Cell Bio First Exam Study Guide
Cell Bio First Exam Study Guide CELL-1010-01
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This 19 page Study Guide was uploaded by Nina Kalkus on Friday February 5, 2016. The Study Guide belongs to CELL-1010-01 at Tulane University taught by Vijayaraghavan, Meenakshi in Fall 2015. Since its upload, it has received 316 views. For similar materials see Intro to Cell & Molec Biology in Business at Tulane University.
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Date Created: 02/05/16
Cell Biology First Exam Study Guide! 7 Characteristics of Life: 1) Cells and Organization 2) Energy & metabolism 3) Response to environment, adaptation 4) Regulation & homeostasis 5) Growth and development 6) Reproduction 7) Biological evolution Cells: macromolecules with information protected by membrane Energy: the capacity to do work Autotrophs vs Heterotrophs make their own food get food from other organisms chemo: energy from chemicals metabolism and cell respiration photo: energy from the sun Catabolism: breakdown/ release of energy Anabolism: making things/ using up energy Development: Change in properties of cells Reproduction: sustain life, represent genes DNA: can replicate, undergo changes, mutations Levels of Organization (all made of matter): 1) Atom (have capacity to maintain properties of elements) 2) Molecule and macromolecules (compounds= 2+ elements) 3) Cell 4) Tissue (same types of cells) 5) Organ (next sublevel= organ system) 6) Organism (species= similar genetic makeup; can reproduce) 7) Population (1 species) 8) Community (interactions between populations of species) 9) Ecosystem (interactions between living systems and abiotic systems) 10)Biosphere Eukaryotic vs. Prokaryotic organelles no nucleus nucleus just mac.mol. & membrane *both have ribosomes Properties of Life: Organization of life: cells (growth and development) Continuity of life: DNA (heredity, storing information) Unity (evolutionary conservation) All modern forms of life display a common set of characteristics (favorable characteristics remain) Based on biological evolution (DNA, all eukaryotes have nucleus & chromosomes) Diversity: Hallmark of Life (speciation) mutations, genetic variations/speciation, 2 sets of DNA to make 1 Evolutionary History: Prokaryotes: 3 billion years ago Eukaryotes: 2 billion years ago Analogous structures vs Homologous structures Analogous: superficially similar, anatomically dissimilar, provide similar functions E.g= bat wings and butterfly wings Homologous: similar in morphology, anatomy, genetics (common ancestry) and embryology, but provide different functions E.g= bat wings and dolphin flippers Vertical evolution vs Horizontal evolution 1 species 2 or more species beneficial mutations insertion of genes from natural selection unrelated species “tree of life” “web of life” Classification→ Taxonomy: the grouping of species based on common ancestry Until 1980, there was only prokaryote vs eukaryote 3 Domains: 1) Bacteria (unicellular prokaryote) 2) Archaea (unicellular prokaryote) *introns & phospholipid bilayer like eukarya 3) Eukarya (unicellular to multicellular eukaryotes) 4 kingdoms: Protista, fungi, plantae, animalia Gene: a segment of DNA that codes for specific function Genome: the complete genetic makeup of an organism carries information to make proteins Genomics: Techniques used to analyze DNA sequences in genomes Proteins: tools of gene expression Proteome: the complete complement of proteins that a cell or organism can make Proteomics: Techniques used to analyze the proteome of a single species and the comparison of proteomes of different species *Clownfish: use their environment and proteome to determine sex largest in group becomes female, 2nd largest becomes male when largest female dies, 2nd largest male becomes female Atoms: nature’s building material fundamental functioning units of matter matter: anything that has mass and occupies space each specific type of atom is a chemical element 3 subatomic particles protons: positive, found in nucleus, same number as electrons neutrons: neutral, found in nucleus, number can vary electrons: negative, found in orbitals, same number as protons orbit: 1 path orbital: region of highest probability of finding electron around nucleus entire atom has no net electrical charge Shells Orbitals Electrons 1= K 1s 2 2= L 2s= (2e), 2p= (6e) 8 3= M 3s, 3p, 3d 18 4= N 4s, 4p, 4d, 4f 32 s= sharp, p= principal, d=diffuse, f= fundamental Periodic Table: Organized by atomic number Rows (periods) correspond to number of electron shells Columns (groups) same number of valence electrons in each causes similarities between electrons in groups Octet rule: outer shell is stable with 8 electrons only exception is hydrogen (outer shell filled with 2) Protons: number of protons in an atom is its atomic number atomic number is also equal to the number of electrons in the atom (net charge=0) Neutrons particles in nucleus that have no charge Electrons number and arrangement of electrons of an atom hold the key to its chemical reactions Isotopes: multiple forms of an element that differ in the number of neutrons same chemical properties different physical properties same number of protons→ same atomic number atomic masses are averages of the weights of different isotopes of element Atomic Mass: protons and neutrons are nearly equal in mass; both are more than 1,800 times the mass of an electron atomic mass= sum of the masses of protons and neutrons atomic mass scale indicates an atom’s mass relative to the mass of other atoms *weight is derived from the gravitational pull on a given mass Chemical bonds and molecules: Molecule= 2 or more atoms bonded together Molecular formula= contains chemical symbols of elements found in a molecule subscript indicates how many of each atom are present Compound= molecule composed of 2 or more elements 3 types of bonds: 1) Covalent atoms share a pair of electrons 1 pair of electrons= single bond 2 pairs of electrons= double bond 3 pairs of electrons= triple bond shared electrons behave as if they belong to each atom→ often the strongest chemical bonds Polar covalent bonds when two atoms with different electronegativities form a covalent bond, shared electrons are more likely to be in the outer shell of the more electronegative atom electronegativity: capacity of an element to draw bonded electrons to itself causes differences in charge across the molecule (one part more negative, another more positive) Example= Water 2) Hydrogen weak polar covalent bonds arise from polar compounds with H represented as dashed or dotted lines collectively can form strong bond overall holds DNA strands together individually, weak bonds can form or break easily substrate and enzyme bonding (don’t want to use a lot of energy to make/break those) 3) Ionic Ion: atom or molecule that has gained or lost one or more electrons now has a net electric charge Cations: net positive charge Anions: net negative charge ionic bond occurs when a cation bonds to an anion Molecules may change shapes: covalent bonds are flexible molecules can rotate around bond angles Free Radicals: molecule containing an atom with a single unpaired electron in its outer shell, has capacity to grab electrons from balanced molecules and make more free radicals formation: radiation, toxins (stressful situations) beneficial aspects: destroy infective agents; e.g hydrogen peroxide harmful effect: killing healthy cells, rupture of cell membrane, genotoxin antioxidants: reduce free radicals, provide extra electrons for FR unpaired electrons Chemical Reactions: substances being changed to other forms “break old bonds, form new ones” need reactants (substances that can react) energy (apply heat→ kinetic energy) catalyst (increase rate of reaction by lowering activation energy) enzymes in body aqueous (liquid environment) equilibrium: when the rate of forward reaction=rate of backward reaction Solution: solute and solvent solute: needs to be dissolved solvent: liquid doing the dissolving weight: used to make % solutions molarity= concentration Water= almost universal solvent polar, cause of many distinct properties when something is dissolved in water, covalent bonds are stronger than ionic bonds polar covalent and ionic bonds dissolve fast, non polar covalent dissolve slow cohesion, solubility, high specific heat, high heat of vaporization, lower density of ice weak acids: partially dissociated in water; strong acid: completely dissociated in plants: vacuole (hydrostatic skeleton) → turgor pressure → rigid cell wall → sturdy structure of plants high specific heat: amount of energy required for 1 g water to be raised 1 degree Celsius why we don’t overheat after meals high heat of vaporization : maintain constant internal temperature (sweat) the amount of energy to vaporize 1 mole of water at its boiling point lower density of ice → high heat of fusion (freezing releases energy) fewer bonds between water molecules and more space colligative: water can stretch its boiling/freezing point depends on number and concentration of substances added to it permits life to exist in extremes hydrolysis and dehydration synthesis cohesion: attraction between water molecule and water molecule causes surface tension why water can go up plant stalks against gravity adhesion: attraction between water molecules and other compounds Hydrophilic: water loving (polar and ionic) Hydrophobic: water fearing (nonpolar→ water pushes them away=hydrophobic exclusion) Amphipathic: both (hydrophilic and hydrophobic) Example: soap → hydrophobic= oil, moisturizes → hydrophilic= acid, washes away may form micelles in water (flower shape) Acids vs. Bases increase release of H+ in water increase release of OH in water some release OH others bind H+ pH≤ 6 pH≥8 *neutral pH= 7* pH= log (H+) effects shapes and functions of molecules effects rates of many chemical reactions effects ability of 2 molecules to bond buffers: can easily be a weak acid/base help keep constant pH water is a weak buffer (equal parts H+ and OH) blood pH: 7.357.45 acidosis→ pH is about 6.4 → vomiting and nausea 10 times more H+ than pH= 7.4 alkilosis→ pH is about 8.4 → muscle tremors 10 times less H+ than pH= 7.4 adjusted by the buffer of carbonic acid, most common buffer, found in blood Organic Molecules: hydrocarbon base Carbon: highly reactive (needs 4 electrons for octet rule) many different nature of compounds C=C bond → very short, difficult to break functional group: groups of atoms with special chemical features that are functionally important not balanced compounds (not fulfilled octet rule) gives chemical characteristics isomers: 2 structures with an identical molecular formula but different structures and characteristics 4 Major types of organic molecules and macromolecules 1) Carbohydrates (4.3 calories/gram) 2) Lipids (9.3 calories/gram) 3) Proteins (4.3 calories/gram) 4) Nucleic Acid *ribozymes→ RNA that act as enzymes Macromolecules: often polymers long molecule built by linking together small, similar subunits dehydration synthesis: lose water to make molecules hydrolysis: insert water to break molecules Macromolecule Covalent bond type Carbohydrate glycosidic Lipid ester Protein peptide Nucleic Acid phosphodiester Carbohydrates: composed of carbon, hydrogen, and oxygen atoms C(H O) n 2 n most carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group well suited for energy storage because of numerous CH bonds lots of energy in covalent CH nonpolar → maximum energy glucose = transport sugar (easiest energy) Monosaccharides: simplest sugars most common are 5 or 6 carbons 5: pentoses (ribose, deoxyribose) 6: hexose (glucose) different ways to depict structures (ringed or linear) Glucose isomers structural: different arrangements of same elements glucose and fructose stereoisomers geometric isomers: above or below ring α and β glucose enantiomers: mirror image D and L glucose Disaccharides: carbohydrates composed of two monosaccharides sucrose, maltose, lactose Polysaccharides: many monosaccharides linked together to form long polymers starch: energy storage found in plants amylose and amylopectin amylose: linear chain of maltose becomes a big clump (movement) water can’t come in for hydrolysis amylopectin: branched more easily accessed by water can’t bunch as easily easier for hydrolysis potatoes: 80% branched, 20% linear cooks faster rice: 100% linear cooks slower cellulose: made up of beta subunits we can’t break this down used for structure in plants sucrose is energy for plants glycosaminoglycans: present in cartilage connected with negative charged ions very charged disaccharides long chains of proteoglycans attached protein sugar complex attract water chitin crabs exoskeleton etc nitrogens and sugar oligosaccharide→ 1215 Lipids: composed mostly of hydrogen and carbon atoms nonpolar → very insoluble in water Fats: mixture of triglycerides (triacylglycerols) formed by bonding glycerol to three fatty acids lose 3 H2 very important for energy storage (longer hydrocarbon chain→ more energy) can be structural in providing cushioning and insulation Fatty acids: saturated vs. unsaturated saturated: saturated w hydrogen no double bonds no kinks unsaturated more double bonds mono and polyunsaturated less hydrogen kinks more liquidlike normally talking about “cis” transfat: more LDL and HDL hydrogen on either side of chain phospholipids: 1 glycerol, 2 fatty acids polar head, nonpolar tail polar: phosphate, nitrogen (amino acid) only hydrophobic molecules can pass through plasma membrane because of tails semipermeability steroids: cholesterol acts like a lipid precursor to hormones waxes: like in the head of a sperm whale... lower the temperature→ solidify more dense, whale can dive deeper raise the temperature→ liquify less dense, volume increase, helps whale float very hydrophobic strictly nonpolar also structural→ honey combs Proteins: composed of carbon, hydrogen, oxygen, nitrogen, and small amount of other elements, notably sulfur workhorses of cell tools for gene expression amino acids are the monomers common structure with variable Rgroup 20 amino acids 8 essential, 12 nonessential essential: not made by the body nonessential: made by the body sidechain determines structure and function 2 ends to amino acids N terminal (nitrogen group) positive C terminal (carboxyl group) negative charges don’t cancel bc R groups R group (functional) can be charged hydrogen functional group and H can switch isomers glycine doesn’t have isomers, bc R group is a hydrogen also special start amino acid code is AUG makes methionine nonpolar peptide bond: between amino acids (CN) R group determines polarity nonpolar amino acids: CH 2or CH3 polar uncharged amino acids: O 2 H charged amino acids: acids or bases aromatic amino acids: aromatic carbon rings with single or double bonds carboxyl of incoming and amino group of existing ⇒ peptide bond Protein Structure: primary, secondary, tertiary, quaternary Primary structure: amino acid sequence, arrangement based on code determined by genes determines how protein is going to function protein can never function in its primary structure Secondary structure: chemical or physical interactions cause folding alpha helixes and beta pleated sheets alpha helix: hydrogen bond to distant amino acids beta pleated sheets: hydrogen bond to adjacent amino acids randomly coiled regions: motifs (super secondary structures) neither alpha helix or beta pleated sheet Tertiary structure: folding gives complex threedimensional shape sometimes the final level of structure 5 factors promoting protein folding 1) hydrogen bonds 2) ionic bonds 3) hydrophobic effects 4) Van der Waals forces 5) Disulfide bridges (covalent, amino acids with sulfur) Quaternary structures made up of 2 or more polypeptides protein subunits multimeric proteins Denaturation vs. Dissociation denaturation: unfolding breaking bonds can happen to tertiary structure and quaternary structure can result in metabolic disorder dissociation breaking apart tertiary polypeptide subunits only happens in quaternary structure doesn’t result in metabolic disorder Protein protein interactions: no covalent bonds forces of attraction→ hydrogen, ionic, hydrophobic, Van der Waals specific binding at surface Domains: tertiary structure parts of protein with own composition of amino acids, own structure, but helps with structure/function of whole protein Nucleic Acids: responsible for the storage, expression, and transmission of genetic information made or carbon, hydrogen, oxygen, nitrogen, and phosphorus phosphate group, 5 carbon sugar, and a single or double ring of carbon and nitrogen atoms known as a base monomer= nucleotide Deoxyribonucleic acid vs. ribonucleic acid DNA: stores genetic information coded in the sequence of their monomer building blocks thymine, adenine, guanine, cytosine 2 stranded double helix (except that viruses have 1 strand) 1 form RNA: involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain uracil, adenine, guanine, cytosine single strand several forms (mRNA, tRNA, etc) Nitrogenous bases: Purines and Pyrimidines purines: 2 rings, adenine and guanine pyrimidine: 1 ring, thymine, cytosine, uracil (missing methyl group that’s in T) Nitrogenous base + sugar = nucleoside nucleoside + phosphate = nucleotide nucleosidephosphate bond= 1st ester bond nucleotidenucleotide bond= 2nd ester bond nitrogenous basenitrogenous base= hydrogen bond DNA + histones → chromosomes, all chromosomes → genome General Features of Cells cells: macromolecules separated from the environment by membrane, having some sort of information Cell Theory: Schwann and Schleiden 1 or many cells= organism smallest unit of life *added by Rudolf: cell division microscope= able to magnify magnification (enlarge): ratio between size of image on microscope to actual resolution (clarity): 2 adjacent objects recognized as distinct from one another contrast (visualize): use dye Light microscope= uses light for illumination (1 beam) smallest size visible: 0.2 ᵰm Phase contrast: no staining Fluorescent: absorb and reflect (at longer wavelength) picks up reflected light Confocal: best resolution among light microscopes uses lasers, move around sample 3D image often coupled with fluorescent dyes Electron microscope= uses electron beam for illumination (2 beams) Transmission: best resolution of all microscopes looks at electrons that pass through sample see the inside of cells Scanning: looks at electrons that scatter from sample outside of cell (topography) Prokaryotic cells: Bacteria and Archaea bacteria: omnipresent cocci: circular structure bacilli: rod structure both found in colonies spirochetes: springlike structure found solitarily archaea: more extreme conditions include complex phospholipids and introns, like eukarya very simple structure lack a membrane nucleus DNA found in single circular double stranded form this is found in nucleoid region, just an area of the cell kept there by proteinprotein interaction plasma membrane: barrier invaginations: folds that increase surface area membrane includes pigments and proteins that allow for special functions cytoplasm: everything inside plasma membrane plasmid: strand of DNA outside nucleoid region nonessential, but gives cells special characteristics capable of inducing horizontal evolution ribosomes: involved in protein synthesis cell wall: outside p.m., support and protection porous for nutrition glycocalyx: traps water, protection syrupy mostly made of carbs prevents cell from dehydrating appendages flagella: long and hairlike, used for movement winds up like a coil spring, releases for energy pilli: short hairlike structures “fertility factor” help transfer plasmids plasmid + pilli = F+ bacteria (can transfer DNA) Gram+ vs. Gram bacteria use iodine to test Gram +: stain purple thick layers of carbs connected by protein (peptido glycan) usually easily digestible by antibodies/antibiotics nonvirulent Gram : stain pink thin layer of peptidoglycan topped by thick layer of lipopolysaccharide very virulent Eukaryotic Cells: more complex Animal and plant cells DNA housed inside nucleus DNA same throughout cells of organism; types of cells differ have autonomous organelles with specific functions Animal cells: lysosome centrosome with centrioles Plant cells: cell wall chloroplasts vacuole Proteome: determines the characteristics of a cell generegulation: some genes “up regulated” → more of that protein some genes “down regulated” → less of that protein persistence and concentration of protein muscles → more of that protein in legs than hands different amino acid composition: alternate splicing 1 gene makes different types of globins → hemoglobin some exons removed Cytoskeleton: support always present in cell unlike spindle fibers, which are only present during mitosis network of three different types of protein filaments microtubules intermediate filaments actin filaments Microtubules Intermediate filaments Actin 25 nm in diameter 10 nm in diameter 7 nm in diameter made up of incapable of dynamic 2 strands of acton coil protofilaments, alpha instability around each other and beta, builds up a once formed, formed made of actin long filament for life monomers originates from the 34 protein subunits negative end= below negative end near the form ropelike plasma membrane nucleus, building onto structures positive end= can be the positive end, no polarity towards nucleus or away from the no motor proteins towards outside of nucleus support organelles cell polar *in Mad Cow Disease, polarity dynamic instability your brain gets dynamic instability (can polymerize and spongy because you myosin: motor protein depolymerize) don’t have that moves over actin dynein and kinesin: 2 intermediate filaments proteins that can rebuilding themselves move on microtubules dynein: moves towards negative end/nucleus kinesin: moves towards positive end/cytoplasm help move things from one organelle to another structural support Motor Proteins: cellular proteins that use ATP as a source of energy to promote movement given by ATP hydrolysis 3 domains called the head, hinge, and tail tail connected to cargo head: venue for ATP hydrolysis connects to the ground (filaments) Flagella and Cilia: flagella are longer than cilia and present singly or in pairs cilia are shorter and tend to cover all surfaces of the cell share the same internal structure both come from basal bodies below the plasma membrane flagella in bacteria vs eukarya: bacteria: corkspring motion made of flagellin eukarya: whiplash motion nexin connects the microtubules and restricts their movement sheaths on dynein restrict their movement built up kinetic energy transfers into whiplash motion of cell made of microtubules with dynein Endomembrane system Secretory system (proteins transported through secretory vesicles) outer membrane endoplasmic reticulum endoplasmic reticulum golgi complex golgi complex lysosome (animals) lysosome (animals) vacuole (plants) vacuole (plants) plasma membrane peroxisome *no peroxisome plasma membrane Nucleus: Ribosomes:
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