Chapter 2: Chemistry of the Cell-USDFall2018-Dr. Karen Koster
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| What are the two ways in which carbon is involved in importnat molecules of biology? | Major component of the backbone/skeleton
Linked covalently in chains or rings
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| What is biological chemistry? | chemistry of living systems
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| What is the valence of carbon? | 4
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| What does a valence of 4 mean for carbon? | it will form four chemical bonds
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| What is the octet rule? | Most atoms want their outer valence shell to have 8 electrons
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| What does a valence of 4 do for carbon? | Gives it structural variation
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| What is mostly likely to form covalent bonds with carbon? | Carbon(4), Oxygen (2), sulfur, hydrogen(1), and nitrogen(3)
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| What is a single bond? | sharing of 1 pair of electrons
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| What is a double bond? | sharing of 2 pairs of electrons
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| What is a triple bond? | sharing of 3 pairs of electrons
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| How is stability expressed? | bond energy
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| What is bond energy? | amount of energy required to break 1 mole (6x10^23) of such bonds
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| How is bond energy expressed? | in calories
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| What is a calorie? | amount of energy needed to rais 1 gram of H20 1 degree
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| What is a hydrocarbon? | molecule containing only hydrogen and carbon
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| Hydrocarbons are essentially ________ in water. | insoluble
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| Hydrocarbons play an importnat role in the structure of what? | biological membranes
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| The interior of every biological membrane is a ________ environment. | nonaqueous
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| what usually projects into the interior of membranes? | hydrocarbon "tails" of phospholipids
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| What gives important implications to permeabilitity barriers of biological membranes? | location of the hydrocarbon "tails" of phospholipids (interior) and the polar heads (exterior)
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| What is a functional group? | specific arrangements of atoms that confer characteristic chemical properties on the molecule they're attached to
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| What bond has the highest bond energy? | C-C triple bond
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| What bond has the second highest energy? | C-C double bond
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| What has the third highest bond energy? | H-C bond
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| What has the fourth highest bond energy? | C-C single bond
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| What has the fifth highest bond energy? | C-N bond
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| What has the lowest bond energy? (as a single bond) | hydrogen bonds
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| What functional groups are negative (acidic) and biological pH? | carboxyl and phosphate
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| What functional groups are positive (basic) at biological pH? | amino
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| What functional groups are neutral at biological pH? | hydroxyl, sulfhydryl, carbonyl, aldehyde
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| What is a carboxyl functional group? | carbon double bonded to O and single bonded to OH
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| What is a phosphate functional group? | phosphate double bonded to O and 3 single bonds to OH
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| What is an amino functional group? | carbon bonded to NH2 (NH3+ at biological pH)
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| What is a hydroxyl functional group? | carbon bonded to OH
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| What is a sulfhydryl functional group? | carbon bonded to SH
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| What is a carbonyl functional group? | carbon double bonded to O (and usually 2 other carbon)
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| What is an aldehyde functional group? | carbon double bonded to O and bonded to an H
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| What is an ion? | atom/molecule that are charged because they have gained/lost a proton
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| What is a polar bond? | unequal sharing of electrons
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| What often makes up a polar bond? (biologically) | Oxygen, sulfur, or nitrogen bound to a carbon or a hydrogen
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| Why do O,S,N cause polar bonds? | Oxygen and sulfur have increased electronegativity
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| What is electronegativity? | affinity for electrons
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| Polar bonds have a ______ water solubility and ______ chemical reactivity. | higher water solubility and higher chemical reactivity
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| What is oxidization? | when carbon containing compounds lose an electron to ather molecules such a smolecular o2
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| Is oxidization a release of energy or absorption of energy? | release of energy
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| What is reduction? | when carbon containing compounds gain an electron
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| Is reduction a release of energy or absorption of energy? | requires energy
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| What structural characteristic gives carbon containing molecules great diversity? | tetrahedral structure
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| Why does the tetrahedral structure of carbon containing molecules matter? | it gives carbon the opportunity for 4 different atoms or groups to be bonded to it in a tetrahedral configuration which leads to 2 possible spatial configurations
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| What are stereoisomers? | mirror images as shown by a plane of symetry
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| What is an asymmetric carbon? | carbon atom with four different substituents
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| How many stereoisomers are possible for each asymetric carbon in a molecule? | 2
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| What is the equation for determining number of stereoisomers in a compound? | 2^n (n is number of asymmetric carbons?
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| Water is a ________ solvent. | universal
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| What is the most abundant component of cells and organisms? | water
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| What weight of cells and organisms is made of water? | 75-85%
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| What is polarity? | unequal distribution of eletrons within a molecule
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| What angle results from polarity? | 104.5 degree (in water)
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| in water oxygen has a _________ charge. | partial negative
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| in water hydrogen has a ________ charge. | partial positive
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| What allows molecules to be attracted to eachother? | polarity
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| What is a hydrogen bond? | partial positive attraction of hydrogen with a highly electronegative atom
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| Each water molecule is hydrogen bonded to ___ other water molecules. | three
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| What gives water its high cohesiveness? | tendency to hydrogen bond
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| What characteristics of water are caused by its tendency to hydrogen bond? (4) | high surface tenison, high boiling point, high specific heat, high heat of vaporization
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| What is specific heat? | amount of heat a substance must absorb per gram to increase the temperature 1 degree Celcius
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| What is the specific heat of water? | 1 calorie per gram
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| What buffers water against large changes in temperature? | energy that goes into water is used to break the hydrogen bonds which acts as a buffer from a large increase in temperature
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| What is heat of vaporization? | amount of energy required to convert 1 gram of a liquid into a vapor
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| Water has a _____ heat of vaporization. | high
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| Water is an excellent general solvent due to its _____. | Polarity
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| What is a solvent? | fluid in which another substance is dissolved
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| What is a solute? | the substance being dissolved in a solvent
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| Many molecules in cells are also ______ and hydrogen bond with water | polar
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| What does hydrophilic mean? | have an affinity for water and readily dissolve
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| Are most small organic molecules hydrophobic or hydrophilic? | hydrophilic
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| What does hydrophobic mean? | low affinity for water and unlikely to dissolve
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| Are lipids hydrophobic or hydrophilic? | hydrophobic
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| Are proteins hydrophobic or hydrophilic? | hydrophobic
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| Are nonpolar molecules generally hydrophobic of hydrophilic? | hydrophobic
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| Are hydrocarbons hydrophobic of hydrophilic? | hydrophobic
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| What are cellular membranes? | essentially a hydrophobic permeability barrier
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| Where are phospholipids found? | cellular membranes
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| Where are glycolipids found? | cellular membranes
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| Where are membrane proteins often found? | cellular membranes
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| What is often found in cellular membranes except those of bacteria? | sterols
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| What is the sterol in animals? | Cholesterol
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| What is the sterol in fungi? | Ergosterol
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| What is the sterol in plants? | Phytosterol
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| What does amphipathic mean? | A molecule/compound has both a hydrophilic and hydrophobic region
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| What two compounds are often amphipathic and where are they found? | lipids and proteins in cell membranes
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| How are phospholipids organized? | often into two layers
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| Where does the polar head of phospholipids face? | outward towards the aqueous environment
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| Where do the hydrophobic tails of phospholipids face? | inward and interacting with eachother to minimalize their interactions with the aqueous environment
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| What membranes have lipid bilayers? | every known biological membranes
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| What causes membran bilayers? | the amphipathic tendency of proteins and lipids, most specifically phosphlipids with their hydrophobic tails facing inwards and their hydrophilic heads facing outwards
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| Lipid Bilayers are _______ permeable. | selectively
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| What does the hydrophobic interior of membranes allow? (3) | Permeability to nopolar molecules
Quite impermeable to most polar molecules
Highly impermeable to ions
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| On a scale from 1-4 for permeability (1=none, and 4+all) how permeable are ions? | 1
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| On a scale from 1-4 for permeability (1=none, and 4+all) how permeable are uncharged polar molecules? | 2
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| On a scale from 1-4 for permeability (1=none, and 4+all) how permeable are small, uncharged polar molecules? | 3
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| On a scale from 1-4 for permeability (1=none, and 4+all) how permeable are ions? | 4
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| Compounds with MW of _____ readilty diffuse across membranes regardless of polarity? | 100
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| What are transport proteins? | specialized transmembrane proteins
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| What is a hydrophilic channel? | channel through an otherwise hydrophobic membrane
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| What is a carrier? | binds a specific solute on one side of the membrane then undergoes a cnformational change to move the soute across the membrane
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| What are macromolecules? | ordered array of linear or branched polymers
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| What does a biological hierarchy? | denotes how biological molecules and structures can be organized into a series of levels with each level building on the preceding
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| Most cellular strctures are composed of small, _____ organic molecules. | watersoluble/hydrophilic
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| What is level one of the hierarchy system? | small organic molecules
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| What is level two of the hierarchy system? | macromolecules
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| What is level three of the hierarchy system? | Supramolecules
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| What is level four of the hierarchy system? | Organelle
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| What is level five of the hierarchy system? | The cell
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| what are some examples of the first level of the hierarchy system? | amino acids, glucose, nucleotides
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| What are some examples of the second level of the hierarchy system? | proteins, cellulose, DNA
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| What are some examples of the third level of the hierarchy system? | membrane, cell wall, chromosome
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| What are some examples of the 4th level of the hierarchy system? | choloroplast/mitochondria, nucleus
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| Will the fifth level of the hierarchy system always be the cell? | yes
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| How are most macromolecules generated? | by the polymerization of small organic molecules into longer chains
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| What is the monomer of polysacchrides? | glucose and other monosaccharides
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| What is the monomer of lipids? | glycerol, fatty acids, or steroids
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| What is the monomer of proteins? | amino acids
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| What is the monomer of nucleic acids? | nucleotide
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| Monomers can be transported across most ______ membranes. | Biological
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| What are the three major kinds of macromolecular polymers in cells? | proteins, nucleic acids, and polysaccharides
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| What are nucleic acids? | informational macromolecules
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| In nucleic acids, the order of the nucleotide monomers is _____. | nonrandom
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| Do amino acids transmit info? | nope
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| what do amino acid monomers do? | they determine the 3D structure of the protein
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| How many different amino acids are there in proteins? | 20
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| What are some roles of proteins? | structure, defense, transport, signalling, catalysis
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| What are polysaccharides? | usually consist of a single repeating subunit or two subunits in strict alternation
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| What is a storag polysacharide used for? | energy storage
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| What are some examples of storage polysaccharides? | starch and glycogen
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| What are some examples of structural polysaccharides? | starch and chitin
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| What is the first basic principle of the polymerization of macromolecules? | they are always synthesized in a stepwise polymerization of similar or identical small molecules called monomers
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| What is the second basic principle of the polymerization of macromolecules? | The additon of each monomer occurs with the removal of a water molecule in a condensation reaction
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| What reaction occurs during polymerization? | condensation reaction
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| What is the third basic principle of the polymerization of macromolecules? | In order for the monomers to be joined they must become activated monomers
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| What is the fourth basic principle of the polymerization of macromolecules? | activation of monomers usually occurs with carrier molecules
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| What is the fifth basic principle of the polymerization of macromolecules? | energy required to couple monomers and carriers is ATP
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| What is the sixth basic principle of the polymerization of macromolecules? | macromolecules have directionality
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| What does directionality mean in terms of macromolecules? | the two ends of the polmer chain are chemically different from one another
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| What does self-assembly mean? | The information required to specify the spontaneous folding and coiling of macromolecules to form more complex structures is inherent in the polmer themselves
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| Once a macromolecule is syntehsized, assembly into compex structures will occur _______ without furthur ______. | spontaneously, energy
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| What is the function of Molecular chaperones? | they assist in protein folding to prevent incorrect molecular interactions
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| Every protein or other macromolecule in the cell is held together by _______ bonds | Covalent
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| What are hydrogen bonds important for? | maintaining 3D structure of proteins and holding together the two strands of DNA
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| What are ionic bonds important for? | they are usually found in fuctional groups and maintain protein structures
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| What are Van der Walls forces? | weak interaction between two atoms that only occur if the atoms are close to eachother
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| What are hydrophobic interactions? | tendency for nonpolar g roups to associate with eachother as they minimize their contact with water
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| What is a polypeptide? | immediate produce of amino acid polymerizaton
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| How does a polypeptide become a protein? | must fold, coil, and go through a conformational change
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| What id denaturation? | unfolding of a polypeptide
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| How do you denature a protein? | apply high temp, high acidity, alkaline conditions, chemical agents or general disruption of the native environment
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| What is renaturation? | return of a polypeptide to its correct structure
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| How do you renature a protein? | return it to conditions in which the native conformation is stable
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| Does self-assembly also apply to more complex structures? | yes
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| What more complex structure go thourhg self-assembly? | ribosomes
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