Bio 192 Exam 2 Review Terms

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108 Terms

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Nucleotide

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

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Pentose sugar

Ribose or deoxyribose, makes up backbone of DNA/RNA

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Nitrogenous base

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

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3' to 5'

Direction in which nucleotides are connected

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Antiparallel

DNA strands run in opposite directions

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DNA denaturation

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

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Major groove

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

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Minor groove

Less accessible groove along the length of the DNA double helix

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Origin of replication

Specific DNA sequence where replication starts

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Helicase

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

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Primase

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

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Ligase

Enzyme that catalyzes the joining of Okazaki fragments

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DNA pol 1

Enzyme that removes RNA primer and replaces it with DNA

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DNA pol 111

Enzyme that forms the continuous leading strand and creates Okazaki fragments

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Replication fork

Y-shaped structure where DNA replication starts and strands separate

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Leading strand

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

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Lagging strand

Synthesized discontinuously, with RNA primers for each fragment

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Okazaki fragment

Fragment of DNA synthesized in the lagging strand

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NTPs

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

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RNA polymerase

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

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Promoter/Transcription terminator

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

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Polyadenylation sequence

Promotes transcript life and prevents degradation

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Template strand

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

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Non-template strand

The strand that is being used as the complementary strand

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Coding strand

Strand that codes for the correct nucleotide sequence for mRNA

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Heterochromatin

Tightly wrapped DNA around histones

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Euchromatin

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

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Histone

Positively charged protein that DNA wraps around

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Nucleosome

Repeating unit of chromatin, negative DNA wrapped around positive histones

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Acetylation

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

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HAT (histone acetyl transferases)

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

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HDAC (histone deacetylases)

Enzyme that deacetylates histones, allowing chromatin to reform

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General transcription factor

Initiates basal transcription complex by binding to the promoter

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Regulatory transcription factor

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

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Pioneer regulatory TF

Unique transcription factor that can bind to enhancers in heterochromatin

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Reporter construct

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

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Reporter gene

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

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DNA methylation

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

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Methyl-cytosine

Most common DNA methylation, occurs on CpG sites

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DNMT (DNA methyltransferase)

Enzyme that adds methyl groups to cytosines

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MBD (methyl-CpG-binding domain)

Recognizes methylated sites on DNA and can recruit HDAC or DNMT

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Hemi-methylated

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

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Palindromic

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

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De novo methylation

Process of adding methyl groups to cytosines in unmethylated DNA

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Post-transcriptional regulation

Includes mRNA processing, stability, and protein activation

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ShRNA (small nuclear RNAs/ribozymes)

Marks the beginning of introns and catalyzes their removal

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Spliceosome

Larger assembly of proteins that removes introns and fuses exons

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Intron

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

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Exon

Coding sequences that are kept in mRNA

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5'/3' UTR

Untranslated region of mRNA outside the coding sequence

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Alternative splicing

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

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5' cap

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

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Poly-A-tail

Part of RNA processing that stabilizes mRNA

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RNA-binding protein

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

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miRNA

Degrades mRNA and inhibits translation

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RISC

Complex that allows miRNA to function

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Chaperones

Provide sheltered environment for protein folding

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Proteasome

Recognizes ubiquitin-tagged proteins and degrades them

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Codon

3-nucleotide sequence that encodes for an amino acid

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Anticodon

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

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Start/stop codon

Initiates translation and stops translation, respectively

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Codon redundancy

Multiple codons can code for the same amino acid

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tRNA/uncharged

tRNA without an attached amino acid

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tRNA charged

tRNA with an attached amino acid

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Small/large rRNA

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

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E site

Holds tRNA that will exit the ribosome

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P site

Holds tRNA with the growing polypeptide chain

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A site

Holds aminoacyl-tRNA

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Aminoacyl tRNA synthetase

Enzyme that matches amino acids with their corresponding tRNA

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G1

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

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G2

Phase where the cell grows in size and prepares for mitosis

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S

Phase of DNA replication

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M

Phase of mitosis

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G0

Phase where DNA exits the cell cycle and never replicates again

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Cell cycle

Process that leads to replication and division of cells for growth

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Cell cycle checkpoints

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

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Interphase

GI, S, G2 phases before mitosis

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Mitosis

Anaphase and telophase stages of cell division

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Centromere

Attachment point for spindle fibers on a chromosome

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Centrosome

Organelle essential for microtubule formation, duplicates during S phase

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Spindle apparatus

Network of microtubules that separates and aligns chromosomes

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Nuclear envelope

Protects nucleus and separates it from cytoplasm

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Cytokinesis

Division of the cytoplasm to form two new cells

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Cell plate

Forms during plant cytokinesis to divide the cell into two

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Kinetochore

Attachment point for microtubules to move chromosomes

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Sister chromatid

Identical copies of a chromosome produced during DNA replication

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Homologous chromosome

Chromosomes with the same genes but different alleles

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Recombination

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

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Ploidy

Number of sets of chromosomes

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Meiosis 1

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

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Meiosis 2

Similar to mitosis, separates sister chromatids and creates genetic diversity

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Kinase

Enzyme that phosphorylates molecules using ATP

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Phosphatase

Enzyme that dephosphorylates molecules

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Cyclin

Protein that activates CDKs

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CDKs

Enzymes that drive cell cycle events and checkpoints

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MPF

Specific CDK complex that drives mitosis

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Signaling intermediates

Molecules/compounds involved in conveying information in a signaling pathway

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Effector

Component that carries out the response of a signal pathway

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Kinase

Enzyme that phosphorylates molecules

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Steroid hormones

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