Bio 192 Exam 2 Review Terms

Nucleotide

Nucleotide

Monomer of DNA/RNA with phosphate group, sugar, and nitrogenous base

Pentose sugar

Ribose or deoxyribose, makes up backbone of DNA/RNA

Nitrogenous base

Building block of nucleic acids, purines (AG) and pyrimidines (CTU)

3' to 5'

Direction in which nucleotides are connected

Antiparallel

DNA strands run in opposite directions

DNA denaturation

Occurs by breaking hydrogen bonds due to changes in pH, temperature, etc.

Major groove

Wider groove along the length of the DNA double helix, accessible for protein binding

Minor groove

Less accessible groove along the length of the DNA double helix

Origin of replication

Specific DNA sequence where replication starts

Helicase

Enzyme that 'unzips' DNA by breaking hydrogen bonds between base pairs

Primase

Enzyme that synthesizes RNA primers and places them on the lagging strand

Ligase

Enzyme that catalyzes the joining of Okazaki fragments

DNA pol 1

Enzyme that removes RNA primer and replaces it with DNA

DNA pol 111

Enzyme that forms the continuous leading strand and creates Okazaki fragments

Replication fork

Y-shaped structure where DNA replication starts and strands separate

Leading strand

Synthesized continuously in the 5' to 3' direction, RNA primer placed at the beginning

Lagging strand

Synthesized discontinuously, with RNA primers for each fragment

Okazaki fragment

Fragment of DNA synthesized in the lagging strand

NTPs

Ribonucleoside triphosphates required for DNA synthesis (ATP, GTP, CTP, UTP)

RNA polymerase

Enzyme that polymerizes RNA and unzips DNA when recruited to the promoter

Promoter/Transcription terminator

Specific gene site that starts/stops RNA polymerase from adding ribonucleotides

Polyadenylation sequence

Promotes transcript life and prevents degradation

Template strand

Non-coding strand used as a template for complementary strand synthesis

Non-template strand

The strand that is being used as the complementary strand

Coding strand

Strand that codes for the correct nucleotide sequence for mRNA

Heterochromatin

Tightly wrapped DNA around histones

Euchromatin

More open DNA compared to heterochromatin, allows for binding to DNA

Histone

Positively charged protein that DNA wraps around

Nucleosome

Repeating unit of chromatin, negative DNA wrapped around positive histones

Acetylation

Process of adding acetyl group to a histone, causing it to turn negative

HAT (histone acetyl transferases)

Enzyme that adds acetyl groups to histones, causing chromatin to open up

HDAC (histone deacetylases)

Enzyme that deacetylates histones, allowing chromatin to reform

General transcription factor

Initiates basal transcription complex by binding to the promoter

Regulatory transcription factor

Binds to enhancers/silencers, has specific DNA binding in the major groove

Pioneer regulatory TF

Unique transcription factor that can bind to enhancers in heterochromatin

Reporter construct

Used to locate enhancers/silencers by attaching to promoters and enhancers

Reporter gene

Gene that visually reports the location of something (e.g., GFP)

DNA methylation

Method of adding a methyl group to DNA to permanently silence gene expression

Methyl-cytosine

Most common DNA methylation, occurs on CpG sites

DNMT (DNA methyltransferase)

Enzyme that adds methyl groups to cytosines

MBD (methyl-CpG-binding domain)

Recognizes methylated sites on DNA and can recruit HDAC or DNMT

Hemi-methylated

When only one strand is methylated, provides a marker for the other strand

Palindromic

DNA sequences that are the same, important for piggyback model and methylation

De novo methylation

Process of adding methyl groups to cytosines in unmethylated DNA

Post-transcriptional regulation

Includes mRNA processing, stability, and protein activation

ShRNA (small nuclear RNAs/ribozymes)

Marks the beginning of introns and catalyzes their removal

Spliceosome

Larger assembly of proteins that removes introns and fuses exons

Intron

Non-coding sequences that are cut out of pre-mRNA

Exon

Coding sequences that are kept in mRNA

5'/3' UTR

Untranslated region of mRNA outside the coding sequence

Alternative splicing

Produces mature mRNA from the same gene by skipping exons or keeping introns

5' cap

Part of RNA processing that adds stability to the mRNA and protects from degradation

Poly-A-tail

Part of RNA processing that stabilizes mRNA

RNA-binding protein

Binds to 3' UTR and can degrade or prevent degradation of mRNA

miRNA

Degrades mRNA and inhibits translation

RISC

Complex that allows miRNA to function

Chaperones

Provide sheltered environment for protein folding

Proteasome

Recognizes ubiquitin-tagged proteins and degrades them

Codon

3-nucleotide sequence that encodes for an amino acid

Anticodon

3-nucleotide sequence on tRNA that is complementary to codon sequences

Start/stop codon

Initiates translation and stops translation, respectively

Codon redundancy

Multiple codons can code for the same amino acid

tRNA/uncharged

tRNA without an attached amino acid

tRNA charged

tRNA with an attached amino acid

Small/large rRNA

rRNA found in small/large ribosomal subunits, involved in translation

E site

Holds tRNA that will exit the ribosome

P site

Holds tRNA with the growing polypeptide chain

A site

Holds aminoacyl-tRNA

Aminoacyl tRNA synthetase

Enzyme that matches amino acids with their corresponding tRNA

G1

Phase where the cell accumulates ribosomes, organelles, and building blocks for DNA

G2

Phase where the cell grows in size and prepares for mitosis

S

Phase of DNA replication

M

Phase of mitosis

G0

Phase where DNA exits the cell cycle and never replicates again

Cell cycle

Process that leads to replication and division of cells for growth

Cell cycle checkpoints

G1 checkpoint ensures enough resources for replication, G2 checkpoint checks for proper replication and damage, metaphase checkpoint checks chromosome attachment

Interphase

GI, S, G2 phases before mitosis

Mitosis

Anaphase and telophase stages of cell division

Centromere

Attachment point for spindle fibers on a chromosome

Centrosome

Organelle essential for microtubule formation, duplicates during S phase

Spindle apparatus

Network of microtubules that separates and aligns chromosomes

Nuclear envelope

Protects nucleus and separates it from cytoplasm

Cytokinesis

Division of the cytoplasm to form two new cells

Cell plate

Forms during plant cytokinesis to divide the cell into two

Kinetochore

Attachment point for microtubules to move chromosomes

Sister chromatid

Identical copies of a chromosome produced during DNA replication

Homologous chromosome

Chromosomes with the same genes but different alleles

Recombination

Process of rearranging DNA from two sources to create new sequences and genetic diversity

Ploidy

Number of sets of chromosomes

Meiosis 1

Prophase (includes crossing over), anaphase (paired chromosomes align), telophase (cell divides into haploid cells)

Meiosis 2

Similar to mitosis, separates sister chromatids and creates genetic diversity

Kinase

Enzyme that phosphorylates molecules using ATP

Phosphatase

Enzyme that dephosphorylates molecules

Cyclin

Protein that activates CDKs

CDKs

Enzymes that drive cell cycle events and checkpoints

MPF

Specific CDK complex that drives mitosis

Signaling intermediates

Molecules/compounds involved in conveying information in a signaling pathway

Effector

Component that carries out the response of a signal pathway

Kinase

Enzyme that phosphorylates molecules

Steroid hormones

Hormones that can pass directly through the membrane and regulate gene expression and metabolism