Unit 1
Chemical Bonds
Intermolecular
Electronegativity < 0.5
Non-Polar
Electronegativity > 0.5
Polar
Ion-dipole
Ions and polar molecules
Dipole-Dipole
Hydrogen Bond
F, O, N
Intramolecular
Covalent
Electronegativity > 0.5
Polar
Electronegativity < 0.5
Non-polar
Ionic Bonds
Salts
Crystals
Interactions
Polar substances
Hydrophilic
Polar and Non-polar
Hydrophobic interactions
Cells
Non-polar substances
Van der Waals
Cell Structures
Biological Molecules
Carbohydrates
Length/Branching
Ring Structure
Structural Isomer
Double Bond Location
Geometric Isomer
Cis Bonding (Hydrogens same side)
Trans Bonding (Hydrogens different side)
Nucleic Acids
Nucelotides
Phosphate Group
Sugar Group
Nitrogenous Group
Nucleoside
Sugar/Nitrogenous Group
Proteins
Amino Acid
Primary/Peptide Bond
Polypeptide
R group (Tertiary/Quatnery)
Enantiomers
Carbon in the Center/Mirror Image/4 different molecules
Lipids
Phospholipid Bilayer
Hydrophobic Tail/ Hydrophilic Head
Amipathic Molecules
Hydrophobic/Hydrophilic Properties
Steroids
Cholesterol
Sex Hormones
Cell Evolution
Oparin's Bubble Hypothesis
Milley-Urey Experiment
Theory of Synthesizing Organic Compounds on Early Earth
Earth's atmosphere had little oxygen and lots of water vapor
As Earth cooled down much of the water vapor condensed into oceans and Hydrogen escaped into space
Volcanoes erupted under the sea, releasing gases
Gases in the bubbles reacted with the atmosphere to create organic molecules
Bubbles released contents into the air
Sun's UV radiation and other energy sources to form more complex organic molecules
More complex organic molecules fell back into the sea in raindrops and process repeats
Jumpstart of Biological Evolution
Synthesis of Amino Acids & Nitrogenous Bases
Protein and Nucleic Acids Formation
Maintaining of Internal Chemistry Different From Their Surroundings
Enzymes That Can Copy DNA
Inheritance
Ribosomes are RNAs That Can Copy Themselves
DNA took over RNA as main nucleic acid because of its stability in a double helix structure
Vacuole
Vesicle
Unit 2
Cell Membranes
Plasma Membrane
Phospholipid Bilayer
Hydrophilic Head/ Polar
Hydrophobic Tail/ Non-Polar
Specific Heat Transitions
Below 32 degrees Celsius
Gel
Above 32 Degrees Celsius
Fluid
Cholesterol
Prevents clumping when colder and prevent spreading when hotter
Proteins
Transport/Transmembrane Proteins
Aquaporin
Helps Water go through easily
Facilitated Diffusion
N-Termius and C-Terminus
Alpha Helicases
Co-transport Chain
Proton down Concentration Gradient
Sucrose down Concentration Gradient
Proton Pump
Requires ATP
Selective Permeability
Ions
Polar
Non-Polar
Large Molecules
Exocytosis
Leaving in Bulk
Endocytosis
Phagocytosis
Pinocytosis
Receptor Mediated
Cell Communication
Physical Contact
Local Signaling
Releasing Signals
Local Signaling
Paracrine Signaling
Synaptic Signaling
Membrane Potential
Ca 2+ makes vesciles
Neurotransmitter opens the ligand gated ion channel
Long Distance
Blood Stream
Hormonal Streaming
Signal Molecule
Receptor
Membrane Receptor
Intracelluar Receptor
Aldosterone
GPCR
G-Protein
Adenylyl Cyclase
cAMP
Protein Kinase A
Phosphodiesterase
Tyrosine Kinase Receptor
Phosphorylated
Ion Channel
Signal Molecule Binds
Stages of Signaling
Reception
Transduction
Response
Amplifies Signal
Kinase
Phosphatase
Energy Transformations
Photosynthesis
Calvin Cycle
Carbon fixation
inorganic CO2
organic CO2
ATP and NADPH
CO2 to G3P
ADP, Pi, and NADP+
light reaction
rubisco
Stromata
light reactions
thylakoid membrane
chemical energy
H2O --> H+
O2
NADP+
NADPH
atmosphere
ADP
ATP
a phosphate group to ADP
phosphorylation
O2 + C6H12O6
How cell make energy
Cell Respiration
Pyruvate Oxidative
Citric Acid Cycle
Organic molecules (glucose)
1 molecule of glucose brings about 30-32 ATP molecules
Glycolysis
1 glucose
2 pyruvate
2 ATP
2 NADH
Oxidative Phosphorylation
Oxidative
ATP Synthase
Electron transport chain
FADH2
NADH
Electron transport and pumping out H+ which create an H+ gradient across the membrane
Chemiosmosis
ATP synthesis powered by the flow of H+ back across the membrane
26-28 ATP
Oxygen
Carbon Dioxide
Energy (ATP and heat)
Water
Unit 3
translation
initiation
small ribosomal unit
mRNA
tRNA + anticodon
amino acid
aminoacyl tRNA synthase
elongation
codon recognition
adds amino acids
peptide bonds
chain gets longer
peptidyl transferase
termination
stop codon recognized
release factor sent
translation
free polypeptide is released
DNA
Replication
Origin of Replication
Replication Fork
Bi-directional
5'-3'
Leading Strand
Lagging strand behind with Okazai Fragments
Mainly contains A's and T's
2 Hydrogen bonds
Prokaroytes
Single ORI and it is Circular
Eukaryotes
Multiple ORI
Proteins
Helicase
Breaks the double strand through hydrogen bonding
Topisomerase
Helps relieve the stress of breaking the double strand
Single Strand Binding Proteins
help keep the strands separated
Primase
Adds Primer to the strand
RNA Primer
DNA Polymerase III
5'-3'
Needs Primer
Proofreading function
Adds DNA Nucleotides from the primer
DNA Polymerase I
Adds DNA nucleotides to the RNA nucleotides
DNA Ligase
Joins the lagging strand together through phophosdiester bonds
Transcription
Prokaryotes
RNA Polymerase
Acts as a Helicase and Primer
Termination Site
Coupled
Cytoplasm
mRNA only
Eukaryotes
Not coupled
Nucleus
pre-mRNA
mRNA
Transcription Factors
Transcription intiation complex
TATA Box
DNA Polymerase II
Acts like a Helicase and Primer
Use the 3'-5' Template Strand
Regulation
Eukaryotes
Specific Transcription Factors
Activators
Increase Gene Expression
Inducers
Decrease Gene Expression
General Transcription Factors
Basal (background) Expression
DNA bending protein
Activators to bind to distal control elements
RNA polymerase binds to promoter
Prokaryotes
Operators
lac Operon
E. coli
Lactose binds to inhibitor, so it doesn't bind to the operator
cAMP formed
CAP active
promoted RNA polymerase binding
Allows transcription
Glucose blocks function of adenylyl cyclase
cAMP not formed
CAP inactive
Transcription blocked
lac z
beta galactosidase
lac y
loctose permease
lac a
Transacetylase
protein pathways
free ribosome
nucleus
peroxisome
mitochondria
plastids
rough ER
golgi apparatus
secreted
plasma membrane
lysosomes
signal peptidase