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BCH 4053 > Exam #2 Material > Flashcards

Exam #2 Material Flashcards

1
Q

Lipids are the biomolecules of choice for storage of metabolic energy because they…

A

Yield a large amount of energy upon oxidation

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2
Q

Assuming the degree of saturation of the acyl chains remains the same, fatty acids with longer acyl chains have ___ melting points

A

Higher

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2
Q

Membranes with unsaturated fatty acids in their components are more flexible and fluid because…

A

Unsaturated fatty acids bend at the double bond preventing close packing.

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4
Q

Glycerolphospholipids are all except:

  • essential components of cell membranes
  • members of the phospholipids
  • also called sphingolipids
  • made up of 1,2-diacylglycerol and a phosphate group
A

Glycerolphospholipids are all except also called sphingolipids.

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5
Q

In passive diffusion, the transported species moves across the membrane in the ___ favored direction without ___.

A

thermodynamically

without a specific transport system/molecule

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6
Q

Secondary active transport across a membrane refers to:

A

Movement of a molecule across a membrane and against its concentration gradient powered by an ion gradient that is created by a different transporter.

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7
Q

Terpenes are composed by joining two ___ units.

A

Isoprene

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8
Q

In a typical Na+, K+ -ATPase, ___ sodium ions are moved from the ___ of the cell while ___ potassium ions are moved in from the ___ of the cell

A

3
inside to outside
2
outside to inside

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9
Q

Which of the following is not a property of integral membrane proteins (intrinsic proteins)?

  • they are inserted into the membrane and sequestered by largely hydrophobic interactions
  • they contain both hydrophilic and hydrophobic surfaces
  • they have significant lateral mobility
  • they are exposed to at least one aqueous surface surrounding the membrane
  • they dissociate from the membrane by treatment with salt solutions
A

NOT true: they dissociate from the membrane by treatment with salt solutions

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10
Q

Hydropathy plots for transport proteins are utilized to reveal…

A

Stretches of amino acid residues that make up hydrophobic regions, which may be directly associated with the lipid bilayer

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11
Q

What is the free energy change for transporting a chloride ion into the cell given the following conditions:

  • Cl- in the cell is 5 mM
  • Cl- out of the cell is 115 mM
  • membrane potential is -70 mV (inside is negative with respect to outside)
  • T = 25 deg cel, R = 8.314 J/Kmol, F = 100 kJ/Vmol
A

-768 J/mol

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12
Q

What is the difference between a deoxyribonucleotide and a dideoxyribonucleotide?

A

A dioxynucleotide is missing a 3’ hydroxyl group on its sugar

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13
Q

What is false about nucleotides?

  • they consist a base and a sugar
  • they are phosphorylated
  • they have beta-N glycosidic bond types
  • they refer to carbons using the symbol ‘ to number the locations of the sugar carbon atoms
A

False: they consist a base and a sugar

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14
Q

Which of the following statements regarding the structure of DNA is correct?

  • the two strands are held together by intra-chain hydrogen bonds
  • the two strands have complementary base pairing
  • the two strands are parallel
  • the hydrogen bonding that holds the helix together is always between two purines or two pyrimidines
  • the ratio of A:G is the same in all organisms
A

The two strands have complementary base pairing

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15
Q

In double stranded DNA containing 32% cytosine, the percentage of adenine would be…

A

18%

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16
Q

DNA double helix structure is stabilized by all of the following except:

  • cations such as Mg 2+ bind to the anionic phosphates
  • the sugar-phosphate backbones are oriented in opposite directions
  • appropriate base pairing builds a polymer whose external dimensions are uniform
  • the glycosidic bonds holding paired bases are directly across the helix from one another
  • bases stack together through hydrophobic interactions and van der Waals forces
A

False: the glycosidic bonds holding paired bases are directly across the helix from one another

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17
Q

Histones are rich in the amino acids ___, and interact with DNA via ___.

A

lysine and arginine

ionic bonds

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18
Q

If a restriction site of 6 bases starts with 5’-TGG, what are the last 3 bases in the sequence?

A

5’-CCA-3’

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19
Q

All are true for DNA polymerase except:

  • copies the sequence of nucleotides of one strand in a complementary fashion
  • copies the sequence of nucleotides of one strand to form a new second strand
  • generates dsDNA from ssDNA
  • Requires a primer with a free 5’-OH end, but the 3’ end may stay phosphorylated
  • synthesizes new strands by adding successive nucleotides in the 5’ to 3’ direction.
A

False: Requires a primer with a free 5’-OH end, but the 3’ end may stay phosphorylated

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19
Q

All are characteristics of DNA gyrase in E. Coli except:

  • It is classified as a topoisomerase
  • It cuts both strands of a dsDNA
  • It hydrolyzes ATP during its reaction mechanism
  • All are true
  • It works to induce negative supercoiling in DNA
A

All are true

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21
Q

Uracil can be formed by the spontaneous deamination of ___.

A

Cytosine

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22
Q

How many supercoils (W) are present for a 2000 base pair circular DNA plasmid with a linking number of 300?

A

100

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23
Q

All are distinctive features of enzymes except:

  • catalytic activity
  • ability to change Delta G
  • regulation
  • specificity
A

Ability to change Delta G

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24
Q

The free energy of activation is defined as:

A

The energy required to raise the average energy of one mole of reactant to the transition state energy.

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25
Q

All of the following statements about noncompetitive inhibition are true except:

  • The inhibitor binds to a different site than does the substrate
  • Increasing the concentration of [S] can overcome inhibition
  • The inhibitor can cause a conformational change in the enzyme
  • They interact with the enzyme as well as the enzyme-substrate complex
  • The V-max value does not remain the same as for a reaction that is not inhibited
A

Increasing the concentration of [S] can overcome inhibition

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26
Q

In ___ inhibition, the inhibitor usually resembles the enzymes substrate.

A

Competitive

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27
Q

Amino Acids with higher hydropathy are more likely to be found in the protein ___.

A

Interior

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28
Q

How can we unfold a protein?

A
  • Heat: enthalpic and entropic reasons
  • pH: disrupt charge interactions and hydrogen bonding
  • Detergents: interact with hydrophobic regions
  • Chaotropic chemicals: increase chaos and unfold. by disrupting hydrophobic reactions (similar to salting out)
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29
Q

Epimers

A

Isomers that differ at one chiral center (example: D-glucose and D-mannose with respect to C-2)

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30
Q

What are some functions of lipids?

A
  • Energy storage
  • Thermal insulation
  • Hormonal regulation
  • Enzymatic cofactors
  • Electron carriers
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31
Q

Unsaturated lipids usually have double bonds in the ___ conformation.

A

Cis

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32
Q

Unsaturated fatty acids have a ___ melting point.

A

Lower

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33
Q

Triacylglycerols, or triglycerides, are the fatty acid ___ of ___.

A

Ester

Glycerol

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34
Q

Functions of Triacylglycerol (triglycerides)

A
  • Major energy source (dietary and storage)
  • Stored in adipocytes
  • Body insulation
  • Source of metabolic water
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35
Q

Plant triacylglycerols are rich in unsaturated fats, which are ___ at room temperature. Animal triacylglycerols are rich in saturated fats, which are ___ are room temperature.

A

Liquid

Solid

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36
Q

Trans fats are unsaturated fats, but the double bond is ___ instead of ___. They are ___ at room temperature.

A

Trans instead of cis.

Solid

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37
Q

Glycerophospholipids are the primary lipid found in ___.

A

Membranes

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38
Q

Sphingolipids are often found in ___. Sphingosine backbone instead of glycerol (doesn’t have an ester linkage to alkyl or ___.)

A

Membranes

Amino Group

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39
Q

What are ceramides?

A

Fatty acids with w/ amide linkage to sphingosine

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40
Q

What are the three classes of ceramides?

A
  • Sphingomyelins: the simplest sphingolipids. They contain phosphate, and are important in nervous tissue.
  • Cerebrosides: ceramides with single sugar headgroups, and occur in small amounts in most membranes.
  • Gangliosides: ceramides with oligosaccharide for headgroup. Large headgroup sticks out of membrane, involved in cell-cell recognition.
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41
Q

Waxes are ___ of long-chain alcohols with long-chain ____.

A

esters

fatty acids

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42
Q

Isoprenes, terpenes, and isoprenoids are built from ___ units. They are found in many vitamins, coenzyme Q, and the waxy coating of leaves.

A

5 Carbon

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43
Q

Cholesterol is the parent compound for 5 families of animal hormones:

  • ___ & ___ : sexual development and hormones
  • ___: pregnancy
  • ___: control of metabolism
  • ___: regulate salt balance
A
  • androgens & estrogens
  • progestins
  • glucocorticoids
  • mineralocorticoids
44
Q

How do lipids and their metabolites act as biological signals?

  1. Glycerophospholipid break down produces a variety of signaling products
  2. ?
  3. Cleaved by phospholipases, and results in products
A
  1. Glycerophospholipid break down produces a variety of signaling products
  2. These bind to different cellular proteins and have a cascade of effects in cellular functions
  3. Cleaved by phospholipases, and results in products
45
Q

Single tailed lipids are more likely to form ___. They have conical rotational cross sections.

A

Micelles

46
Q

Double tailed lipids are more likely to form ___. They have rectangular rotational cross sections. (glycerophospholipids, sphingolipids)

A

Bilayers

47
Q

Ionizable lipids allow for package of ___. They are positively charged at low pH.

A

RNAs

48
Q

In Sanger sequencing, incorporation of ___ terminates DNA Polymerase

A

Dideoxynucleotides

49
Q

An enzyme has a maximal activity at pH 6.0 and the mechanism involves a proton transfer. The amino acid ___ is most likely involved.

A

Histidine

50
Q

A two substrate enzymatic reaction in which one product is produced before the second substrate binds to the enzyme, has a ___ mechanism.

A

Ping pong double replacement

51
Q

All of the following are true of type 2 endonucleases EXCEPT
A)they have target sequences called palindromes
B)they can create sticky or blunt ends at cleavage sites
C)They cleave leaving 5’ phosphate and free 3’ OH
D) nomenclature based on enzyme Size

A

nomenclature based on enzyme Size

52
Q

Which of the following best describes the structure of a nucleosome?

a) approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside
b) approximately 15 bp of DNA wrapped around an octamer of H1 with H2A,B, H3 and H4 on the outside
c) approximately 150 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
d) approximately 1500 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
e) approximately 200 bp of DNA wrapped around a tetramer of H2A,H2B,H3, and H4 with H1 on the outside

A

approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside

53
Q

Which of the following is (are) characteristic of the (Na+-K+)-ATPase?
I. It binds Na+ and K+ simultaneously prior to binding ATP
II. It is covalently modified by phosphorylation at an Asp residue when Na+ is present.
III. Transport of Na+ and K+ occur in a 1:1 ratio, thus maintaining a balanced gradient until opening of the gated portion of the channel.
IV. It is essential for excitation of nerve cells.

a) I, II, IV
b) II, III, IV
c) II, IV
d) II, III
e) II

A

II, IV

54
Q

Which of these amino acid groups would not make a good nucleophilic catalyst?

a) amino
b) sulfhydryl
c) imidazole
d) methyl
e) hydroxyl

A

Methyl

55
Q

A new serine protease was discovered that preferentially cleaves a peptide bond adjoining a negatively charged side chain. Which of the following is true?

a) The specificity pocket would mimic that of chymotrypsin.
b) The specificity pocket would mimic that of trypsin.
c) The specificity pocket is likely lined with amino acids such as Arg and Lys.
d) It likely reacts much slower than chymotrypsin.
e) It likely reaction much faster than chymotrypsin.

A

The specificity pocket is likely lined with amino acids such as Arg and Lys.

56
Q

There are ___ residues per turn in an alpha helix.

A

3.6

57
Q

The coiled coil ___ proteins help drive membrane function.

A

SNARE

58
Q

Above its phase transition temperature, membrane lipids are said to be in the ____ state while below they are said to be in the _____ state

A

liquid crystalline, gel

59
Q

An electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH?

a. Ser/Asn
b. Asp/Glu
c. Arg/Cys
d. Lys/Asp
e. Val/Ile

A

Lys/Asp

60
Q

Which of the following amino acids would generally not be found in an α-helix?

a. Ala
b. His
c. Leu
d. Pro
e. Met

A

Proline

61
Q

The porin proteins (e.g., maltoporin) utilize the ____ structural motif.

a. single transmembrane α-helix
b. multiple transmembrane α-helixes
c. single β-sheet both c or d are OK
d. multiple β-sheet
e. none of the above

A

C or D

62
Q

List the three most common experimental techniques for protein sequence determination.

A

X-ray crystallography, Cryo-EM, NMR

63
Q

The _____________ in ion channels is responsible for their specificity for particular ions

A

selectivity filter

64
Q

Nucleotides necessary for Sanger sequencing include dNTPs and ___.

A

DDNTP

65
Q

In addition to Watson/Crick pairing, another form of base pairing that can be found in triple helical DNA and RNA structures is…

A

Hoogsteen Base Pairing

66
Q

A closed circular DNA has a linking number of 10 and a writhe of -1. If the writhe was
decreased by an additional -1, the resulting twist is

A

12

67
Q

The oxyanion hole in serine proteases stabilizes the ___.

A

Transition state or tet intermediate

68
Q

The ___ groove in B-form helices is narrower than in A-form helices.

A

Minor

69
Q

Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes often employ ____________ to assist with catalysis.

A

Cofactors or metal ions

70
Q 
Nucleotides have a nitrogenous base linked to a sugar by a:
A. α-anhydride bond.
B. β-ester bond.
C. α-N-amide bond.
D. β-N-glycosidic bond.
E. α-N-hemiacetal bond.
A

β-N-glycosidic bond.

71
Q

All are properties of nucleosomes EXCEPT:
A. protein spools neatly wrapped with DNA.
B. fundamental structural unit in chromatin.
C. protein spools made up of pairs of histones H2A, H2B, H3 and H4 octameric aggregates.
D. DNA binds histones by ionic bonds of positively charged amino acids and the negative charged phosphate groups.
E. all are true

A

All are true

72
Q

Which of the following methods will allow you to determine if a substance used mediated transport?
A. Measure the rate of transport to determine if it is high or low relative to other transport systems.
B. Evaluate the ion flux at several different concentrations of the substance and look for hyperbolic dependence.
C. Monitor transport rates at a variety of concentrations and confirm a linear dependence.
D. Compare rate of transport in an in vitro system to those in vivo.
E. None of the above.

A

Evaluate the ion flux at several different concentrations of the substance and look for hyperbolic dependence.

73
Q 
Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pKa values of each amino acid are equal to the pKa value for the free amino acid in solution, i.e. they are not being changed by the local environment of the enzyme.)
I. leucine
II. lysine
III. aspartic acid
IV. histidine
A. I, II, III
B. I, II
C. I
D II
E. I, III
A

I, II, III

74
Q

Lipids in bilayer exhibit transverse (flip-flop) and ___ diffusion.

A

Lateral

75
Q

Membrane fluidity is affected by ___. It goes from a liquid crystal state to a gel state.

A

Temperature

76
Q

The melting temperature (Tm) in a membrane ___ with lipid chain length and degree of saturation. The melting temp. of most bio. membranes is ___.

A

Increases

10-40 deg cel.

77
Q

At high temps, cholesterol ____ the membrane and ___ the melting point. At low temps, it intercalates between phospholipids and prevents them from ___ and stiffening.

A

Stabilizes; raises

Clustering

78
Q

Integral membrane proteins can only be extracted from the membrane using ___ or chaotropic agents.

A

Detergent

79
Q

Peripheral membrane proteins can be disassociated from the membrane using high ___ or changes in pH.

A

Salt

80
Q

Peripheral membrane proteins associate ___ with the membrane, and integral membrane proteins associate ___ with the membrane

A

Loosely

Tightly

81
Q

Membrane lipids are distributed ___. Membrane lipid distribution is mediated by phospholipid ___.

A 
Asymmetrically
Translocases (flippases, floppases, scramblases).
82
Q

The mechanism for transporting membrane proteins and secreted proteins is the ___ ___. It starts at translation.

A

Secretory pathway

83
Q

Vesicle fusion is mediated by ___. R-SNARES are conserved ___ usually on the vesicle. Q-SNARES are conserved ___, usually on the target membrane. Together they form a ring that drives fusion.

A

SNARES
Arginine
Glutamine

84
Q

in passive diffusion thermodynamics, the free energy difference between two sides of a membrane is given by:

A

Aout→Ain

ΔG=RTln[Ain] / [Aout]

Where ΔG is called the chemical potential difference

85
Q

In thermodynamics for charged species, the formula is:

A

Aout-> Ain

ΔG=RTln[Ain] / [Aout]+ZFΔΨ

OR

∆G = RT ln([Cprod]/C[react]) + ZFΔΨ

Where:
ΔΨ−membrane potential
F-Faraday’s constant=96,485J⋅V−1⋅mol−1
Z- charge

86
Q

In passive-mediated transport, the species moves down the ___ gradient. It is usually faster than passive processes, and there is a ___ ___ or other carrier involved.

Important features:

  • rate of transport is ___.
  • Specificity towards transported species
  • Can have specific inhibitors
A

Electrochemical
Membrane protein
Saturable

87
Q

Ion channel characteristics:

  • Have a ___ ___, in which an A.A. binds specifically to that substrate. It can often bind to multiple copies of the substrate at once.
  • Aqueous cavity/funnels that restrict dimensions of pore
  • has a “gate”
A

Selectivity filter

88
Q

KcsA is a pH gated ___ channel in ___. It opens in response to low pH in the cell to help maintain osmolarity and conduct cell signaling.

A

K+ ; bacteria

89
Q

Tautomer

A

Isomers that differ in the position of an atom (usually a hydrogen) that readily interconvert

90
Q

Nucleases are enzymes that cleave ___ bonds. Endonucleases cleave ___ in the middle of strands.

A

Phosphodiester

Nucleic acids

91
Q

Differences between DNA and RNA:

  • DNA contains ____ instead of ribose.
  • DNA contains thymine instead of ___.
A

2-deoxyribose

Uracil

92
Q

A form DNA is found in ___ conditions.

A

Dehydrated

93
Q

Z DNA has a ___ handed helix. It has high salt.

A

Left

94
Q

All major and minor grooves in DNA are defined by ___ of the base and sugar.

A

N-glycosidic bonds

95
Q

___ has more degrees of freedom than proteins. There is the potential for lots of flexibility but restricted because of sterics in double helix.

A

DNA

96
Q

In base conformation, purines can form syn and anti, but pyrimidines can only form ___. In A and B DNA, all bases are ___. In Z DNA, G is syn and C is anti.

A

Anti

Anti

97
Q

In Hoogsteen base pairs, the purine ___ is a hydrogen-bond acceptor.

A

N-7

98
Q

Forces stabilizing nucleic acid structures are:

A
  • Hydrogen bonding
  • Electrostatic interactions
  • Van der Waals
  • Hydrophobic interactions
99
Q

Enzymes called ___ can introduce or remove supercoils. They can change the linking number.

A

Topoisomerases

100
Q

Linking number =

A

Linking number = # of Twists + # of Writhes

101
Q

Type I topoisomerases introduce ___ supercoils, and Type II topoisomerases ___ supercoils.

A

More

Relax

102
Q

DNA gyrase is a topoisomerase that introduces ___ ___ into DNA.

A

Negative supercoils

103
Q

Superhelical density formula

A

σ=(L-L0)/L0

Where L0–linking number in the relaxed (non-supercoiled) form

104
Q

DNA supercoiling is important for?

A
  • Packaging DNA in all organisms
  • Histones in chromatin in eukaryotes
  • Unwinding pressure during replication and transcription
105
Q

Histone complexes are dominated by ___ & ___.

A

Arginine and Lysine

BCH 4053 (5 decks)

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