments
* Symmetric orientation across the membrane
* α-helical membrane-spanning motifs.
* β-sheet membrane-spanning motifs
* Covalently attached lipid moities

Symmetric orientation across the membrane

Which of the following statements describes a membrane protein best?

* The membrane proteins typically have hydrophilic residues located on their surface and hydrophobic residues buried in the interior.
* There must be a bundle of seven α-helices in a membrane protein to have a stable conformation in the membrane.
* Membrane proteins self-insert into the membrane once they are folded.
* The section of a membrane protein that spans the membrane either consists of α-helices or is a β-barrel.

The section of a membrane protein that spans the membrane either consists of α-helices or is a β-barrel.

Cholesterol is an component of mammalian cell membranes. What effect does cholesterol have on the membrane?

* Cholesterol does not change the transition (melting) temperature of membranes, but it broadens the transition between gel state and liquid crystalline state.
* Cholesterol increases the transition (melting) temperature of membranes, but it broadens the transition between gel state and liquid crystalline state
* Cholesterol decreases the transition (melting) temperature of membranes, but it broadens the transition between gel state and liquid crystalline state.
* Cholesterol does not change the transition (melting) temperature of membranes, but it tightens the transition between gel state and liquid crystalline state.

Cholesterol does not change the transition (melting) temperature of membranes, but it broadens the transition between gel state and liquid crystalline state.

Regions on cell membranes called lipid rafts form because ________.

* Membrane proteins form them
* Cholesterol and proteins bind to form them
* Certain membrane protein patches aggregate
* Cholesterol preferentially associates with sphingolipids

Cholesterol preferentially associates with sphingolipids

Which statement is FALSE about lipid-anchored membrane proteins?

* The protein portion that can be removed by treatment with phospholipase most resembles an integral membrane protein.
* Like integral membrane proteins, they are permanently associated with the membrane.
* The covalent link to the membrane can involve the phosphate group of the lipid anchor.
* They are found on either leaflet of the plasma membrane.

The protein portion that can be removed by treatment with phospholipase most resembles an integral membrane protein.

Which statement is FALSE about lipid rafts?

* They are patches of cholesterol associated with sphingolipids.
* They are distributed non-uniformly on the mammal cell surfaces.
* Membrane proteins help maintain the integrity of membrane rafts.
* They occur mostly on the outer mitochondrial membrane.

They occur mostly on the outer mitochondrial membrane.

Which statements about the makeup of biological membranes are true? \n


1. They are composed of bilayers in which the polar head group of the lipid is oriented toward the solvent and the lipophilic tails are pointed inward toward the interior of the membrane.
2. All fatty acids can form micelles.
3. The major classes of lipids that make up membranes include glycerophospholipids, sphingolipids, and glycoglycerolipids.
4. The hydrophobic interior is typically twice as thick as the polar, hydrophilic head groups.

* Statements 1, 2, and 4 are true.
* Statements 1, 2, and 3 are true.
* Statements 2, 3, and 4 are true.
* All of the listed statements are true.

Statements 1, 2, and 4 are true.

Which of following lipids can be a major component of biological membranes?

* Progesterone
* Phosphatidylinositol
* Phosphatidylcholine
* Phosphatidic acid

Phosphatidylcholine

Some of the lipid groups appear similar, but changing a few components significantly alters their biological properties.

Identify similarities and differences between the *general* structures of glycerophospholipids and sphingolipids. If you were to draw the most basic form of each, which pieces are required to define a lipid as either type?

Lipids may be either hydrophobic or ________.

* Amphoteric
* Inorganic
* Hydrophilic
* Amphipathic

Amphipathic

Linolenic acid has cis double bonds with the formula CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH. Write out the abbreviated systematic numbering for this fatty acid.

* 18:3Δ3,6,9
* 18:3Δ9,15,12
* 18:3Δc9,12,15
* 18:3Δ10,12,15

18:3Δc9,12,15

Please finish the sentence. \n Soaps are...

* long-chain fatty acids that are esterified to a long-chain alcohol.
* triacylglycerols
* salts of fatty acids.
* esterified to a glycerol head group

salts of fatty acids.

Trans fatty acids have physical properties like those of ________.

* Unsaturated fatty acids
* ω-3 fatty acids
* Saturated fatty acids
* cis-fatty acids

Saturated fatty acids

Saturated fatty acids are different to unsaturated fatty acids because they ________.

* Have short hydrophobic tails
* Exhibit free rotation about the carbon-carbon bonds in the hydrocarbon tail
* Have no C=C double bonds
* Have an even number of carbon atoms

Have no C=C double bonds

Which of these is NOT a lipid?

* RNA
* phospholipid
* cholesterol
* wax
* steroids

RNA

Which of these is rich in unsaturated fats?

* olive oil
* lard
* a fat that is solid at room temperature
* beef fat
* butter

olive oil is a plant oil, and most plant oils are rich in unsaturated fats

A function of cholesterol that does not harm health is its role _____.

* as a component of animal cell membranes
* the most abundant male sex hormone
* All of cholesterol's effects cause the body harm.
* as the primary female sex hormone
* in calcium and phosphate metabolism

as a component of animal cell membranes

Which of the following statements is FALSE?

* Most types of fat in many animals is used in energy production.
* Some unsaturated fatty acids are liquid at physiological temperatures.
* The longer the chain length of a saturated fatty acid, the higher the melting temperature.
* The difference in melting temperature between a saturated fatty acid and an unsaturated fatty acid with the same chain length is only a few degrees C.

The difference in melting temperature between a saturated fatty acid and an unsaturated fatty acid with the same chain length is only a few degrees C.

In an aqueous environment the hydrocarbon tails of lipids tend to associate by entropy-driven ________ and by Van der Waals interactions.

* Electrostatic effects
* Hydrophobic effects
* Hydrophilic effects
* Covalent effects

Hydrophobic effects

________ are the simplest lipids but they may be a part of or a source of many complex lipids.

* Carbohydrates
* Terpenes
* Fatty acids
* Triglycerols

Fatty acids

The antibody binds to the specific antigen at the binding site formed by...

* the variable domain of the light chain.
* the constant domains of the heavy *and* light chains.
* the variable domain of the heavy chain.
* the variable domains of the light *and* heavy chains.

the variable domains of the light *and* heavy chains.

How many Fab fragments can be produced from proteolytic cleavage of a single IgG molecule?

* 1
* 2
* 3
* 4

2

What physiological effect would you predict from a mutation that replaced the cysteine with serine in the constant part of the immunoglobulin light chain that is involved in disulfide-bond formation with the heavy chain?

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The immunoglobulin domain is a stable scaffold containing two antiparallel β- sheets upon which to display loops that are ________.

* Hyperbolic
* Hypervariable
* Hyperlistic
* Hyperbaric

Hypervariable

Which statements regarding shape and charge complementarity are true? \n


1. Charge complementarity occurs when specific noncovalent binding interactions occur between two contacting surfaces.
2. The charge complementarity refers to noncovalent bonding interactions such as charge-charge, hydrogen-bonding, or van der Waals interactions.
3. Shape complementarity refers to the intimate contact made between an antibody and its target antigen.
4. Shape and charge complementarity explain exclusively the interactions between an antibody and its target antigen.

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* Only statements 2, 3, and 4 are true.
* Only statements 1, 2, and 3 are true.
* All of the listed statements are true.
* Only statements 1, 2, and 4 are true.

Only statements 1, 2, and 3 are true.

The specific interaction between an antibody and antigen occurs by virtue of both shape and ________ complementarity. \n

* Charge
* Structure
* Size
* Binding affinity

Charge

The hypervariable loops on the antibody that determine the binding to its antigen is called ________.

* Constant region
* Variable region
* Leucine region
* Complementarity determining regions

Complementarity determining regions

Which immune cells is virulent to HIV?

* T cells
* B cells
* Competent cells
* MHC

T cells

Which statements about immunoconjugates are true? \n


1. Immunoconjugates are hybrid drugs that link a cytotoxic agent to an antibody.
2. The cytotoxic agent is usually attached to the constant region of the antibody.
3. The antibody has a high affinity to its target.
4. Immunoconjugates are in clinical trials, but none has been approved yet.

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* All answers are right
* 1, 2, and 3
* 2 and 3
* 1 and 2

1, 2, and 3

Describe the profile you would expect for a biological catalyst. Complete the sentences to explain why an enzyme is different than an inorganic catalyst.

**Match the words in the left column to the appropriate blanks in the sentences on the right.**

Define what is meant by the following species.

**Match the species in the left column to the appropriate blanks in the sentences on the right.**

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Label the missing components on the diagram below.

Complete the sentences to explain why is it important that ESES is not too much more stable than E+SE+S.  Determine how this is related to the lock and key versus induced fit models of enzyme function.

Enzymes can accelerate reactions by ________.

* Positioning a metal ion to bind only to the substrate
* Raising the energy for activation
* Preventing the removal or addition of protons
* Binding a substrate or substrates

Binding a substrate or substrates

In a favorable reaction, the free energy of the products is ________ the free energy of the reactants. \n

* Less than
* Greater than
* Same as
* Has no bearing on

Less than

Catalysts affect the ________ of a chemical reaction.

* Energy of activation to the transition state
* Energy of product formation
* Energy of substrate formation
* Thermodynamics

Energy of activation to the transition state

In a first order enzyme-catalyzed reaction, the velocity of the reaction is proportional to the ________, while in a zero order enzyme-catalyzed reaction, the velocity of the reaction is proportional to the ________.

* Speed of the reaction; concentration of substrate
* Concentration of substrate; amount of enzyme
* Amount of enzyme; concentration of substrate
* Concentration of substrate; speed of the reaction

Concentration of substrate; amount of enzyme

The main difference between chemical and enzyme kinetics is that ________.

* Enzyme reactions depend on the concentration of the enzyme and its recycling
* Enzyme reactions are altered by pH
* The rate constant for the formation of products is k2
* Enzyme reactions depend on the concentration of the substrate

Enzyme reactions depend on the concentration of the enzyme and its recycling

Consider the following reaction: \n A → B \n Which of the following statements about this reaction are correct? \n


1. If you double the concentration of reagent A, you will double the rate.
2. The reaction rate (or velocity) is dependent only on the concentration of A.
3. The units for the first-order rate constant are M s–1.
4. A plot of the log\[A\] versus time yields an inverse hyperbola.

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* Only statements 1 and 2 are correct.
* Only statements 2 and 4 are correct.
* Only statements 1, 3, and 4 are correct.
* Only statements 1, 2, and 3 are correct.

Only statements 1 and 2 are correct.

Show that the half-life for a first-order reaction is inversely proportional to the rate constant, and determine the constant of proportionality.

**Match the items in the left column to the appropriate blanks in the sentences and the equation on the right.**

In general, enzymes are what kinds of molecules?

* proteins
* minerals
* nucleic acids
* lipids
* carbohydrates

proteins

Enzymes work by _____.

* adding energy to a reaction
* adding a phosphate group to a reactant
* decreasing the potential energy difference between reactant and product
* increasing the potential energy difference between reactant and product
* reducing EA

reducing EA

An enzyme _____.

* can bind to nearly any molecule
* increases the EA of a reaction
* is a source of energy for endergonic reactions
* is an organic catalyst
* is a inorganic catalyst

is an organic catalyst

What name is given to the reactants in an enzymatically catalyzed reaction?

* products
* EA
* reactors
* substrate
* active sites

substrate