SECOND-TEST-ON-MOLECULAR-BIOLOGY...

maaria_07

Biología Celular y Molecular

1º Grado en Ingeniería Biomédica

Escuela Politécnica Superior. Campus Leganés

Universidad Carlos III de Madrid

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 No se permite la explotación económica ni la transformación de esta obra. Queda permitida la impresión en su totalidad.
SECOND TEST ON MOLECULAR BIOLOGY. 19 May 2021

NAME Maria de Evan

UC3M number 100450937
DNI 06609716E
EACH QUESTION SCORES 2 POINTS
THE TEST LASTS 90 MIN (10:30-12:00). THEN YOU HAVE 10 MIN TO UPLOAD IT (PDF
FORMAT) TO AULA GLOBAL AND SEND IT TO jjorcano@ing.uc3m.es
(TIME LIMIT 12:10)

1. You are 60 years old and you are a tourist in Los Angeles. The metropolitan area of Los
Angeles, Long Beach and Glendale, has been defined as one of the worst air quality

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areas of USA, with an overhead of 1322 deaths related to pollution per year.
Moreover, this region also has the worst index relative to ozone concentration and
small particles in air in the country. Cite all possible DNA damages that will be hitting a
cell of your body at the moment that you decide to go to the beach and eat a
hamburger. Cite also all the associated repair mechanisms.

Three possible DNA damages are really possible to occur

1.Oxidation, caused by radiation and air pollution, is repaired by base excision repair
(BER)
2.Alkylation, that consists of the addition of an ethyl or methyl and is caused by
environmental carcinogens. This damage is repaired by nuclear excision repair (NER)
and photoreactivation repair (which is activated by light)
3. Thymine dimers, that is caused by light exposure and UV radiation, and affect the
backbone of the nucleotide chain. This type of damage is repaired by nuclear excision
repair (NER)

It also may occur other damages as single and doble strand break:
-Single strand break, which is caused by ROS and UV radiation, is repaired by a
mechanism where PNK enzyme, DNA polymerase and DNA ligase take part
-Doble strand break, that is caused by exogenous agents (radiation, genotoxic
chemicals), can be repaired by two different procedures, non-homologous end joining
and homologous recombination

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 2. Describe all types of signaling proteins that you can recognize in the following draw:

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Relay proteins: pass the message to the next signaling component. They switch between two
states (on/off). When they are activated, they are able to transmit the message (RAS)

Messenger proteins: Proteins with ability to translocate to the nucleus once activated and

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induce transcription of particular genes. They are normally situation at the end of the
transcription chain. (ERK1/2)

Anchoring proteins: maintain specific signaling proteins at a specific location by tethering them
to a membrane. They normally lack from enzymatic activity. Contain a variety of protein- and
lipid- binding domains that allow to maintain binding partners at a short distance, facilitating
the creation of a larger signaling complex attached to a lipid bilayer. (RAF)

Adaptor proteins: link one signaling protein to another without themselves participating in the
signaling event. Adaptors use different domains to couple one signaling protein to another.
Contain a variety of protein-binding domains that allow to maintain binding partners at a short
distance, facilitating the creation of a larger signaling complex in the vicinity of activated
receptors. (Grb2)

Modulator proteins: modify the activity of intracellular signaling proteins and regulate the
strength of signaling along the pathway. Their presence says how much time, different
components, should be activated. (MEK1/2)

Amplifier/transducer proteins: usually either enzymes or ion channels that enhance the signal
they receive by converting it to a different form. In general, they are proteins that produce or
transport second messengers, small organic molecules that can be produced in large range and
rapidly diffuse through the cytosol (RTK)

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 3. A) Explain why if you are given a protein sequence, you cannot predict the exact RNA
sequence that was used by the cell to generate that sequence.

Each 3 nucleotides form a codon, and each codon codifies for an amino acid. There are more
codons than amino acids and, therefore, the code is redundant, which means that more than
one codon codifies for one amino acid. This makes it impossible to predict the codon sequence
based on the sequence of amino acids.

B) Now, you have just sequenced a short segment of DNA. Find the longest open reading
frame (ORF) of the resulting protein.

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1º strand of the DNA: 5'-TCAATGTAACGCGCTACCCGGAGCTCTGGGCCCAAATTTCATCCACT-3'

2º strand of the DNA: 3’-AGTTACATTGCGCGATGGGCCTCGAGACCCGGGTTTAAAGTAGGTGA-5´

mRNA: 5´- UCAAUGUAACGCGCUACCCGGAGCUCUGGGCCCAAAUUUCAUCCACU-3'

protein: N-met-C

As the start codon is next to the stop codon, we have a chain that consist only in one amino acid.

4. Below is the double-stranded DNA sequence of part of a hypothetical yeast genome, which
happens to contain a very small gene. Transcription starts at the Transcription Start Site (TSS)

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after the promoter (shown in yellow), and proceeds in the direction of the arrow. Transcription
stops at the end of the Transcription Terminator (shown in blue).

a) Which strand of DNA shown, the top or the bottom, is the template strand?

Bottom

b) What is the sequence of the mRNA produced from this gene? Label the 5’ and 3’ ends.
5’-GAGCCAUGCAUUAUCUAGAUAGUAGGCUCUGAGAAUUUAUCUC-3’

c) What is the sequence of the protein produced from the mRNA in (b)? Label the N and C
termini.

We must start by the start codon (AUG)

N-met-his-tyr-leu-asp-ser-arg-leu-C

If a mutation were found where a T/A (top/bottom) base pair were added immediately after
the T/A base pair shown in bold.

d) What would be the sequence of the mRNA?

5’-GAGCCAUGCAUUUAUCUAGAUAGUAGGCUCUGAGAAUUUAUCUC-3’

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 e) What would be the sequence of the protein?

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N-met-his-leu-ser-arg-C

If a similar mutation were produced after the 5th nucleotide:

f) How will change the mRNA?

5’-GAGCCUAUGCAUUUAUCUAGAUAGUAGGCUCUGAGAAUUUAUCUC-3’

g) How will change the protein sequence?

N-met-his-tyr-leu-asp-ser-arg-leu-C.
It is exactly the same as the first one because the mutation is not included in the part we are
translating

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5.- A mutation in DNA generates a UGA stop codon in the middle of the mRNA coding for a
particular protein. A second mutation in the cell’s DNA leads to a single nucleotide change in a
tRNA that allows the correct translation of the protein; that is, the second mutation
“suppresses” the defect caused by the first. The altered tRNA translates the UGA as
tryptophan.
A) What nucleotide change has probably occurred in the mutant tRNA molecule?

After the first mutation, the mRNA presents a stop codon, which is UGA. After the second
mutation, that codon instead of codifying for a STOP codon, now codifies for Trp codon (UGG),
there has been a switch between a Guanine for an Adenine. Therefore, the tRNA that should
be bounded now to that codon is ACC instead of ACU.

B) What consequences would the presence of such a mutant tRNA have for the translation of
the normal genes in this cell?

If the mutant tRNA is allowed to translate, then the sequence of amino acids of that particular
protein will be altered (i.e will not be as the original one). This will lead to a defective protein
molecule which will have different types of consequences. This change could be light and not
cause any huge genetic disorders in the person. However, this change could have a bigger
impact in the synthesis of the protein and end up leading to occurrence of a diseases in the
person.

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