E1 Bioinformatics

Which component is NOT part of a nucleotide?

A. Phosphate

B. Sugar

C. Nitrogenous base

D. Amino acid

D. Amino Acid

The backbone of DNA consists of:

A. Nitrogenous bases and sugars

B. Sugars and phosphates

C. Amino acids

D. Bases and phosphates

B. Sugars and phosphates

Which bond connects the sugar-phosphate backbone?

A. Hydrogen bond

B. Peptide bond

C. Phosphodiester bond

D. Ionic bond

C. Phosphodiester bond

Hydrogen bonds connect:

A. Sugars

B. Phosphates

C. Complementary nitrogenous bases

D. Ribosomes

c. Complementary nitrogenous bases

How many hydrogen bonds connect G and C?

A. 1

B. 2

C. 3

D. 4

C. 3

Which DNA strand is read during transcription?

A. Coding strand

B. Template strand

C. mRNA

D. cDNA

B. Template strand

RNA polymerase synthesizes RNA in which direction?

A. 3'→5'

B. 5'→3'

C. Either direction

D. 1'→5'

B. 5’ to 3’

Which statement about the coding strand is TRUE?

A. It is complementary to mRNA.

B. It is identical to the template strand.

C. It has nearly the same sequence as mRNA except T is replaced by U.

D. It contains uracil.

C. It has nearly the same sequence as mRNA except T is replaced by U.

Which process is represented by DNA → RNA?

A. Translation

B. Replication

C. Transcription

D. Splicing

C. Transcription

Which process is represented by RNA → Protein?

A. Replication

B. Translation

C. Transcription

D. Mutation

B. Translation

Which molecule contains introns?

A. Mature mRNA

B. cDNA

C. Genomic DNA

D. Protein

C. Genomic DNA

Why does cDNA not contain introns?

A. Introns are destroyed during DNA replication.

B. cDNA is synthesized from mature mRNA after splicing.

C. cDNA contains only promoter regions.

D. Introns become proteins

B. cDNA is synthesized from mature mRNA after splicing

What happened when a shorter nucleotide sequence was used in BLAST?

A. Bit score increased and E-value decreased.

B. Both stayed the same.

C. Bit score decreased and E-value increased.

D. Both became zero.

C. Bit score decreased and E-value increased.

Which BLAST program should be used to compare amino acid sequences?

A. Nucleotide BLAST

B. Protein BLAST

C. CLUSTAL Omega

D. GenBank

B. Protein BLAST

Normal adult hemoglobin contains:

A. Four alpha chains

B. Four beta chains

C. Two alpha and two beta chains

D. One alpha and three beta chains

C. Two alpha and two beta chains

The human HBB gene is located on:

A. Chromosome 21q

B. Chromosome 11p15.4

C. Chromosome 7q31

D. Chromosome Xp

B. Chromosome 11p15.4

Which program is used to generate a phylogenetic tree from multiple aligned sequences?

A. Protein BLAST

B. Nucleotide BLAST

C. CLUSTAL Omega

D. GenBank

C. CLUSTAL Omega

A lower BLAST E-value indicates:

A. A less significant match.

B. A match more likely to occur by chance.

C. A more statistically significant match.

D. A shorter sequence.

C. A more statistically significant match. (genuine biological relationship)

Which sequence correctly represents the central dogma?

A. DNA → Protein → RNA

B. RNA → DNA → Protein

C. DNA → RNA → Protein

D. Protein → RNA → DNA

C. DNA → RNA → Protein

Using a shorter query sequence usually causes the E-value to:

A. Decrease

B. Increase

C. Stay the same

D. Become zero

B. Increase

In sequence alignment tools like BLAST, the E-value (Expectation value) indicates the number of chance alignments you can expect to find in a database. Because shorter query sequences have a higher probability of matching database sequences purely by chance, the E-value increases

Using a shorter query sequence usually causes the Max (bit) score to:

A. Increase

B. Stay the same

C. Decrease

D. Become zero

C. Decrease

In BLAST searches, the max bit score is length-dependent. Because shorter query sequences provide fewer potential matching segments and less overall scoring potential, using a shorter sequence will typically result in a lower max bit score and a higher E-value

A higher Max (bit) score indicates:

A. Poor alignment

B. Better alignment

C. More mutations

D. Shorter sequence

B. Better alignment

In sequence alignment tools like BLAST, the bit score is a statistical measure of the similarity between your query sequence and the matched database sequence. A higher score means there are more identical matches and fewer mismatches or gaps, showing a stronger, more significant relationship.

Bioinformatics is the use of:

A. Microscopes

B. Computers to analyze biological data

C. PCR

D. Gel electrophoresis only

B. Computers to analyze biological data

Which statement is TRUE about AUG?

A. It always starts translation.

B. It always codes for methionine.

C. It is a stop codon.

D. It codes for glycine.

B. It always codes for methionine.

Translation occurs at the:

A. Nucleus

B. Ribosome

C. Golgi

D. Mitochondria

B. Ribosome

Which is NOT a stop codon?

A. UAA

B. UAG

C. UGA

D. AUG

D. AUG

AUG codes for:

A. Glycine

B. Methionine

C. Alanine

D. Leucine

B. Methionine

The universal start codon is:

A. UGA

B. UAA

C. AUG

D. UAG

C. AUG

A codon consists of:

A. 2 nucleotides

B. 3 nucleotides

C. 4 nucleotides

D. 5 nucleotides

B. 3 nucleotides

UTR stands for:

A. Universal Translation Region

B. Untranslated Region

C. Universal Transcription Region

D. Unknown Translation Region

B. Untranslated Region

Introns are:

A. Coding regions

B. Removed during RNA processing

C. Ribosomes

D. Codons

B. Removed during RNA processing

Exons are:

A. Removed from RNA

B. Noncoding regions

C. Coding regions

D. DNA enzymes

C. Coding regions

RNA is synthesized in which direction?

A. 3'→5'

B. 5'→3'

C. Either

D. None

B. 5'→3

RNA polymerase reads DNA in which direction?

A. 5'→3'

B. 3'→5'

C. Both

D. Neither

C. 3'→5'

Which process converts RNA into protein?

A. Replication

B. Translation

C. Transcription

D. Splicing

B. Translation

The product of transcription is:

A. Protein

B. DNA

C. mRNA

D. Amino acid

C. mRNA

The product of translation is:

A. DNA

B. RNA

C. Protein

D. Codon

C. Protein

DNA strands run:

A. Parallel

B. Antiparallel

C. Perpendicular

D. Randomly

B. Antiparallel

Genetic information is stored in the:

A. Sugar

B. Phosphate

C. Nitrogenous bases

D. Hydrogen bonds

C. Nitrogenouse bases

Which pair of bases are purines?

A. Cytosine and Thymine

B. Adenine and Guanine

C. Adenine and Cytosine

D. Guanine and Thymine

B. Adenine and Guanine

Which base pair is the strongest?

A. A-T

B. A-U

C. G-C

D. C-T

C. G-C

How many hydrogen bonds connect guanine and cytosine?

A. 1

B. 2

C. 3

D. 4

C. 3

RNA is usually:

A. Double-stranded

B. Triple-stranded

C. Single-stranded

D. Circular

C. Single-stranded

Template DNA

3'-TAC GGA TTT CCG-5'

What is the mRNA?

A. AUG CCU AAA GGC

B. TAC GGA TTT CCG

C. ATG CCT AAA GGC

D. AUG GGA UUU CCG

A

Coding DNA

5'-ATG CCT AAA GGC-3'

What is the mRNA?

A. TAC GGA UUU CCG

B. AUG CCU AAA GGC

C. UAC GGA UUU CCG

D. ATG CCU AAA GGC

B

Template DNA

3'-AAA CGT TGC-5'

Which mRNA is correct?

A. UUU GCA ACG

B. AAA CGU UGC

C. UUU CGA ACG

D. TTT GCA ACG

A

Why are there three possible reading frames?

A. DNA has three strands

B. Translation can begin at nucleotide 1, 2, or 3

C. RNA polymerase reads three strands

D. Every gene has three proteins

B. Translation can begin at nucleotide 1, 2, or 3

An Open Reading Frame (ORF) is:

A. A DNA mutation

B. A possible protein-coding sequence

C. A promoter

D. A chromosome

B. A possible protein-coding sequence

Template DNA

3'-TAC CCG AAA TGA-5'

What is the mRNA?

A. AUG GGC UUU ACU

B. AUG CCC AAA UGA

C. TAC CCG AAA TGA

D. AUG GGG UUU UGA

A

Template DNA

3'-TAC TTT ACT-5'

The correct mRNA is:

A. AUG AAA UGA

B. AUG UUU ACU

C. TAC AAA UGA

D. AUG AAA ACU

A

If the DNA coding strand is

5'-ATG GCT TAA-3'

The mRNA sequence is

A. AUG GCU UAA

B. UAC CGA AUU

C. TAC GCT TAA

D. AUG GCA UAA

A

Which statement is TRUE?

A. Translation occurs before transcription.

B. DNA is translated directly into protein.

C. Transcription produces mRNA, which is translated into protein.

D. RNA polymerase makes proteins.

C. Transcription produces mRNA, which is translated into protein.

Template DNA:

3'-TAC GGT CCA TTT GAA-5'

What is the correct mRNA?

A. AUG CCA GGU AAA CUU

B. TAC GGT CCA TTT GAA

C. ATG CCA GGT AAA CTT

D. AUG GGU CCA UUU GAA

A

ORF Finder is used to

A. Find promoters

B. Find all possible protein-coding regions

C. Translate DNA into RNA

D. Assemble chromosomes

B. Find all possible protein-coding regions

Which strand is actually read during transcription?

A. Coding strand

B. Template strand

C. mRNA

D. Protein

B. Template strand

The coding strand differs from mRNA because

A. RNA contains uracil instead of thymine.

B. RNA is complementary.

C. RNA has different codons.

D. There is no relationship.

A. RNA contains uracil instead of thymine.

Using a shorter nucleotide query generally causes

A.

Higher Max Score

Lower E-value

B.

Lower Max Score

Higher E-value

C.

Both increase

D.

No change

B. Lower Max Score

Higher E-value

cDNA is synthesized from

A.

DNA

B.

Protein

C.

Mature mRNA

D.

tRNA

C. Mature mRNA

The mRNA sequence is

AUG AAA UGA

Translation produces:

A. Met-Lys-Stop

B. Met-Ala-Stop

C. Lys-Met-Stop

D. Met-Gly-Stop

A

Coding strand:

5'-ATG GCT TTT CCG-3'

What is the mRNA?

A. AUG GCU UUU CCG

B. UAC CGA AAA GGC

C. TAC GCT TTT CCG

D. AUG GCA UUU CCG

A.

Notice that you did not reverse the coding strand. You simply replaced T with U because the coding strand already has the same sequence as the mRNA (except DNA uses T and RNA uses U). This is exactly what Dr. Falah emphasized in lecture: the coding strand and mRNA are almost identical, while the template strand is the one RNA polymerase actually reads.

Coding DNA

5'-GGCATGCAATGA-3'

What is the correct mRNA?

A. GGCAUGCAAUGA

B. CCGUACGUUACU

C. GGCTTGCAATGA

D. CCGAUGCAAUGA

A