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Silent mutations are DNA mutations that do not result in a ..., Study notes of Molecular biology

The basics a) Define the term "silent mutation". Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein.

Typology: Study notes

2021/2022

Uploaded on 09/12/2022

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1. The basics
a) Define the term "silent mutation"
Silent mutations are DNA mutations that do not result in a change to the amino acid
sequence of a protein
b) What is the "central dogma" of molecular biology?
Biological information flows in only one direction, from DNA to RNA to proteins.
Replication (DNA) ->Transcription (DNA-RNA)->Translation (RNA->protein)
!
!
!
c) Identify the longest open reading frame in the following DNA sequence and translate it
into an amino-acid sequence (note: translation table provided at the end of the exam)
!
TGCGTATGTATGTCAGACGGTGAGACGCTTGCGGGCTAAGCGACG
ATG TCA GAC GGT GAG ACG CTT GCG GGC TAA
M S D G E T L A G
2. Sequence alignment
a) Describe the recurrence and location of answer for global alignment between two
sequences.
Recurrence:
Bottom rightmost cell
pf3
pf4
pf5

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  1. The basics a) Define the term "silent mutation" Silent mutations are DNA mutations that do not result in a change to the amino acid sequence of a protein b) What is the "central dogma" of molecular biology? Biological information flows in only one direction, from DNA to RNA to proteins. Replication (DNA) - >Transcription (DNA-RNA)->Translation (RNA->protein) c) Identify the longest open reading frame in the following DNA sequence and translate it into an amino-acid sequence (note: translation table provided at the end of the exam) TGCGTATGTATGTCAGACGGTGAGACGCTTGCGGGCTAAGCGACG ATG TCA GAC GGT GAG ACG CTT GCG GGC TAA M S D G E T L A G 2. Sequence alignment a) Describe the recurrence and location of answer for global alignment between two sequences. Recurrence: Bottom rightmost cell

b) Perform a global multiple sequence alignment on the following sequences and report the alignment and Sum-of-Pairs score. Use Seq1 as Sc in both (center of star tree). MATCH = +1, MISMATCH = - 1 , GAP = - 1. Seq1: AGT Seq2: ACT Seq3: AGAT Seq1: AGT Seq2: ACT Seq1: AG-T Seq3: AGAT

AG-T

AC-T

AGAT

S(-,-) = 0 (if not we double count)

4. Genome alignment Briefly describe what is depicted in the dot plot below: A large scale inversion event between genome A & genome B.

A

B

4. Data structures: Suffix trees a) Given the following string, construct a suffix tree of ATGTAG a) Label the path of the string GTAG in the above suffix tree. Give the time complexity of finding a query of length ‘n’.

A

G

T

G

TGTAG

TAG

G

GTAG

AG

G