Attributes of Living Systems: Exam 1

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What is the core theme of biology?: Evolution
Define: Molecule: 2 or more atoms held together by covalent bonds
Define: Matter: Anything that has mass and takes up space. Composed of elements.
Define: Element: A subsance that can't be broken down into other subsances by chemical reactions. Composed of atoms.
Define: Atom: The smallest unit of matter that has properties of an element.
What number of chemical elements are essential for life?: 25
96% of living matter is composed of which four elemnts?: Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C)
Hint: remember HONC!
What are atoms made up of?: Protons (+1 charge)
Neutrons (0 charge)
Electrons (-1 charge)
How much do protons, nuetrons and electrons weigh, respectively?: protons: 1 dalton, nuetrons: 1 dalton, electrons: ~0
Define: Atomic Number: The number of protons per atom. The Atomic number is characteristic for each element. written Lower left of element
Define: Atomic weight. What is the unit?: number of protons + the number of nuetrons. written upper left of element

The unit is Dalton (Da)
How can atoms be modified?: 1) gain or lose electrons
2) isotopes
Define: Ion: Atom gains or loses electrons and becomes charged
Define: Isotopes: Two atoms with the same number of protons but different number of nuetrons. Some can be radioactive.
What is the maxiumun number of electrons that the first electron shell can hold?: 2 electrons
What is the maximun number of electrons the second electron shell can hold?: Shell 2 and up can hold 8 electrons each.
What are the electrons in the outermost shell called?: Valence electrons
Why do atoms interact with one another?: to achieve a full vallence shell
The formation of chemical bonds between atoms results in what?: Molecules and compounds
What are the 3 chemical bonds important in biology?: Covalent bonds, Hydrogen Bonds, and Ionic bonds
Define: Covalent Bond: formed when valence electrons are shared by two atoms. Includes single and double bonds
Define: Nonpolar bond: bond between 2 atoms of the same element or same electronegativity
Define: Polar Bond: bond between two atoms with different electronegativity. Electrons are pulled closer to the atom with more electronegativity, making it slightly negative and the other slightly positive. Ex: water molecules
Define: Hydrogen Bond: Weak bond formed between 2 POLAR molecules. Slightly positive hydrogen atom is attracted to slightly negative atom of another polar molecule. Can be between 2 different molecules of within the same molecule
Why are hydrogen bonds important in biology?: 1. Chemical Reactions
2. Stabilize large molecules (DNA, proteins)
3. Water properties
Define: Ionic Bond: formed when electrons are transferred from one atom to another. Both atoms become charged ions. Strong but dissolves in water.
Define: Cation: atom that lost an electron due to ionic bond. (postive ion)
Define: Anion: Atom that gained an electron due to ionic bond. (negative ion)
What do cations and anions form when they attracted one another?: Salts
What is the difference between salts and molecules?: Molecules have a fixed number of atoms while salts can vary.
What happeneds during a chemical reaction?: Bonds between atoms in reactants are broken, atoms are rearranged, and new bonds are formed
Define: Mass Conservation Law: All atoms present in the reactants are present in the products
Define: Chemical Equilibrium: foward and reverse reactions occur at equal rate. Concentration of reactants remains constant, but not necessarily equal to concentration of products.
What is considered the molecule of life?: Water
Water is essential to what?: All living organisms
What percentage of water are organisms composed of?: 70-95%
What percentage of earths surface is covered by water?: 75%
How long was life in water before its transition to land?: 3 billion years
How is oxygen ultimately derived?: From water, via photosynthesis.
Why is the polarity of water so important?: it allows hydrogen bonds to form between water molecules.
How many other water molecules is each water molecule capable of bonding to?: Four others
Hydrogen bonds give water what properties that are essential to life?: 1. Cohesion
2. High Specific Heat
3. Solid is less dense than liquid
4. Ability to act as a solvent
Define: Cohesion: linkage of molecules by hydrogen bonds. bonds are constantly breaking and reforming
What percent of water molecules are bonded together at body temperature?: about 15%
What is it that gives water more structure than other liquids?: Hydrogen bonds
What allows the transport of water against gravity in plants?: Cohesion. Evaporation of water at leaves pulls water up from roots.
Define: Heat: TOTAL amount of kinetic energy in a body of matter
Define: Temperature: Heat intensit due to AVERAGE kinetic energy
Define: Specific Heat: the amount of heat that must be absorbed or lost for 1 gram of a substance to change temperature by 1 degree celsius. S.H. of Water = 1 calorie
How does heat effect the bonds in water?: Heat absorbed breaks hydrogen bonds. The formation of bonds releases heat.
Why is water denser than ice?: In ice, each molecule is bonded to 4 others, forcing the molecules to be spaced farther apart in ice than in liquid.
Why is it important that ice floats?: Prevents large bodies of water from freezing and it insulates the water to maintain a habitable environment.
What makes water a good solvent?: It forms hydrogen bonds with ions and polar molecules.
Define: Hydrophyllic: has an affinity for water. Has polar or ionic bonds
Define: Hydrophobic: has no affinity for water. Has non-polar bonds
Define: Solution: liquid composed of 2 or more substances
Define: Solute: the substance that is dissolved in a solution
Define: Solvent: the liquid that dissolves the solute
What are the important properties of solutions?: 1. concentration
2. acidity
Define: Concentration: the amount of solute per volume of solvent.
Unit: molar (M)
- 1 M = 1 mole of soluter per liter solvent
- 1 mole = 6.02 x 10^23
Define: Molecular Weight (Mw): = the weight of its atoms in daltons

= the weight of 1 mole of it (in grams)
What determines the acidity of a solution?: The concentration of Hâº ions. Some water molecules dissociate into Hâº and OHâ». if unequal, the solution is either acidic or basic. greater # of Hâº â†’ more acidic
In pure water, what are the concentrations of H⁺ and OH⁻ equal to?: both equal to 10⁻⁷ M
What is the ion product constant K_w?: [H⁺] x [OH⁻] = 10^-14
What is the pH of acidic solutions, nuetral solutions, and basic solutions, respectively?: Acidic: [H⁺] higher, pH lower, pH<7
Nuetral: pH = 7
Basic: [H⁺] lower, pH higher, pH>7
What are the dissociative porperties of strong acids/ bases versus weak acids/bases?: Strong acids/bases dissociate completely
Weak acids/bases dissociate reversibly
Define: buffers: weak acids/bases that can take up or donate [H⁺]. they help cells regulate pH. Ex: carbonic acid
What is considered the backbone of life?: Carbon
What distguishes living (organic) matter from non-living (inorganic) material?: Carbon compounds
Carbon atoms bond to the atoms of what elements?: hydrogen (H), Oxygen (O), nitrogen (N), sulfer (S), phosphorus (P) and itself.
The differences in carbon compounds result in what?: Species differences and individual variability
What does the diversity of organic compounds come from?: How the atoms are arranged
Why is carbon special?: Because it can covalently bond with up to four different atoms. (Tetravalent)
Define: Hydrocarbons: molecule that consists of only carbon and hydrogen. Hydrophobic due to nonpolar H-C bond. Key part of fossil fuels. Energy stores for cells- fats.
How can carbon skeletons vary?: 1. Length
2. Branching
3. Double bonds
4. Rings
What does the function of organic molecules depend on?: structure
Define: Isomers: compounds with the same molecular formula but different structures
What are the different types of Isomers?: 1. structural isomers
2. geometric isomers
3. enantiomers
define: structural isomers: different arrangment of covalent bonds
define: geometric isomers: different arrangement of atoms around a double bond
define: enantiomers: isomers are mirror images of each other
define: Functional groups: atoms attached to the carbon skeleton that give a molecule its chemically reactive properties
What are the six different functional groups?: 1. Hydroxyl group
2. carbonyl group
3. Carboxyl group
4. Amino group
5. Sulfhydryl group
6. Phosphate Group
List: Characteristics of hydroxyl group: - (-OH)
- H covalently bonded to O
- compounds w/ hydroxyl groups are alcohols
- polar covalent bonds improve the solubility of organic molecules
List: Characteristics of Carbonyl group: - C=O
- oxygen atom joined to carbon skeleton by double bond
- if on end of skeleton, compound is an aldehede
- if not, compound is a keytone
List: Characteristics of Carboxyl Group: - (-COOH)
- carbon atom double bonded to an oxygen atom and single bonded to hydroxyl group
- Acid because electronegativities of two oxygen atoms increase dissociation of H⁺
List: Characteristics of Amino Group: - (-NHâ‚‚)
- Nitrogen atom bonded to two hydrogen atoms
- base because ammonia can pick up Hâº
Define: Carboxylic Acids: compounds with carboxy groups
Define: Amines: compounds with amino groups
Define: Alcohols: Compounds with hydroxyl groups
Define: Aldehyde: compounds with cabonyl group at END of carbon skeleton
Define: Ketone: compounds with carbonyl group that is NOT at an end of the carbon skeleton
Define: Thiol: Compound with sulfhydryl group. Help stabilize protein structure.
Define: Organic Phosphates: Compounds with phosphate groups
List: Characteristics of Sulfhydryl Group: - (-SH)
- Sulfer atom bonded to hydrogen atom
List: Characteristics of Phosphate Group: - (-POâ‚„)
- phosphorus bonded to four oxygen atoms, bonded to carbon skeleton via one of the oxygen atoms
- Anions w/ negative charge between two oxygen atoms
*- Transfer energy between organic molecules
Define: Macromolecules: large molecules, 1000's of atoms
What are the four main classes of Macromolecules?: 1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acid
Define: Polymer: strings of monomers. Make up most macromolecules.
How are polymers formed?: each monomer is added to the chain of monomers by a condensation (dehydration) reaction. A new bond is formed by removing a molecule of H2O
How are macromolecules broken down?: By hydrolysis. Hydrolysis adds a water molecule which breaks a bond and releases a monomer.
Define: Carbohydrates: sugars and sugar polymers
What are the types of carbohydrates?: 1. monosaccharides
2. disaccharides
3. polysaccharides
List: Characteristics of monosaccharides: - generic formula: CHâ‚‚O
- one carbonyl group and multiple hydroxyl groups attatched to a carbon skeleton
-* cellular fuel
How can monosaccharides differ?: 1. location of carbonyl groups
2. length of carbon skeleton
3. arangment of atoms around the carbon skeleton
Define: Glycosidic linkage: covalent bond formed betwween two monosacharrides by a dehydration reaction
What determines whether a monosaccharide is an aldose or a ketose?: the location of the carbonyl group
What are the possible lengths of a carbon skeleton?: 3C- triose
5C- pentose
6C- hexose
What do most monosaccharides form in solution?: rings
Define: Disaccharides: 2 monosaccharides joined by a glycosidic linkage
List: Characteristics of polysaccharides: - 100s to 1000s of monosaccharides joined by glycosidic linkages
-* energy storage or structural elements
What is the primary monosaccharide of most polysaccharides?: Glucose.
What forms is glucose found in?: 1. α glucose
2. β glucose
What is the fuel storage polysaccharide for plants?: Starch
What is the fuel storage polysaccharide for animals?: Glycogen
What is starch made of?: α Glucose monomers
What is the major structural polysaccharide of plant cell walls?: Cellulose
What is cellulose made of?: β glucose monomers
How are the shapes of starch and cellulose different?: Starch is helical in shape while cellulose is flat and can hydrogen bond with other cellulose molecules
Define: Lipids: macromolecules but not polymers.
What are lipids primarily made of?: Hydrocarbons
What kind of bonds are found in lipids?: non-polar
What are the important classes of lipids?: 1. Fats
2. Phospholipids
3. Steriods
What are fats composed of?: glycerol and fatty acids
What is glycerol composed of?: 3 carbon alcohols
Define: Fatty Acid: long hydrocarbon w/ a carboxyl group
Define: Triaglycerol: three fatty acids bonded to one glycerol
Define: Ester Linkage: Bond between glycerol and fatty acid
Define: Phospholipids: composed of glycerol, fatty acids, and a phosphate group
Which part of the phospholipid is hydrophillic and which part is hydrophobic?: The phosphate head is hydrophillic. The fatty acid tail is hydrophobic.
Define: Phospholipid Bilayer: 2 layers of phospholipids with tails to the inside and heads on the outside facing H2O.
Key component of cell membrane
Define: Steriods: lipids characterized by 4 fused carbon rings. Differ by the functional groups attachted to the carbon rings.
List: Characteristics of cholesterol: - A steriod
- precursor from which other steriods are synthesized
- common component of animal cell membranes
Describe enzymes: -Type of protein
-function: acceleration of reactions
Describe Structural proteins: -Type of protein
-function: structural support
Describe Storage proteins: Type of protein
-amino acid
-energy storage
Describe transport proteins: Type of protein
function: transport of other compounds
Describe hormones and receptors: type of protein
function: cell signaling
describe contractile proteins: function: movement
describe antibodies: type of protein
-function: defense against pathogens
What are proteins made of?: Made up of Amino acids (monomers) that join to form a polypeptide. One or more polypeptides form a protein
Define: Amino Acids: monomers of polypeptides
How many important amino acids are there?: 20
What are the components of all amino acids?: an α carbon (center carbon), an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group)
What does the R group of an amino acid do?: Determines the functional properties
Describe nonpolar amino acids: side chains are made of hydrocarbons
describe polar amino acids: side chains have strongly electronegative atoms: sulfer or oxygen
describe charged (ionic) amino acids: side chains are ionized
-acidic if there is a negative charge in side chain
-basic if there is a positive charge in side chain
How are polypeptides formed?: Amino acids are joined by a peptide bond (condensation reaction). Polypeptide has repeated backbone with side chains attatched.
What are the four stages of protein formation?: 1. Primary Structure
2. Secondary Structure
3. Tertiary Structure
4. Quaternary Structure
Describe the primary structure: determined by the sequence of amino acids
Describe the secondary structure: caused by hydrogen bonds between different regions of the polypeptide backbone.
- α helix or β pleated sheet
Describe the tertiary structure: arises from interactions between amino acid side chains
What are the four interactions that occure in the tertiary structure?: 1. hydrophobic interactions
2. hydrogen bonds
3. ionic bonds
4. disulfide bridges
Describe the quaternary structure: Results from aggregation of 2 or more polypeptides
Last step in making a functional protein
what environmental factors does protein structure depend on?: pH, temperature, and ion concentrations
Define: denaturation: loss of protein structure
What are the different types of nucleic acids?: - Deoxyribonucleic Acid (DNA)
- Ribonucleic Acid (RNA)
Define: Nucleotides: monomers that compose nucleic acids. Each has one 5-carbon sugar (pentose), a nitrogenous base, and a phospate group.
What are the 2 kinds of 5-carbon sugars in nucleotides?: deoxyribose (sugar in DNA)
ribose (sugar in RNA)
What are the 5 kinds of nitrogenous bases?: Purines: adenine and guanine
Pyrimidines: cytosine, thymine, and uracil
What are the nitrogenous bases in DNA?: adenine, cytosine, guanine, and thymine
What are the nitrogenous bases in RNA?: adenine, cytosine, guanine, and urasil
Define: Polynucleotides: nucleic acids
formed by joining of nucleotide monomers via phosphodiester linkage.
Describe: Characteristics of DNA: - double stranded helix
- polynucleotide strands joined by hydrogen bonds between nitrogenous bases.
- carries hereditary information
Describe: Characteristics of RNA: - single stranded
- important for protein synthesis
What are considered the fundamental units of life?: cells
How big are most cells?: 1-100 μm

μm= 10⁻⁶ m
nm= 10⁻⁹ m
Why are cells so small?: large surface area to volume ratio is needed to exchange of oxygen, nutrients, and waste
What are the three types of domains?: 1. domain bacteria
2. domain archaea
3. domain eukarya
What domain(s) fall into the category of prokaryotic cells?: domain bacteria and domain archaea
What domain(s) fall into that category of eukaryotic cells?: domain eukarya
What is domain bacteria?: single cell organisms
What is domain archea?: oganisms living under extreme conditions
what is domain eukarya?: multicellular organisms
Define: Plasma Membrane: a selective barrier for exchange of oxygen, nutrients, and waste.
What do ALL cells have?: Cytosol (cell fluid), chromosomes, ribosomes, cytoplasm, and a plasma membrane
What characterizes a general prokaryotic cell?: lack of membrane bound organelles. Has a nucleoid and cell wall.
Define: Nucleoid: region where DNA is located in a prokaryotic cell
Define: Cell wall: rigid structure surrounding plasma membrane.
What characterizes a general eukaryotic cell?: membrane bound organelles. DNA enclosed by a membrane-bound nucleous.
What are the differences between prokaryotes and eukaryotes?: Prokaryotes lack a nucleus, lack organelles, and are small cells. Eukaryotes have a membrane bound nucleus that contains several chromosomes, have organelles and are large cells.
How did prokaryotes get to be eukaryotes?: Endosymbiosis. Symbiotic relationship between large (eater) prokaryote and small (eaten) prokaryote, eventually becomes a eukaryote
What are the 4 components of eukaryotic cells?: 1. Genetic Organelles
2. Endomembrane system
3. metabolic organelles
4. cytoskeleton
What are the genetic organelles in a eukaryotic cell?: 1. nucleus
2. ribosomes
define: Nucleus: membrane-bound organelle that contains chromosomes (DNA)
define: Ribosomes: organelles (not membrane-bound) where protien synthesis occurs
What are the components of the nucleus?: 1. nuclear envelope
2. nuclear lamina
3. chromosomes
4. chromatin
5. nucleolus
6. pore complexes
define: nuclear envelope: 2 phospholipid bilayers on top of one another
define: nuclear pores: channels through entire nuclear envelope. transport substances across membrane
define: nuclear lamina: net of proteins gives structure to the nucleus
define: chromatin: DNA and proteins. makes up chromosomes
define: nucleolus: non-membrane bound component of the nucleus. ribosomal RNA (rRNA) is made here.
Where are free ribosomes located?: suspended in cytosol
Where are bound ribosomes located?: attached to endoplasmic reticulum.
Where are the protiends of free ribosomes and bound ribosomes used?: Free ribosomes- protein is used in cytosol
bound ribosomes- protein is used in organelles, added to plasma membrane or secreted from cell.
What are the organelles of the endomembrane system responsible for?: transport of proteins
What are the components of the endomembrane system?: 1. Nuclear envelope
2. endoplasmic reticulum
3. golgi apparatus
4. lysosomes
5. vacuoles
6. plasma membrane
Define: Endoplasmic Reticulum: network of membranes folded into cisternae. smooth ER and rough ER.
List: Characteristics of smooth ER: -no ribosomes are attached.
-lipid synthesis
-carbohydrate metabolism
-detoxification
-storage of calcium ions
List: Characteristics of rough ER: -bound ribosomes attached
-protein modification and transport
-membrane synthesis
What are 'transport vesicles' made out of?: endoplasmic reticulum membrane
What are the functions of the golgi apparatus?: -receives proteins and lipids from ER
-modifies ER products and sunthesizes new macromolecules
-releases macromolecules in transport vesicles
define: lysosomes: stacks of enzymes. Only function at pH 5 (in acidic solution)
Where are enzymes made?: In rough ER
Where are enzymes modified?: In golgi apparatus
What is the purpose of lysosomes?: hydrolysis of macromolecules
Define: phagoctosis: cellular eating. Cell eats by engulfing peices of food
Define: autophagy: recycling cell's own macromolecules
Define: Vacuoles: storage compartments
Define: Food Vacuoles: formed by phagocytosis
Define: contractile vacuoles: found in freshwater protists, pump excess water out of cell
Define: Central vacuole: found in plants
store pigments
diverse storage compartment
aids in cells growth
What is the membrane flow through the endomembrane system?: Rough ER
â†“
transport vesicles
â†“
golgi apparatus
â†“
plasma membrane
Define: metabolic organelles: responsible for metabolic processes, import macromolecules from cytosol
What are the three metabolic organelles?: 1. Peroxisomes
2. Mitochondria
3. Chloroplasts
List: Characteristics of Peroxisomes: -single membrane
-break down fatty acids into fuel used by mitochondria
-detoxy alcohol and other toxins
Define: Mitochondria: convert macromolecules into cellular energy (ATP) by respiration
Define: Chloroplasts: convert solar energy into fuel (macromolecules) by photosynthesis
What parts of cells are semiautonomous?: mitochondria and chloroplasts have their own DNA and ribosomes. They get macromolecules from cytosol
Define: Thylakoids: interconnected sacs
Define: Grana: stacks of thylakoids
What are the three compartments of a chloroplast?: 1. Intermembrane space: between inner and outer membranes
2. Stroma
3. Thylakoid space
Define: Stroma: fluid filled space that contains DNA, ribosomes and enzymes
Define: Cytoskeleton: Network of proteins throughout the cytoplasm
What are the functions of the cytoskeleton?: -Mechanical Support
-Communication bewteen inside of cell and outside of cell
-Movement
-Regulate cell activity
What are the 3 components of the cytoskeleton?: 1. microtubules
2. microfilaments
3. intermediate filaments
List: Characteristics of microtubules: -thickest fibers of cytoskeleton
-hollow tubes made of tubulin (rigid support structure)
Where do microtubules grow out from?: the centrosome
What are microtubules responsible for?: Movement of cell components via motor proteins
Describe the movement of a flagellum: undulating movement force is parellel to axis of flagellum
Describe the movement of cilia: oar-like movement, force is perpendicular to axis of cilia
How do cilia and flagella move?: -adjacent microtubule pairs are linked by dynein
-changed in dynein shape move microtubule pairs relative to one another
-cross-linking proteins cause bending
List: Characteristics of microfilaments: -thinnest fibers of cytoskeleton
-solid rods made of actin
-forms 3-D network inside cell membrane
Describe function of microfilaments in muscles: motor proteins (myosin) in between actin filaments shorten muscle during contraction
describe function of microfilaments in amoeboid movement: - 3D network of microfilaments inside membrane give cytosol gel-like consistency
- contraction of actin/myosin complex extend pseudopodium
describe cause of cytoplasmic streaming in plants: caused by actin/myosin interactions and sol/gel transformations
List: Characteristics of intermediate filaments: -coiled rods made of keratin.
-provide support for cytoskeleton
-important for maintaining shape
What are plant cell walls made of?: Cellulose embedded in a network of polysaccharides and proteins
What are the functions of plant cell walls?: protects cell, regulates water uptake, maintains cell shape, allows growth against gravity
List: Characteristics of primary cell wall: -laid down by growing cell
-provides protection and flexibility
List: characteristics of secondary cell wall: -laid down by mature cell
-stronger and thicker than primary
List: Characteristics of middle lamella: -sticks 2 adjacent cells together
Define: Extracellular Matrix: network of proteins and carbohydrates (glycoproteins)
What makes up the majority of the extracellular matrix?: collagen
Define: Proteoglycan molecule: molecule with core protein and carbohydrate branches
Define: proteglycan complex: complexes of long polysaccharides and proteoglycan molecules
Define: Fibronectin: attaches ECM to membrane proteins
Define: Integrins: membrane proteins that connect ECM and cytoskeleton

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