BIO 311C

Occurs in the Cytoplasm
(Coupled with Translation, mRNA is made and immediately translated)

Stages of Transcription

Initiation
- The beginning of transcription that occurs when the enzyme RNA polymerase binds to the promoter. (RNA Polymerase)

RNA Polymerase
- The RNA polymerase seen in prokaryotes. (Makes new strand of mRNA in 5' to 3' direction)

Elongation
- This step follows initiation as RNA polymerase moves downstream, unwinding the DNA and elongating the RNA transcript in the direction of 5' to 3'. (Uses condensation/ dehydration reactions)

Termination
-This step occurs when the RNA transcript is released, and the polymerase detaches from the DNA. This happens once the RNA polymerase reaches the termination site on the DNA.

Template Strand
- The DNA strand that is used to form the new RNA strand. (Template strand is in the 3' to 5' direction because transcription occurs in the 5' to 3' direction.)

Transcription Start Point
- The nucleotide in DNA where transcription starts.

Upstream
- To the left of the transcription start site, nucleotides are numbered by negative numbers.

Promoter
- Region on the DNA upstream of the start site where RNA polymerases bind to.

Downstream
- To the right of the transcription start site, nucleotides are numbered by positive numbers.

Occurs in the Nucleus
(Not coupled with Translation, translation occurs in the cytoplasm.)

Stages of Transcription

Initiation
- The beginning of transcription that occurs when the enzyme RNA polymerase binds to the promoter. (RNA Polymerase II)

TATA Box
- A eukaryotic promoter commonly includes a TATA box, which is a nucleotide sequence containing TATA that is about 25 nucleotides upstream from the transcription start point.

Transcription Factors
- In eukaryotes, the addition of these proteins is required in order for RNA polymerase II to bind to the promoter. One recognizes the TATA box and binds to the promoter.

RNA Polymerase II
- The RNA polymerase seen in eukaryotes which is used to produce pre mRNA, snRNA, and micro RNA. (Makes new strand of mRNA in 5' to 3' direction)

Transcription Initiation Complex
- Additional transcription factors bind to the DNA along with RNA polymerase II, forming this complex. RNA synthesis can now begin at the start point on the template strand.

Elongation
- This step follows initiation as the transcription initiation complex moves downstream, unwinding the DNA and elongating the RNA transcript in the direction of 5' to 3'. (Uses condensation/ dehydration reactions)

Termination
- This step occurs in eukaryotes differently as an AAUAAA sequence signals the cell to make a cut in the newly formed pre mRNA and release it from the DNA.

Ribonuclease
- The enzyme that makes the cleavage to form the pre-mRNA.

pre-mRNA Processing

5' Cap
- A modified guanine (G) nucleotide added to the 5' end of the pre-mRNA that will be used for translation.

Poly A Tail
- A tail of 100-200 A's that is added to the 3' end of pre-mRNA, near the AAUAAA sequence. This poly A tail helps with the stability of the mRNA.

Poly A Polymerase
- The enzyme that adds the poly A tail to the pre-mRNA. (Requires ATP)

RNA Splicing

Introns
- Non-coding sequences that are removed during RNA splicing.

Spliceosomes
- Complexes of RNA and proteins that bind junctions of the introns and makes cuts to release introns from the DNA. The exons are then joined together.

Alternative Splicing
- Due to the presence of introns, different combinations of exons can be generated through the removal of different introns to form different mRNAs.

Exons
- Coding sequences of mRNA that are used to encode proteins.

Forms Glycosidic Linkage

Forms Ester bonds

Forms Phosphodiester Bond

Forms Peptide Bond

Sucrose

DNA

RNA

Nucleobase

Amino Acid

Laws Of Thermodynamics

Gibbs Free Energy

ΔG can be

Endergonic

Exergonic

ΔG<0

ΔG>0

ΔG=0

Reactions Have

Enzyme/Substrate

Denatures by

Competitive

Noncompetive

Allosteric Regulation

Cooperativity

Feedback

Release factor

Protein is released in the ER lumen.

Signal peptidase

Enzyme that cleaves the signal peptide

Protein is now in the ER

Protein gets shipped out through vesicles and then fuze onto the first phase of Golgi

Ribosomes
- Comprised of ribosomal RNA and protein. Produces proteins

Free Ribosomes
- Ribosomes suspended in the cytosol

Bound Ribosomes
- Ribosomes that are on the outside of the ER

Nucleus
- Storage site for DNA

Chromosome
- One long DNA molecule that forms when a cell is prepared to divide (CONDENSED Chromatin)

Chromatin
- Material consisting of DNA and histone proteins

Nucleolus
- Site of ribosomal RNA synthesis

Nuclear Envelope
- Double membrane enclosing the nucleus; continuous with the ER

Nuclear Pores
- Small openings lined with porin proteins that assist in transport

Lamina
- Protein filament meshwork that lines the inner surface of nuclear envelope and keeps its structure

Endomembrane System
- Regulates protein traffic and performs metabolic functions

Lysosomes
- Organelles packed with enzymes that promote the hydrolysis of biological molecules

Phagocytosis
- Extending a cell's membrane to engulf a foreign cell or food particle

Autophagy
- A process that uses hydrolysis enzymes to recycle cell's own organic material

Vacuoles
- Large vesicles that are meant to store substances

Food Vacuoles
- Formed when cells engulf food or other particles

Contractile Vacuoles
- Pump excess water out of cells

Central Vacuoles
- Found in plant cells and serves as a repository for inorganic ions and water

Endoplasmic Reticulum

Rough ER
- Secretes glycoproteins, distributes transport vesicles, and is considered the membrane factory of the cell

Smooth ER
- Synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium ions

Golgi Apparatus
- Modifies products of the ER and moves them to their final destination

Trans Face
- Releases cargo after making changes

Cis Face
- Receives cargo shipped out by ER

Plasma Membrane
- To protect the cell from the surrounding environment and regulate the materials that enter and exit from the cell

Endosymbiont Theory
- Origins of mitochondria and chloroplasts. Prokaryotic (non-photosynthetic and photosynthetic) cells engulfed by eukaryotic cells and formed symbiotic relationships with them. (Energy)

Mitochondria
- A double membrane organelle that produces ATP through cellular respiration

Cristae
- Folds within the mitochondria

Intermembrane Space
- Space between inner and outer membranes

Matrix
- Space inside the inner membrane where DNA is

Chloroplast
- A double membrane organelle that synthesizes food through photosynthesis

Granum
- Stack of thylakoids

Thylakoid
- Membranous sac

Stroma
- Internal fluid

Peroxisomes
- A single membrane organelle that is packed with enzymes that produces various metabolic functions like extracting hydrogen from certain molecules and adding them to oxygen to form hydrogen peroxide, which is then turned to water.

Microtubules
- Thickest of the three, hollow rods made of a protein called tubulin. Grow in length by adding tubulin dimers; very dynamic

Functions:
- Maintenance of Cell Shape
- Cell Motility
- Chromosomal Movement in Cell Division
- Organelle Movement

Flagella
- Mobility structure that is limited to one or few per cell. (Cell motility, composed of microtubules (9 doublets surrounding 2 microtubules))

Cilia
- Mobility structure that occurs in large numbers on cell surface. (Cell motility, composed of microtubules (9 doublets surrounding 2 microtubules))

Centrosomes
- "Microtubule organizing center" that helps with cell division. (Composed of 9 sets of triplet microtubules)

Intermediate Fibers
- Intermediate diameter compared to the three, very diverse and made up of different proteins. These structures are more permanent (Ex: Nuclear Lamina)

Function:
- Maintenance of cell shape
- Anchorage of nucleus and certain organelles
- Nuclear Lamina

Microfilaments/Actin Fibers
- Thinnest of the three, two thin intertwined strands of actin

Function:
- Maintenance of Cell Shape
- Muscle Contraction
- Cellular Movement/ Amoeboid Movement
- Cytoplasmic Streaming

Cell Junctions

Plasmodesmata
- Channels present between plant cells that go through cell walls, allowing the transfer of water and other nutrients (Plant)

Tight Junctions
- Membranes of adjacent cells tightly connected with proteins preventing the movement of any fluid or substance (Animal)

Desmosomes
- Connections between cells through proteins that allow some substances to go between cells (Animal)

Gap Junctions
- Allows everthing to move between cells (Animal)

Cell Wall
- Provides structure for plant cell

Primary Cell Wall
- Relatively thin and flexible

Middle Lamella
- Thin layer between the primary walls of adjacent cells

Secondary Cell Wall
- (In some cells) added between the plasma membrane and primary cell wall

Extracellular Matrix
- Comprises of a lot of different proteins and is a network that provides structure for animal cells

Structure

Fluid Mosaic Model
- Describes phospholipids as a fluid component of the membrane while different types of proteins (mosaic) are present in the bilyaer.

Phospholipids
- An amphipathic molecule that is contains a hydrophilic head and two hydrophobic tails. Hydrophilic heads are positioned to be in contact with extracellular and intracellular fluids while hydrophobic tails orient themselves inside the bilayer.

Membrane Fluidity

Temperature
- Temperature affects membrane fluidity. Above specific phase transition temperature, the lipid is in a liquid crystalline phase and below the lipid is in a gel phase.

Cholesterol
- Cholesterol also affects membrane fluidity. Its presence between phospholipids reduces movement at moderate temperatures and prevents phospholipids from packing tightly at low temperatures.

Hydrocarbon Tails
- The type of hydrocarbon tails affects membrane fluidity. Unsaturated fatty acids allow the membrane to more freely and saturated fatty acids pack tightly so the membrane cannot move as much.

Membrane Proteins

Peripheral Proteins
- Proteins that are anchored to the membrane.

Integral Proteins
- Proteins that are partially or fully inserted into the membrane.

Transmembrane Proteins
- Proteins spanning the entire membrane. N-terminus on extracellular side and C-terminus on intracellular side.

Function

Functions of Membrane Proteins
- Transport
- Enzymatic Activity
- Signal Transduction
- Cell-Cell Recognition
- Intercellular Joining
- Attachment to Cytoskeleton and ECM

Selective Permeability
- The ability for a cell membrane to control which molecules can pass through it.

Passive Transport
- Membrane transport that does not require energy and utilizes a concentration gradient to exchange small nonpolar and small uncharged polar molecules across the membrane. (With Concentration Gradient)

Osmosis
- The diffusion of free water across a selectively permeable membrane, going from an area of higher solute concentration to an area of lower solute concentration.

Tonicity
- The ability of a surrounding solution to cause a cell to gain or lose water.

Animal Cells
- Due to no cell wall, animal cells fare best in isotonic environments unless they have special adaptations.

Hypertonic Solution
- Solute concentration is greater than that inside the cell; cell loses water. (Shriveled)

Isotonic Solution
- Solute concentration is the same as the inside of the cell, no net water movement. (Normal)

Hypotonic Solution
- Solute concentration is less than that inside the cell; cell gains water. (Lysed)

Plant Cells
- Cell walls in plant cells help maintain water balance.

Hypertonic Solution
- Solute concentration is greater than that inside the cell; cell loses water. (Plasmolyzed)

Isotonic Solution
- Solute concentration is the same as the inside of the cell, no net water movement. (Flaccid)

Hypotonic Solution
- Solute concentration is less than that inside the cell; cell gains water. (Turgid)

Diffusion
- The tendency for molecules of any substance to spread out evenly into the available space because of thermal motion, moving from an area of high concentration to an area of low concentration.

Facilitated Diffusion
- Membrane transport that does not require energy but does utilize a transport protein and a concentration gradient to exchange large, uncharged molecules across the membrane. (With Concentration Gradient)

Channel Proteins
- Proteins that provide corridors or channels that allow a specific molecule or ion to cross the membrane

Aquaporin
- A channel protein that is present in the membrane that helps facilitate water through the membrane by use of aqua pores.

Carrier Proteins
- Proteins that undergo a subtle change in shape, alternating between two shapes. The shape change may be triggered by the binding and release of the transported molecule.

Active Transport
- Membrane transport that utilizes energy to move ions against their concentration gradients.

Electrogenic Pump
- A transport protein that helps create a voltage difference across membranes.

Sodium-Potassium Pump
- Typically, the outside of the cell has an abundance of Na+ and the inside of the cell has an abundance of K+, so if the cell needs to take out more Na+ or bring in more K+ it needs to do it against the concentration gradient. For every 3 Na+ transported outside the cell, 2 K+ ions are transported inside. (Requires ATP)

Proton (H+) Pump
- A pump that transports H+ against its concentration gradient. As positive charge leaves the cell, we see a slight negative charge develop inside the cell and a slight positive charge develop outside the cell.

Cotransport
- When active transport of a solute indirectly drives transport of other substances. (Ex: H+/Sucrose Cotransporter)

Bulk Transport
- The use of vesicles to move large molecules such as polysaccharides and proteins in bulk cross the membrane .

Exocytosis
- Transport vesicles migrate to the membrane, fuse with it, and release their contents.

Endocytosis
- Contents collect onto the plasma membrane, and they fuse into a transport vesicle where the contents travel within the cell.

Phagocytosis
- When a cell engulfs large food particles by extending part of its membrane out. The ingested particle is now in a food vacuole where it will fuse with lysosomes and be digested.

Pinocytosis
- When a cell takes in extracellular fluid from outside in vesicles. This allows the cell to take in any dissolved molecules.

Receptor-Mediated Endocytosis
- A very specialized form of pinocytosis that allows the cell to acquire bulk quantities of a specific substance. This can occur due to the presence of receptors on the plasma membrane which allow for the binding of specific solutes.