EXAM 1 Flashcards
What are fatty acids described as?
Amphipathic
This means that within the molecular structure, one end is polar and the other is non-polar.
Which gene sequences are termed orthologs?
Glucose-6-phosphate gene sequences from a human and a chimpanzee
These sequences are highly conserved.
When is a reaction always spontaneous?
The change in free energy, delta G, is negative.
What is a hydrogen bond acceptor?
An atom, ion, or molecule component of a hydrogen bond which does not supply the bridging hydrogen atom.
What are hydrogen bond donors bound to?
Hydrogen, specifically N or O atoms.
Which reaction is not spontaneous and could be driven by ATP hydrolysis?
Pyruvate + Pi <—-> phosphoenolpyruvate (+31.5 kJ/mol)
Also includes Glucose + Pi <—-> glucose 6 phosphate (+13.8 kJ/mol).
What differentiates the biochemical standard state from the standard state?
pH of 7.
How are changes in enthalpy (H) and entropy (S) related to changes in free energy (G)?
Delta G = Delta H - T delta S.
Which reaction is entropically favored?
ATP —> ADP + Pi.
What is true regarding coupled reactions?
The overall free energy of a coupled reaction is the difference of the free energies for the individual reactions.
Which biochemical reaction is endergonic?
Glutamate + NH4+ —> Glutamine; Delta G = +14.2 kJ/mol
Also includes L-Malate + NAD+ —> Oxaloacetate + NADH + H+; Delta G = +29.7 kJ/mol.
What is an example of decreasing entropy?
An anabolic pathway.
What is the energy charge (EC) for a cell with ATP = 0.5 mM, ADP = 12.2 mM, AMP = 80 µM?
0.52.
How would EC change in cells without the hyperactive adenylate kinase mutation?
The EC would increase.
What does the first law of thermodynamics state about pressure and volume?
Pressure and volume do not change.
How much does 100.0 mol of ATP weigh?
50.7 kg.
What is the maximum number of amino acids that six mRNA codons could encode?
6.
What problems arise from mutations in the gene encoding G6P dehydrogenase?
Nucleotide biosynthesis.
How can someone with G6P dehydrogenase deficiency mitigate symptoms?
Consume more five carbon containing foods.
What are the main components of the plasma membrane?
Phospholipids.
How many fatty acids do the main chemical components of the plasma membrane contain?
Two.
Which chemical contains completely oxidized carbon atoms?
Carbon dioxide.
What nucleotides are parts of interacting molecular structures?
C - G.
To break a base pair, ______ energy needs to be invested than is required to break a base pair that consists of two hydrogen bonds.
More.
An organism that grows at high temperatures is likely to have greater ______ content compared to A/T.
G/C.
What amino acid substitution is likely from the CF genetic mutation?
A positively charged amino acid is substituted by a non-polar amino acid.
What has become increasingly common for CF patients due to treatment advancements?
Gene therapy, lung transplant, inhaled antibiotics.
Why are fatty acids important for cell membrane formation?
They are amphipathic.
Which two primates are most related based on morphological phylogeny?
Chimp and gorilla.
Which two primates are most related based on molecular phylogeny?
Human and chimp.
Which type of phylogeny is more powerful for measuring genetic relatedness?
Molecular.
Genes that evolved from one another following duplication are called ______, and comparing them in humans and chimpanzees shows ______.
Paralogs; orthologs.
Which term includes both orthologous and paralogous?
Homologous.
Which functional group is NOT capable of multiple protonation states?
Methyl.
What changes first when the genetic expression pattern of a eukaryotic cell changes?
The transcriptome.
In terms of energy conservation, direct regulation of synthesis is more efficient for ______.
Transcriptome.
What areas were enhanced by the sequencing of the human genome?
All of these areas were enhanced.
What describes fatty acids’ amphipathic nature?
One end is polar and the other end is nonpolar.
Which enzymes are involved when yeast converts pyruvate into ethanol?
Alcohol dehydrogenase, pyruvate decarboxylase.
An increase in acetaldehyde correlates with ______ production.
An increase in ethanol.
Which pairs are not standard DNA base pairs?
Adenine-guanine, cytosine-thymine, uracil-thymine.
Is there enough information to determine the type of strand for the polynucleotide 5’-AGGGCAACCGGCCGGAAACGACCAGACAAAAAAAAAAGC-3’?
Not enough information.
What base pairs with cytosine in DNA?
guanine
What is the expected base pairing for adenine?
thymine
What is the molecular formula for glucose?
C6H12O6
If the molecular formula of a carbohydrate is C6H12O6, then it is most likely considered to be a _______.
monosaccharide
Within a eukaryotic cell, the _________ is the organelle with highly invaginated membrane structures that sequester ribosomes for protein synthesis.
endoplasmic reticulum
What is the concentration of [OH-] in a solution of 0.025 M HCl?
4.0 × 10-13 M
The mobility of lipids in membranes is best described by _______.
fast lateral diffusion and slow transverse diffusion
Which of the following is an example of a weak acid?
Vinegar, CH3COOH
Which properties of water are true? (Select all that apply)
- Water is polar and an excellent solvent because of its hydrogen-bonding properties.
- Water is less dense as a solid than as a liquid.
- Water is liquid over a wide range of temperatures.
What characteristic do molecules found in biological membranes have that allows for the maintenance of low entropy?
amphipathic
What common substance has molecular properties similar to the molecules found in biological membranes?
detergent
What response is observed in a person experiencing acidosis?
- more CO2 exhaled (hyperventilation)
- diminished HCO3- excretion
When a protein enzyme folds in an aqueous solution, which of the following is correct?
Non-polar amino acids are found in the interior of the protein.
If a cell is placed in a hypotonic solution, then _______.
water will flow into the cell
Placed in a hypertonic solution, a living cell will _______.
shrink as water leaves the cell
What is directly responsible for maintaining turgor pressure in a leaf?
osmotic pressure
Which of the following is correct about biological membranes?
Phospholipid head groups are directed toward the aqueous environment.
If all the threonines of an antifreeze protein were changed to valines, the protein would _______.
not bind water and would lose antifreeze properties
How can reactions that create order occur according to the Second Law of Thermodynamics?
- A favorable enthalpy change overcomes entropic penalty.
- The unfavorable reaction is coupled to a favorable one.
What is the correct chronological order of proton hopping events that form the ‘water wire’?
C ’ E ’ B ’ D
What is the approximate distance each proton ‘hops’ between molecules?
1.5 Å (1 × 10-10 m)
What distance does proton A appear to travel through the water wire to reach the position marked F?
1 nm
What step is performed when preparing for both RNA-seq analysis and a gene microarray?
Isolate mRNA from whole cell lysate.
Which gene expression assay requires that the sequence of genes be known in advance?
gene microarray
On a gene microchip assay, a _______ level of green fluorescence corresponds to more transcripts present upon cell lysis.
greater
The HindIII-DNA complex contains ___ amino terminus/termini and ___ carboxy terminus/termini.
two; two
How much space along the longitudinal axis of DNA does the HindIII enzyme occupy when bound?
approximately one major groove and one neighboring minor groove, which in total is approximately 40 angstroms
What effect would methylation of the HindIII target DNA have on the binding probability?
decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site
If the same experiment were performed in the presence of 1.5 M NaCl, the new curve would be positioned _______.
to the right of the current curve
Which type of chromatin is usually associated with non-coding DNA?
heterochromatin
Which type of chromatin is usually associated with the centromere of a chromosome?
heterochromatin
What is the melting temperature of DNA affected by?
The presence of sodium ions and G-C content
Higher G-C content leads to higher melting temperatures due to three hydrogen bonds.
Which type of chromatin is associated with the centromere of a chromosome?
heterochromatin
What genetic anomaly causes Hutchinson-Gilford Progeria Syndrome (HGPS)?
A shortened version of a certain nuclear protein to be synthesized by the cell.
Is the genetic anomaly that leads to HGPS a single-nucleotide polymorphism?
true
What type of mutation is associated with the genetic anomaly that leads to HGPS?
deamination
What is the relationship between G-C content and DNA melting temperature?
Higher G-C content results in a higher melting temperature due to three hydrogen bonds.
What can be inferred about a thermophilic microbe living at >75°C regarding G-C content?
higher G-C content compared to a similar microbe living at 37°C
Which chemical component of nucleotides interacts with sodium ions?
phosphate group
What distinguishes monocistronic from polycistronic genes?
Polycistronic genes are multiple genes under a single promoter transcribed into a single RNA, while monocistronic genes encode only a single protein.
What conclusion can be drawn from DNA melting curves regarding nucleic acid length?
Shorter-length nucleic acid has a lower melting temperature than that of longer-length DNA.
Based on VNTR DNA analysis, which suspect should be further pursued?
suspect B only
What effect do chemotherapy drugs targeting topoisomerase enzymes have?
These drugs negatively impact DNA replication so that these cells experience a cell cycle arrest.
If the DNA template strand is 5’-AGGCT-3’, what would the new strand read?
3’-TCCGA-5’
Where is adenine located within a molecular structure?
as part of a base pair; at the 3’ end in one polynucleotide strand
What is the distance from the guanine amide oxygen to the cytosine amine nitrogen?
2.61 angstroms
How many hydrogen bonds connect complementary DNA strands in the given nucleic acid?
8
Which terms are considered synonyms regarding DNA integrity?
renatured : annealed, melted : denatured
If a sample of double-stranded DNA is 20% guanine, what percent adenine is it?
30%
What percent of a DNA sample with 20% guanine is purine nucleotide chemistry?
50%
Single-stranded nucleic acid is expected to absorb _______ ultraviolet light than double-stranded nucleic acid.
more
What happens to the quantity of light absorbed at wavelength 260nm as temperature increases?
The quantity of light absorbed at wavelength 260nm is expected to increase.
A __________ mutation will not lead to a change in the protein product of a gene.
Silent
Which amino acid is categorized as a charged amino acid?
R
What does a Ramachandran plot show?
The allowable phi (Φ) and psi (Ψ) angles for a peptide.
What is the isoelectric point (pI) of lysine with given pKa values?
10.1
Which amino acid is most likely found on the exterior of a protein?
Ser
The type of reaction that forms a peptide bond is _______.
condensation
What are heat shock proteins classified as?
chaperones
What type of chaperone is Hsp70?
clamp type
Amino acids are polymerized via a _______ reaction.
condensation
Which statement is true regarding keratin in hair and fingernails?
Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails.
What must happen during a hair perm?
Reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds.
What are the four groups that amino acids can be divided into?
charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic
What restricts the rotation of the peptide bond?
partial double bond character
What are the four groups that amino acids can be divided into?
A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic
Rotation in the peptide backbone is around the two bonds that flank adjacent ___ atoms.
C±
What is the molecular geometry of the amide nitrogen and carbonyl carbon in a peptide plane?
The amide nitrogen is trigonal planar and the carbonyl carbon is also trigonal planar
What is the most plausible explanation for the bending of the peptide plane observed?
Some other restraint is causing the peptide plane to adopt an unfavorable state. The favorable energetics of the other restraint offset the energetic unfavorability of the skewed peptide plane
From the nucleotide sequence 5’-GCCUCCAAACCCCUCCA-3’, what peptides could be encoded?
A. Pro-Pro-Asn-Pro-Ser, C. Ala-Ser-Lys-Pro-Leu, D. Leu-Gln-Thr-Pro-Pro
Which amino acids contain sulfur?
B. cysteine, E. methionine
Which amino acid is able to form disulfide bonds?
Cysteine
Which bond type has partial double bond character?
D. A peptide bond
What is a major consequence of the partial double bond character of the peptide bond?
Greatly reduced rotational freedom compared to the Æ (phi)/È (psi) torsion angles
Hsp70 is a ___ chaperone. GroEL-GroES is a ___ chaperone.
Hsp70 = clamp type chaperone, GroEL-GroES = chamber type chaperone
Which statement is correct regarding Hsp70 and GroEL-GroES?
A. Both Hsp70 and GroEL-GroES utilize ATP to assist in protein refolding
For Anfinsen’s studies of RNaseA folding, which statement is not correct?
C. Removal of ²-mercaptoethanol, followed by removal of urea, resulted in active RNaseA
If RNase were heated to twice its Tm in the absence of ²-mercaptoethanol and then cooled to 4 °C, what state would it be in?
A. native state
What is the folded state of ovalbumin in a cooked egg?
D. irreversibly denatured
If the hydrophobic part of a membrane is roughly 60 Å thick, how many amino acids are necessary to form the shortest possible transmembrane spanning α-helix?
40 amino acids
How many amino acids are necessary if the transmembrane helix is at an angle of 24° from being perpendicular to the plane of the membrane?
44 amino acids
Which residues would you likely find in a transmembrane spanning α-helix?
A. leucine, C. isoleucine
What does the amino acid sequence of a protein lead to regarding folding pathways?
A. The amino acid sequence of a protein leads to a limited number of possible folding pathways
What is the quaternary structure of a hexamer made of three different homodimers?
C. A2B2C2
What is the quaternary structure of a hexamer composed of two homotrimers?
A3B3
The GroEL-GroES complex is classified as which types?
B. a chaperone, C. an ATPase
What type of chaperone is GroEL-GroES?
C. chamber type
If a mutation occurred in the GroEL gene that abolished ATP binding, what functional consequence would you predict?
C. The GroEL complex would form but would not act as a chaperone
How many ATP molecules are hydrolyzed during a full cycle of GroEL-GroES-aided protein folding?
B. 14
Quaternary structures provide increased functionality to proteins in which of the following ways?
B. They provide structural properties not present in individual subunits, C. They increase efficiency of biochemical processes
Which amino acid sequences could form an amphipathic helix?
A. TVVEAIDRLVDT
Many diseases, including Alzheimer’s disease, are associated with what phenomenon?
C. protein aggregation
Which of the following is NOT accurately classified as a motif?
D. FERM domain fold
What would be observed if you overexpressed a GFP fusion protein in E. coli?
D. The E. coli would have a green appearance when observed in white light
Why would GFP not be a good choice of light-interacting protein for a creature that lives exclusively in a cold, dark sea cave?
C. GFP would not emit green light since there is no blue light for it to absorb and re-emit
Disulfide bonds are covalent interactions formed between which amino acid residues?
E. Cys
What would happen to an existing surface-exposed disulfide bond in a typical cytoplasmic protein in a more oxidizing environment?
A. There would be no change since the disulfide bond is already oxidized
Which secondary structure elements are stabilized by hydrogen bonds?
A. α-helices, B. antiparallel β-sheets, C. parallel β-sheets
If a mutation occurred in which a codon changed to that for proline, what would you expect if the codon were found in a region that formed an α-helix?
Which secondary structure elements are stabilized by hydrogen bonds?
A. ± helices
B. antiparallel ² sheets
C. parallel ² sheets
These elements are crucial for protein structure and stability.
What effect would a mutation changing a codon to that for proline in a region that formed an ±helix have?
A. The proline would disrupt the ± helix.
Proline’s unique structure can introduce kinks in helices, affecting overall protein folding.
