Cell and Molecular Biology BIO 2210: Everything after midterm 2

DNA

What molecule encodes genetic information?

Chromatin

DNA in eukaryotes is compacted into this structure, composed of repeating units of DNA and protein

Nucleosome

The fundamental unit of chromatin

Histones

What DNA gets wrapped around

Histone tails

N-terminal segments of histones that protrude from the nucleosome

Methylation

Leads to tighter DNA packing

Acetylation

Leads to looser DNA packing

Heterochromatin

Highly packed chromatin

Euchromatin

Loosely packed chromatin

Centromeres

Appear as constriction of chromosomes, important for chromosome movement in cell division

Telomeres

Found at the tips of chromosomes, repetitive “sacrificial” DNA that is lost when DNA is replicated

Nuclear matrix

Fibrous protein network that extends throughout the nucleus and maintains its shape

Nuclear lamina

Meshwork of protein fibers that lines the inner surface of the inner nuclear membrane

Nucleolus

The most prominent structure within the nucleus where the ribosomal subunits are assembled

Gene

A hereditary factor that specifies an inherited trait; template for the synthesis of an RNA molecule

mRNA

RNA that encodes for proteins

Central dogma of molecular biology

The principle of directional information flow from DNA to RNA to protein

Transcription

A DNA template is used to make RNA

Reverse transcription

An RNA template is used to make DNA

Reverse transcriptase

Enzyme that catalyzes reverse transcription

Retrotransposons

Mobile genetic elements within the genomes of most eukaryotes

Retroviruses

Have RNA genomes that must be reverse transcribed to make DNA

Regulatory elements

Found in genes, acts as instructions for when and where to transcribe the gene

rRNA

Component of ribosomes

tRNA

Used during protein synthesis

Genetic code

Set of rules that describes the relationship between base sequence in a DNA polymer and the order of amino acids in a polypeptide

Template strand

The strand of DNA used to synthesize RNA

Codon

Triplet of RNA nucleotides

AUG

The start codon

Open reading frame

Triplets between the start and stop codon

UAA, UAG, UGA

The stop codons

Mutations

Changes in the base sequence of a DNA molecule

Promoters

DNA sequences that indicate where RNA polymerase should start transcribing

Primary transcript

The name for newly made RNA

Translation

The process of a ribosome using a mRNA template to guide the synthesis of a polypeptide

Ribosomes

Carry out the process of polypeptide synthesis

mRNA

Molecules that encode the amino acid sequence and are read by the ribosome

tRNA

Used to deliver amino acids to the ribosome

Svedberg unit

Larger numbers usually reflect greater mass (S)

A site

Binds the newly arriving tRNA with its attached amino acid

P site

Binds the tRNA that carries the growing polypeptide chain

E site

Where the tRNA leaves the ribosome after depositing their amino acid

Anticodon

A 3 nucleotide sequence that is complementary to a codon

Aminoacyl tRNA

Term for when the amino acid is covalently attached to the tRNA

Wobble base pairs

Can form between the 3rd base of a codon and the corresponding base in its anticodon

Inosine

Can form wobble base pairs with C, U, or A

Pluripotent

Stem cells in the embryo that can become any cell type in the body

General transcription factors (GTFs)

Bind core promoters and recruit RNA polymerase

Regulatory transcription factors

Determines local chromatin structure

Activators

Transcription factors that increase transcription by activating promoters

Repressors

Transcription factors that decrease transcription by repressing promoters

Euchromatin

When promoters are found in this type of chromatin (relaxed/loose), they are more active

Heterochromatin

When promoters are found in this type of chromatin (tightly compacted), they are repressed

MyoD

A regulatory transcription factor that confers muscle cell identity

DNA methylation

A way to silence genes, involves the covalent addition of methyl groups to cytosine

XIST

Noncoding RNA that coats one X chromosome, and causes heterochromatin to form, which silences the genes on that chromosome

Barr body

Term for the silent X chromosome that is visibly compacted

ER signal sequence

Targets nascent (new) proteins to the rough ER during synthesis

Nuclear localization signal

Post-translational signal for import into the nucleus

Proteasome

A protein complex that degrades proteins

Ubiquitin

Covalent attachment of this protein targets proteins for degradation

Rett syndrome

Normal development for 6-18 months, but then see neurological regression, loss of speech, loss of purposeful hand movement, social interaction impairments

Semiconservative replication

Each newly formed DNA molecule consists of one old strand and one newly synthesized strand

Daughter strands

Term for the new strands of DNA formed

Helicase

Enzyme that unwinds DNA and separates strands

Primers

Small RNA fragment that provides a starting point for polymer synthesis

Primase

Enzyme that makes the RNA primers

DNA polymerase

Enzymes that copies DNA molecules

DNA ligase

Enzyme that “glues” DNA fragments together

Leading strand

DNA strand that grows as a continuous chain from 5’ to 3’

Lagging strand

DNA strand that must grow in the opposite direction

Okazaki fragments

Term for the small fragments formed from the lagging strand

Proofreading

How the errors made by DNA are fixed

3’ to 5’ exonuclease

DNA polymerases have _____ activity

Mutations

Are the result of unfixed errors in DNA replication

Telomeres

Expendable DNA at the end of chromosomes, ensure that DNA replication does not lead to a loss of genes

Telomerase

Maintains and regenerates telomeres

Cell division

One cell gives rise to 2 daughter cells

Cell cycle

An ordered series of events in which the cell copies its chromosomes and divides into 2 cells

Interphase

Stage in cell cycle that contains G1, S, and G2 phase

G1 phase

Cell cycle phase: Preparation for S phase, longest/most variable length, decides whether and when the cells will divide again

S phase

Cell cycle phase: DNA synthesis stage

G2 phase

Cell cycle phase: Preparation for M phase

Quiescent cells

Cells that do not divide

G0 phase

Cell cycle phase: temporarily arrested in G1 phase, able to divide but waiting for a signal

Post-mitotic

Cell cycle phase: no longer able to re-enter the cell cycle, most cells in an adult are found here

Senescent

Forced irreversible cell cycle arrest, these cells are often cleared by the immune system, but accumulate as we age

Cyclin-dependent kinases (CDKs)

Protein phosphorylation by ____ drives progression through the cell cycle

Sister chromatids

Term for pairs of duplicated chromosomes

Mitosis

The division of sister chromatids into new nuclei

Cytokinesis

The formation of two new cells

Prophase

Mitosis stage: when chromosomes are condensed and become visible

Prometaphase

Mitosis stage: breakdown of the nuclear envelope, centromeres have moved to opposite sides of the cell, kinetochores assemble at the centromeres of DNA, the mitotic spindle attaches to kinetochores

Metaphase

Mitosis stage: fully condensed chromosomes are aligned in the center of the cell

Anaphase

Mitosis stage: two stages:

A: sister chromatids are pulled towards opposite poles by microtubules

B: Poles move away from each other by the force of microtubules

Telophase

Mitosis stage: when daughter chromosomes arrive at poles of the mitotic spindle, chromosomes decondense and nucleoli reappear, nuclear envelope reforms, cytokinesis takes place which results in 2 cells

Cleavage

Term for cytoplasmic division, is caused by a contractile ring of actin microfilaments below the plasma membrane

Myosin motor protein

Tightens the contractile ring until the daughter cells are separated