Exam #2 Material Flashcards
Lipids are the biomolecules of choice for storage of metabolic energy because they…
Yield a large amount of energy upon oxidation
Assuming the degree of saturation of the acyl chains remains the same, fatty acids with longer acyl chains have ___ melting points
Higher
Membranes with unsaturated fatty acids in their components are more flexible and fluid because…
Unsaturated fatty acids bend at the double bond preventing close packing.
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
Glycerolphospholipids are all except also called sphingolipids.
In passive diffusion, the transported species moves across the membrane in the ___ favored direction without ___.
thermodynamically
without a specific transport system/molecule
Secondary active transport across a membrane refers to:
Movement of a molecule across a membrane and against its concentration gradient powered by an ion gradient that is created by a different transporter.
Terpenes are composed by joining two ___ units.
Isoprene
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
3
inside to outside
2
outside to inside
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
NOT true: they dissociate from the membrane by treatment with salt solutions
Hydropathy plots for transport proteins are utilized to reveal…
Stretches of amino acid residues that make up hydrophobic regions, which may be directly associated with the lipid bilayer
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
-768 J/mol
What is the difference between a deoxyribonucleotide and a dideoxyribonucleotide?
A dioxynucleotide is missing a 3’ hydroxyl group on its sugar
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
False: they consist a base and a sugar
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
The two strands have complementary base pairing
In double stranded DNA containing 32% cytosine, the percentage of adenine would be…
18%
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
False: the glycosidic bonds holding paired bases are directly across the helix from one another
Histones are rich in the amino acids ___, and interact with DNA via ___.
lysine and arginine
ionic bonds
If a restriction site of 6 bases starts with 5’-TGG, what are the last 3 bases in the sequence?
5’-CCA-3’
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.
False: Requires a primer with a free 5’-OH end, but the 3’ end may stay phosphorylated
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
All are true
Uracil can be formed by the spontaneous deamination of ___.
Cytosine
How many supercoils (W) are present for a 2000 base pair circular DNA plasmid with a linking number of 300?
100
All are distinctive features of enzymes except:
- catalytic activity
- ability to change Delta G
- regulation
- specificity
Ability to change Delta G
The free energy of activation is defined as:
The energy required to raise the average energy of one mole of reactant to the transition state energy.
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
Increasing the concentration of [S] can overcome inhibition
In ___ inhibition, the inhibitor usually resembles the enzymes substrate.
Competitive
Amino Acids with higher hydropathy are more likely to be found in the protein ___.
Interior
How can we unfold a protein?
- 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)
Epimers
Isomers that differ at one chiral center (example: D-glucose and D-mannose with respect to C-2)
What are some functions of lipids?
- Energy storage
- Thermal insulation
- Hormonal regulation
- Enzymatic cofactors
- Electron carriers
Unsaturated lipids usually have double bonds in the ___ conformation.
Cis
Unsaturated fatty acids have a ___ melting point.
Lower
Triacylglycerols, or triglycerides, are the fatty acid ___ of ___.
Ester
Glycerol
Functions of Triacylglycerol (triglycerides)
- Major energy source (dietary and storage)
- Stored in adipocytes
- Body insulation
- Source of metabolic water
Plant triacylglycerols are rich in unsaturated fats, which are ___ at room temperature. Animal triacylglycerols are rich in saturated fats, which are ___ are room temperature.
Liquid
Solid
Trans fats are unsaturated fats, but the double bond is ___ instead of ___. They are ___ at room temperature.
Trans instead of cis.
Solid
Glycerophospholipids are the primary lipid found in ___.
Membranes
Sphingolipids are often found in ___. Sphingosine backbone instead of glycerol (doesn’t have an ester linkage to alkyl or ___.)
Membranes
Amino Group
What are ceramides?
Fatty acids with w/ amide linkage to sphingosine
What are the three classes of ceramides?
- 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.
Waxes are ___ of long-chain alcohols with long-chain ____.
esters
fatty acids
Isoprenes, terpenes, and isoprenoids are built from ___ units. They are found in many vitamins, coenzyme Q, and the waxy coating of leaves.
5 Carbon
Cholesterol is the parent compound for 5 families of animal hormones:
- ___ & ___ : sexual development and hormones
- ___: pregnancy
- ___: control of metabolism
- ___: regulate salt balance
- androgens & estrogens
- progestins
- glucocorticoids
- mineralocorticoids
How do lipids and their metabolites act as biological signals?
- Glycerophospholipid break down produces a variety of signaling products
- ?
- Cleaved by phospholipases, and results in products
- Glycerophospholipid break down produces a variety of signaling products
- These bind to different cellular proteins and have a cascade of effects in cellular functions
- Cleaved by phospholipases, and results in products
Single tailed lipids are more likely to form ___. They have conical rotational cross sections.
Micelles
Double tailed lipids are more likely to form ___. They have rectangular rotational cross sections. (glycerophospholipids, sphingolipids)
Bilayers
Ionizable lipids allow for package of ___. They are positively charged at low pH.
RNAs
In Sanger sequencing, incorporation of ___ terminates DNA Polymerase
Dideoxynucleotides
An enzyme has a maximal activity at pH 6.0 and the mechanism involves a proton transfer. The amino acid ___ is most likely involved.
Histidine
A two substrate enzymatic reaction in which one product is produced before the second substrate binds to the enzyme, has a ___ mechanism.
Ping pong double replacement
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
nomenclature based on enzyme Size
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
approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside
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
II, IV
Which of these amino acid groups would not make a good nucleophilic catalyst?
a) amino
b) sulfhydryl
c) imidazole
d) methyl
e) hydroxyl
Methyl
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.
The specificity pocket is likely lined with amino acids such as Arg and Lys.
There are ___ residues per turn in an alpha helix.
3.6
The coiled coil ___ proteins help drive membrane function.
SNARE
Above its phase transition temperature, membrane lipids are said to be in the ____ state while below they are said to be in the _____ state
liquid crystalline, gel
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
Lys/Asp
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
Proline
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
C or D
List the three most common experimental techniques for protein sequence determination.
X-ray crystallography, Cryo-EM, NMR
The _____________ in ion channels is responsible for their specificity for particular ions
selectivity filter
Nucleotides necessary for Sanger sequencing include dNTPs and ___.
DDNTP
In addition to Watson/Crick pairing, another form of base pairing that can be found in triple helical DNA and RNA structures is…
Hoogsteen Base Pairing
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
12
The oxyanion hole in serine proteases stabilizes the ___.
Transition state or tet intermediate
The ___ groove in B-form helices is narrower than in A-form helices.
Minor
Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes often employ ____________ to assist with catalysis.
Cofactors or metal ions
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.
β-N-glycosidic bond.
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
All are true
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.
Evaluate the ion flux at several different concentrations of the substance and look for hyperbolic dependence.
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
I, II, III
Lipids in bilayer exhibit transverse (flip-flop) and ___ diffusion.
Lateral
Membrane fluidity is affected by ___. It goes from a liquid crystal state to a gel state.
Temperature
The melting temperature (Tm) in a membrane ___ with lipid chain length and degree of saturation. The melting temp. of most bio. membranes is ___.
Increases
10-40 deg cel.
At high temps, cholesterol ____ the membrane and ___ the melting point. At low temps, it intercalates between phospholipids and prevents them from ___ and stiffening.
Stabilizes; raises
Clustering
Integral membrane proteins can only be extracted from the membrane using ___ or chaotropic agents.
Detergent
Peripheral membrane proteins can be disassociated from the membrane using high ___ or changes in pH.
Salt
Peripheral membrane proteins associate ___ with the membrane, and integral membrane proteins associate ___ with the membrane
Loosely
Tightly
Membrane lipids are distributed ___. Membrane lipid distribution is mediated by phospholipid ___.
Asymmetrically Translocases (flippases, floppases, scramblases).
The mechanism for transporting membrane proteins and secreted proteins is the ___ ___. It starts at translation.
Secretory pathway
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.
SNARES
Arginine
Glutamine
in passive diffusion thermodynamics, the free energy difference between two sides of a membrane is given by:
Aout→Ain
ΔG=RTln[Ain] / [Aout]
Where ΔG is called the chemical potential difference
In thermodynamics for charged species, the formula is:
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
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
Electrochemical
Membrane protein
Saturable
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”
Selectivity filter
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.
K+ ; bacteria
Tautomer
Isomers that differ in the position of an atom (usually a hydrogen) that readily interconvert
Nucleases are enzymes that cleave ___ bonds. Endonucleases cleave ___ in the middle of strands.
Phosphodiester
Nucleic acids
Differences between DNA and RNA:
- DNA contains ____ instead of ribose.
- DNA contains thymine instead of ___.
2-deoxyribose
Uracil
A form DNA is found in ___ conditions.
Dehydrated
Z DNA has a ___ handed helix. It has high salt.
Left
All major and minor grooves in DNA are defined by ___ of the base and sugar.
N-glycosidic bonds
___ has more degrees of freedom than proteins. There is the potential for lots of flexibility but restricted because of sterics in double helix.
DNA
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.
Anti
Anti
In Hoogsteen base pairs, the purine ___ is a hydrogen-bond acceptor.
N-7
Forces stabilizing nucleic acid structures are:
- Hydrogen bonding
- Electrostatic interactions
- Van der Waals
- Hydrophobic interactions
Enzymes called ___ can introduce or remove supercoils. They can change the linking number.
Topoisomerases
Linking number =
Linking number = # of Twists + # of Writhes
Type I topoisomerases introduce ___ supercoils, and Type II topoisomerases ___ supercoils.
More
Relax
DNA gyrase is a topoisomerase that introduces ___ ___ into DNA.
Negative supercoils
Superhelical density formula
σ=(L-L0)/L0
Where L0–linking number in the relaxed (non-supercoiled) form
DNA supercoiling is important for?
- Packaging DNA in all organisms
- Histones in chromatin in eukaryotes
- Unwinding pressure during replication and transcription
Histone complexes are dominated by ___ & ___.
Arginine and Lysine
