Biology Chapter 15

Proofreading

A mechanism for error correction during DNA synthesis in which a DNA polymerase recognizes and removes a wrong deoxyribonucleotide added during DNA replication and then continues synthesis An important mechanism for achieving accuracy in DNA synthesis

Capsid

A protein shell enclosing the genome of a virus particle

Single-Stranded DNA Binding proteins (SSBPs)

A protein that attaches to separated strands of DNA during replication, preventing them from re-forming a double helix

Primer

A short, single-stranded RNA molecule that base-pairs with a DNA template strand and is used as a starting point for DNA synthesis by DNA polymerase Primase is one type of RNA polymerase

Parental Strands

A strand of pre-existing DNA that is used as a template during DNA synthesis

Mismatch repair

A type of DNA repair used to correct mismatched base pairs in DNA that result from mistakes in DNA synthesis Mismatch repair is the final layer of error detection and correction

Genome

All the hereditary material (DNA in cells, DNA or RNA in viruses) in a virus, cell, or organism, including but not confined to genes

Telomerase

An enzyme that adds DNA to the ends of chromosomes (telomeres) to prevent their shortening by standard DNA synthesis; catalyzes DNA synthesis guided by an RNA template that is part of the enzyme Telomeres are made of short stretches of bases that are repeated over and over. In human telomeres, for example, the base sequence TTAGGG is repeated thousands of times An enzyme called telomerase that carries its own template is involved in replicating chromosomes Without telomerase, the chromosomes of somatic cells, the vast majority of cells in an organism, should gradually shorten with each mitotic division and become progressively smaller as an individual ages The idea that chromosomes get shorter and shorter in cells without telomerase led to the hypothesis that the number of cell divisions possible for a somatic cell is limited by the initial length of its telomeres Many cancer biologists have proposed that telomerase activity allows unlimited division of cancer cells Telomerase is needed only to replicate the ends of a linear DNA. Because bacterial DNAs are circular, they lack ends and don't require telomerase

DNA polymerase

An enzyme that catalyzes synthesis of DNA from deoxyribonucleoside triphosphates. This protein catalyzes DNA synthesis. They can only work in one direction. DNA polymerase can add deoxyribonucleotides only to the 3' end of a growing DNA chain. As a result, DNA synthesis always proceeds in the 5' → 3' direction

DNA Helicase

An enzyme that catalyzes the breaking of hydrogen bonds between nucleotides of DNA, "unzipping" a double-stranded DNA molecule

RNA polymerase

An enzyme that catalyzes the synthesis of RNA from ribonucleotides using a DNA template RNA polymerases, unlike DNA polymerases, do not require a primer to begin synthesis

DNA Ligase

An enzyme that joins pieces of DNA by catalyzing the formation of a phosphodiester bond between the pieces

Topoisomerase

An enzyme that prevents the twisting of DNA ahead of the advancing replication fork by cutting the DNA, allowing it to unwind, and rejoining it. Breaks and rejoins the DNA double helix to relieve twisting forces caused by the opening of the helix

Primase

An enzyme that synthesizes a short stretch of RNA to use as a primer during DNA replication. (leading) Catalyzes the synthesis of the RNA primer (lagging) catalyzes the synthesis of the RNA primer on an Okazaki fragment

DNA Synthesis

DNA synthesis involves a condensation reaction that forms a phosphodiester bond DNA synthesis requires an input of energy The potential energy of the deoxyribonucleotide monomers is first raised by reactions that add two phosphate groups to form deoxyribonucleoside triphosphates (dNTPs) Have a high potential energy, making the formation of the phosphodiester bonds in a growing DNA strand exergonic

Synthesis at the replication fork occurs in three step

Helicase opens the double helix, SSBPs stabilize the exposed single strands, and topoisomerase removes twists downstream of the fork DNA polymerase synthesizes the leading strand after primase has added an RNA primer The lagging strand is synthesized in Okazaki fragments that eventually are joined together

Sliding Clamp

Holds DNA polymerase in place during strand extension

Conservative replication

If the bases of both strands temporarily turned out from the helix, they could serve as a template for the synthesis of an entirely new double helix all at once. This hypothesis, called conservative replication, would conserve the original parental molecule and create a daughter DNA molecule consisting entirely of newly synthesized strands.

Dispersive replication

If the parental double helix were cut at frequent intervals and DNA was synthesized in short sections, then there would be a mix of new and old segments along each replicated molecule. Stretches of old DNA would be interspersed with new DNA down the length of each daughter strand.

Lagging strand/discontinuous strand

In DNA replication, the new strand of DNA that is synthesized discontinuously (as a series of short pieces that are later joined) in a direction moving away from the replication fork.

Leading Strand

In DNA replication, the new strand of DNA that is synthesized in one continuous piece in a direction that follows the replication fork. Also called the continuous strand. Straightforward.

Okazaki Fragments

Short segment of DNA produced during replication of the lagging-strand template. The Okazaki fragments are eventually linked together to produce the lagging strand in newly synthesized DNA

Replication Fork

The Y-shaped site at which a double-stranded molecule of DNA is separated into two single strands for replication Active DNA synthesis takes place at the replication forks of each replication bubble. DNA synthesis is bidirectional - it occurs in both directions at the same time

Complementary base pairing

The association between specific nitrogenous bases of nucleic acids stabilized by hydrogen bonding.

Telomere

The end of a linear chromosome that contains a repeated sequence of DNA

Replisome

The macromolecular machine that copies DNA; includes DNA polymerase, helicase, primase, and other enzymes

Origin of Replication

The site on a chromosome at which DNA replication begins Bacterial chromosomes have only one origin of replication, and they form a single replication bubble Eukaryotes have multiple origins of replication along each chromosomes, forming multiple replication bubbles

Daughter Strand

The strand of DNA that is newly replicated from a template strand of DNA

Semiconservative replication

The way DNA replicates, with each strand of an existing DNA molecule serving as a template to create a new complementary DNA strand

The End Replication Problem

When the replication fork reaches the end of a linear chromosome, a eukaryotic DNA polymerase synthesizes the leading strand all the way to the end of the parent DNA template. As a result, leading-strand synthesis results in a double-stranded copy of the DNA molecule. On the lagging strand, primase adds an RNA primer close to the end of the chromosome DNA polymerase synthesizes the final Okazaki fragment of the lagging strand. An enzyme that degrades ribonucleotides removes the primer. DNA polymerase is unable to add DNA near the end of the chromosome because it cannot synthesize DNA without a primer. As a result, the single-stranded DNA that is left stays single-stranded.

Dna double helix

considered one molecule even though it's made of two strands The DNA molecule is stabilized in two ways: (1) by complementary base pairing, and (2) by hydrophobic interactions between the bases inside the helix

DNA Polymerase III

extends the leading strand/extends the Okazaki fragment. also repairs mismatches

DNA polymerase I

removes the RNA primer and replaces it with DNA