527 exam 1 material

Glutamine (Q)

Lysine (K)

Aspartic Acid (D)

C. N-R-D-E-Q-G-T-Y-W

A small peptide has the following sequence: Asparagine-Arginine-Aspartate-Glutamate-Glutamine-Glycine-Threonine-Tyrosine-Tryptophan Which of the following is the correct sequence using the one-letter abbreviations for amino acids?

A. R-N-A-E-Q-G-T-Y-W

B. N-R-D-E-Q-G-W-Y-T

C. N-R-D-E-Q-G-T-Y-W

D. A-R-D-Q-E-G-T-Y-W

C. -1

You have discovered a new amino acid. It is an alpha-amino acid and has a side chain containing a terminal carboxylic acid group with pKa =6. The net charge of this amino acid at physiological pH will be:

A. +1

B. 0

C. -1

D. +2

Glutamic Acid (E)

Threonine (T)

Proline (P)

Leucine (L)

Arginine (R)

B. H bonding between amino acid backbone atoms

What type of bonding is critical for stabilizing protein alpha helices?

A. H bonding between amino acid side chain atoms

B. H bonding between amino acid backbone atoms

C. Disulfide bonds between cysteines

D. Charge-Charge interactions between positively and negatively charged side chains

Anti- parallel beta sheet

Option A

D. negative heterotrophic allosteric effector

Select the term that best applies to the following sentence: Carbon dioxide is a __________ of hemoglobin

A. competitive inhibitor B. positive heterotrophic allosteric effector

C. reducing agent

D. negative heterotrophic allosteric effector

B. adopt multiple conformations that can be stabilized by different ligands

G protein-coupled receptors are globular proteins that can produce multiple downstream signaling events because they:

A. are structurally important components of the plasma membrane

B. adopt multiple conformations that can be stabilized by different ligands

C. form long polymers D. are affected by cooperative binding of ligands

C. α-helices dimerize via hydrophobic interactions that are further cross-linked by disulfide bonds between cysteine residues

Which statement best explains the mechanical strength and insolubility of αkeratin in hair and nails? A. Repeating G-X-Y triplets form triple helices stabilized by hydroxyproline

B. Parallel β-sheets stack via extensive hydrogen bonding between strands

C. α-helices dimerize via hydrophobic interactions that are further cross-linked by disulfide bonds between cysteine residues

D. Extensive O-glycosylation of serine/threonine increases water binding

Aldopentose

Aldohexose

Ketohexose

A. Sucrose contains an α-1, β-2 glycosidic bond while isomaltulose contains an α-1,6 glycosidic bond, meaning the process of digesting the two sugars is different

Valine (V)

Methionine (M)

tryptophan (W)

D. G (glycine)

A beta-carbon is present in every proteinogenic amino acid except:

A. P

B. A

C. I

D. G

B. 4

You have discovered a new amino acid. It is an alpha-amino acid and has a side chain containing a terminal carboxylic acid group with pKa =6. The pI of this amino acid is approximately:

A. 8

B. 4

C. 5

D. 2

D. They form between the alpha carbon and amino group of amino acids

Which of the following is not a property of peptide bonds:

A. They have partial double bond characteristics

B. They are planar

C. The can exist in cis and trans forms

D. They form between the alpha carbon and amino group of amino acids

A (the graph on the left)

Histidine (H)

B. Secondary

"The local arrangement of amino acids in space" is a broad description of what level of protein structure?

A. Primary

B. Secondary

C. Tertiary

D. Quaternary

A. L

The stereochemical form of amino acids used by human beings is:

A. L

B. D

C. Both

D. Neither

oxidized disulfide bone

D. pH 8

What is the approximate pI of histidine?

A. pH 2

B. pH 4

C. pH 6

D. pH 8

Amino Acid U

C. Globular proteins are more conformationally dynamic than fibrous proteins

Which of the following properties applies to Globular proteins as opposed to Fibrous proteins? A. Globular proteins are elongated compared to fibrous proteins B. Globular proteins tend to be less soluble than fibrous proteins C. Globular proteins are more conformationally dynamic than fibrous proteins D. Globular proteins are extensively and heavily crosslinked compared to fibrous proteins

Phenylalanine (F)

Isoleucine (I)

Tyrosine (Y)

Serine (S)

Asparagine (N)

Histidine (H)

Cysteine (C)

Glycine (G)

Alanine (A)

C. 0

At physiological pH (7.4), what is the net charge of the amino acid H?

A. +2

B. +1

C. 0

D. -1

ECGK

C. 9

You have discovered a new amino acid. It is an alpha-amino acid and has a side chain containing a terminal amino group with pKa =8. The pI of this amino acid is approximately:

A. 8

B. 4

C. 9

D. 2

D. The Histidine carries a net positive charge at pH 2 but no net charge at pH 7.4

You are studying a protein found in stomach acid (pH 2). The protein has enzymatic functions that are reliant on a charged Histidine residue in the protein. Why might this protein not be functional at pH 7.4?

A. The Histidine carries a net positive charge at pH 2 but a negative charge at pH 7.4

B. The Histidine carries a net negative charge at pH 2 but a positive charge at pH 7.4

C. The protein is denatured at pH 7.4

D. The Histidine carries a net positive charge at pH 2 but no net charge at pH 7.4

D. E6 to V

Which of the following mutations in hemoglobin is an example of a change that would result in sickle cell anemia

A. I9 to V

B. A14 to I

C. E6 to D

D. E6 to V

C. As one molecule of oxygen binds Hb, it induces conformational changes in Hb subunits that make it easier for another molecule of oxygen to bind

Which of the following statements provides the best description of oxygen binding to hemoglobin (Hb):

A. Hb always exists in a relaxed form and allows four oxygen molecules to bind simultaneously B. Each of the four Hb subunits binds oxygen independently and without affecting the other subunits

C. As one molecule of oxygen binds Hb, it induces conformational changes in Hb subunits that make it easier for another molecule of oxygen to bind

D. The affinity of Hb for oxygen is constant

A. higher

Select the best option to complete the following sentence" Myoglobin has a(n) __________ affinity for oxygen compared to hemoglobin

A. higher

B. lower

C. equal

D. variable

C. triple stranded left handed helices

Collagen does not form a traditional alpha-helical secondary structure. Instead it adopts what structure? A. anti-parallel beta-sheets

B. parallel beta-sheets C. triple stranded left handed helices

D. unstructured loop

D. hydroxyproline

Select the option that best applies to the sentence below: Collagen is rich in __________, a property that lends itself to extensive hydrogen bonding between collagen chains.

A. proline

B. glycine

C. leucine

D. hydroxyproline

C. Elastin

Desmosine is crucial to the function of which fibrous protein?

A. Collagen

B. Keratin

C. Elastin

D. Actin

B. 3.6

An alpha-helix is an example of secondary protein structure. On average, how many amino acids per helical turn are there in an alpha helix?

A. 1.6

B. 3.6

C. 5.6

D. 7.6

B. two heavy chains and two light chains

The structure of an antibody is made up of: A. one heavy and one light chain

B. two heavy chains and two light chains

C. three heavy chains and three variable light chains

D. One heavy chain and two light chains

C. Immunoglobulin

You are given a sample to analyze by SDS-PAGE. The sample contains a single type of protein. It is in a solution containing saline, SDS and 2-mercaptoethanol. The sample does not contain an enzyme. You run the sample using SDS-PAGE and perform the relevant analysis. The result you get is two bands or lines on the gel: the first band has a molecular weight around 50 kDa and is heavier than the second band which has a molecular weight of around 25 kDa. What type of protein might be contained in this sample?

A. Collagen

B. Hemoglobin

C. Immunoglobulin

D. Actin

B. NMR can capture multiple protein conformations

One advantage of NMR vs X-ray crystallography when determining protein structure is:

A. NMR has higher resolution

B. NMR can capture multiple protein conformations

C. NMR has solved the majority of protein structures

D. NMR can resolve membrane protein structure easily

A. X-ray crystallography often provides higher resolution

One advantage of X-ray crystallography over NMR in solving protein structures is:

A. X-ray crystallography often provides higher resolution

B. X-ray crystallography is performed in solution C. X-ray crystallography is more physiologically relevant

D. X-ray crystallography provides multiple snapshots of protein conformations

B. Larger molecules elute first because they are excluded from the pores and travel the shortest distance through the column

In size-exclusion chromatography, which statement best describes the elution order of molecules from the column

A. Smaller molecules elute first because they can access more of the porous volume within the stationary phase, increasing their path length

B. Larger molecules elute first because they are excluded from the pores and travel the shortest distance through the column

C. Molecules elute based on their chemical affinity for the stationary phase

D. Molecules elute based on the size of their chemical charge and interaction with the stationary phase

Graph D

A. A reduction in 2,3-bisphosphoglycerate in red blood cells will increase the affinity of hemoglobin for oxygen, making it more difficult for red blood cells to off load sufficient oxygen in tissues, so more red blood cells are needed.

Erythrocytosis is a pathological condition characterized by a higher than normal concentration of red blood cells in patients. A rare genetic cause of this disease is a mutation in the enzyme Bisphosphoglycerate mutase, which is the enzyme responsible for production of 2,3-bisphosphoglycerate. The mutation substitutes an arginine for histidine in the active site and renders the enzyme inactive. This leads to a significant decrease in the amount of 2,3-bisphosphoglycerate in red blood cells, and an increase in the amount of red blood cells to cope with this. Why might the body produce more red blood cells in response to a reduction in 2,3-bisphosphoglycerate levels?

A. A reduction in 2,3-bisphosphoglycerate in red blood cells will increase the affinity of hemoglobin for oxygen, making it more difficult for red blood cells to off load sufficient oxygen in tissues, so more red blood cells are needed.

B. A reduction in 2,3-bisphosphoglycerate in red blood cells will decrease the affinity of hemoglobin for oxygen, making it more difficult for red blood cells to off load sufficient oxygen in tissues, so more red blood cells are needed.

C. A reduction in 2,3-bisphosphoglycerate in red blood cells will decrease the affinity of myoglobin for oxygen, making it more difficult for red blood cells to off load sufficient oxygen in tissues, so more red blood cells are needed.

D. A reduction in 2,3-bisphosphoglycerate in red blood cells will increase the affinity of myoglobin for oxygen, making it more difficult for red blood cells to off load sufficient oxygen in tissues, so more red blood cells are needed

D. S to G

C. Lipid 2 is unsaturated with cis-double bonds

Two newly discovered fatty acids each have 20 carbon molecules in their tails. Lipid 1 has a higher melting temperature than Lipid 2. Which of the following options would best describe why this might be the case?

A. Lipid 2 is unsaturated with trans-double bonds

B. Lipid 1 is unsaturated with cis-double bonds

C. Lipid 2 is unsaturated with cis-double bonds

D. Lipid 2 is longer than lipid 1

C. Both

Steroids can have which of the following effects?

A. Genomic

B. Non-genomic

C. Both

D. Neither

A. 1'

Nucleotides are bonded to a nitrogenous base via a glycosidic bond to which carbon in the sugar backbone?

A. 1'

B. 2'

C. 3'

D. 5'

Glycerophospholipid

Section A

Prostaglandin

B. A stretch of K &R amino acids in the protein structure

A soluble protein that you are studying localizes to the inner leaflet of the plasma membrane in cells. You treat the cells with an inhibitor that blocks enzymes from adding lipid groups to protein. Your protein of interest still localizes to the membrane. What is the most likely property of the protein that facilitates this interaction?

A. A stretch of E &D amino acids in the protein structure

B. A stretch of K &R amino acids in the protein structure

C. The protein can circumvent the inhibitor and still be modified with a lipid addition

D. The protein is a transmembrane protein

B. Targets protein to localize at the cell membrane

A lipid modification is added to a protein, in a manner similar to the addition of a farnesyl group to the oncoprotein K-Ras. What is the effect of this modification?

A. Causes protein degradation

B. Targets protein to localize at the cell membrane

C. Causes protein to form higher order structures

D. Makes proteins available for transport around the body

A. Size exclusion chromatography

Which of the following methods separates protein based on only size?

A. Size exclusion chromatography

B. Ion exchange chromatography

C. Affinity chromatography

D. Native-PAGE

B. False

Lipids form form large covalent polymers like proteins, nucleic acids

A. True

B. False

B. Glucose

Which of the following is not a component of glycerophospholipids?

A. Glycerol

B. Glucose

C. Phosphate

D. Fatty acid

B. Phosphatidylethanolamine

Which of the following glycerophospholipids has no net charge/is neutral at pH 7.4?

A. Phosphatidic acid

B. Phosphatidylethanolamine

C. Phosphatidylserine

D. Phosphatidylinositol

B. Negative

Lipids with what charge tend to be more concentrated in the inner leaflet of the plasma membrane?

A. Positive

B. Negative

C. No charge

C. Unequal

The distribution of different types of lipids is _________ between the outer and inner leaflets of the plasma membrane?

A. Even

B. Equal

C. Unequal

D. None of the above

C. Cone

A newly discovered phospholipid has a physically small polar head group similar to phosphatidic acid, and two unsaturated hydrocarbon tails. What shape is this lipid likely to adopt?

A. Cylindrical

B. Inverted cone

C. Cone

D. None of the above

B. Lipid 1 is unsaturated with cis-double bonds

Two newly discovered fatty acids each have 20 carbon molecules in their tails. Lipid 1 has a lower melting temperature than Lipid 2. Which of the following options would best describe why this might be the case?

A. Lipid 2 is unsaturated with trans-double bonds

B. Lipid 1 is unsaturated with cis-double bonds

C. Lipid 2 is unsaturated with cis-double bonds

D. Lipid 2 is longer than lipid 1

C. HDL

Which of the following Lipoproteins transports cholesterol accumulating in tissues to the liver?

A. Chylomicron

B. LDL

C. HDL

D. VLDL

A. Sphingolipids

You have extracted and isolated an unknown lipid from the dermis of patients with atopic dermatitis. This lipid contains a backbone with at least two hydroxyl groups, connected to a fatty acid tail via an amide bond. What family of lipids does this likely belong to?

A. Sphingolipids

B. Steroids

C. Phospholipids

D. Prostaglandins

D. All of the above

Which of the following vitamins is fat soluble?

A. Vitamin A

B. Vitamin D

C. Vitamin K

D. All of the above

B. I, F, V and A

Apolipoproteins are protein components of lipoproteins. What amino acids might you expect to find in the lipid binding portion of apolipoproteins? A. E &D

B. I, F, V and A

C. K and R

D. None of the above

B. -1

At physiological pH (7.4), what is the net charge of the amino acid E?

A. -2

B. -1

C. 0

D. +1

C. Valine

D. Phenylalanine

F. Isoleucine

G. Alanine

I. Leucine

Which of the following amino acids are hydrophobic? A. Tyrosine

B. Serine

C. Valine

D. Phenylalanine

E. Glutamate

F. Isoleucine

G. Alanine

H. Lysine

I. Leucine

Option A

Option D

B. S

O-linked glycosylation of proteins occurs on which of the following amino acid residues?

A. N

B. S

C. C

D. K

Option A

B. D

In humans, which stereoisomer of sugars if generally preferred?

A. L

B. D

C. Both

D. Neither

A. Glycosidic

In polymers of monosaccharides, individual monomers are linked by what type of bond?

A. Glycosidic

B. Phosphodiester

C. Hydrogen

D. Ester

C. Aldehyde

You have discovered a new monosaccharide. It gives a positive result when subjected to Tollen's and Benedict's tests. What functional group does this new sugar possess?

A. Sulfhydryl

B. Amine

C. Aldehyde

D. Phosphate

Beta-D-Glucose

C. 4

Glucose is a 6 carbon sugar. How many stereocenters does LINEAR glucose have?

A. 2

B. 3

C. 4

D. 5

A. Aldehydes and Ketones

Carbohydrates contain two important functional groups that can tautomerize when catalyzed to do so by enzymes. What are the two functional groups?

A. Aldehydes and Ketones

B. Amines and Ketones

C. Amines and Aldehydes

D. Tertiary alcohols and Ketones

D-Fructose

D-Glucose

C. No because cooperativity is dependent on the conformation of each monomeric unit affecting the next subunit in the tetramer

Hemoglobin is a tetrameric protein that binds to four Oxygen molecules via a porphorin ring present in each hemoglobin monomer. Hemoglobin binds to oxygen in a cooperative manner. If Hemoglobin were a monomeric protein i.e. only one subunit not four, do you think it would still act in a cooperative manner?

A. Yes because each monomer has a porphorin ring that binds to oxygen

B. Yes because the amino acid sequence of the monomer would be the same as the monomers in the tetrameric form

C. No because cooperativity is dependent on the conformation of each monomeric unit affecting the next subunit in the tetramer

D. No because 2,3-bisphosphoglycerate would not bind to monomers.

C. Q-G-E-T-Y-W-N-R-D

A small peptide has the following sequence: Glutamine-Glycine-Glutamate-Threonine-Tyrosine-Tryptophan-Asparagine-Arginine-Aspartate Which of the following is the correct sequence using the one-letter abbreviations for amino acids?

A. Q-G-E-T-Y-W-R-N-A

B. E-G-Q-T-Y-W-R-N-D

C. Q-G-E-T-Y-W-N-R-D

D. Q-E-G-T-Y-W-N-R-D

L

D-Ribose