Attributes of Living Systems: Exam 1
Terms
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- What is the core theme of biology?
- Evolution
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Define:
Molecule - 2 or more atoms held together by covalent bonds
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Define:
Matter - Anything that has mass and takes up space. Composed of elements.
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Define:
Element - A subsance that can't be broken down into other subsances by chemical reactions. Composed of atoms.
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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?
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Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C)
Hint: remember HONC! - What are atoms made up of?
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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
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Define:
Atomic Number - The number of protons per atom. The Atomic number is characteristic for each element. written Lower left of element
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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?
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1) gain or lose electrons
2) isotopes -
Define:
Ion - Atom gains or loses electrons and becomes charged
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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
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Define:
Covalent Bond - formed when valence electrons are shared by two atoms. Includes single and double bonds
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Define:
Nonpolar bond - bond between 2 atoms of the same element or same electronegativity
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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
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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?
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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.
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Define:
Cation - atom that lost an electron due to ionic bond. (postive ion)
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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
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Define:
Mass Conservation Law - All atoms present in the reactants are present in the products
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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?
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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.
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Define:
Heat - TOTAL amount of kinetic energy in a body of matter
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Define:
Temperature - Heat intensit due to AVERAGE kinetic energy
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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.
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Define:
Hydrophyllic - has an affinity for water. Has polar or ionic bonds
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Define:
Hydrophobic - has no affinity for water. Has non-polar bonds
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Define:
Solution - liquid composed of 2 or more substances
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Define:
Solute - the substance that is dissolved in a solution
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Define:
Solvent - the liquid that dissolves the solute
- What are the important properties of solutions?
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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 H⺠ions. Some water molecules dissociate into H⺠and OHâ». if unequal, the solution is either acidic or basic. greater # of H⺠→ 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?
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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?
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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)
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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?
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1. Length
2. Branching
3. Double bonds
4. Rings - What does the function of organic molecules depend on?
- structure
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Define:
Isomers - compounds with the same molecular formula but different structures
- What are the different types of Isomers?
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1. structural isomers
2. geometric isomers
3. enantiomers -
define:
structural isomers - different arrangment of covalent bonds
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define:
geometric isomers - different arrangement of atoms around a double bond
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define:
enantiomers - isomers are mirror images of each other
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define:
Functional groups - atoms attached to the carbon skeleton that give a molecule its chemically reactive properties
- What are the six different functional groups?
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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 H⺠-
Define:
Carboxylic Acids - compounds with carboxy groups
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Define:
Amines - compounds with amino groups
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Define:
Alcohols - Compounds with hydroxyl groups
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Define:
Aldehyde - compounds with cabonyl group at END of carbon skeleton
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Define:
Ketone - compounds with carbonyl group that is NOT at an end of the carbon skeleton
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Define:
Thiol - Compound with sulfhydryl group. Help stabilize protein structure.
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Define:
Organic Phosphates - Compounds with phosphate groups
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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?
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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.
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Define:
Carbohydrates - sugars and sugar polymers
- What are the types of carbohydrates?
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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?
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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?
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3C- triose
5C- pentose
6C- hexose - What do most monosaccharides form in solution?
- rings
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Define:
Disaccharides - 2 monosaccharides joined by a glycosidic linkage
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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?
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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
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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?
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1. Fats
2. Phospholipids
3. Steriods - What are fats composed of?
- glycerol and fatty acids
- What is glycerol composed of?
- 3 carbon alcohols
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Define:
Fatty Acid - long hydrocarbon w/ a carboxyl group
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Define:
Triaglycerol - three fatty acids bonded to one glycerol
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Define:
Ester Linkage - Bond between glycerol and fatty acid
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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.
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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.
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List:
Characteristics of cholesterol -
- A steriod
- precursor from which other steriods are synthesized
- common component of animal cell membranes - Describe enzymes
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-Type of protein
-function: acceleration of reactions - Describe Structural proteins
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-Type of protein
-function: structural support - Describe Storage proteins
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Type of protein
-amino acid
-energy storage - Describe transport proteins
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Type of protein
function: transport of other compounds - Describe hormones and receptors
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type of protein
function: cell signaling - describe contractile proteins
- function: movement
- describe antibodies
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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
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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
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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?
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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
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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?
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1. hydrophobic interactions
2. hydrogen bonds
3. ionic bonds
4. disulfide bridges - Describe the quaternary structure
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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
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Define:
denaturation - loss of protein structure
- What are the different types of nucleic acids?
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- 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?
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deoxyribose (sugar in DNA)
ribose (sugar in RNA) - What are the 5 kinds of nitrogenous bases?
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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
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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?
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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?
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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
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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.
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Define:
Nucleoid - region where DNA is located in a prokaryotic cell
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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?
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1. Genetic Organelles
2. Endomembrane system
3. metabolic organelles
4. cytoskeleton - What are the genetic organelles in a eukaryotic cell?
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1. nucleus
2. ribosomes -
define:
Nucleus - membrane-bound organelle that contains chromosomes (DNA)
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define:
Ribosomes - organelles (not membrane-bound) where protien synthesis occurs
- What are the components of the nucleus?
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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
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define:
nuclear pores - channels through entire nuclear envelope. transport substances across membrane
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define:
nuclear lamina - net of proteins gives structure to the nucleus
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define:
chromatin - DNA and proteins. makes up chromosomes
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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?
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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?
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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.
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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?
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-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
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Define:
phagoctosis - cellular eating. Cell eats by engulfing peices of food
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Define:
autophagy - recycling cell's own macromolecules
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Define:
Vacuoles - storage compartments
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Define:
Food Vacuoles - formed by phagocytosis
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Define:
contractile vacuoles - found in freshwater protists, pump excess water out of cell
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Define:
Central vacuole -
found in plants
store pigments
diverse storage compartment
aids in cells growth - What is the membrane flow through the endomembrane system?
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Rough ER
↓
transport vesicles
↓
golgi apparatus
↓
plasma membrane -
Define:
metabolic organelles - responsible for metabolic processes, import macromolecules from cytosol
- What are the three metabolic organelles?
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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
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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
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Define:
Grana - stacks of thylakoids
- What are the three compartments of a chloroplast?
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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?
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-Mechanical Support
-Communication bewteen inside of cell and outside of cell
-Movement
-Regulate cell activity - What are the 3 components of the cytoskeleton?
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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
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- 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
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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