Genetics Exam 2

3’ end of DNA

The end of a polynucleotide strand with a 3’ hydroxyl (–OH) group; DNA is extended in this direction during synthesis.

5’ end of DNA

The end of a polynucleotide strand with a 5’ phosphate group.

antiparallel

The two DNA strands run in opposite directions (one 5’→3’, the other 3’→5’)

base pairing

The specific matching of complementary bases: A with T (or U) and C with G

biomolecule

A molecule produced by living organisms that performs essential functions such as energy storage, structure, or genetic information storage

carbohydrates

Biomolecules made of sugars that primarily provide quick energy (e.g., glucose, starch

centromere

The highly condensed chromosome region where sister chromatids are held together and spindle fibers attach

Chargaff’s Rule

In double-stranded DNA, the amount of A = the amount of T and the amount of G = the amount of C due to complementary base pairing

chromatin

DNA combined with proteins that helps package DNA in the nucleus.

chromosome

A condensed structure of DNA and protein that organizes genetic material; only present during cell division

complementary

The sequence of one DNA strand determines the sequence of the other due to base pairing rules

dNMP (deoxyribonucleoside monophosphate)

A nucleotide with one phosphate group; the form incorporated into DNA

dNTP (deoxyribonucleoside triphosphate)

A nucleotide with three phosphate groups; the high-energy form used during DNA synthesis

deoxyribose

the 5-carbon sugar in DNA that has an H at the 2’ carbon

DNA

A biomolecule that stores the genetic instructions for an organism’s development and function

euchromatin

Less condensed chromatin where most gene expression occurs.

genome

The complete set of DNA in an organism.

heterochromatin

Highly condensed chromatin with little to no gene expression.

hydrogen bonds

Weak bonds that hold complementary base pairs together between DNA strands, allowing strands to separate when needed

lipids

Biomolecules involved in long-term energy storage, insulation, and signaling; include fats and oils

macromolecule

A large molecule made of many smaller subunits

molecule

A group of atoms bonded together by sharing or exchanging electrons.

molecular genetics

The branch of biology that studies the structure and function of genes at the molecular level, focusing on how DNA, RNA, and protein products interact to control cellular and organismal functions

monomer

A small, basic molecule that can bond with others to form a larger chain (building block)

nitrogenous base

the variable part of a nucleotide (A, T (or U), C, or G) that encodes genetic information

nucleic acids

Biomolecules (DNA and RNA) that store and transmit genetic information.

nucleotide

The monomer of DNA, made of a sugar, phosphate group, and nitrogenous base.

phosphate group

A component of a nucleotide attached to the 5’ carbon that helps form the DNA backbone

phosphodiester bond

A strong covalent bond linking nucleotides along the sugar-phosphate backbone

polymer

A long chain made of repeating monomers.

polymerization

The chemical process of linking monomers together to form a polymer

polynucleotide

A polymer made of many nucleotides linked together (a single DNA or RNA strand)

primary structure of DNA

The linear sequence (order) of nucleotides in a single DNA strand.

protein synthesis

The process by which DNA provides instructions to build proteins.

proteins

Biomolecules made of amino acids that perform structural and functional roles in cells

purine

A nitrogenous base with two rings (adenine or guanine).

pyrimidine

A nitrogenous base with one ring (cytosine or thymine).

secondary structure of DNA

The three-dimensional double helix formed by two complementary DNA strands

supercoiling

The over- or under-winding of DNA to help it fit in the cell and regulate access

telomere

The highly condensed region of a chromosome that acts as a protective end to prevent DNA degradation and fusion.

tertiary structure of DNA

The higher-order folding and packaging of DNA into supercoils and chromosome

bidirectional replication

DNA replication proceeds in two directions from each origin, with replication forks moving away from each other

DNA ligase

An enzyme that joins Okazaki fragments together to form a continuous DNA strand.

DNA polymerase I

The enzyme that replaces the RNA primers with DNA nucleotides.

DNA polymerase III

The enzyme that builds new DNA strands by adding nucleotides in the 5’→3’ direction.

DNA replication

The process of making an exact copy of DNA before cell division.

enzyme

A protein that catalyzes (speeds up) chemical reactions by building or breaking bonds without being used up

helicase

An enzyme that unwinds DNA by breaking hydrogen bonds between base pairs

lagging strand

The DNA strand that is synthesized discontinuously in short fragments away from the replication fork

leading strand

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

multiple origins of replication

The presence of many starting points along eukaryotic chromosomes where DNA replication begins simultaneously

Okazaki fragments

Short DNA segments formed on the lagging strand that are later joined together.

origin of replication

A specific location on DNA where replication begins.

primer

A short RNA sequence that provides a starting point for DNA polymerase to begin synthesis.

primase

An enzyme that synthesizes RNA primers needed to start DNA replication

replication bubble

The region where DNA has been unwound and replication is actively occurring.

replication fork

The Y-shaped regions where DNA strands are being separated and copied

semi-conservative replication

Each new DNA molecule contains one original (parent) strand and one newly synthesized (daughter) strand.

semi-discontinuous replication

DNA replication where one strand (leading) is continuous and the other (lagging) is built in fragments

single-strand binding proteins (SSBs)

Proteins that stabilize separated DNA strands and prevent them from rejoining.

S phase

Synthesis phase: The stage of the cell cycle, during interphase, when DNA replication occurs

template strand

The original DNA strand used as a guide to build a new complementary strand

topoisomerase

An enzyme that relieves tension and supercoiling ahead of the replication fork

coding strand

The DNA strand that has the same sequence and direction as the RNA transcript (except T is replaced with U)

consensus sequence

A common DNA sequence pattern across multiple genes and species that serves as an ideal binding site for proteins (e.g., promoter regions)

downstream

DNA sequence located after the transcription start site (+1), in the direction of transcription.

elongation (transcription)

The stage of transcription where RNA polymerase adds nucleotides to build the RNA strand

exon

In eukaryotes, a coding region of a gene that remains in the final mRNA and contributes to protein sequence

gene

A specific DNA sequence that contains instructions to produce a functional product (protein or RNA).

initiation (transcription)

The stage where transcription factors and RNA polymerase bind to the promoter in order to begin RNA synthesis.

intron

In eukaryotes, a non-coding region of a gene that is transcribed but removed during RNA processing

mRNA (messenger RNA)

The RNA molecule that carries genetic information from DNA to the ribosome for protein synthesis

pre-mRNA

The initial RNA transcript that contains both exons and introns before processing.

promoter

A DNA consensus sequence where transcription factors and RNA polymerase bind to begin transcription

RNA (ribonucleic acid)

A nucleic acid made of ribose sugar, phosphate group, and nitrogenous bases (A, U, C, G) that plays a role in gene expression

RNA polymerase

The enzyme that synthesizes RNA by adding nucleotides in the 5’→3’ direction using a DNA template

RNA processing

The modification of pre-mRNA (e.g., intron removal) to produce mature mRNA

template strand

The DNA strand used by RNA polymerase to build a complementary RNA transcript

terminator

A DNA consensus sequence that signals RNA polymerase to stop transcription

termination (transcription)

The stage where transcription ends and RNA polymerase is released from DNA

transcription

The process of copying genetic information from DNA into RNA.

transcription bubble

The region where DNA is unwound and RNA is being synthesized (~25 bases long)

transcription factors (TFs)

Proteins that bind to DNA and help initiate transcription by recruiting RNA polymerase

transcription start site (TSS)

The first nucleotide of a gene that is transcribed into RNA (+1 position)

transcription unit

A segment of DNA that contains the instructions necessary to transcribe a single RNA molecule (includes promoter, coding region, terminator)

upstream

DNA sequence located before the transcription start site (toward the promoter), and labeled with negative numbers

alternative splicing

A post-transcription process where different combinations of exons are joined, allowing one gene to produce multiple proteins

branch point

A conserved adenine nucleotide within an intron where the lariat structure forms during splicing

lariat structure (RNA splicing)

A looped intermediate structure formed when an intron folds back on itself during RNA splicing.

mature mRNA

The final processed messenger RNA molecule that is ready for translation (contains only exons, a 5’ cap, and a poly(A) tail).

Poly(A) tail

A string of adenine nucleotides added to the 3’ end of mRNA that increases stability and aids export and translation.

polyadenylation

The process of adding a poly(A) tail to the 3’ end of a pre-mRNA.

Poly(A) polymerase

The enzyme that adds adenine nucleotides to form the poly(A) tail.

RNA endonuclease

An enzyme that cleaves RNA, such as cutting the 3’ end during polyadenylation

RNA splicing

The process of removing introns and joining exons of an RNA transcript to form a continuous coding sequence

spliceosome

A complex of RNA and proteins that recognizes splice sites and removes introns during RNA splicing

splicing sites

Specific nucleotide sequences (consensus sequences) at exon–intron boundaries that direct the spliceosome

3’ splice site

The location at the end of an intron where the second splicing cut occurs

5’ splice site

The location at the start of an intron where the first splicing cut occurs.

5’ cap

A modified guanine nucleotide added to the 5’ end of a pre-mRNA that helps with stability, export and initiating translation