Republic of the Philippines
NUEVA VIZCAYA STATE UNIVERSITY
Bayombong, Nueva Vizcaya
COLLEGE OF TEACHER EDUCATION
Graduate Program
SEGS-CHEMISTRY OF LIFE
PROBLEM SET
(DNA, RNA, and Nucleotides,
Enzymes and Metabolism
Submitted by:
EMEROS R.CASTILLO
Ph.D. (SEGS), student
Submitted to:
DAISY V. RIVERA, Ph. D.
Subject Instructor/Professor
1. Name the following Nucleotides (5 points)
A strand of DNA has the following sequence:
a. Guanosine 5’-diphosphate
5' TCG TTT ACG ATC CCC ATT TCG TAC TCG 3'
b. Adenosine 3’, 5’-monophosphate
a) what is the sequence of its complementary strand?
Given: 5' TCG TTT ACG ATC CCC ATT TCG TAC TCG 3'
2. Protein coding: Consider the following mRNA: Complementary: 3' AGC AAA TGC TAG GGG TAA AGC ATG AGC 5'
AGU CUC UGU CUC CAU UUG AAG AAG GGG AAG GGG Strand
The sequence of the complementary strand is (notice the 5’→ 3’ orientation):
AGU GCU CUG UCU CCA UUU GAA GAA GGG AAG GGG
5' TCG AGT ACG AAA TGG GGA TCG TAA ACG 3'
a) indicate the amino acid sequence which would be coded (read from 5’ to b) what is the base sequence of mRNA transcribed from the first strand?
3’). Use the table containing the genetic code. Answer:
Answer: The RNA sequence obtained after the transcription of the DNA sequence
provided will be identical to the sequence of the complementary strand, with the
Ser - Leu - Cys - Leu - His - Leu - Lys - Lys - Gly - Lys - Gly exception of the presence of uracil in place of thymine:
5' UCG AGU ACG AAA UGG GGA UCG UAA ACG 3'
b) you obtain mutations which consist of additions or deletions of one
nucleotide. If we insert G between the third and fourth nucleotide, and we
eliminate the 10th nucleotide from the right (it is a G), what would be the c) what is the coded amino acid sequence?
peptide sequence?
The amino acid sequence is obtained after first separating the mRNA sequence into
codons:
5' UCG AGU ACG AAA UGG GGA UCG UAA ACG 3'
G
AGU GCU CUG UCU CCA UUU GAA GAA GGG AAG GGG Ser-Ser-Thr-Lys-Trp-Gly-Ser-Stop
Ser - Ala - Leu - Ser - Pro - Phe - Glu - Glu - Gly - Lys - Gly
d) what is the coded amino acid sequence if the second T from the 3’ end of the DNA
is deleted?
3. Protein coding.
Deleting the second T from the 3’ end of the DNA molecule gives us the concentrations of the electron donors and electron acceptors contribute
following nucleotide sequence: significantly to the value of E'°. Under nonstandard conditions, the potential can
either add to an already favorable ΔE'° or be such a large positive number as to
“overwhelm” an unfavorable ΔE'°, making ΔE favorable.
T
5' TCG TTT ACG ATC CCC ATT TCG ACT CGA 3' Calculate first the ΔE'° for the reaction.
Transcribing this DNA will give us (5’ → 3’ orientation):
ΔE'° = (E'° of electron acceptor in the reaction) ꟷ (E'° of electron donor in the
5' UCG AGU CGA AAU GGG GAU CGU AAA CGA 3' reaction).
And the corresponding protein sequence will be:
c.) Favorable.
Ser-Ser-Arg-Asn-Gly-Asp-Arg-Lys-Arg
ΔE'° = (E'° for pyruvate/lactate) ꟷ (E'° for NAD+/NADH)
4. Which of the following reactions would you expect to proceed in the direction = ꟷ 0.185 V ꟷ (ꟷ 0.320 V)
shown, under standard conditions, assuming that the appropriate enzymes are
present to catalyze them? Discuss briefly your choice. (10 points) = 0.135 V
d.) Favorable.
a) Malate + NAD+ → oxaloacetate + NADH + H+
b) Acetoacetate + NADH + H+ → β-hydroxybutyrate + NAD+ ΔE'° = (E'° for pyruvate/lactate) ꟷ (E'° for acetoacetate/β-hydroxybutyrate)
c) Pyruvate + NADH + H+ → lactate + NAD+ = ꟷ 0.185 ꟷ (ꟷ V 0.346 V)
d) Pyruvate + β -hydroxybutyrate → lactate + acetoacetate = 0.161 V
e) Malate + pyruvate → oxaloacetate + lactate
5. In a laboratory experiment, two groups of rats are fed two different fatty acids
f) Acetaldehyde + succinate → ethanol + fumarate as their sole source of carbon for a month. The first group gets heptanoic acid
(7:0), and the second gets octanoic acid (8:0). After the experiment, a striking
Answer difference is seen between the two groups. Those in the first group are healthy
and have gained weight, whereas those in the second group are weak and have
It is important to note that standard conditions do not exist in the cell. The value lost weight as a result of losing muscle mass. What is the biochemical basis for
of ΔE'°, as calculated in this problem, gives an indication of whether a reaction this difference? Discuss (5 points)
would or would not occur in a cell without additional energy being added
(usually from ATP); but ΔE'° does not tell the entire story. The actual cellular
Answer: ATP + H2O → ADP + Pi
The β oxidation of heptanoic acid (which has an odd number of carbons) In a cell at steady state, for every mole of ATP hydrolyzed, a mole of ATP is
produces the three-carbon intermediate propionyl-CoA, which can be converted formed by condensation of ADP + Pi. There is no net change in [ATP] and thus
by propionyl-CoA carboxylase to methylmalonyl-CoA, then to succinyl-CoA. no net production of H2O.
This four-carbon product of fatty acid oxidation can then be converted to
oxaloacetate in the citric acid cycle, and the oxaloacetate can be used for
gluconeogenesis—thus providing the animal with carbohydrate as well as
energy from fatty acid oxidation. Animals fed octanoic acid (with an even
number of carbons) degrade it completely to acetyl-CoA by three rounds of β
oxidation. This provides energy via the citric acid cycle but does not provide
starting material for gluconeogenesis. These animals are therefore deficient in
glucose, the primary fuel for the brain and an intermediate in many biosynthetic
pathways.
6. Sources of H2O Produced in β Oxidation. The complete oxidation of palmitoyl-
CoA to carbon dioxide and water is represented by the overall equation
Palmitoyl-CoA + 23O2 + 108Pi + 108 ATP + 23H2O →
CoA + 16CO2 + 108ATP + 23H2O
Water is also produced in the reaction
ADP + Pi → ATP + H2O
But not included as a product in the overall equation. Why?
Answer:
ATP hydrolysis in the cell’s energy-requiring reactions uses water, in the
reaction
