Biochem Exam 1 study guide

Simple sugars are made of which elements?

Carbon, oxygen, hydrogen

Mutations in adenylate kinase have led to a hyperactive enzyme that ultimately ends up elevating ADP levels in a cell.Calculate the EC (energy charge) given the following atypical adenylate concentrations for the cell containing the mutant adenylate kinase: ATP = 0.5 𝑚𝑀mM, ADP = 12.2 𝑚𝑀mM, AMP = 80 𝜇𝑀μM.

0.52

The standard conditions for Gibbs free energy are

1 atm, 298 K, 1 M

Examine the table and then order the following amino acids based on their propensity (highest to lowest) to form α helices.

1. Glutamate 2. Alanine 3. Lysine 4. Isoleucine 5. Glycine 6. Proline

What does chromatin in eukaryotic nucleus contain?

DNA packaged with protein

A polypeptide has a high pI value. Which statement below best describes what might be contributing to he observed high pI value?

A large number of arginine and lysine residues.

The partial sidechain of asparagine or glutamine is shown above. For the three atoms marked A, B, and C, indicate whether they serve as donors, acceptors, or neither for hydrogen bonds. (Choose THREE total answers (one each for A, B, C) from the list of nine possibilities)

A- neither B- acceptor C- donor

Protein folding allows proteins to adopt a conformation that is functional. Which interaction(s) is critical for folding?

A. Hydrogen bond formation B. Van der Waals interaction C. Salt-bridge formation/ionic interactions ANS. is D. A, B, and C

From the partial nucleotide sequence given below, what peptides could be encoded? 5'-GCCUCCAAACCCCUCCA-3'

Ala-Ser-Lys-Pro-Leu Pro-Pro-Asn-Pro-Ser Leu-Gln-Thr-Pro-Pro

Which of the following would be an example of decreasing entropy?

An anabolic pathway

Which amino acids are positively charged

Arginine and Lysine

For the yeast biochemical pathway, identify fermentative reactants and products by dragging the chemical names to their respective structures.

B. Glucose C. Ethanol A. Carbon Dioxide

The titration curve for the amino acid glutamate is shown above. Refer to this figure to answer the following question. The form of glutamate shown above predominates at what point on the titration curve?

C

Proton hopping allows for the rapid apparent movement of protons (H+) through aqueous solution. From first to last in the figure above, what is the correct chronological order of proton hopping events (B-E) that form the "water wire" between proton A and proton F?

C → E → B → D

Eight (1-8) characteristics that describe either histone proteins or restriction endonucleases are provided below. Select the letter in which the eight characteristics are classified as belonging to histone proteins (H) or restriction endonucleases (R). H = histone proteins R = restriction endonucleases 1. DNA sequence dependent binding 2. Bind 147 bp of DNA 3. Bind and cleave short (6-8 bp) of DNA 4. DNA sequence independent binding 5. Protect bacteria against infection 6. Part of nucleosomes in eukaryotes 7. Used in cloning (recombinant DNA technology 8. Are enzymes

C. R H R H R H R R

Which of the following is the correct formula for glucose?

C6H12S6

Amino acids have different functional groups and thus can perform different chemistry. Which of these group is not a functional group found in an amino acid?

CH3

Organisms on Earth are considered _________ life forms.

Carbon

Which THREE of the following biochemical relationships are correct statements illustrating the hierarchical organization of molecular life?

Carbon, hydrgogen, and oxygen are the most abundant elements in biomolecules. Insects degrade organic materials on the forest floor and generate nitrogen compounds that are used by tree seedlings as nutrients. Metabolic pathways are considered more complex than biomolecules but less complex than ecosystems.

For a circular, unbroken piece of DNA, which of the following is true?

Decreasing the writhe increases the twist to keep the linking number constant.

Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into the appropriate categories.

Hydrophobic: 1. methionine 2. isoleucine 3. valine 4. phenylalanine Hydrophilic: 1. aspartate 2. lysine

DNA methylase enzymes transfer a methyl group to C-5 of a cytosine or to N-6 of an adenine within a DNA sequence recognized by the enzyme. What effect, if any, would this have on the establishment of the HindIII-DNA complex that is shown in this molecular structure?

If the HindIII target DNA were methylated, then it would decrease the probability of binding between HindIII and DNA and would decrease the endonuclease activity at that methylated site.

Two proteins have the same overall fold, but different amino acid sequences. These proteins likely derived from a common ancestor.

TRUE

For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change?

The EC would increase.

If a semi-conservative mutation occurred in the GroEL gene that abolished ATP binding, what functional consequence would you predict?

The GroEL complex would form but would not act as a chaperone.

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha-amino group of a protein has a pKa of about 8.0 when it is exposed to H2O on the outside of a protein. Would you expect the pKa to be higher or lower than 8.0 if the alpha-amino group were buried in the hydrophobic interior of the protein and why?

The alpha-amino group would be uncharged at neutral pH, which is favorable and therefore it would be lower.

If a cell is placed in a hypotonic solution, then _____________.

water will flow into the cell.

What is the H+ concentration at the following pH values?

pH = 2 -> [H+] = 10 mM pH = 6 -> [H+] = 1 µM(or 1 micromolar) pH = 7 -> [H+] = 100 nM(the same as 1×10-7 M) pH = 8 -> [H+] = 10 nM pH = 12 -> [H+] = 1 pm

The figure below shows an example of which functional group?

phosphoryl

Getting your hair permed must involve which of the following?

reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds

When a gene sequence is cloned from mRNA, the mRNA is first isolated from the cell and then converted into a double-stranded sequence using the enzyme______________.

reverse transcriptase

A __________ mutation will not lead to a change in the protein product of a gene.

silent

Identify the four building block biomolecules from the list to the right, and then match them with the best description of their primary cellular function.

simple sugars: cell recognition nucleotides: enzyme catalysis fatty acids: cell membranes amino acids:neurotransmission

A reaction is always spontaneous if

the change in free energy, ΔG, is negative.

Shown here is a complex between HindIII and DNA. Consider its molecular structure and manipulate the molecule according to the instructions below to answer the following questions. The HindIII-DNA complex that is shown in this molecular structure contains _______ amino terminus/termini and ______ carboxy terminus/termini. An amino terminus sequence KSALEKLLSL is associated with a(n) _________ . Use the sequence view from the dropdown menu and determine the location of KSALEKLLSL within the folded polypeptide.

two two a-helix

As DNA unwinds and denatures, absorbance is predicted to_______________.

increase.

For the alanine titration curve shown below, which best describes point A?

isoelectric point

For the alanine titration curve shown below, which best statement best describes point A?

isoelectric point

Of these three parameters regarding DNA twist, which is calculated by adding the other two parameters together?

linking number (Lk)

Using the table below, determine the kind of gene mutation illustrated in which a T in the second codon is changed to a G in the same position, i.e, what does the T-->G change lead to in terms of mutations? ATG_AAT_CAC, ATG_AAG_CAC

missense mutation

Fatty acids are amphipathic, meaning that within the molecular structure,

one end is polar and the other end is nonpo

Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf?

osmotic pressure

Energy conversion in living systems is required for what three types of work?

osmotic work, chemical work, mechanical work

Which of the following is correct about topoisomerases?

Type II topoisomerases reduce positive supercoiling generated during replication or transcription.

DNA is more stable than RNA; why?

Under basic conditions the 2'-OH group on the sugar ring in RNA enables phosphodiester bond cleavage

Two amphipathic α helices in a dilute aqueous solution are likely to ______________.

form a coiled coil structure with the hydrophobic amino acid side chains interacting with each other down the middle.

When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments?

gel electrophoresis

Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution _______________.

had no solutes.

The transfer of a phosphate from ATP to another molecule produces a(n)

high-energy intermediate

This question describes features of two pairs of Watson-Crick base pairs? Identify the letter that has the correct answers to the following questions: 1. What is the base stacking energy for this set of base pairs? 2. How many hydrogen bonds total are present in this set of two base pairs? 3. What are the two dominant energetic forces that stabilize interactions between the base pairs?

- 5.44 kJ/mol 5 hydrophobic effect; van der Waals

How many ATP molecules are hydrolyzed during a full cycle of GroEL-GroES-aided protein folding?

14

A histidine residue is in a hydrophobic environment in the interior of a protein. If the pKa of the imidazole group of this histidine is 5.5, what would be the ratio of deprotonated imidazole sidechain to protonated imidazole sidechain at pH 7?

31.6/1

Given the DNA sequence of 3 '-CAT-5', what is the complementary sequence in mRNA? Make sure you think about hydrogen bond formation

5 '-GUA-3 '

Predict the complementary strand of the following DNA sequence:5' ATCTGAATCT 3'

5' AGATTCAGAT 3'

ATP is critical to allow chemical reaction to proceed; it is for this reason we produce how much ATP per day:

50 kg

If a typical person hydrolyzes 100.0 mol of ATP per day, how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol.)

50.7 kg

A 20 bp duplex with __________ content at __________ will have the highest absorbance at 260 nm.

60 percent A-T 50 degrees C

Use the table below to determine how many possible RNA sequences written in the 5' to 3' direction could code for the tripeptide Met-Pro-Ala-Leu?

96

Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur?

A favorable enthalpy change overcomes entropic penalty. The unfavorable reaction is coupled to a favorable one.

The ΔG°of ATP hydrolysis is -30.5 kJ/mol. Which of the following reactions are not spontaneous and could be driven by being coupled to hydrolysis of ATP (one ATP molecule per individual reaction)?

Dihydroxyacetone phosphate (DHAP) ⇔ glyceraldehyde-3-phosphate (GAP) (+7.5 kJ/mol) Glucose + Pi ⇔ glucose-6-phosphate (+13.8 kJ/mol)

Rank the following cellular features and/or activities in terms of their decreasing complexity compared to one another. The most complex should be positioned on top, and the least complex should be positioned on the bottom.

Ecosystem Cells Metabolism Macromolecules Elements & functional groups

Name the four non-covalent interactions that occur within and between molecules

Hydrogen bonds, van der Waals interactions, ionic (electrostatic) interactions, hydrophobic effect

Rhodopsin is made up of amphipathic α helices and is embedded in the lipid membrane. __________ amino acids are likely to be found on the interior-facing helical surface.

Hydrophilic

For the reaction: A + B ↔ C + D, which of the following is correct?

Keq = [C][D]/[A][B]

Fibrous proteins are multi-subunit complexes that constitute some of the most abundant proteins in nature, including keratin, silk fiber, and collagen. Keratin is a homodimer of two helical polypeptides that are wrapped around each other to form what is called a coiled coil. The keratin helix itself is right-handed; however, the coiled coil dimer is formed from the helices wrapping around each other in a left-handed direction. The ∼300-amino-acid core polypeptide of each keratin subunit consists of a 7-amino-acid repeating unit, in which the first, and usually the fourth, amino acid is hydrophobic. This repeat provides a hydrophobic strip that rotates anticlockwise around the surface of the helix. Two helices have to twist around each other in order to line up those two hydrophobic strips. Thus, the helices pack together with an extensive hydrophobic interface. The strength of keratin comes from covalent cross-linking between coiled coil dimers as a result of disulfide bridge formation between cysteine residues. Many different types of keratins are found in nature, which differ primarily in the number of cysteine residues. Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true?

Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails.

Identify the THREE conditions in the list below that BEST describe low energy charge in a cell.

Low ATP concentrations. The energy charge ratio is below 0.70. High AMP concentrations.

Which one of the following amino acid residues would most likely be buried in the interior of a water-soluble protein?

Lys, Ser, Arg

If the value of ΔG (actual change in free energy) for a reaction is positive, the reaction will:

Not be spontaneous

Which of the following is correct about biological membranes?

Phospholipid head groups are directed toward the aqueous environment.

Currently, there is much interest in studying the different "omes". Which of the following "ome" is matched with its correct biomolecule?

Proteome - proteins

Plasmids are small, circular DNA molecules that are essential for what?

Replication of nucleus

Which of the following is most likely to be found on the exterior of a protein?

Ser

Which of the following statements about Ramachandran plots is true?

They show that b-sheet and a-helices occupy different O and Y angles.

Water is critical for life and is considered the universal solvent because of its unique properties. However, when temperatures drop below the freezing point of water, ice crystals form and can be lethal to cells. Cold-blooded organisms that live in cold climates have evolved mechanisms to cope with freezing temperatures, one of which is the synthesis of antifreeze proteins that block ice crystal growth. The larval antifreeze protein contains multiple stretches of 12 amino acids, repeating the sequence threonine-cysteine-threonine. The placement of the threonines in the repeating amino acid sequence positions hydroxyl groups at precisely the spacing needed to maximize hydrogen bond formation with the water at the leading edge of the ice crystal, and thereby blocks further growth of the crystal lattice. If all the threonines of an antifreeze protein were changed to valines, what would happen to the protein's ability to bind and form complexes with water?

The protein would not bind water and would lose antifreeze properties.

DNA binding proteins are most commonly

Their surfaces are commonly positively charged

Which THREE of the following statements about autotrophs and heterotrophs on Earth are true?

There are no metabolic differences between autotrophs and heterotrophs. Autotrophs depend on heterotrophs to oxidize sugar and release CO2 into the atmosphere. --->Heterotrophs depend on autotrophs for conversion of light energy to chemical energy. --->Heterotrophs are dependent on autotrophs to generate O2 from H2O in order to support aerobic respiration. Heterotrophs that do not eat autotrophs every day will die in a short time --->The majority of autotrophs on Earth require aerobic respiration in order to survive.

How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment?

They have rigid cells walls.

Energy charge is the relationship between [ATP], [ADP] and [AMP]. Cells regulate the energy charge between 0.7 - 0.9. An energy charge of 0.7 - 0.9 means:

[ATP] larger than either [ADP] or [AMP]

The GroEL-GroES complex is

a chaperone. an ATPase.

DNA samples from four individuals are cleaved with the same endonuclease, and the fragments are separated by gel electrophoresis (as shown above). The DNA is incubated with a probe complementary to part of the DNA.Lanes I, II, III, and IV are the samples from individuals I, II, III, and IV, respectively. Individual I has five restriction sites - A, B, C, D and E (see diagram above). a) Which individual has a point mutation that eliminates restriction site C only? b) Which individual has a point mutation that eliminates restriction sites B and C? c) Which individual has a point mutation that eliminates restriction site A?

a) II b) IV c) cannot be determined

What is the principal type of secondary structure seen in the structure:

a- Helix

The interior stacking of the DNA bases in the double helix provides stability through

hydrophobic and van der Waals interactions.

Which two functional groups are involved in producing a peptide bond?

amino and carboxyl

Fatty acids are important for cell membrane formation because they are

amphipathic.

Fatty acids are important for cell membrane formation because they are _________.

amphipathic.

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

Pyruvate decarboxylase converts pyruvate into _______________.

carbon dioxide and acetaldehyde.

Calcium, Magnesium, Potassium and Sodium are all essential ions. They are also

cations

What type of chaperone is GroEL-GroES?

chamber type