Biology Study Notes PDF

What are the characteristics of living things? 1.Consists of cells 2.Store/Process info (DNA genome passed down) 3.Transform energy 4. Grow and reproduce 5. Adapt and evolve How are organisms classified? In Taxonomic Ranks: According to a binomial system Genus - Species (*species: group capable of i...

What are the characteristics of living things? 1.Consists of cells 2.Store/Process info (DNA genome passed down) 3.Transform energy 4. Grow and reproduce 5. Adapt and evolve How are organisms classified? In Taxonomic Ranks: According to a binomial system Genus - Species (*species: group capable of interbreeding) What are the three concepts of the Cell Theory 1.all organisms are composed of cells 2.smallest thing that can be alive 3.Cells arise only from preexisting cells What are Emergent Properties? "Whole is greater than the sum of parts" Cells may look the same but as you get a bigger picture differences start appearing between animals. What is the order of things at a population level? Population-> species -> community -> ecosystem -> biosphere What is an atom ? What are valence electrons? Smallest stable part of the cell Valence electrons are on the outermost ring and are the ones which interact with other atoms What is an element? What is the difference between Atomic number and mass? Element: Substance which can't be broken down Atomic number: # of protons Atomic mass: sum of mass of protons and neutrons Whats the difference between mass and weight? Mass : amount of a substance Weight : the force exerted on gravity on substance What are isotopes? What are ions? Isotopes have a different number of protons than the original. Ions have a different number of electrons. Which bond is the strongest and which is the weakest? Covalent ----> Ionic ----> Hydrogen (sharing of H atom) strongest weakest Why is water so essential for life? +cohesion: water is attracted to water (surface tension) +adhesion: Water bonds to other molecules (capillary action) +Specific Heat: has a high specific heat capacity (helps organisms maintain a constant temp) +Ice is less dense than water +universal solvent +polarity makes for a solvent and organizes molecules (ampipathic lipid bilayer) What are the three domains of living organisms? BACTERIA (prokaryote) ARCHAEA (prokaryote) EUKARYA (eukaryote) What are the classes of Eukarya? ^Plantae: Have cell walls,cellulose, and use photosynthesis ^Fungi: Cells walls of chitin, get energy by secreting digesting enzymes then absorbing products they release from the external environment. ^Animalia: Lack cell walls, obtain energy through ingesting other organisms ^Protista: All unicellular Eukaryotes except yeasts (which are fungi) What are molecules and what are compounds ? Molecules: Groups of atoms held together in a stable association. Compounds: Molecules with more than one type of element. What are the four macromolecules? *Carbohydrates: energy, storage, structure *Nucleic Acids: genetic info *Proteins: Enzymes, structure support *Lipids: energy storage, membrane structure, signaling What are the building blocks of carbohydrates? MONOSACCHARIDES Contain C, H, O in a 1:2:1 ratio bonds store energy What are the building blocks of Nucleic Acids NUCLEOTIDES phosphate+ sugar + nitrogenous base Sugar: DNA is deoxyribose and RNA is ribose What are the building blocks of proteins? AMINO ACIDS -Amino group -carboxyl (functional) group -single hydrogen -R group (determines chemical properties and is unique to each amino acid) What are the four structures of a protein? 1. Primary Structure: Based on gene code & made up of covalent bonds (such as peptide bonds) 2. Secondary Structure: "Alpha sheet" and "beta helix" formed by hydrogen bonds 3.Tertiery Structure: Driven by hydrophobic interactions and interactions between side chains. Quaternary Structure: Only created if more than one polypeptide chain is present What is the cell hierarchy? Atoms --> molecules --> macromolecules --> organelles --> cell What do prokaryotes contain in the cell? -DNA -membrane -ribosomes (NO membrane-enclosed organelles, including mitochondria) -preform respiration -preform photosynthesis What is the difference between plant cells and animal cells? PLANT Cell wall and membrane huge central vacuole chloroplasts ANIMAL No cell wall only membrane What is the difference between the cytoplasm and the cytosol? -cytoplasm includes all material inside of membrane -cytosol includes all material inside membrane except organelles NUCLEUS -Protect DNA -separate RNA synthesis from protein synthesis ER -protein synthesis -lipid synthesis -Ca ++ Storage -detoxification *proteins made on rough ER are destined to be exported GOLGI APPARATUS -carbohydrate processing -synthesis of cell wall LYSOSOMES -breakdown substances - PH=5 PEROXISOMES -Enclose a variety of enzymatic reactions The Eukaryotic cytoskeleton is made up of...... a. Actin Filaments (contraction) b. Microtubules (Mitosis, movement) c. Intermediate Filaments What are the cell wall materials? plant: cellulose fungi:Chitin What is compartmentalization? Where many organelles work together What is the cis face? The opening of the Golgi Apparatus Cell size We want a high surface/volume ratio so things can easily be transported in/out of cell. The extracellular Matrix - made up of proteins and carbohydrates Cell Membrane -Made up of phospholipids (lipid bilayer) -Saturated fatty acids: One double bond - very rigid -Unsaturated Fatty Acids: more than one double bond creates kinks in the membrane thus making it more fluid. -Phospholipids have hydrophilic head and hydrophobic tail. Protiens in the cell membrane *integral protiens *peripheral protiens *cholesterol in membrane Protiens can be inside the membrane, or attached to a lipid. Peripheral proteins are associated to integral proteins. What can/can't get through the cell membrane CAN -small, non polar (O2, CO2, N2) -Small uncharged polar molecules CANT large (polar/nonpolar) molecules ions Diffusion -Requires no energy (passive transport) *Osmosis (aquaporins) * facilitated diffusion *gated transport Active Transport -requires energy *ion pump Coupled Transport -Use energy stored in ion content (ion moving down a gradient helps other molecule move up) Symporters: ion and molecule move in same direction. Antiporters: Move in opposite directions Endocytosis > Pinocytosis (cell drinking) > Receptor mediated >Phagocytosis (Cell eating ) What are the types of Cell Signaling ^ Direct Contact Signaling:(fast) gap junctions for cells who function as a group ^Paracrine Signaling:(fast) still local, but molecules diffuse through extracellular fluid ^Autocrine: (fast) For the cells self (same cell signaling) ^Endocrine: (slower) Long Distance Longer lasting responses Hormones ^Synaptic Signaling: neurotransmitting fast, long distance Cell Signal Reception Process -Peptides, proteins, neurotransmitters bind to cell signal receptors on outside of cell -hydrophobic signals can go into cell -many steroid receptors control gene expression (typically transcription factors) Types of Receptors Effector Protiens (enzymes, channel) Molecular Switches (Kinases, G Proteins) second messengers (CAMP, Ca +) What are the three classes of cell surface receptors. 1. Channel Linked Receptors (gated ion channels) Ligand--> Channel opens 2. Enzymatic Receptor Turns on protein inside cells Receptor Tyrosine Kinase (RTK) Activation Ligand binds to receptor ---> dimerization (acossiates w other receptor protein) and the two phosphoralize each other (autophosphorilate) --> response proteins bind to the phosphorylated tyrosines G-Protein Coupled Receptors Ligand--> G-Protein Coupled receptor is--> G-protien is phosphorilized (GDP turns to GTP)-->g-protien goes to enzyme --> Enzyme is activated Depending on the Effector Protien/enzyme , some things can happen... What are some of the reactions? cAMP Signaling pathway: Adenyl Cyclase is enzyme activated --> produces cAMP--> activates PKA PI/Ca++ Signaling Pathway Phospholipase --> splits PIP2 into two parts (DAG & PIP3) --> PIP3 opens gates of chanel proteins --> Ca++ moves out --> High concentration on Ca++ in cytosol activates targets What is the difference between Kinase and Phosphatase? Kinase-Sticks phosphate on Phosphatase: Removes phosphate Steroids -Non polar, lipid soluble soluble structure (cholesterol) -Goes through membrane --> causes complex it binds to to move into the nucleus. -Complex affects transcription Kinase Cascades -Mitogen Activated Protien (MAP) Kinases; series of protein Kinases which phosphorylate each other in succession -Amplifies signal What is Thermodynamics? Branch of chemistry concerned with energy changes. Two types of energy: Kinetic Potential Law of Thermodynamics 1. Energy cannot be created nor destroyed can only change form 2. Entropy (disorder) is continuously increasing as more and more conversions happen G= H-TS H: Enthalpy T:Absolute Temp S: Entropy Dehydration vs hydrolysis Dehydration: Formation of bonds Hydrolysis: Breaking of bonds ATP ATP synthesis depends on exergonic reactions to be formed ATP hydrolysis provides energy for endergonic cellular process. Activation Energy Extra energy needed needed to initiate reaction What are Ribozymes? RNA molecule which preforms enzymatic activities Intramolecular: Acts on self Intermolecular : Acts on another molecule Influences on an enzyme -Amount of substrate -amont of enzyme -PH -Temp What are allosteric Enzymes? Enzymes that exist in active/inactive forms. What are the types of inhibitors? Competitive: Bind directly to active site Non Competitive: bind to there place and change the shape What is metabolism? Total of all chemical reactions carried out by organism Anabolic vs Catabolic Anabolic: Expend energy (build molecules) Catabolic: harvesting energy (break molecules) Cofactor vs coenzyme Cofactor: inorganic Coenzyme: Organic Autotrophs vs Heterotrophs Autotrophs: make own energy Heteretrophs: get energy from autotrophs What is Cellular Respiration Extracting energy from chemical bonds present in organic molecules What are the types of Respiration Aerobic Anaerobic Fermentation What are the two types of phosphorilation Substrate-level phosphorilation: Transfer of Phosphate directly to ADP from another molecule Oxidative Phosphorilation: Use of ATP synthase and concentration gradient GLYCOLYSIS * 2 phosphates added to ends of glucose *Broken into two 3-carbon molecules *Each G3P is oxidized by NAD+ and P is broken off (2 ATP, 2 NADH) mitochondrial matrix PYRUVATE OXIDATION *Removal of CO2 from pyruvate leaves a 2 carbon Acetyl-group *Acetyl Group is attached to CoA (2 NADH) mitochondrial matrix KREBS CYCLE *Acetyl CoA picked up by oxaloacetate *rearrangement and decarboxylation result in release of CO2 and NADH (6 NADH, 2 FADH2, 2 ATP) mitochondrial matrix What is chemiosmosis? Uses H+ proton gradient to create energy (28 ATP) What is total net ATP yield? Bacteria: 32 Eukaryotes: 30 What are the two types of fermentation. What is the point of fermentation? Alchohol Fermentation: (yeast) Produces ethanol Lactic Acid Fermentation:Produces lactic acid Purpose is to recycle NADH Catabolism of Proteins deamination to remove amino group Catabolism of fats -Broke down into fatty acids and glycerol -Fatty Acids--> Acetyl Group by beta-oxidation What is the equation for photosynthesis? CO2+H2O --> C6H12O6+H2O+O2 Where do the light dependent reactions occur and where do the dark reactions occur? Light: Thylakoid (where Chlorophyll is ) Dark: Stroma We have an expert-written solution to this problem! What are the three main pigments? Chlorophyl A : main pigment Chlorophyl B: accessory pigment carotenoids: reflects orange act as antioxidants What is a photosystem? Collection of pigments/protiens in membrane 1. Antenna Complex: gathers photons and feeds e- to 2. reaction center: passes excited e- out of photosystem How do the light reactions work? Light hits photosystem II --> photons go to reaction center--> and H2O is split/donates electrons--> electrons go through an ETC (b6F complex) and H+ gradient is formed--> PLASTOCYANIN --> plastocyanin goes to photosystem I --> electron pair is re-excited -->goes down another ETC but no gradient is formed--> FERADOXIN --> NADP is reduced to NADPH What is Cyclic phosphorylation? Electrons from PSI are circled back through 1st ETC to create more ATP What are the three steps of the Calvin Cycle? 1. Carbon Fixation: CO2 comes into cycle and binds to RubP by Rubisco 2.Reduction: PGA reduced to G3P by NADPH 3. Regeneration: 3 G3P are used to regenerate rubisco What are the alternative ways plants preform photosynthesis? C4: Plant shuttles CO2 to different place CAM: Open at night when cool and store CO2 in vacuole Which bases are Purines and which are Pyrimidines? Purines: Adenine , Guanine ( 3 ring) Pyrimidines: Cytosine, Thymine (2 ring) What kind of backbone does DNA have Phosphodiester backbone Messelson Stahl Experiment proved semiconservative model Griffith Infected mice Hershey Chase marked protien with radioactive sulfur and DNA with P Chargaffs Rules A=T G=C Wilkins and Franklin Discovered DNA is helical What are the main 3 Polymerases in DNA replication? What are the other main enzymes? 1. DNA poly 1: replaces primers with DNA 2. DNA Poly 2: DNA repair 3. DNA Poly 3: main replication enzyme Helicase: Unwinds DNA SSBS : coats strands to keep them apart DNA Gyrase: Keeps DNA from Twisting Primase: makes the primer DNA: Ligase seals Okazaki Fragments Replication is Semidiscontinuous Meaning there is a leading strand that is synthesized continuously and a lagging strand which is synthesized in Okazaki Fragments. How does DNA replication occur in prokaryotes ? Replication fork is made by replisome There is a b-clamp on the lagging strand Eukaryotic Replication. -There is a larger amount of DNA and multiple chromosomes so multiple origins are used. -Telomeres are special structures found at the end of the chromosome to protect the ends.(made by telomerase) What are the five main types of RNA? Messenger RNA: codes for protien Ribosomal RNA: ribosome components, create peptide chains/proteins Transfer RNA: Adaptors btwn mRNA and amino acids SnRNA: Pre mRNA splicing miRNA: regulates gene expression RNA Polymerase Adds nucleotides 5-3' Doesn't need a primer positioned upstreamed of gene to be transcribed INITIATION Promoter sequence (TATA box) recognized --> DNa is unwound--> RNA binds and transcription bubble forms ELONGATION RNA adds to 3' end U replaces T Transcription bubble: RNA poly unwinds and reattaches before and after TERMINATION RNA base pairs with itself to form hairpin structure