Bio 202 Section 3

Phage

A type of virus that infects bacteria

What are the three components of a nucleotide?

• Sugar (deoxyribose or ribose)

• Phosphate group on the 5’ carbon

• Nitrogenous base on the 1’ carbon

Where is the hydroxide group located on a nucleotide?

The 3’ carbon

Semiconservative replication

DNA replication where the original parental strand is pulled apart and each half of the original strand serves as a template to make a new complimentary strand

Conservative replication

DNA replication where some enzyme reads a DNA strand and leaves it intact, but makes a new, separate, double-stranded DNA molecule

Dispersive replication

DNA replication where the original DNA molecule gets pulled apart and chopped into pieces, and new DNA is then synthesized to stitch those pieces together

Meselson and Stahl

Determined the correct method of DNA replication (semiconservative) by using different isotopes of nitrogen to distinguish different rounds of DNA replication by weight

Origin of replication

Place where DNA replication begins

Replication bubble

Place where DNA replication is occurring; circle formed by the two individual strands of the original DNA

Replication fork

Transition point from the separated single strands of DNA to where the original molecule is still double-stranded

Helicase

Protein that catalyzes the breaking of hydrogen bonds between the base pairs of DNA to open the double helix

Single-strand DNA-binding proteins (SSBPs)

Proteins that stabilize single-stranded DNA, keeping the strands from re-annealing

Topoisomerase

Protein that breaks and rejoins the DNA double helix by making knicks in one side of the sugar-phosphate backbone or the other to relieve twisting forces caused by the opening of the helix

Primase

Protein that catalyzes the synthesis of the RNA primer

DNA polymerase III

Protein that extends the leading strand of DNA

RNA primer

Initiation site created by primase that provides an OH group for DNA polymerase to add nucleotides to

Leading strand

DNA strand synthesized continuously 5’ to 3’ in the same direction as helicase

Lagging strand

DNA strand synthesizes in pieces 5’ to 3’ in the opposite direction that helicase is moving

Okazaki fragment

Small section containing an RNA primer and the DNA being made off of it that is made during the synthesis of the lagging strand during DNA replication

DNA polymerase I

Protein that binds to the primase section of an Okazaki fragment, chews away the RNA, and replaces the ribonucleotides with deoxyribonucleotides to connect the fragments together

DNA ligase

Protein that forms the final phosphodiester bond linking the end of one Okazaki fragment with the next in the chain

Replisome

All of the things happening simultaneously at a replication fork (helicase, primase, topoisomerase, DNA polymerase III, DNA polymerase I, DNA ligase, etc.)

Telomerase

Enzyme that extends the end of the end of the template DNA strand to allow one more Okazaki fragment to be made by making a single-stranded region long enough for primase to make a primer

Telomere region

The end of a chromosome

Senescence

When cells die of old age; triggered when the telomeres get so short that the DNA that is lost begins to impact important regions of the chromosome

Mismatch

When a base on one strand doesn’t match what’s on the complimentary strand

Nucleotide excision repair

Family of enzymes will detect bumps or bends in the DNA molecule, cut out the region that is damaged, and fill in the gaps to correct the mistake

Nucleotide mismatch repair (proofreading)

DNA polymerase III has the ability to detect bumps caused by base-pair mismatches, remove the last base it added, and begin again

Mitosis

Form of cell division in eukaryotes that results in two daughter cells that are mostly identical to the original

Meiosis

Form of cell division in eukaryotes that results in four daughter cells with half as much DNA as the original

Binary fission

Method by which bacterial cells divide, producing two cells that are nearly identical to the original

Cell cycle

A series of stages that cells go through on their way to dividing

G1

The longest phase of the cell cycle, when cells are functioning normally and are the most active metabolically

S

Phase of the cell cycle when DNA synthesis (replication) takes place

G2

Phase of the cell cycle when cells prepare for division

M

Phase of the cell cycle where cells undergo nuclear division (division of chromosomes) and cytokinesis (physically splitting the cell in half)

G0

When cells exit the cell cycle at some point and stop actively dividing (post mitotic)

Interphase

Any part of the cell cycle other than M phase

M-phase promoting factor (MPF)

Complex of a Cdk1 and cyclin B that pushes cells from G2 to M phase

Cdk

Cyclin-dependent kinase; regulated by the phosphorylation of two different sites

Cyclins

Regulatory proteins that control the progression of cells through the cell cycle by activating CDKs

G1 checkpoint

Regulates the decision of cells to exit G1 and enter S phase

G2 checkpoint

Regulates the decision to enter mitosis

M phase checkpoint

Checkpoint shortly before nuclear division

How is the G1 checkpoint passed?

If:

• Cell size is adequate

• Nutrients are sufficient

• Social signals are present

• DNA is undamaged

How is the G2 checkpoint passed?

If:

• Chromosomes have replicated successfully

• DNA is undamaged

• Activated MPF is present

How is the M phase checkpoint passed?

If:

• Chromosomes have attached to the spindle apparatus

• Chromosomes have properly segregated

• MPF is absent

Apoptosis/apitosis

Form of cellular suicide when a cell repeatedly fails to get past a checkpoint

Mitogens

Signaling molecules that bind to receptors that activate the G1 cyclin/Cdk complex, triggering a signaling pathway that directly drives progression through the cell cycle

Growth factors

Signaling molecules that bind to receptors that activate a signaling pathway that results in increased uptake of nutrients from the environment and increased metabolism of those nutrients to make proteins, lipids, sugars, etc.

Retinoblastoma (Rb)

Protein that acts as a checkpoint that stops cells from dividing prematurely by blocking the G1 to S-phase transition in the cell cycle by inhibiting E2F

E2F

Transcription factor that activates the genes that encode the proteins necessary for S-phase (helicase, primase, topoisomerase, DNA polymerase, etc.)

p53

Protein that is activated by being phosphorylated once DNA damage is detected, which goes into the nucleus and acts as a transcription factor to turn on the expression of genes, one of which encodes p21

p21

Protein that is CKI that binds to the G1 and S-phase cyclin/Cdk complexes and prevents them from interacting with their targets, even if they are activated

CKI

Cyclin-dependent kinase inhibitor

Cancer

Loss of cell cycle regulation

Benign tumor

Form of cancer where cells are dividing in an unregulated way, but they have not left the area that they originated in

Malignant tumor

Form of cancer where cells are dividing rapidly and leaving their environment and spreading to new locations

Centrosomes

Microtubule organizing structures that form the spindle apparatus

Spindle apparatus

Microtubule structure that forms to separate sister chromatids between daughter cells

What happens during the prophase of mitosis?

• Chromosomes condense but are still contained in the nuclear envelope

• Microtubules are beginning to be reorganized into the spindle apparatus

What happens during the prometaphase of mitosis?

• Chromosomes are condensed

• Nuclear envelope has broken down

• Microtubules from each side of the spindle apparatus attach to chromosomes at the kinetochore

Kinetochore

Complex of proteins that assemble onto the centromeres to serve as a point of attachment for the microtubules onto the chromosome

What happens during metaphase of the mitosis?

• Chromosomes complete migration to the middle of the cell

• Each chromosome is attached to a microtubule from each half of the spindle apparatus

• First M-phase checkpoint

First M-phase checkpoint

Checkpoint from metaphase to anaphase that won’t proceed unless all chromosomes are in the middle and attached to the spindle apparatus

What happens during anaphase of mitosis?

• Attachments between sister chromatids break

• Microtubules connecting chromatids to the spindle apparatus shorten, so the unreplicated chromosomes get pulled to opposite ends of the cell

• Second M-phase checkpoint

Second M-phase checkpoint

Before the transition from metaphase to anaphase, MPF has to no longer be active because it will inhibit some events in anaphase and later

What happens during telophase of mitosis?

• Cell rebuilds nuclear envelopes around chromosomes

• Chromosomes begin to decondense

• Spindle apparatus begins to break down

• Cytokinesis

Cytokinesis

Cytoplasm between the two nuclei formed during mitosis divides, producing two new daughter cells with identical sets of chromosomes

Kinetochore microtubules

Connect to the kinetochores

Interpolar/overlap microtubules

Project towards the middle of the cell but do not interact with chromosomes and instead interact with microtubules from the other side of the spindle apparatus

Aster microtubules

Link the spindle apparatus to the periphery of the cell on the opposite side

Cleavage furrow

Point where the pinching is occurring during cytokinesis

Cell plate

New cell membrane/wall structure formed in the middle of plant cells during the cytokinesis

Chromosome

A structure containing genetic information in the form of genes

Chromatin

The material that makes up eukaryotic chromosomes consisting of a DNA molecule complexed with histone proteins

Chromatid

One double-stranded DNA copy of a replicated chromosome with its associated proteins

Sister chromatids

The two attached, double-stranded DNA copies of a replicated chromosome that contain identical genetic material

Centromere

A specialized region of a chromosome where sister chromatids are most closely joined to each other

Centrioles

Cylindrical structures consisting of microtubule triplets located inside the centrosomes

Genome

The entire genetic information of a cell that is stored in the sequence of bases in DNA

Genes

Specific regions of a chromosome made up of sequences of bases that contain the information to make a unique RNA

Ploidy

The number of copies of a particular chromosome type a cell has

Homologous chromosomes

Two versions of the same type of chromosome that are the same size and shape, and have the same gene content, but may have different alleles for some genes

Diploid (2n)

Cells that have 2 of each chromosome type in the cell

Haploid

Cells that have just 1 of each chromosome type in the cell

Alleles

Alternate versions of the same gene that have non-identical base pair sequences

Karyotype

The number and types of chromosomes in a cell

Sex chromosome

Chromosome associated with an individual’s sex

Autosome

Any chromosome other than a sex chromosome

Sexual reproduction

Two different individuals contribute genetic material to the next generation

Somatic cells

Cells that are not gametes and do not give rise to gametes

Germ cells

Cells that give rise to the egg or the sperm

What does the first round of division in meiosis separate?

Members of a homologous pair

What does the second round of division in meiosis separate?

Sister chromatids

Non-sister chromatids

Chromatids between two different members of the same homologous pair

Unreplicated chromosome

A chromosome that consists of one double-helical molecule of DNA packaged with proteins for compactness

Replicated chromosome

A chromosome after DNA replication consisting of 2 identical sister chromatids each containing one double-helical DNA molecule packaged with proteins for compactness

Bivalent/tetrad

Homologous replicated chromosomes that are joined together during prophase I and metaphase I of meiosis

n

How many of each chromosome type there are