q4 final biotech correct (copy)

How many species have been named in the last 250 years?

2 million

What are two differences between DNA and RNA?

DNA contains thymine and deoxyribose; RNA contains uracil and ribose.

What is true about transcription?

Transcription makes RNA from DNA and occurs in the nucleus.

What is the importance of the CO1 gene?

It encodes a protein critical to the electron transport chain.

What accounts for higher interspecies variability in the CO1 sequence?

Degeneracy of the genetic code.

What nucleotide position is most impactful when changed?

1st position.

If the expected nucleotide variation is 2%, how many differences will there be in 600 bp?

12 differences.

Why is it important that CO1 has regions of variability and conservation?

Variability distinguishes species; conservation allows primer binding.

What does Proteinase K do?

Cleaves peptide bonds in proteins to help release DNA.

What is the purpose of RNase A?

To digest RNA during DNA purification.

How do we obtain the CO1 sequence?

Extract DNA, PCR amplify CO1, purify, and sequence.

What charge does the silica matrix have?

Neutral (but binds DNA via Na⁺ cation bridge in high salt).

Why does DNA bind to the silica column?

Na⁺ ions create a cation bridge between negatively charged DNA and silica.

What is the purpose of lysis in DNA extraction?

To break open cells and release DNA.

What is the purpose of the binding step?

To attach DNA to the silica membrane in the spin column.

What is the purpose of the wash step?

To remove proteins, salts, and other impurities.

What is the purpose of the elution step?

To release purified DNA from the silica column using water or buffer.

Why does DNA migrate toward the positive electrode in electrophoresis?

DNA is negatively charged due to its phosphate backbone.

What creates the wells in an agarose gel?

A sample comb.

What is the purpose of loading buffer in gel electrophoresis?

To weigh down the sample and track migration with dyes.

Bromophenol Blue migrates at the same rate as what size DNA fragment?

Approximately 300 base pairs.

Why is ethidium bromide useful for visualizing DNA?

It intercalates between DNA base pairs and fluoresces under UV light.

What is the purpose of the wash step in DNA extraction?

To remove unbound contaminants from the column.

What is the purpose of the elution step in DNA extraction?

To release purified DNA from the silica column.

Why does DNA migrate during electrophoresis?

DNA is negatively charged and moves toward the positive electrode.

What is used to create wells in an agarose gel?

Sample combs.

What is the purpose of loading buffer?

It helps the DNA sink and contains tracking dye like bromophenol blue.

Bromophenol Blue migrates with what size DNA fragment in a 1% gel?

Approximately 300 base pairs.

Why is ethidium bromide (EtBr) useful for visualizing DNA?

It intercalates into DNA and fluoresces under UV light.

What is the purpose of running a gel with gDNA?

To verify the presence and quality of genomic DNA.

PCR is based on what natural process?

DNA replication.

During which phase of the cell cycle does DNA replication occur?

S phase.

What is needed for PCR?

Template DNA, DNA polymerase, primers, dNTPs, and buffer.

What are the steps of PCR?

Denaturation, annealing, and extension.

What is the expected size of the CO1 amplicon?

Approximately 650 base pairs.

Why run a DNA ladder on a gel?

For size comparison.

True or false: the forward primer generates the top strand.

True.

Why are ddNTPs useful in sequencing?

They terminate synthesis because they lack a 3' hydroxyl group.

What happens if you use only ddNTPs in a sequencing reaction?

You’d get only 1 bp fragments; you need both dNTPs and ddNTPs for a ladder of different lengths.

What is the first step in sequence editing?

Trimming low-quality bases from the ends.

Why are sequence quality scores low at the ends?

Due to poor resolution of short DNA fragments.

What does the forward sequencing reaction generate?

The sense strand of CO1.

What does the 'N' represent in a DNA sequence?

An ambiguous nucleotide (uncertain base).

What is a contig?

A continuous sequence assembled from overlapping reads.

What are the stop codons in mitochondrial DNA?

UAA, UAG, AGA, AGG.

What indicates a sequencing error when evaluating CO1?

A stop codon appearing in all three reading frames.

What is the importance of DNA barcoding?

Identifying species, conserving biodiversity, and monitoring ecosystems.

What does iBOL stand for?

International Barcode of Life project.

What is BOLD?

Barcode of Life Database, used for storing barcode sequences.

What is the process of barcoding bees?

Collect samples, extract DNA, PCR amplify CO1, sequence.

What are proteins made of?

Amino acids.

What is not a characteristic of amino acid side chains?

Cytotoxicity (this is a property of substances, not side chains themselves).

Where are the instructions to make CO1 found?

Mitochondrial DNA (mtDNA).

What are the bonds within and between DNA strands?

Phosphodiester bonds link nucleotides; hydrogen bonds link complementary strands.

What is meristics?

A traditional method of identifying species based on physical traits.

What are the categories of amino acids?

Basic, nonpolar/hydrophobic, polar uncharged, and acidic.

How do proteins form?

By linking amino acids with peptide (covalent) bonds and releasing a water molecule (condensation reaction).

What is DNA → RNA called, and where does it occur?

Transcription; occurs in the nucleus.

What is RNA → protein called, and where does it occur?

Translation; occurs in the ribosome.

Where does RNA polymerase bind to start transcription?

Promoter regions on the DNA.

Why was CO1 chosen for DNA barcoding?

It’s a protein-coding gene that is conserved across species yet variable enough to distinguish between them.

Why was mitochondrial DNA (mtDNA) chosen for barcoding?

It has high copy number, no introns, and more genetic differences between species.

What organism is agarose derived from?

Red algae, specifically Gracilaria.

At what wavelength is ethidium bromide (EtBr) excited?

Around 300 nm.

At what wavelength does EtBr emit light?

Around 600 nm.

Why must DNA be isolated after PCR before sequencing?

Residual PCR components can reduce sequencing quality.

Why do ddNTPs terminate synthesis in sequencing?

They lack a 3' hydroxyl group, preventing addition of more nucleotides.

What does an electropherogram represent?

The raw output of a DNA sequencing reaction.

What does each peak on an electropherogram represent?

A nucleotide (base) in the sequence.

How are sequencing quality scores determined?

By the shape and resolution of the peaks on the electropherogram.

What is a drawback of the Sanger (chain termination) method of sequencing?

It is inefficient for samples with many species; separating sequences is labor-intensive and costly.