MCAT Nucleic Acids

To do: Start at Repair of DNA

What are the two main types of nucleic acids in living organisms?

Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA)

What is the structural difference between DNA and RNA?

DNA lacks a Hydroxyl at the 2’ carbon

Genome

The genetic content of a cell

What are the monomers called for DNA or RNA?

Nucleotides

What are the there components of a nucleotide?

A Nitrogenous base, a pentose (5 carbon) sugar, and a phosphate group.

What are the 4 nucleotides of DNA?

ATCG

What are the 4 nucleotides of RNA?

AUCG

What are the base pairings for DNA?

A to T, C to G

What are the base pairings for RNA?

A to U, C to G

What is the purpose of DNA?

the genetic information of the cell

What is the purpose of RNA?

A short-lived sequence used for converting DNA to proteins without moving the DNA itself

Why are nitrogenous bases considered organic molecules?

They contain carbon and nitrogen

Why are nucleotides considered bases?

They have an amino group that can attack Hydrogens, reducing the acidity of their environment

What is the full base name of A?

Adenine

What is the full base name of T?

Thymine

What is the full base name of C?

Cytosine

What is the full base name of G?

Guanine

Which contains a Phosphate group? Nucleotide or Nucleoside?

Nucleotide

Which pentose sugar is used in DNA and RNA?

Ribose

Where is the phosphate group attached on a ribose?

To the 5’ carbon

What is a nucleoside?

Only contains a nitrogenous base and a pentose sugar

What is a Purine, and which bases fall under this category?

2 rings, A and G

What is a Pyrimidine, and which bases fall under this category?

3 rings, C, U, and T

Which base is this?

Adenine

Which base is this?

Guanine

Which base is this?

Ctyosine

Which base is this?

Uracil

Which base is this?

Thymine

What is the structure of Ribose?

5 carbons and a 5 member ring, but Oxygen connects the 1’ and 4’ carbons, leaving the 5’ hanging off of the 4’ carbon. Hydroxyls are attached to both the 2’ and 3’ (RNA) or just the 3’ (DNA)

In what form does DNA usually exist?

A right handed double helix, with the strands running anti parallel to each other, forming major and minor grooves every 10 base pairs

What model describes the structure of DNA?

Watson-Crick Model

How do the complementary strands of DNA bind to each other?

Hydrogen bonds between their bases

In what form does RNA usually exist?

A single strand

How many H bonds are formed between A and T?

2

How many H bonds are formed between C and G?

3

What atoms are involved in H bonds? (Other than Hydrogen, duh)

Fluorine, Nitrogen, and Oxygen

How is base pairing used for proof reading in DNA replication?

Wrongly paired bases will fail to H bond correctly and create a bump

What is Replication?

The process by which DNA is copied during cell division

What is a Gene?

The basic functional unit of heredity

What is a Trait?

A physical feature of an organism

What is DNA denaturation?

Breaking the H bonds between complimentary strands and separating them

How is DNA denaturation induced?

High temperatures and certain chemicals

What is Reannealing?

Gradually decreasing temperature so denatured DNA strands can H bond again

What is hybridization?

Two DNA strands rejoin via H bonding in a position that is different than usual

What type of conservative replication does DNA undergo?

Semiconservative, each daughter helix contains one original and one new strand

Where does DNA replication start?

Origins of replication

What enzyme unzips DNA by disrupting H bonds?

Helicase

What reaction does Helicase use to break H bonds between paired bases?

ATP Hydrolysis

What is it called when DNA is unzipped at an origin of replication?

A replication bubble, with two replication forks, one on each side

What is the function of DNA polymerase?

Adding free nucleotides onto a complimentary template strand

Which direction does DNA pol add in?

5’ to 3’

Which direction does DNA pol read the template strand?

3’ to 5’

How does DNA pol have intrinsic proof reading activity?

3’ to 5’ exonuclease activity

What links adjacent nucleotides in DNA or RNA?

Phosphodiester linkage

To what part of a nucleotide does DNA pol add the next nucleotide?

To a 3’ Hydroxyl group

What is a phosphodiester bond?

3’ OH to 5’ phosphate group

Can DNA pol add in any direction?

No, only 5’ to 3’

How is the lagging strand synthesized?

DNA primase synthesizes a short RNA primer, to which DNA pol can add nucleotides in its proper direction, forming Okazaki fragments

What are Okazaki fragments?

Short sequences of RNA and DNA that make up the broken lagging strand

How are Okazaki fragments joined into the complete lagging strand?

DNA pol 1 (prokaryotes) or Flap Endonuclease 1 (Eukaryotes) removes the RNA primer, DNA pol fills the gap, then DNA ligase joins the fragments

Which direction do replication forks move?

They move in opposite directions on both strands, so there are 4 replication processes happening in a single replication bubble (2 leading and 2 lagging strands)

Topoisomerase

Enzymes that prevent supercoiling DNA ahead of the replication forks by introducing breaks

What is Conservative replication?

The two parental strands of DNA stay together, while the new DNA is made up of completely new strands

What is DIspersive replication?

The original and new helices have bits of the parental strands dispersed throughout

What do Single Stranded binding proteins do?

coat the DNA around the replication fork to prevent rewinding of the DNA

What does the sliding clamp do?

helps hold DNA pol in place as it adds nucleotides

What enzymes are involved in lagging strand synthesis?

DNA primase and DNA pol 3

What does DNA pol 3 do?

Adds nucleotides in 5’ to 3’ direction

What does DNA pol 1 do?

Replaces nucleotides where exonuclease removed the RNA primer

What does DNA pol 2 do?

Repairs DNA

What is the difference between enzymes involved in prokaryotic vs eukaryotic replication?

Eukaryotes may subdivide a single prokaryotic enzyme into multiple

What is supercoiling?

Over or underwinding of the DNA helix that creates strain

What is an origin of replication?

A specific site in DNA where replication begins

What is the difference in numbers of origins of replication in prokaryotes vs eukaryotes?

Eukaryotes can have multiple origins of replication while circular prokaryotic DNA only has 1

What is a replisome?

A replication bubble in circular prokaryotic DNA

What is the difference in structure and replication between prokaryotic DNA and eukaryotic DNA?

Eukaryotic DNA is linear and thus the ends cannot be completely replicated, leading to shortening

What are the repeating end segments of Eukaryotic DNA called and what is their purpose?

Telomeres provide a buffer so that no important genes are accidentally lost

What enzyme can extend telomeres?

Telomerase

What is the end-replication problem?

An RNA primer cannot be synthesized for the very end of DNA, leading to the loss of genetic information that is coded there

In which cells is Telomerase active and inactive?

Active in germ cells, deactive in somatic cells

What are Germ cells?

Specialized cells that give rise to gametes (eggs and sperm)

What are somatic cells?

Any biological cell making up the body of an organism that isn’t a reproductive cell

What kind of polymerase is Telomerase?

RNA dependant DNA polymerase (extends DNA using RNA as a template)

What is the Central Dogma?

DNA makes RNA makes Proteins

What type of organism goes against the Central Dogma?

Retroviruses, which can convert their RNA to DNA and insert it into the host genome

What is a dimer?

Two of the same purine form H bonds with each other on the same strand rather than to the complimentary strand

What are Thymine dimers caused by?

UV radiation

How is a dimer repaired?

Nucleotide excision repair: Helicase unzips the DNA, excinuclease cuts them out, DNA pol fills the gap, and DNA ligase mends the cuts

What enzymes does base excision repair use?

glycosylases

What do Glycosylases do?

Each Glycosylase detects and removes a specific kind of damaged base

What chemical reaction can convert a Cytosine to Uracil?

Deamination

What chemical reaction is this?

Deamination

What is the most serious type of DNA damage?

A double stranded break

What are the two pathways for repairing a double stranded DNA break?

non-homologous end joining and homologous recombination

What is non-homologous end joining, and what are its drawbacks?

The two ends of a double stranded DNA break are glued back together, this can add in extra nucleotides at the cut site

What is homologous recombination, and what are its drawbacks?

DNA from a homologous chromosome or chromatid is used to repair the break, and usually doesn’t cause mutations

What is the difference between chromosomes and chromatids?

During DNA replication, a chromosome will be made up of 2 sister chromatids, forming an X shape, that separate to go into the two daughter cells

What are the steps of Mitosis?

Prophase, Metaphase, Anaphase, and Telophase

What is the acronym for Mitosis?

PMAT

What occurs during Prophase?

Chromosomes condense, the mitotic spindle forms, and the nuclear membrane begins dissolving