exam 2 (lec. 7-12) Flashcards
How many methods are commonly used in protein purification?
A. 0
B. 1
C. 2
D. 3
D. 3
I have a dimer of 20 kDa protein. What size permeable membrane should I use?
A. 10 kDa
B. 15 kDa
C. 30 kDa
D. 50 kDa
B. 15 kDa
Which is NOT an affinity purification type residue?
A. Antibody
B. Cationic
C. DNA
D. Ligand
B. Cationic
What do larger spots represent in 2D gels?
Larger Proteins
The primary sequence of protein is the:
A. Amino Acid code
B. Helices and sheets
C. Protein structure
D. Protein Complex
Amino Acid code
Two enzymes were used to cleave the fragment and the pieces generated were TS, ACGTY, and KANRVW or ANR, VTWS, and ACGTYK. What is the starting fragment?
A. ACGTYKVWTSPNR
B. ACGTYKANRVWTS
C. KANRVWACGTYTS
D. TSACGTYKANRVW
B. ACGTYKANRVWTS
Which amino acid is the least common:
A. Met
B. Phe
C. Ser
D. Val
A. Met
Which proteases were used to generate the previous fragments?
A. Chymotrypsin and Pepsin
B. Thermolysin and Pepsin
C. Trypsin and Chymotrypsin
D. Trypsin and Endopeptidase V8
C. Trypsin and Chymotrypsin
Can you cleave a protein with trypsin and identify the protein if previously known?
A. True
B. False
A. True
Given the genetic code and the number of known proteins, how many amino acids must you sequence from the N-terminal to identify a protein?
A. 1
B. 10
C. 100
D. The whole protein
B. 10
An anion exchange resin purifies a protein based largely on:
A. Hydrophobicity
B. Negative Charge
C. Positive Charge
D. Size
B. Negative Charge
Given the following trypsin fragments YR, QMK, FAMK, and GMDIK and the CNBR fragments of K, KFAM, YRGM, and DIKQM, what is the starting fragment?
A. FAMKQMKYRGMDIK
B. KFAMYRGMDKQMK
C. GMDIKFAMKYRQMK
D. YRGMDIKQMKFAMK
D. YRGMDIKQMKFAMK
The sickle cell mutation is an example of what type of protein mutation:
A. Conserved
B. Non-conserved
C. Silent mutatino
D. Cannot tell
B. Non-Conserved
Which PAM score is more closely related?
A. 5
B. 25
C. 40
D. 50
5
Do genes which have been duplicated have the same general function?
The same role in the organism?
A. No and No
B. No and Yes
C. Yes and No
D. Yes and Yes
C. Yes and No
The homologous A and B domain of the catalytic subunit likely occurred because of:
GENE DUPLICATION
All the proteins represented come from mammals.
A. True
B. False
B. False
In the previous graph, the further away the vertical line is from the protein the:
A. more related the protein is
B. the more unrelated the protein is
C. does not say anything about relatedness
D. the more homology a protein has
B. the more unrelated the protein is
The more complete the grey line is the more ___ an amino acid is.
A. conserved
B. hydrophobic
C. Acidic
D. structurally important
A. Conserved
The Ramachandran plot shows what of protein?
Structure/Angles/Steric Hindrance
Protein alpha helices by and large are:
A. composed of prolines
B. left-handed
C. right-handed
D. all have consistent distances between AA’s
C. Right-handed
Beta sheets
a. have a distance of 7 angstroms between residues
b. can be parallel or anti paralle
c. amino acid sidechains alternate location
d. all of the above statements are true
d. all of the above statements are true
Loops in proteins are:
a. the least mutated areas
b. always rigid
c. flexible
d. never random coils
c. Flexible
Given the Chou-Fasman chart, Tyr is most likely to be:
a. found in alpha helix
b. found in a beta sheet
c. both structures about equally
d. not enough information
b. Found in a beta sheet
Given the Chou-Fasman chart, the sequence EIMALQDP is most likely a(n):
a. alpha helix
b. beta sheet
c. random coil
d. cannot tell
a. Alpha helix
The amino acids (EIMALQDP) would likely be found in which region of the plot:
a. 1
b. 2
c. 3
d. 4
b. 2
What amino acid would likely be found in region 4?
a. Gly
b. Glu
C. Pro
D. Tyr
A. Gly
Where is keratin structure NOT found?
A. Bone
B. Feather
C. Hair
D. Nails
A. Bone
Which amino acid is NOT part of silk?
A. Ala
B. Gly
C. Phe
D. Ser
C. Phe
Which modified amino acid is found in collagen?
A. Gly
B. Glu
C. Pro
D. Phe
C. Pro
Which vitamin is necessary for modification of proline?
A. Vitamin A
B. Vitamin B
C. Vitamin C
D. Vitamin D
C. Vitamin C
Which group does the following amino acid, Aspartic Acid, belong to?
Polar
Which structural protein is found as beta sheet?
A. Collagen
B. Keratin
C. Silk
D. None of the above
C. Silk
For amino acids with neutral (non-ionizing) R groups, at any pH below the pI of the the amino acid, the population of amino acids in solution will:
have a net POSITIVE charge
What is the primary function of SDS in SDS-PAGE?
A. to visualize proteins under UV
B. To denature proteins and impart a negative charge
C. To impart a uniform positive charge
D. None of the above
E. To provide conducitivity for the gel
B. To denature proteins and impart a negative charge
Given pK1 = 2.35 and pK2 = 9.87, select its correct charge at pH 13.
-1
pH > pka’s
if pH<pka’s, +1
if pk1<pH<pk2, 0
pH = pk1, 1/2
pH = pk2, -1/2
Two dimensional electrophoresis is a combination of which two techniques?
A. Ion-exchange chromatography and SDS-Page
B. Isoelectric focusing and affinity chromatography
C. Isoelectric focusing and ion-exchange chromatography
D. Affinity and SDS-PAGE
E. Isoelectric focusing and SDS-Page
E. Isoelectric focusing and SDS-PAGE
Most proteins are purified using characteristics such as:
A. Size
B. Solubility
C. Charge
D. Specific binding affinity
E. All of the above
E. All of the above
The secondary structure of a protein is primarily maintained by:
A. Hydrogen bonds
B. All of the above
C. Van der Waals
D. Hydrophobic bonds
E. Ionic Bonds
A. Hydrogen Bonds
The backbone of a protein has an alternating ____ sequence.
C-C-N
In what order would the amino acids Arg, His, and Leu be eluted from a carboxymethyl column at pH 6?
Leu, His, Arg
In what order would Glu, Lys, and Val be eluted from a diethyl aminoethyl (positively charged resin) column at pH8?
Lys, Val, Glu
KVE
The quaternary structure of hemoglobin has how many peptides?
a. 1
b. 2
c. 3
d. 4
d. 4
2 alpha and 2 beta subunits
In order to follow the purity of an enzyme, you need:
a. a method to measure the activity
b. an antibody against the enzyme
c. to be able to run SDS/Page
d. None of the above
a. a method to measure the activity
Which type of protein purification is, generally, the most expensive
a. affinity purification
b. ion exchange
c. phase separation
d. size exclusion
Affinity purification
The primary sequence of a protein is
a. the local special alignment of amino acids without regards to side chains
b. the linear sequence of amino acids
c. the 3-dimensional structure of the peptide
c. 2 or more peptide chains associated with a protein
The linear sequence of amino acids (AA code)
In order to purify a protein, you:
a. must use an affinity column
b. must protect against denaturation of the protein
c. must allow cleavage of the protein by proteases
d. all of the above
b.must protect against denaturation of the protein
For protein isolation, you need:
a. a good source of protein
b. a sensitive detection method
c. both the above
d. neither the above
c. both the above
Which is a strategy of purification?
a. charge
b. polarity
c. solubility
d. all of the above
d. all of the above
Which is NOT a type of chromatography?
a. liquid
b. gas
c. solid state
d. affinity
c. Solid State
The first protein sequenced was
a. myoglobin
b. hemoglobin
c. insulin
d. beta galactosidase
c. INSULIN
think pig OINK!
What is the max. number of amino acids that can be sequenced using Edman degradation?
a. 25
b. 50
c. 75
d. 100
b. 50!
Mr.Edmand is 50 yrs old
Which is the least common amino acid in proteins?
a. Ala
b. Gly
c. Glu
d. Trp
d. TRP!
tripping is unlikely in sneakers
Which enzyme will cleave near a Tyr residue?
a. chymotrypsin
b. endopeptidase v8
c. thermolysin
d. trypsin
Chymotrypsin
Residues that chymotrypsin cleaves: Phe, Trp, Tyr
In sickle cell anemia, the normal hemoglobin’s amino acid of Glu is mutated to ___
a. Asp
b. Cys
c. Phe
d. Val
Val
Sickle cell anemia serves a protective role against malaria which normally occurs in:
a. Congo
b. England
c. Germany
d. South Africa
a. Congo
Which drink was historically used to combat malaria?
a. beer
b. gin and tonic
c. jack daniels and coke
d. tequila and lime
Gin and tonic
Myoglobin’s main role is to:
a. cleave proteins
b. generate ATP
c. store oxygen
d. transport oxygen throughout the body
Store oxygen
DNA mutation rates are:
a. constant
b. dependent on the organism’s lifespan
c. depend on the size of the genome
d. random
a. constant
Protein families are:
a. composed of homologous proteins
b. have mutations to key structural amino acids
c. not related evolutionarily
d. show mutations to enzymatically important residues
a. composed of homologous proteins
In a phylogenetic tree, each branch represents:
a. common ancestors
b. conservative mutations
c. non conservative mutations
d. related proteins
a. common ancestors
Which is a conservative mutation?
a. Ala to Phe
b. Glu to Asp
c. Leu to Lys
d. Thr to Trp
b. Glu to Asp
Evolution through gene duplication:
a. produce related proteins
b. once duplicated, individual genes can mutate into separate genes
c. result in proteins which evolve with different properties
d. all of the above
d. all of the above
Protein mutation rates:
a. are constant
b. differ bc of varying rates of DNA mutations
c. differ bc of differing RNA mutation rates
d. vary due to mutations to necessary amino acids
d. vary due to mutations to necessary amino acids
Which region of the Ramachandran plot is indicative of a beta sheet?
a. 1
b. 2
c. 3
d. 4
a. 1
An alpha helix has how many amino acids per turn?
a. 2.2
b. 3
c. 3.6
d. 4
c. 3.6
A left-handed helix is compromised mostly of:
a. Ala
b. Phe
c. Pro
d. Thr
Pro
Pro/left = liberal
In the NM nomenclature for helices, the M stands for:
a. the # of amino acids in a turn
b. the pitch of the helix
c. The number of atoms that complete the cyclic system that is enclosed by the hydrogen bond
d. none of the above
c. The number of atoms that complete the cyclic system that is enclosed by the hydrogen bond
The repeat distance in beta sheets is __ angstroms
a. 2
b. 3.5
c. 7
d. 10
c. 7
An anti-parallel beta sheet ___ stable than a parallel beta sheet
a. has the same stability as
b. is equally as
c. is less
d. is more
d. is more
Which is composed of triple left-handed helices forming a right-handed coil?
a. collagen
b. keratin
c. hemoglobin
d. silk
a. Collagen
Which has a high content of proline?
a. collagen
b. keratin
c. myoglobin
d. silk
a. collagen
Bone tendon contains which of the following:
a. collagen
b. keratin
c. myoglobin
d. silk
a. Collagen
British sailors were given lime juice in the age of sail to prevent which disease?
Scurvy
Which region of the diffraction pattern gives the highest resolution in crystallography?
a. 1
b. 2
c. 3
d. 4
1 (outermost region)
Which is NOT an advantage of crystallography?
a. can obtain the structure of large macromolecules and complexes
b. can get the position of AA sidechains
c. Determined structure is dynamic
d. can get to 4.5 angstroms resolution
c. Determined structure is dynamic
Which protein denaturing method associates with nonpolar amino acids blocking water interactions?
a. heat
b. detergents
c. pH
d. Chaotropes
b. Detergents
Which method can solve the phase problem of crystallography?
a. Isomorphous replacement
b. Direct methods
c. Molecular replacement
d. all of the above
d. all of the above
There is an estimate of about how many different folding motifs for proteins:
a. 50
b. 100
c. 500
d. 1000
1000
Which amino acid is the most hydrophobic?
a. Asp
b. Gly
c. His
d. Val
d. Val
Val, she’s scared of water
The GroESL (chaperonin) system uses how many ATP when refolding a protein?
a. 2
b. 10
c. 14
d. 28
14
Which of the following is true regarding SDS-PAGE gels?
a. the proteins that run on the gel have a negative charge
b. the proteins are separated according to molecular weight
c. the proteins run on the gel are in their native conformation
d. two of the above (a and b)
d. two of the above (a and b)
What is required for hydroxyproline formation?
a. Thiamin
b. Cobalamin
c. Ascorbic Acid
d. Nicotinic Acid
c. Ascorbic Acid
What is true of peptide bonds?
a. most assume a cis conformation
b. they have ~60% double bond character
c. they are planar
d. none of the above
They are planar
Which amino acid has the highest propensity for a helical conformation?
a. P
b. G
c. C
d. A
P(Proline)
Which amino acid has the highest propensity for beta sheet conformation?
a. E
b. V
c. P
d. S
E (Glutamate)
What advantage(s) does NMR provide over X-ray crystallography in characterizing protein structure?
a. NMR can be used for proteins that don’t crystallize
b. NMR can be used for proteins over 200 kDa
c. Both A and B
d. None of the above
a. NMR can be used for proteins that don’t crystallize
Which is composed of mostly beta sheets?
a. Collagen
b. Keratin
c. Myoglobin
d. Silk
d. Silk
think how strong silk is and structure of beta sheets
Ni2+ columns bonds to poly histidine residue tags placed onto a protein for purification, what kind of purification is this considered?
a. Affinity purification
b. Ion exchange
c. Phase separation
d. size exclusion
a. Affinity purification
You have a protein with a pI of 9. You are running at pH of 7.2. Which would be the best type of resin should you use to purify it?
a. anion exchange resin
b. cation exchange resin
c. Ni2+ resin
d. size exclusion resin
b. Cation Exchange Resin
Which amino acid would Trypsin cleave at:
a. Arg
b. Leu
c. Met
d. Phe
Arg
Which protein denaturing method solubilizes hydrophobic region of proteins?
a. heat
b. detergents
c. pH
d. chaotropes
Chaotropes
Given the following chart and an amino acid sequence of RCIVWRMQTY, what is the most likely secondary structure to form?
Alpha helix
Which amino acid is least likely to be found on the exterior of the protein?
a. Ser
b. Lys
c. Met
d. Asn
Met
What do vertical grey lines denote about the amino acid position? The amino acid position may be important:
a. enzymatic
b. structurally
c. for binding small molecules
d. all of the above
d. all of the above
Which filament protein has crosslinked Lys?
a. collagen
b. keratin
c. silk
d. none of the above
Collagen
Which protein is unable to expand due to its structure?
a. collagen
b. keratin
c. silk
d. none of the above
Silk
Which protein forms bone?
a. collagen
b. keratin
c. silk
d. none of the above
Collagen
Which is a drawback of crystallography?
a. You need to find crystallization conditions
b. The structure is static
c. You have to determine the phase of the crystal
d. All of the above
d. All of the above
What is an advantage compared to x-ray crystallography?
a. able to easily determine structure of 20kDa proteins
b. Able to determine the structure of membrane proteins
c. Able to get resolutions at 1.5 angstroms
d. able to get dynamic structures
Able to determine the structure of membrane proteins
An advantage of NMR is:
a. large proteins structure can be determined
b. the structure is dynamic
c. all side chains are well defined
d. proteins must be labeled
b. The structure is dynamic
Which is a beta hairpin turn?
a. A
b. B
c. C
d. Not shown
B (figure 6.8b)
consists of antiparallel strands connected by relatively tight reverse turns
About how many folds do half the proteins fit into?
A. 30
B. 100
C. 300
D. 1000
30
A protein’s structure is determined by its:
a. bound molecules
b. enzymatic activity
c. primary structure
d. secondary structure
c. Primary structure
The GroESL protein folding system takes about how much energy (kJ/mol) to refold a protein?
a. 21
b. 42
c. 210
d. 420
d. 420
Which disease is caused by misfolded proteins?
a. Osteogenesis imperfecta
b. Prions
c. Scurvy
d. Sickle Cell Anemia
b. Prions
In what order would Arg, Asp, Cys, and Ser be eluted from a diethylaminoethyl column at pH 8.5?
ASCA
Arg, Ser, Cys, Asp
Protein Y has an absorptivity of 0.5 mL-mg-1-cm at 280 nm. What is the absorbance at 280 nm of a 2mg-mL-1 solution of protein Y?
1
(0.5 mL)(2 mg-mL)
Protein Y has an absorptivity of 0.06 mL-mg-1-cm-1 at 280 nm. What is the absorbance at 280 nm of a 4.0 mg mL-1 solution?
0.24
(0.06 mL)(4.0 mg-mL)
