Unit 7 on ramps bio review

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Rosalind Franklin's role in discovery of DNA

Rosalind Franklin was one of the scientists that used X-ray crystallography to suggest the helix structure of DNA. Watson used her data to figure out the structure of DNA. She died before she could be nominated for the Noble Prize for her work and could also have been uncredited because of her gender.

Watson and Crick are credited with discovering the structure of DNA. However, the most important result of their discovery was providing a mechanism for the replication of DNA. Explain.

By showing that DNA is a complementary, double-stranded helix, we were able to determine that each strand served as a template for the synthesis of a new strand during DNA replication.

Summarize Chargaff’s results and explain them in terms of the structure of DNA.

Chargaff’s results: in one DNA molecule ...A=T and G=C therefore A+G = C+T Contribution to structure of DNA: Chargaff’s rule explains the complementary pattern of double-stranded DNA and the uniform diameter.

How does Chargaff’s ratio explain the uniform diameter of DNA?

Chargaff’s ratio says that a dual ring purine always hydrogen bonds to a single ring pyrimidine in the complementary molecule. Base pairing between purines or pyrimidines across complementary molecules would create areas 4 rings across and areas 2 rings across. If a purine were able to bind to a purine, the diameter would be larger in areas, and if a pyrimidine could bind to a pyrimidine it would be smaller.

Semi Conservative Model

When DNA replicates, the products are two identical DNA molecules. Each newly synthesized DNA molecule contains one original strand and one newly synthesized strand

Complementarity Model

makes process of DNA replication complete and more accurate. The original strand is a template for the newly synthesized complementary strand. Allows each strand to be templates for predictable synthesis.

Specific reaction catalyzed by DNA polymerase

condensation reactions to form phosphodiester bonds between nucleotides

To which end of the leading strand does DNA polymerase add nucleotides? To which end of the lagging strand?

DNA polymerase always adds nucleotides to the 3’ end (for leading and lagging)

What is an Okazaki fragment? Where do we find Okazaki fragments?

Okazaki fragment: DNA strands synthesized discontinuously away from the replication fork... located on lagging strand

Origin of Replication in bacteria

site where replication bubble is formed and expands to make two new DNA molecules. Where DNA replication begins.

ORIs in eukaryotes

sites where replication bubbles form and expand to make two new DNA molecules. Where DNA replication begins. There are many in eukaryotes, making DNA replication faster.

Helicase

separates the two strands of a DNA molecule from each other

Single-stranded binding protein

keep the DNA strands from rejoining after Helicase separates them

Topoisomerase

prevents the DNA ahead of the replication fork from getting too wound while helicase opens the DNA molecule.

Primase

creates short RNA primer that triggers synthesis of new DNA strand from its 3’ end

DNA Polymerase 3

adds nucleotides to RNA primer using the existing DNA strand as a template

DNA Polymerase 1

removes the RNA primer and replaces it with DNA

DNA ligase

Links DNA fragments together where RNA primer was originally (ex: Okazaki fragments or leading to lagging strand)

Why can’t we see ligase in the image above?

Ligase is used to link the newly synthesized DNA fragments together. In the picture above, no new DNA has been synthesized from the template strand yet.

how the sequence data of DNA is used to direct the primary structure of a protein

The sequence of bases is transcribed to an RNA sequence that is translated at the ribosome to a sequence of amino acids.

G1 phase

Cell growth and differentiation. Most variable phase in length between different types of cells. Cells in G0 phase are cells that never leave G1 phase and never divide, such as nerve cells.
Phosphorylation of glucose, polymerization of tubulin or actin, sub-pho of ATP in cytoplasm.

S phase

Synthesis and replication of chromosomes/DNA. Longest phase in interphase and doubles DNA content. Replicated DNA is found in chromatin state until condensing into identical chromatids at the start of mitosis.
Polymerization of DNA, translation of histone mRNAs, actions of all the DNA replication machinery.

G2 phase

Synthesis of molecules other than DNA, needed for cell division. Centrosome duplication in preparation to form the mitotic spindle. Synthesis of molecules and organelles needed for division. Active metabolic state as cell prepares for mitosis, and least variable phase between different types of cells.
Phosphorylation of ADP, synthesis of microtubule components, cyclin synthesis.

Requirements for cell division

1. Receipt of a signal to direct the cell to divide

2. DNA replication

3. Mitosis

4. Cytokinesis

Interphase

It takes up the majority of the cell cycle, intense metabolic activity takes place continuously during all phases making proteins, generating membranes, performing respiration, and building cytoskeleton continuously.

Centromere

The name of the region in which identical chromatids that are the product of DNA replication are attached to each other.

Centrioles

Rod like objects that help organize cell division and are found within the centrosomes of certain eukaryotes.

Centrosome

The small non membrane bound organelle in the cytoplasm that duplicates and move to opposite ends of the cell when division begins. Provides the mitotic spindle.

Mitosis phases

Prophase, prometaphase, metaphase, anaphase, telophase.

Prophase

Chromosomes condense and become visible, spindle fibers emerge from the centrosomes. Nuclear envelope breakdown and nucleolus disappears.

Prometaphase

Chromosomes continue to condense, kinetochores appear at the centromeres. Mitotic spindle microtubules attach to kinetochores, and centrosomes move toward opposite poles.

Metaphase

Mitotic spindle is fully developed, centrosomes are at opposite poles of the cell, chromosomes are lined up at the metaphase plate, each sister chromatid is attached to a spindle fiber originating from opposite poles.

Anaphase/chromatid disjunction

Cohesin proteins binding the sister chromatids together break down, sister chromatids (now called chromosomes) are pulled toward opposite poles. Non-kinetochore spindle fibers lengthen, elongating the cell.

Telophase

Chromosomes arrive at opposite poles and begin to decondense, nuclear envelope material surrounds each set of chromosomes. The mitotic spindle breaks down.

Kinetochore Microtubules

Attatches to each chromatid at the kinetochore and aid in chromosome movement

Polar or Nonkinetochore microtubules

Overlaps with each other midway between the 2 poles of the cell and aid in cell elongation.

Astral microtubules

Attaches the centrosomes to the cell poles and help with spindle orientation.

Cytokinesis

Cell divisions is completed, the process in which the cytolpasm and its components are separated equally into the 2 daughter cells.
Animal cells: A cleavage furrow separates the daughter cells.
Plant Cells: A cell plate separates the daughter cells.

Plant cytokinesis

A cell plate forms through the fusion of golgi-derived vesicles, which then develops into a new cell wall, effectively partitioning the cytoplasm into 2 daughter cells.

Identical chromatids

Chromosomes that carry different genes

A cell ready to divide, a homologous pair of chromosomes consists of…

Two chromosomes and four chromatids

When a cell leaves the cell cycle and becomes inactive

G0 phase

What role does DNA replication play in the cell cycle

It generates identical chromatids that are distributed in identical cells.

Mitotic Spindles

Separates chromatids by attaching fibers to the kinetochores of the chromosomes. Theses chromosomes then end up in separate daughter cells.

Why does eukaryotes need mitosis but prokaryotes do not

ukaryotes have a nucleus, so mitosis is needed in order to dissolve and then reform the nuclear membrane around the chromosomes in each daughter cell. Prokaryotes on the other hand, do not have a nucleus and can just split apart.

Animal cytokinesis

Cleavage furrow formation because of contractile ring of microflaments. Cleavage furrow doesn’t happen in plants because the presence of the cell wall, which is rigid and not very bendable, in plant cells prevents the cell from forming cleavage furrows.

3 molecules someone would expect to find at or near the cell plate of a plant cell

Phospholipid in vesicle, cellulose, membrane proteins.

What following situatation would be least likely to promote cell division

The cell is completely surrounded by other cells.

Cyclin

A class of proteins that activate cyclin-dependent kinases.

Predict the effect on the target protein if a cyclin undergoes a mutation and is not broken down. 

The target protein will be phosphorylated all the time.

G1 checkpoint

Cell is big enough to begin DNA replication

S checkpoint

DNA replication is complete and accurate.

G2 checkpoint

Cell has doubled the quantity of chromatin and organelles.

M checkpoint

Chromosomes consist of two chromatids attached at the centromere.

Which molecules primarily regulates the cell cycle checkpoints?

Cyclins

Positive regulators

Promotes passage through the cell cycle

Negative regulators

stops or slows passage through the cell cycle.

Proto-oncogenes

Genes that code for positive regulators of the cell cycle. These genes can become oncogenes when they are mutated so that they over-stimulate cell division or survival.
Oncogene products can include: Transcription factors, growth factors, cyclins and Cdks.

Tumor-suppressor genes

Codes for negative cell cycle regulators. They are the “brakes” of the cell cycle, and when they under go certain mutations, those brakes can become non-functional.

Tumor Suppressor genes include: Retinoblastoma (RB) - mutations can lead to tumors of the retina.

p53 - mutations found in over 50% of human cancers.

Overstimulation of the cell cycle with loss of inhibition results

Abnormally high rates of cell division.

Cyclins and Cdk

Positive regulators, they are two families of protein. Cyclins are proteins that fluctuate in concentration throughout the cell cycle. They are able to regulate the cell cycle by binding and activating a family of enzymes called Cdks.

Retinoblastoma protein (RB)

Negative regulator, acts at the G1 checkpoint by monitoring cell size, binds a transcription factor E2F that is required for passage to S phase, when Rb is phosphorylated it can no longer bind the transcription factor E2F. The transcription factor E2F binds to DNA and promotes gene expression.

p53

Negative regulator, that acts at the G1 checkpoint. When damaged DNA is detected, p53 responds in many ways:

1. halts the cell cycle by producing another protein called p21, which inhibits Cdk/cyclin complexes.

2. stimulates enzymes to repair the DNA

3. triggers apoptosis (cell death) if the DNA can’t be repaired.

Metastasis

where individual cancer cells break away and start a new tumor somewhere else.

Benign

Tumor doesn’t invade surrounding tissue… it’s not spreading so it’s non-cancerous.

Malignant

Tumor is invading surrounding tissue… it is spreading so it’s cancerous.

Why don’t cancer cells undergo apoptosis?

Damage or change in genetic material of these cells leads to changes in gene expression and metabolism that result in cancer cells ignoring cell signals to undergo apoptosis.