Genetics Exam 1

What are the three components of a nucleotide?

A sugar, a phosphate group, and a nitrogenous base.

How can you distinguish the sugar, phosphate, and base in a nucleotide drawing?

Sugar is a pentose ring that has a phosphate group (PO₄) attached on one side, and a ringed nitrogen-containing structure that is either a purine or pyrimidine on the other side.

What are purines and which bases are purines?

Purines are double-ring bases: adenine (A) and guanine (G).

What are pyrimidines and which bases are pyrimidines?

Pyrimidines are single-ring bases: cytosine (C), thymine (T), uracil (U).

How does DNA differ from RNA in structure?

DNA has deoxyribose (sugar pentose connects with an H) and thymine; RNA has ribose (sugar pentose connects with an OH) and uracil.

How does DNA connect?

The two DNA strands are connected to each other through nitrogenous base pairing (the ladder steps), while each strand’s backbone alternates between sugar and phosphate (the ladder rails). These are linked through phosphodiester linkages.

What does DNA strand directionality mean?

DNA strands have a 5′ end (the phosphate) and a 3′ end (the OH on the sugar).

What bases pair together in double-stranded DNA?

A pairs with T; C pairs with G. A and T have 2 hydrogen bonds, while G and C have 3.

How do bases relate in single-stranded vs double-stranded DNA?

Single-stranded DNA has no fixed pairing; double-stranded DNA follows complementary base pairing.

Why do DNA and RNA strands have directionality?

Because nucleotides are linked through the 5′- and 3′- carbons of the sugar.

Why can DNA replication only proceed in one direction?

DNA polymerase can only add nucleotides to a free 3′-OH group. Meaning that DNA polymerase adds a deoxyribose nucleotide on the 3’.

In what direction does DNA polymerase synthesize/add DNA?

5′ → 3′.

Given one DNA strand, how do you determine the complementary strand?

Use antiparallel orientation and complementary base pairing.

Why is base pairing specific between strands?

Hydrogen bonding patterns and molecular structure allow only A–T and C–G pairing.

What is a replication bubble?

A region of DNA where strands are separated and replication is occurring bidirectionally.

What enzyme separates the DNA strands?

Helicase.

What do single-stranded Binding proteins (SSBs) do?

Stabilize separated DNA strands by coating the separated strands to prevent the DNA from re-annealing or re-forming a double helix.

What enzyme relieves torsional strain ahead of the replication fork?

Topoisomerase. Clips the DNA a little ahead of the helicase so the DNA can rotate feely to release the tension so it does not tangle or break.

What is the replication fork?

The Y-shaped region where the DNA double helix is being unwound and the new DNA strands are synthesized.

What is the leading strand?

The strand synthesized continuously toward the replication fork. (synthesized 5’ to 3’ from a single RNA primer)

What is the lagging strand?

The strand synthesized discontinuously away from the fork. (synthesized 5’ to 3’ from multiple RNA primers).

What is an RNA primer?

A short single stranded sequence of ribonucleotides that act as a crucial starting point for complimentary and antiparallel nucleotides.

What enzyme makes RNA primers?

Primase

What are Okazaki Fragments?

Fragments of RNA primers on the lagging strand are copied from the leading strand to help it catch up in DNA replication.

Which enzyme synthesizes most of the DNA from the RNA primers?

DNA Polymerase III

Whih enzyme removes RNA primers and replaces them with DNA?

DNA polymerase I

What does DNA ligase do?

Seals the gaps of the Okazaki fragments together.

What happens in helicase fails?

DNA strands cannot seperate.

What happens in Primase fails?

DNA polymerase cannot initiate synthesis.

What happens in DNA polymerase III fails?

DNA synthesis stops.

What happens if DNA ligase fails?

Okazaki fragments remain unconnected.

How has DNA replication been studied experimentally?

Using labeled nucleotides and visualization of replication bubbles.

Why is replication of chromosome ends difficult?

RNA primers cannot be replaced at the 5’ end of the lagging strand.

What are telomeres?

Repetitive DNA sequences at chromosome ends.

How do eukaryotes solve the end-replication problem?

By using telomerase.

What is telomerase?

Telomerase is an RNA-dependent DNA polymerase that carries its own RNA template and adds repetitive DNA sequences to the 3′ end of linear chromosomes, allowing complete replication of chromosome ends.

Why does tolomerase add to the 3’ end?

Because DNA polyermase can only add nucleotirde in the 5’ to 3’ direction, so by extending the 3’ to 5’ template, the 5’ to 3’ template also extends.

What type of cells use tolermerase?

Cells that divide frequently and shorten their chromosmes often like germ cells (sperm and egg cells), stem cells, skin cells, intestinal lining cells, blood cells, and cancer cells.

What type of cells do not use telomerase?

Most somatic or body cells, so the older we get the shorter our chromosomes get.

What is the main idea behind Sanger sequencing?

Requires a single stranded template that is heated up to break up the helix. Sanger sequencing starts with a DNA primer (so no RNA is removed or extra enzymes are needed) to start off the DNA polymerase for sequencing. Uses around 200 deoxynucleotides (dNTPs) as normal building blocks for every dideoxynucleotides (ddNTPs) since ddNTPs lack a 3-OH group for o further DNA synthesis. This produces large fragments that reveal the DNA sequence when separated by size.

How does Shotgun sequencing differ from Sanger Sequencing?

It sequences millions of fragments simultaneously. DNA is broken into many small fragments and a computer then reassembles the fragments by finding small overlapping DNA sequences and stitching them together like a puzzle. This is what was used for the first human genome project.

How do you read a DNA sequencing gel?

From bottom to top.

What does each band in a sequencing gel represent?

A DNA fragment ending in a specific base.

What is PCR used for?

Amplifying a specific DNA region. It can make billions of copies of a specific region of DNA by using just two primers.

What are the three steps of PCR?

Denaturation (heat breaks the helix), anneling (primers form hydrogen bonds with complementary nucelotides), and extension (taq polymerase extends the strands adding antiparallel and complementary nucleotides from the primers).

How is PCR similar to DNA Replication?

It uses DNA polymerase and primers.

How is PCR different from DNA Replication?

It uses heat instead of helicase enzymes to split the helix and uses a special DNA polymerase called taq polymerase that can withhold the heat.

What determines the region amplified in PCR?

The primer sequences tell us the beginning and end of the region.

How do you predict the PCR Product?

The DNA sequence between the primers, and including the primers is the amplified region of DNA.

How many DNA molecules result after 32 PCR cycles?

Around 2 billion.

What is an STR?

A short tandem repeat of nucleotides.

What is DNA fingerprinting?

DNA fingerprinting identifies individuals by analyzing STR regions that vary in repeats, since every human has a different number of STRs in their fingertips. This helps us identify missing people, solve crimes, link ancestry, and much more due to humans being 99.9% genetically similar.

How is DNA fingerprinting performed?

PCR amplification of STR region followed by size comparison.

Why might DNA fingerprinting not uniquley indetify an indiviudal.

If few too STRs are tested a profile might not be unique enough because humans can share the same alleles. There are around 20-40 STR loci’s that agencies use to identity individuals and only testing 1 STR gives a 1/10 probability of people this DNA could match, making it pretty common to match with any individual. While testing 10+ STRs, the the probability reduce to 1/850 quintillion, making it very certain that it is linked to an individual.

What experimental system was first used to idenfity genes at the molecular level?

Bacteriopahe infections in bacteria.

What is a bacteriophage?

A virus that infects bacteria.

What is a plaque?

A clear area where bacteria have been lysed or killed.

What is wild-type phage behavior?

Produces small plaques, does not kill much of the virus.

What is a mutant-type behavior?

Produce large plaques, kills most of the virus and does not function.

What does diploidy allow scientists to study?

Dominance and complementation

What is diploidy?

Having two copies of each gene usually one copy from mom and the other from dad, these help establish dominance and recessive traits.

What is a pseudo diploid?

A cell that has dipolody or contrains two copies of a gene.

What is complementation?

When two recessive mutations complement or fix each other and now work because the problems are in different genes so now the normal phenotype appears.

If a mutation complements, what does that mean?

The mutation where in different copies of the pseudo diploid and the normal phenotype appears.

If a mutation fails to complement, what does that mean?

The mutation are in the same copy of the pseudo diploid and the normal phenotype does not appear as the mutation takes over.

How can complementation tests reveal recombination within a gene?

Recombination between different mutations within the same gene can restore a functional copy of the gene, producing a normal (wild-type) phenotype.

What is the advantage of working with diploids over haploid?

They can mask mutations due to containing two genes, unlike haploids that only carry one.

Where in the bacteriophage produced by an infection is the P32 isotope found?

the DNA or the Bacteria

Where in the bacteriophage produced by an infection is the S35 isotope found?

the Protein or Extracellular Fluid

Which nucleotides denature more?

A and T denature and break more, while C and G denature less and are harder to break.

What happens if there is a double-strand break in DNA?

The DNA can either go back to normal, get deleted completely, or get inverted.

How do you determine the order of genes that are closest to farthest from replication?

The faster a cell replicates, the closer it is to the replication site, while the slower a cell replicates, the further away it is from the replication site.

If there is a normal nucleotide length but a wrong sequence at the end of a chromosome, where is the mutation?

In the RNA template.

If there is a normal nucleotide sequence but a wrong length at the end of a chromosome, where is the mutation?

In the enzyme telomerase.

If there is a wrong nucleotide sequence but a wrong length at the end of a chromosome, where is the mutation?

A major mutation in telomerase function.

What do STR gel bands represent?

Each band represents how many alleles are in a STR. (Humans are diploid, so we have 1 at minimum and 2 at maximum).