Glossary of Attributes of Living Systems: Exam 1
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- What is the core theme of biology?
- 2 or more atoms held together by covalent bonds
- Anything that has mass and takes up space. Composed of elements.
- A subsance that can't be broken down into other subsances by chemical reactions. Composed of atoms.
- The smallest unit of matter that has properties of an element.
- What number of chemical elements are essential for life?
- 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
- The number of protons per atom. The Atomic number is characteristic for each element. written Lower left of element
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
- Atom gains or loses electrons and becomes charged
- 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
- formed when valence electrons are shared by two atoms. Includes single and double bonds
- bond between 2 atoms of the same element or same electronegativity
- 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
- 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
- formed when electrons are transferred from one atom to another. Both atoms become charged ions. Strong but dissolves in water.
- atom that lost an electron due to ionic bond. (postive ion)
- Atom that gained an electron due to ionic bond. (negative ion)
- What do cations and anions form when they attracted one another?
- 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
Mass Conservation Law
- All atoms present in the reactants are present in the products
- 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 is essential to what?
- All living organisms
- What percentage of water are organisms composed of?
- What percentage of earths surface is covered by water?
- 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
- 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.
- TOTAL amount of kinetic energy in a body of matter
- Heat intensit due to AVERAGE kinetic energy
- 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.
- has an affinity for water. Has polar or ionic bonds
- has no affinity for water. Has non-polar bonds
- liquid composed of 2 or more substances
- the substance that is dissolved in a solution
- the liquid that dissolves the solute
- What are the important properties of solutions?
- 1. 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
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⁺ ions. Some water molecules dissociate into H⁺ and OH⁻. if unequal, the solution is either acidic or basic. greater # of H⁺ → 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
- 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?
- 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)
- 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
3. Double bonds
- What does the function of organic molecules depend on?
- compounds with the same molecular formula but different structures
- What are the different types of Isomers?
- 1. structural isomers
2. geometric isomers
- different arrangment of covalent bonds
- different arrangement of atoms around a double bond
- isomers are mirror images of each other
- 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
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
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
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⁺
Characteristics of Amino Group
- - (-NH₂)
- Nitrogen atom bonded to two hydrogen atoms
- base because ammonia can pick up H⁺
- compounds with carboxy groups
- compounds with amino groups
- Compounds with hydroxyl groups
- compounds with cabonyl group at END of carbon skeleton
- compounds with carbonyl group that is NOT at an end of the carbon skeleton
- Compound with sulfhydryl group. Help stabilize protein structure.
- Compounds with phosphate groups
Characteristics of Sulfhydryl Group
- - (-SH)
- Sulfer atom bonded to hydrogen atom
Characteristics of Phosphate Group
- - (-PO₄)
- 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
- large molecules, 1000's of atoms
- What are the four main classes of Macromolecules?
- 1. Carbohydrates
4. Nucleic Acid
- 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.
- sugars and sugar polymers
- What are the types of carbohydrates?
- 1. monosaccharides
Characteristics of monosaccharides
- - generic formula: CH₂O
- 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
- 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
- What do most monosaccharides form in solution?
- 2 monosaccharides joined by a glycosidic linkage
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?
- What forms is glucose found in?
- 1. α glucose
2. β glucose
- What is the fuel storage polysaccharide for plants?
- What is the fuel storage polysaccharide for animals?
- What is starch made of?
- α Glucose monomers
- What is the major structural polysaccharide of plant cell walls?
- 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
- macromolecules but not polymers.
- What are lipids primarily made of?
- What kind of bonds are found in lipids?
- What are the important classes of lipids?
- 1. Fats
- What are fats composed of?
- glycerol and fatty acids
- What is glycerol composed of?
- 3 carbon alcohols
- long hydrocarbon w/ a carboxyl group
- three fatty acids bonded to one glycerol
- Bond between glycerol and fatty acid
- 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.
- 2 layers of phospholipids with tails to the inside and heads on the outside facing H2O.
Key component of cell membrane
- lipids characterized by 4 fused carbon rings. Differ by the functional groups attachted to the carbon rings.
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
- 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
- monomers of polypeptides
- How many important amino acids are there?
- 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
- loss of protein structure
- What are the different types of nucleic acids?
- - Deoxyribonucleic Acid (DNA)
- Ribonucleic Acid (RNA)
- 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
- nucleic acids
formed by joining of nucleotide monomers via phosphodiester linkage.
Characteristics of DNA
- - double stranded helix
- polynucleotide strands joined by hydrogen bonds between nitrogenous bases.
- carries hereditary information
Characteristics of RNA
- - single stranded
- important for protein synthesis
- What are considered the fundamental units of life?
- 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
- 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.
- region where DNA is located in a prokaryotic cell
- 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
- What are the genetic organelles in a eukaryotic cell?
- 1. nucleus
- membrane-bound organelle that contains chromosomes (DNA)
- organelles (not membrane-bound) where protien synthesis occurs
- What are the components of the nucleus?
- 1. nuclear envelope
2. nuclear lamina
6. pore complexes
- 2 phospholipid bilayers on top of one another
- channels through entire nuclear envelope. transport substances across membrane
- net of proteins gives structure to the nucleus
- DNA and proteins. makes up chromosomes
- 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
6. plasma membrane
- network of membranes folded into cisternae. smooth ER and rough ER.
Characteristics of smooth ER
- -no ribosomes are attached.
-storage of calcium ions
Characteristics of rough ER
- -bound ribosomes attached
-protein modification and transport
- 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
- 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
- cellular eating. Cell eats by engulfing peices of food
- recycling cell's own macromolecules
- storage compartments
- formed by phagocytosis
- found in freshwater protists, pump excess water out of cell
- found in plants
diverse storage compartment
aids in cells growth
- What is the membrane flow through the endomembrane system?
- Rough ER
- responsible for metabolic processes, import macromolecules from cytosol
- What are the three metabolic organelles?
- 1. Peroxisomes
Characteristics of Peroxisomes
- -single membrane
-break down fatty acids into fuel used by mitochondria
-detoxy alcohol and other toxins
- convert macromolecules into cellular energy (ATP) by respiration
- 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
- interconnected sacs
- stacks of thylakoids
- What are the three compartments of a chloroplast?
- 1. Intermembrane space: between inner and outer membranes
3. Thylakoid space
- fluid filled space that contains DNA, ribosomes and enzymes
- Network of proteins throughout the cytoplasm
- What are the functions of the cytoskeleton?
- -Mechanical Support
-Communication bewteen inside of cell and outside of cell
-Regulate cell activity
- What are the 3 components of the cytoskeleton?
- 1. microtubules
3. intermediate filaments
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
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
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
Characteristics of primary cell wall
- -laid down by growing cell
-provides protection and flexibility
characteristics of secondary cell wall
- -laid down by mature cell
-stronger and thicker than primary
Characteristics of middle lamella
- -sticks 2 adjacent cells together
- network of proteins and carbohydrates (glycoproteins)
- What makes up the majority of the extracellular matrix?
- molecule with core protein and carbohydrate branches
- complexes of long polysaccharides and proteoglycan molecules
- attaches ECM to membrane proteins
- membrane proteins that connect ECM and cytoskeleton
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