Bio midterm 2

Gene

A segment of DNA that contains the instructions for making a specific protein or RNA molecule.

Base pairing

The specific hydrogen bonding between purines and pyrimidines in DNA or RNA (A with T or U, G with C).

Complementary base pairing

The matching of DNA or RNA bases through hydrogen bonds: 1. Puridines pair with pyrimidines. 2. A pairs with T (or U in RNA), and G pairs with C.

Also stacking of base pairs has van der waals interactions that support the structure

Antiparallel

The orientation of the two strands of DNA running in opposite directions (5' to 3' and 3' to 5').

Genome

Complete set of genetic material (DNA) in an organism

Chromosome

long organized structure of DNA and protein that contains many genes; humans have 46 chromosomes in somatic cells

Somatic cell

any cell in the body not sperm or egg; contains full set of chromosomes

Histone

A family of proteins that associate with DNA in the nucleus and help condense it into chromatin.

Nucleosome

The fundamental unit of chromatin, consisting of DNA wrapped around a core of histone proteins

Chromatin

A complex of DNA and protein found in eukaryotic cells that condenses to form chromosomes during cell division

ATP Dependent chromatin remodeling complex

A protein complex that uses the energy from ATP hydrolysis to reposition or restructure nucleosomes

Histone tail

The flexible N-terminal region of a histone protein that extends out from the nucleosome and can be modified to affect DNA/gene accessibility

Homologous chromosome

Pairs of matching chromosomes, one inherited from each parent, found in somatic cells, containing the same genes in the same order but potentially different alleles (versions of a gene

Aneuploidy

A genetic condition characterized by an abnormal number of chromosomes (missing: monosomy or extra: trisomy)

Semiconservative replication

Each new DNA molecule consists of one original strand and one newly synthesized strand

Origin of replication

A-T rich sequence(s) in the genome where DNA replication begins

Replication bubble

The unwound and open region of a DNA molecule where replication occurs

Replication fork

The Y-shaped structure formed where the DNA is split into two strands for replication. Occurs at each end of the replication bubble

Helicase

Enzyme that unwinds the DNA double helix at the replication fork

Single-strand binding protein???????????

Proteins that bind to and stabilize single-stranded DNA to prevent re-annealing???????

Topoisomerase

An enzyme that relieves tension ahead of the replication fork by cutting and rejoining DNA strands

Primase

An enzyme that synthesizes short RNA primers needed to start DNA synthesis.

DNA polyemerase

The enzyme that synthesizes new DNA strands by adding nucleotides to a primer or pre-existing strand

Sliding clamp

A protein that holds DNA polymerase in place during strand extension

Telomerase

An enzyme that extends the ends of linear chromosomes (telomeres)

Leading strand

The DNA strand that is synthesized continuously in the direction of the replication fork

Lagging strand

The DNA strand synthesized discontinuously away from the replication fork

Okazaki fragment

Short DNA fragments synthesized on the lagging strand

End replication problem

The inability of DNA polymerase to fully replicate the ends of linear chromosomes, leading to gradual shortening

Nuclease

An enzyme that removes nucleotides from DNA, often used in repair

Repair polymerase

A DNA polymerase that fills in gaps with nucleotides during repair processes

Ligase

An enzyme that seals breaks in the DNA backbone by forming phosphodiester bonds

Mismatch repair

A repair mechanism that corrects mismatch errors missed by DNA polymerase proofreading

Excision repair

A repair system that corrects DNA errors/damage caused by spontaneous base changes, radiation, oxidation, or chemicals

Depurination

Loss of a purine base (adenine or guanine) from the DNA backbone

Happens billions of times per second

Deamination

Removal of an amino group from a base, often converting cytosine to uracil

Mutation

Permanent change in the DNA sequence

Pyrimidine dimers

Covalent linkages between adjacent pyrimidine bases (usually thymine), often caused by UV light

Double-stranded DNA break

A severe form of DNA damage involving breaks in both strands of the DNA helix

Nonhomologous end joining

A repair pathway that joins broken DNA ends without requiring a homologous template

Homologous recombination

A precise repair pathway using a homologous DNA sequence as a template

Sister chromatid

One of two identical copies of a single replicated chromosome, joined together by a common centromere

DNA Duplex

The double-stranded structure of DNA formed by complementary base pairing between two strands

Polymerase chain reaction

A technique used to amplify a specific DNA segment exponentially using cycles of heating and cooling

Primer

A short strand of DNA (DNA used in PCR) or RNA that provides a starting point for DNA synthesis

Anneal or hybridize

The process by which primers bind to their complementary sequences on the template DNA during PCR

PCR cycle

One round of denaturation, annealing, and extension steps in PCR, repeated multiple times to amplify DNA

PCR product

The DNA fragment that is amplified during the PCR process

Agarose gel electrophoresis

A technique used to separate DNA fragments by size using an electric field in an agarose gel matrix

Plasmid

A small, circular DNA molecule used as a vector to carry foreign DNA into a host cell

Restriction enzyme

An enzyme that cuts DNA at specific recognition sequences, often used in cloning

Cloning (molecular)

The process of creating identical copies of DNA fragments by inserting them into a plasmid vector and then into host cells to be copied

Sanger sequencing

A method of DNA sequencing that uses chain-terminating nucleotides to generate DNA fragments of varying lengths

Chain-terminating nucleotides

Modified nucleotides (missing the 3’ OH) that stop DNA synthesis when incorporated, used in Sanger sequencing