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Polyadenylation
adding a poly-A tail at the 3' end of mRNA to export from nucleus
Splicing
removing introns and joining the exrons to produce mature mRNA: spliceosomes
Capping
Adding 5' methylated cap to the 5' end of mRNA to help ribosome bind during translation
synthesized mRNA is ready for translation once transcription is complete
RNA polymerase binds to promoter
RNA polymerase II
microRNA
snRNA
pre mRNA
RNA polymerase
Elongation
RNA polymerase II synthesizes pre-mRNA
RNA polymerase moves along DNA template synthesizing RNA (5’ TO 3’)
Termination
RNA polymerase reaches termination and mRNA transcript is released
splicing and addition of a poly-A tail
Pre-mRNA processes into mature mRNA
DNA is a template for RNA synthesis
RNA polymerase synthesizes RNA
Enhancers and silencers
They bind to specific regulatory sequences located far from promoter
Activators and repressors
bind to specific DNA sequences to regulate transcription
Operons
allows for coordinated expression of genes involved in related functions.
Sequences where RNA polymerase binds to a initiate sequence on DNA
Regulatory sequences that increase transcription rate
Protein that inhibits transcription by binding to DNA
Proteins that enhance transcription by binding to enhancer regions
Nonoverlapping - Nucleotides are read in sets of 3
Degenerate - Multiple Codons code for the same Amino Acid
Universal - Most Organisms Use this to form Proteins
Initiation of Translation
Translation Initiation Complex
Small and Large Ribosomal Subunits
Initiation Factors
Prokaryotes: 70S Eukaryotes: 80S
rRNA
Endomembrane System Pathways
Destinations (From Free Ribosomes)
Endoplasmic Reticulum
Secretion
Outside Cell
Examples of Secreted Proteins
Digestive Enzymes
Amylase
Extracellular Matrix Proteins
Collagen
Serum Proteins
Albumin
Milk Proteins
Casein
Peptide Hormones
Insulin
Lysosome
Glycoproteins: Carbohydrate groups are added to a protein in the ER by enzymes
SRP
Signal Peptidase: Cleaves SRP Signal Molecule
Organelles
Peroxisomes
Single stranded binding proteins keep the seperated strands apart so that nucleotides can bind
DNA gyrase moves in advance of helicase and relieves strain and prevents the DNA supercoiling again
Each strand of parent DNA is used as template for the synthesis of the new strands. Synthesis always occurs in 5'-> 3' direction on each new strand.
Leads to formation of okasaki fragments
To synthesise a new strand first an RNA primer is synthesized on the parent DNA using RNA primase
Next DNA polymerase III adds the nucleotides (to the 3' end) added according to the complementary base pairing rules; adenine pairs with thymine and cytosine pairs with guanine.
Nucleotides added are in the form of as deoxynucleoside triphosphate. Two phosphate groups are released from each nucleotide and the energy is used to join the nucleotides in to a growing DNA chain.
DNA polymerase I then removes the RNA primers and replaces them with DNA
DNA ligase next joins Okazaki fragments on the lagging strand. Because each new DNA molecule contains both a parent and newly synthesized strand DNA replication is said to be semiconservative.
Signal Amplification
cAMP binds to a Protein Kinase, which activates another, and etc...
Cell Response
Signal Reception
Stages of Signaling
1. Reception 2. Transduction 3. Response
Binding of a Signal to a Receptor Protein
Receptors
Intracellular Receptors
Steroid Hormone Interaction
Receptor Protein Activated by Binding to Hormone (Ex: Aldosterone)
Activated Hormone-Receptor Complex moves into the Nucleus and activates genes controlling Sodium and Water Flow
Transcription Factor
Signal Molecule is Nonpolar/Hydrophobic and Small; can cross the membrane on its own.
Membrane Receptors
Ion Channel Receptor
Tyrosine Kinase Receptor
Protein Kinase: Enzymes that catalyze the transfer of phosphate groups from ATP to proteins.
G-Protein Coupled Receptor
G-Protein
Guanosine (Di/Tri)-phosphate (GDP/GTP)
GDP: Deactivates G-Protein
GTP: Activates G-Protein
Phosphatase: Enzyme that catalyze the removal of phosphate groups by hydrolysis
Signal Molecule is Hydrophilic (Charged/Polar); cannot cross a membrane on its own.
First Messenger: Receptor that Receives a hydrophilic signal in the membrane.
Second Messenger: Another molecule that helps the message travel inside the cell
cAMP (Cyclic AMP): Synthesized from ATP
Signal/Ligand
Ex: Aldosterone
Types of Signal Release
Long-Distance Signaling
Local Signaling
Synaptic Signaling
Neurotransmitters
Post-Synaptic Cell
Presynaptic Neuron
Light Reactions
Solar to chemical
NADPH
O2
Calvin Cycle
ADP + P
NADP+
Sugar
Organic molecules + O2
Cellular respiration in mitochondria
Glycolysis
Produce pyruvate
Glucose
Glucose 6-phosphate
Fructose 6-phosphate
Fructose 1, 6-bisphosphate
4 ATP + 2 NADH formed
2 ATP used
CO2 + H2O
Heat
1) Resting State: most Na+ channels closed, and most but not all K+ channels are also closed
2) Depolarization: some Na+ channels open, leading to inflow, depolarizing membrane; if it reaches threshold voltage, action potetnial is trigger and fulfilled
3) Rising Phase: K+ channels remain closed; Na+ influx makes inside of membrane positive
4) Falling Phase: Na+ Channels become inactive; K+ channels open, making inside of cell negative again
5) Undershoot: Na+ Channels close; some K+ channels open; returns to resting state with the help of Na+/K+ pump
Repolarization: as the positive charge leaves the cell, inside starts to get less positive
Hyperpolarization: inside of the cell becomes more negative than resting membrane potential
opening of gated K+ channels; INSIDE MORE NEGATIVE
Depolarization: reduction in the magnitude of the membrane potential
opening of gated Na+ channels; INSIDE LESS NEGATIVE
Gated: open and close in response to stimuli
Voltage-gated: open/close to change in membrane potential
Ligand-gated: open/close when neurotransmitter binds to channel
Stretch-gated: "sense stretch"; open when mechanically deformed
Ungated: always open
cell loses water; shriveled
cell gains water; lysed
Endocytosis: taking in something inside cells in bulk
Receptor Mediated Endocytosis: specialized endocytosis that enables the cell to acquire bulk quantities of specfic substances
Pinocytosis: cell takes in extracellular fluid from outside in vesicles
dissolved molecules
Phagocytosis: when a cell engulfs large food particles/other cells by extending part of its membrane out
leads to becoming a food vacuole, digeswted afyer fusing with lysosomes
Exocytosis: transport vesicles migrate to the membrane, fuse, and release their contents
used in secretory cells to export products
occurs when active transport of a solute indirectly drives transport of other substances
Example Na+/K+ Pump: abundance of Na+ outside the cell & abundance of K+ inside; to even out, goes against the concentration gradient by 3 Na+ transported out the cell and 2 K+ inside the cell
Facilitated Diffusion: passive transport aided by proteins to help diffuse across the membrane
Carried out by channel and carrier proteins
Carrier: undergo a subtle change in the shape that translocates the solute-binding site across the membrane
Channel: provide corridors or channels that allow a specific molecule or ion to cross the membrane
Osmosis: diffusion of free water across a selectively permeable membrane
Diffusion: the tendency for molecules of any substance to spread evenly into the avaliable space as a result of thermal motion; high to low concentration
Cholesterol
amphipathic
present in all animal cell membranes
type of Hydrocarbon tail affects fluidity
More Saturated: tightly packed; cannot move as well(viscous)
More Unsaturated: not tightly packed, movement in the membrane
Each Phospholipid has a Specific Phase Transition Temperature
Below Temp: lipids is gel phase & is rigid
Above Temp: lipid is liquid crystalline phase & is fluid
Amphipathic: hydrophobic fatty acid tail and hydrophilic head
Different Types of Bonds: different types of phospholipids due to fatty acids, group attached to phosphate etc.; primarliy noncovalent
Van der Waals
Hydrophilic head due to prescene of phosphate group
Isocitrate
a-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Oxaloacetate
Membrane-Bound organelles
Both
r
Cytoskeleton
Golgi Apparatus
Nucleus
Mitochondria
ER
Plants only
Vacuoles
Chloroplasts
Animals only
Lysosomes
No membrane-Bound organelles
Extremophiles
Ether bond in lipids
Circular chromosome
Histones associated DNA
Lack membrane bound orgenelles
Some
Fimbriae, Pili
Endoscope
Flagella
All
Cell wall
Periplasmic space
Nucleoid
Ribosomes
Plasma Membrane
Acids increase Hydronium concentration (More H3O+ or H+ groups).
pH + pOH = 14
Every increase or decrease in pH is a tenfold increase or decrease of the concentration of H+ ions.
Bases decrease Hydronium Concentration (More OH- groups).
Dissolves most substances
Substances in Water
Polar Substances
Polar and Ionic Compounds Dissolve in Water
Nonpolar Substances
Water Forms a Cage Around Nonpolar Molecule
Floats on Water; Insulation of Ice for Waters Below
Stable Hydrogen Bonds; Ordered
Most Dense at 4 Degrees Celsius
Evaporative Cooling
Temperature Moderation
Water Transport in Plants
High Surface Tension
Strong Dipole-Dipole Interactions between H and O, F, or N (Partial Positive H with Partial Negative O, F, N).
Crystalline Structures (Salts)
Electronegativity Differences (Greater differences give more polar bonds)
four types of basic groups
Basic (+)
Acidic (-)
Nonpolar
contains H, CH, or carbon ring; hydrophobic
Polar
contains OH, SH, or NH groups
made of main chain and side chain
has a central cabron surrounded by amino, carboxyl, hydrogen, and R group
connected through phosphodiester bonds/linkages through condensation/dehydration reactions
Nucleosides
does not have a phosphate group
nitrogenous base
pyrimidines: C, T(U in RNA)
purines: A, G
phosphate
5 carbon sugar
single-stranded
A,G,C,U
doubled stranded
A, G, C, T
directs synthesis of messenger RNA and control protein synthesis (gene expression)
translation:information from the mRNA is used to make proteins
transcription: information in the DNA is used to make mRNA
provides directions for its own replication
LDL: low density protein or "bad cholesterol
increased by saturated fats and trans fat
HDL: high density lipoprotein or "good cholesterol"
four fused rings
Unsaturated
one or more double covalent bonds are found within carbon chain; do not have hydrogen atoms at every position
Trans: trans fatty acids
Cis: presence of double bonds; slight kinks
liquid at room temp
come from plant sources
can contain one tupe of different types of fatty acids
Saturated
increased incidence of cardiovascular disease
no double covalent bonds between carbons; saturated with hydrogen atoms
found in animal sources
solid at room temp
connected through ester linkage
Ester Linkages: connects each fatty acid to an OH in glycerol
compact way for animals to carry their energy stores with them
made of glycerol and three fatty acids
Polysacchrides: formed when 100 or more monosaccharides are bonded together through glycosidic linkages
Structure
Chitin
Cellulose
made of beta-Glucose; no branching; insoluble fiber
Storage
Dextran
Disaccharide: formed when a dehydration reaction joins two monosaccharides
Glycosidic Linkage: formed through covalent bond
Monosaccharides: simplest sugars; made of C, H, OH, and CO groups
Aldoses: CO groups at the middle of the chain
Ketoses: CO group is in the middle of the chain
Enantiomers: mirror images of one another
Geometric Isomers
Trans Isomer: opposite side
Cis Isomer: same side
Structural Isomers: differ in the covalent arrangement of their atoms
