Deductive reasoning - big concept to specific situation (example: antibiotic resistance in bacteria to explain evolution/survival of the fittest) 

Inductive reasoning - small concept to big concept (ex: beaks on birds to evolution) 

Characteristics of living systems - made of cells, store and process information, transform energy, grow and reproduce, adapt and evolve 

Cell theory - all organisms made of ells, cells smallest living things, cells arise from preexisting cells 

Important chemical elements in living systems - CHON(P)

Cohesion - attraction between water molecules, allows for surface tension, form droplets 

Adhesion - attraction between water molecules and other substances, drives capillary action 

Function of enzymes - polymerases, proteases 

Movement proteins - actin, myosin

Structural proteins- collagen, keratin 

Defense proteins - antibodies, venoms 

Nucleic Acids - building blocks for DNA, phosphodiester bond, 6-carbon sugar base, phosphate 5’, hydroxyl 3’ 

Proteins - made of AA, n-term (amino) c-terminus (carboxyl), peptide bond AA

Carbohydrates - made of monosaccharides, disaccharide bonds,

Polar - water lover, hydrophilic

Nonpolar - hydrophobic 

Primary structure = amino acids

Secondary structure = flat sheet (b-sheet) or cylinder structure (a-helix), consist of hydrogen bonds 

Tertiary structure = nonpolar buried in the middle of a protein, polar on surface of the structure 

Quarternary structure = 2 or more polypeptide chains, between polypeptide chains 

Nucleoid - prokaryotic, no membrane, DNA hanging out 

Nucleus - eukaryotic w/ membrane, nucleus inside 

Nucleolus - region inside nucleus, makes RNA structure for ribosomes 

Prokaryotic - archaea and bacteria, unicellular and small and lack internal compartments; may have capsule, pili, flagella 

Eukaryotic - animal and plant cells, has nucleus, ER and golgi apparatus, peroxisomes, and mitochondria; plants have chloroplasts and cell wall 

Rough Endoplasmic Reticulum (ER) - network of membranes covered w/ ribosomes, involved in the synthesis and modification of proteins, transports proteins to other parts of the cell 

Smooth Endoplasmic reticulum (ER) - network of membranes w/o ribosomes, involved in lipid synthesis, detox of harmful substances and stores Calcium ions 

Golgi apparatus - modifies, sorts, packages proteins from the ER and transports them to destinations (in or out of the cell) 

Lysosomes - aid in breakdown of old organelles, digestions of particles, trashcan

Peroxisomes - oxidation of fatty acids, biosynthetic reactions, detox 

Vacuoles - store water, nutrients, water; in plants, central vacuole helps maintain cell structure; in animal cells, vacuoles are smaller and more specialized for storage/waste removal 

Endosymbiosis - theory that forms mitochondria and chloroplasts; bacteria that performed oxidative metabolism (mito) or photosynthesis (chloro) 

Cytoskeletal filaments - eukaryotic structure only, provide support, shape and organization to the cell 

Actin - sliding mechanism for muscle contraction, microfilaments 

Internal microtubules - cell organization and division, 

External microtubules - cell swimming cilia and flagella 

Intermediate filaments - keratin (skin) and lamins (surround nucleus of cells) 

Cell membranes - composed of lipids and proteins, phospholipids provide structure of membrane and proteins provide functions; carbs sugar coat the surface of the membrane

How do membranes form? - polar hydrophilic head and 2 hydrophobic tails

Unsaturated - double bonds/kink in the chain

Saturated - no double bonds 

Michelle - hydrophobic lipid tails cluster in the middle; heads from a h-bond with water 

Bilayer - forms cell membranes, phospholipids held together by non-covalent interactions, selective permeability

Fluid mosaic model - 2D membrane where proteins are inserted or dissolved. extracellular on top and cytosolic face @ bottom 

Integral membrane proteins - embedded in bilayer; transmembrane or lipid-anchored proteins

Peripheral membrane proteins - noncovalently bond to transmembrane proteins/phospholipid heads

Receptor proteins - allow cell to detect signal molecules and initiate cell’s response 

Cell Identity - give ID, allows cell to be recognized by other cell

Enzymes - associate w/ different membranes, promotes chemical reactions to either face of membrane 

Cell Adhesion - allow cell to attach to another cell or extracellular matrix

Cytoskeletal attachment - allows cell to transmit changes in cytoskeleton, changes in plasma membrane 

Transport - movement of hydrophilic molecules from one side of membrane to other 

Passive transport - no energy, molecules travel down gradients 

Active transport - requires energy to travel up gradient 

Coupled transport - movement of ion down gradient provides energy for another molecule to travel up its gradient 

Symporters - ion and molecule transported in same direction across membrane 

Antiporters - ion moves down its gradient, transports molecule in opposite direction 

Osmosis - movement of water down its concentration

Hypertonic - pulls water out of cell, cell shrivels 

Hypotonic - water floods cell, cell bursts 

Endocytosis - allows eukaryotic cells to ingest larger martial from extracellular environment 

Pinocytosis - cell drinking 

Receptor-mediated - binds to specific receptor, triggers membrane to fold inward and form vesicle

Phagocytosis - cell eating 

pH - go up pH, go lower in H+, factors of 10 

Kinetic energy - energy of motion 

Potential energy - stored energy 

Oxidation - loss of electrons

Reduction - gain of electrons 

1st Law of thermodynamics - energy cannot be created or destroyed 

2nd Law of thermodynamics - entropy is continuously increasing 

+delta G - products have more energy than reactants, not spontaneous, ENDERGONIC 

-delta G - produced have less energy than reactants, spontaneous, EXERGONIC

Activation energy - energy required to initiate chemical reaction 

How can you increase reaction rate? - heat molecules or use catalyst to lower activation energy 

Catalysts - speed up reaction without being consumed or changed in the process, lower the activation energy, enzymes are biological catalysts

Inhibitor - molecule that binds to and decreases activity of an enzyme 

Competitive inhibitor - competes w/ substrate for active site 

Noncompetitive inhibitor - binds to enzyme at allosteric site that can cause shape changes that makes enzyme unable to bind to substrate

Biochemical pathways - reactions that occur in a sequence, product of one rxn is the substrate for the next rxn

feedback inhibition - end product of the pathway binds to an allosteric site on first enzyme in pathway 

ATP - source of chemical energy, main energy for all cells

ATP & control of protein - provides energy for multiple processes such as activation or deactivation of proteins. 

Phosphorylation - many proteins, like enzymes, are activated or inhibited through the addition or removal of phosphate groups; can change proteins shape, activity, stability or location 

Autotrophs - makes own ATP and organic molecules via photosynthesis

Heterotrophs - lives on organic molecules produced by autotrophs 

E-carriers - buckets that carry electrons and dump them elsewhere. (NAD+ to NADH) 

Glycolysis - occurs in cytosol, generates 2 ATP molecules and 2 NADH molecules, breaks glucose into 2 pyruvate 

Pyruvate Oxidation - occurs in mitrochondiral matrix, pyruvate into acetylCoA before entering krebs cycle, releases one CO2, reduced NAD+ to NADH

Krebs Cycle - occurs in matrix, forms citric acid with acetyl-CoA with oxaloacetate, 2 CO2 released, produces NADH, FADH2 and ATP 

ETC - occurs in inner membrane, protein complexes in mitochondrial membrane, uses NADH and FADH2 electrons to power movement of H ions across the membrane to create a proton gradient, drives the synthesis of ATP, produces majority of the cell’s ATP 

Chemiosmosis - process by which ATP is produced using the proton gradient of H+ ions across membrane. ETC pumps H+ into the intermembrane space and these protons flow back into the matrix through ATP synthase, central to oxidative phosphorylation

aerobic respiration - oxygen as final electron acceptor

Anaerobic respiration - inorganic molecules (like sulfur) as final electron acceptor, less ATP is produced 

Fermentation - glycolysis is only source of ATP, organic molecule as final electron acceptor, reduces organic molecules to regenerate NAD+ 

Catabolize Proteins - proteins broken into AA, undergo deamination to remove amino group, remainder converted into a molecule that can enter glycolysis or krebs cycle 

Catabolize fats - fats broken into fatty acids and glycerol, fatty acids are converted into acetyl group by B-oxidation, each acetyl group combines with CoA to make acetyl-CoA, enters krebs cycle 

Photosynthesis - the inverse chemical formula of cellular respiration, energy for almost all life on earth comes from this process; occurs in chloroplasts

Light dependent reactions- require light, occur in thylakoid, capture energy from sunlight, make ATP and reduces NADP+ to NADPH, produces O2 as byproduct 

Light Independent Reactions - doesn’t require light, occurs in stroma, use ATP and NADPH to synthesize organic molecules from CO2 

Chlorophyll A - main pigment in plants, absorbs violet blue and red light, only pigment that converts light energy into chemical energy 

Chlorophyll B - accessory pigment, absorbs blue and red-orange light, adds to range of absorbed light 

Carotenoids - accessory pigment, absorbs blue and green light, adds to range of absorbed light, functions as an antioxidant 

Photosystem II - absorbs light to excite electrons which are then passed into the ETC, splits water molecule to replace lost electrons to produce NADPH for calvin cycle 

Photosystem I - absorbs light to re-energize electrons used to produce NADPH

How do light dependent reactions generate ATP and NADPH? - Absorption of light and electron excitation, ATP generation in photophosphorylation, protons flowing through ATP synthase to make ATP, NADPH produced by PSI which takes high energy electrons NADP+ with H+ to make NADPH. 

Calvin Cycle - allows carbon fixation, RuBP + CO2 -> 2 PGA, PGA -> G3P, G3P used to regenerate Rubisco; 3 turns with the input of 3 CO2 to have enough carbon to produce new G3p; 6 turns to incorporate enough carbon for 1 glucose 

Photorespiration - Carboxylation leads to carbon fixation and favored under normal conditions; oxidation leads to photorespiration and favored in dry conditions 

C4 - use spatial solution, corn/sugarcane, 

CAM - succulent plants, time-based, opens at night 

Nucleotides consist of - adenine, thymine, cytosine, guanine, a phosphate group and a 5’ carbon sugar. 

Where is a phosphodiester bond formed? - between phosphate and 3’ (OH) of another nucleotide 

Watson and Crick DNA model - 2 nucleotide strande, complementary base pairs, constant diameter, strands are anti-parallel 

DNA polymerase - enzyme that synthesizes DNA by adding nucleotides to a growing DNA strand during replication, works in 5’ to 3’ direction and requires template strand and primer to start synthesis, has a proofreading ability to ensure accuracy of DNA replication by correcting errors in base pairing

Continuous replication - synthesis of leading strand during DNA replication, same direction as the fork unwinds which means DNA polymerase can synthesize without interruption 

Discontinuous replication - occurs on the lagging strand during DNA replication, so the lagging strand is synthesized in Okazaki fragments, these strands are later joined together by DNA ligase (glue) to form a continuous strand 

Components required for DNA replication - DNA gyrase that relieves tension in strands, helicase unwinds the double helix, primase makes RNA primer, Polymerase III elongates, reads 3’ to 5’, synthesizes 5’ to 3’, DNA ligase is glue 

Telomeres - DNA sequences at the end of chromosomes that protect them from damage (shoelace caps!) and prevent loss of important genetic info during replication. 

Telomerase - enzyme that extends length of telomeres, extends the parental strand 

Transcription - RNA synthesis, DNA to RNA

Translation - protein synthesis, RNA to protein/AA

Messenger RNA (mRNA) - codes for proteins 

Robosomal (rRNA) - components of robosomes, catalyze protein synthesis 

Transfer (tRNA) - adaptors between mRNA and AA 

Small Nuclear (snRNA) - pre-mRNA splicing 

MicroRNA (miRNA) - regulates gene expression 

Initiation phase - subunit recognizes promoter, DNA unwinds ahead of start site, subunit released after ~10 subunits 

Elongation phase - DNA synthesis 5’ to 3’ 

Termination phase - RNA base pairs w/ itself to create ‘hairpin’ formation, disrupts DNA/RNA/DNA pol interaction 

Eukaryotic transcription - occurs in nucleus, 3 different RNA polymerase, termination phase not well defined, primary transcripts are processed to produce mature mRNA 

Introns - non-coding regions that don’t need to be translated 

Exons - coding regions that specify amino acids 

Alternative splicing - single primary transcript may be spliced into different mRNAs by inclusion of different set of exons, can produce different proteins from a single gene

Critical features of genetic code - Initiation, elongation, termination, AA specified by sequence of 3 nucleotides (Codon), 

Function molecules and phenotype - proteins are important to cell structure and function, and affect phenotype of an organism. A single nucleotide change in the gene that codes for hemoglobin changes the cellular phenotype from round to sickle-shaped. 

Silent mutation - change to DNA nucleotide doesn’t alter AA 

Missense mutation - change to DNA nucleotide changes AA 

Nonsense mutilation - changes DNA nucleotide to a stop codon 

Point mutilation - mutation that alters a single base 

Frameshift mutilation - insertion of deletion mutation, changes downstream reading frame often with major consequences 

Gene expression is controlled by 3 mechanisms - transcriptional regulation, post-transcriptional regulation, post-translational regulation 

Positive control of transcription - activator protein is present, RNA polymerase can bind to binding site 

Negative control of transcription - repressor protein is present, RNA polymerase cannot bind

Promoter region - DNA sequence upstream from transcription start site, RNA polymerase binds to the core promoter 

Regulatory Proteins - affect ability of RNA polymerase to bind to the promoter/initiate transcription 

Core promoter region - bound by sigma factor of RNA polymerase 

Activator binding site - bound by positive control w/ activator proteins, can be closer to core promoter or further away 

Operons - always have a promoter, but may have any number of activating binding sites and operators 

Lac operon protein - produces proteins required for lactose metabolism 

Lac repressor protein ___ transcription when lactose is ____ - inhibits, absent 

CAP activator protein ___ transcription when glucose is ____ - promotes, absent 

Induction - occurs when transcription from lac operon is stimulated by presence of lactose in the environment, environmental molecule stimulates transcription 

Repression - occurs when tryptophan in the environment inhibits transcription from trp operon, molecule inhibits transcription

Chromatin - influence gene expression, DNA + histone organized into nucleosomes and then assembled in chromatin structure, changes in chromatin structure can occur by medical modification of histones or by ATP dependent movement of nucleosomes 

Transcriptional regulation what is transcribed? - regulation by transcription factors, DNA accessibility 

Post-transcriptional regulation what is translated? - regulation by mRNA processing, translation inhibition 

Post-translational regulation how does protein function - regulation of protein stability, activity 

Binary Fission - prokaryotic cells reproduce, replicate DNA and separate into 2 daughter cells 

Mitosis - nonsexual cell division, end product diploid 

Meiosis - sexual repo, end product haploid (sperm/eggs) 

Haploid - complete set of chromosomes, necessary to define the species 

Diploid - 2 complete set of chromosomes 

Centromere - point at which chromatids stick together; kinetochore located 

Kinetochore - ‘glue’ on centromere that stick to microtubules 

Cohesion proteins - rubber bands holding sister chromatids together 

Eukaryotic chromosomes - composed of chromatin, single chromosome is one continuous DNA molecule, there are 2 types of chromatin present in nucleus 

Heterochromatin - tightly packed, inaccessibly, methylated histones, 

Euchromatin - loosely packed, accessible, acetylated histones 

M phase - nuclear division + cytoplasmic division 

G1/S checkpoint - cell decides to divide, primary point for external signal influence 

G2/S checkpoint - commitment to mitosis, double check DNA replication 

Spindle checkpoint - cell ensures all chromosomes are attached to spindle, split before you check (nondisjunction)

G2 phase - centrosome duplicates, prep for M phase 

Prophase - bipolar spindle assembles chromosomes conffense 

Prometaphase - chromosomes attach to MTs, orient & congress 

Metaphase - chromosome align at the spindle equator 

Anaphase - sister chromatids separate, move to opposite poles

Telophase - chromosomes decondense nucleus begins to reform 

Cytokinesis - cleavage furrow in animals, cell plate in plants