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#2 ELONGATION: The RNA polymerase moves downstream towards transcription, unwinding the DNA and elongating the RNA transcript in a 5' to 3' direction.

RNA polymerase moves along the DNA untwisting the double helix and exposing approximately 10-20 DNA nucleotides at a time to pair it with RNA nucleotides.

#3 TERMINATION: RNA transcript is released and the RNA polymerase detaches from the DNA.

In Eukaryotes the RNA polymerase II transcribes a polyadenylation signal sequence.

This specifies a polyadenylation signal (AAUAAA) into the pre-mRNA bounding it by specific proteins in the nucleus.

AAUAAA cut the RNA transcript free from the polymerase and releases the pre-mRNA.

RNA Processing

The ends of the pre-mRNA are modified. The 5' end is synthesized first and receives a 5' cap. The 5' cap is a modified form of a guanine nucleotide.

Polyadenylate polymerase adds 50-250 Adenine nucleotides to the 3' end of the pre-mRNA to make a poly-A tail.

In Prokaryotes a RNA sequence called the terminator signals the end of transcription.

While transcription is occurring, DNA strands are re-forming a double helix.

Transcription in Prokaryotes

In cytoplasm

In Prokaryotes, the RNA polymerase recognizes where to start.

In nucleus

In a Eukaryotic promoter there is a TATA box: A nucleotide sequence that contains approximately 25 TATA nucleotides upstream from the starting point in the promoter.

Transcription factors (proteins) recognize the TATA box and bind to the DNA strand prior to the RNA polymerase II binds.

Additional transcription factors bind along to the RNA polymerase II.

RNA polymerase binds to the promoter (upstream)of a gene, unwinding the DNA to use the strand going from 3' to 5' as the template strand.

Transcription Initiation Complex: when transcription factors and RNA polymerase become bound to the promoter.

Direction of transcription = downstream The other direction = upstream

#1 INITIATION: RNA polymerase initiates RNA synthesis at the starting point on the template strand.

Transcription in Eukaryotes

Sites where Transcription Occurs

single celled eukaryotes

yeast:

use chemical signaling to identify cells of opposite mating type and initiate the mating process. The two mating types and their corresponding chemical signaling molecules, or mating factors, are called a and 𝛂.

Cell Signaling

Cells and Organelles

Main topic

Eukaryotes

Animal Cells:

Endoplasmic Reticulum (ER): a network of membranous sacs; the ER membrane separates the internal compartment of the ER

Smooth ER: outer surface, lacks ribosomes, functions in metabolic processes (synthesis of lipids, metabolism of carbohydrates, detoxifies drugs and poisons, breaks down hormones

Rough ER: studded with ribosomes on the outer surface of the membrane, makes secretory proteins

Nucleus: contains most of the DNA; DOUBLE MEMBRANE

Chromatin: material consisting of DNA and proteins; visible in cell division as individual condensed chromosomes

Nucleolus: nonmembranous structure involved in production of ribosomes

Nuclear envelope: DOUBLE MEMBRANE enclosing the nucleus, separating its contents from the cytoplasm, pierce by nuclear pores that serve as "holes" that regulate entry and exit of materials through envelope; continuous with ER

Ribosomes: complexes that synthesize proteins; NO MEMBRANE

Bound Ribosomes: attached to the outside of the ER or nuclear envelope & make proteins for insertion into membranes

Free Ribosomes: suspended in the cytosol, proteins of these function within cytosol

Golgi Apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products

Trans face: shipping department of Golgi, gives rise to vesicles that pinch off and travel to other sites

Cis face: receiving department of Golgi, located near the ER, transport vesicles used to more from ER to Golgi, ER lumen and membrane fuse with the Golgi membrane

products of the ER are modified, stored, and then sent to other destinations

Extracellular Matrix: helps cells to bind together and regulates several cell functions; made out of glycoproteins and carbohydrates.

Cells attach to the matrix with the help of fibronectin- binds to cell-surface receptor proteins (integrins) in the membrane

Contains collagen (glycoprotein) that forms strong fibers outside the cells

Centrosome: region where the cell's microtubules are initiates; contains a pair of centrioles

Flagellum: motility structure present in some animal cells; composed of microtubules

Cytoskeleton: reinforces cell shape, functions in cell movement, and components are made of protein; located in cytoplasm

Microfilaments: thin solid rods that are built from actin molecules; help maintain cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility, and cell division

Actin-protein interactions help cytoplasmic streaming (the circular flow of cytoplasm within cell)

Actin filaments and Myosin (motor protein) interact to cause contraction of muscle cells

Intermediate filaments: maintain cell shape, anchorage of organelles, and help with formation of nuclear lamina

Microtubules: hollow rods constructed from globular proteins called tubulins; maintain cell shape, cell motility in cilia and flagella, chromosome movements in cell division, and organelle movements

Dyneins have two "feet" that "walk" along the micotubules and use ATP to cause bending movement

Large motor proteins called dyneins are attached along each outer microtubule double and are responsible for the bending movement of flagella and cilia

Microvilli: projections that increase the cell's surface area

Peroxisomes: produces hydrogen peroxide as a by-product and then converts it to water; single-membrane organelle

Mitochondrion: organelle where cellular respiration occurs and most ATP is generated; double-membrane organelle

Inner membrane: coiled with infoldings (cristae) and divides the mitochondrion into TWO internal compartments

Mitochondrial Matrix: enclosed by the inner membrane, contains different enzymes and mitochondrial DNA and ribosomes

Intermembrane Space: narrow region between the inner and outer membrane

Outer membrane is SMOOTH

Lysosomes: digestive organelle where macromolecules are hydrolyzed (add water molecule); has hydrolytic enzymes and are single-membrane organelles

Autophagy: lysosomes fuse with vesicle containing damaged organelles and hydrolytic enzymes are used to recycle the cell's own organic material

Phagocytosis: lysosomes fuse with a food vacuole and hydrolytic enzymes digest the food particles

excessive leakage from A LOT of lysosomes leads to self-digestion of cell

Plant Cells:

Ribosomes

Rough and Smooth ER

Nucleus/Chromatin, nucleolus, and nuclear envelope

Sites where DNA Replication Occurs

Each cell has an ORI (origin of replication) where DNA replication begins; prokaryotes have one ORI and eukaryotes have many

1) Helicase: enzyme that untwists the 2 strands at the replication fork

2) Single-stranded Binding Proteins: bind to the unpaired DNA strands and keep them from re-pairing

3) Primase: enzyme that synthesizes a complementary RNA primer using the parent strand as the template; new DNA strand will start at the 3' end of the primer

4) DNA Polymerase III: enzyme that adds a DNA nucleotide to the 3' end of the primer and continues to add complementary DNA nucleotides to the template strand

5) DNA Polymerase I: removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

6) DNA Ligase: joins final nucleotide of DNA replacement to the first DNA nucleotide of the adjacent Okazaki fragment

Nuclease: a DNA-cutting enzyme that cuts a segment of DNA strand that contains damage; the gaps are filled with nucleotides using undamaged strand

Sliding clamp: converts DNA Poly. III from being distributive (falling off) to processive (staying on)

Replicates the leading strand 5' to 3' direction; continously; only one primer Replicates the lagging strand away from replication fork, 5' to 3' direction, and discontinously synthesized in a series of Okazaki fragments, who each need a primer

Adds each monomer through dehydration reactions; is able to proofread its own work

Needs a primer & can only replicate 5' to 3' end

Topoisomerase: enzyme that helps relieve the strain by breaking, swiveling, and rejoining DNA strands

Subtopic

Golgi Apparatus

Mitochondrion

Peroxisomes

Cytoskeleton: only microfilaments and microtubules

Central Vacuole: functions include storage, breakdown of waste products, hydrolyze macromolecules, and plant growth

Plasmodesmata: cytoplasmic channels through cell walls that connect the cytoplasms of adjacent cells

Chloroplast: photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules; DOUBLE MEMBRANE

Stroma: fluid outside the thylakoid, contains the chloroplast DNA, ribosomes, and enzymes

Membranes of the chloroplast divide the chloroplast into 3 compartments: intermembrane space, stroma, and thylakoid space

Thylakoids: another membranous system inside chloroplasts in the form of flattened, interconnected sacs; thylakoids are stacked; each stack is called a granum

Cell Wall: outer layer that maintains the cell's shape and protects the cell from mechanical damage

Secondary Cell Wall: between membrane and primary cell wall; has strong, durable matrix for cell protection and support

Primary Cell Wall: thin and flexible wall