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URI / Biology / CMB 210 / hydrolysis bond

hydrolysis bond

hydrolysis bond

Description

School: University of Rhode Island
Department: Biology
Course: Biochemistry for Nutrition
Professor: Xifoung lin
Term: Spring 2017
Tags: biochemistry
Cost: 50
Name: Exam 1 Notes
Description: Life characteristics, bonds, monomer/polymers, cell structure, oxidation/reduction, pH, acids/bases
Uploaded: 02/14/2017
17 Pages 190 Views 0 Unlocks
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Why do we say that life is information-based?




What is the basic structural, functional, and biological unit of life?




What are the 3 characteristics that distinguish living creatures from inanimate objects?



Checklist for CMB210 Exam1 Lecture 1: 1. What are the 3 characteristics that distinguish living creatures  from inanimate objects? 1.) Living objects are chemically  complex/organized 2.) living creatures extract energy  (nutrients) from the environment aWe also discuss several other topics like qmb 3200 fsu
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nd export waste products of  metabolism (like CO2 when we exhale) 3.) living organisms  have the capacity to precisely self-replicate and self-assemble.  2. What is the basic structural, functional, and biological unit of  life? The cell.  3. Why do we say that life is information-based? Life is  information based because biologicaql information is stored  within DNA. A chromosome (of which we have 23 pairs) have  many genes. Series of amino acids within living organisms  codes for specific proteins, is encoded with a gene, which gives each organisms a specific trait. A gene (encoded by AA acids,  and a gene is a protein that codes for information) is a  sequence of nucleotides on chromosomes that encodes linear  sequence of amino acids of a protein—again, which codes for  specific information about an organism).  4. What is a “gene”? unit sequence of nucleotides on  chromosomes that encodes the linear sequence of amino acids  of a protein 5. What is an “organic compound”? What is the matrix of life? An  “organic compound” is a compound that uses carbon to form  covalent bonds to a few other elements (CHOSeN + P). Water is the matrix of life (0.15 M NaCl)  6. What are the important ions in living organisms? Do they form  covalent bond? Important ions in living organisms are Na+, K+, Ca2+, and Cl-. They DO NOT FORM COVALENT BONDS.  7. What are the principal elements of biochemical compounds  forming covalent bonds to carbon? CHOSeN + P  8. What are the most abundant elements in the cell? The most  abundant elements in the cell are C, O, H, and N.  9. What are the 4 classes of biomolecules? What are the names of their monomers and polymers? The 4 classes of biomolecules  are: 1.) Amino Acid 2.) Monosaccharide 3.) Nucleotide 4.) Fatty  Acid. The polymer of amino acids are proteins, the polymer of monosaccharides (like glucose) are polysaccharides, the  polymer of nucleotides are nucleic acids (DNA,  RNApolynucleotides) and there is not a polymer of the  monomeric unit fatty acids.  10. What are the general functions of the four biopolymers? The  general function of proteins are catalysts and structure  (actin/myosin are proteins for muscle contraction). The function of polysaccharides are for energy storage for glucose (use  inbetween meals), structure outside the cell (cartilage that  cushions bone) and intercellular communication. The function  of polynucleotides, or nucleic acids, are DNA/RNA production.  DNA stores genetic information as “bases” of nucleic acids. The specific sequence of “bases” determines sequence of amino  acids in a protein. The function of RNA is for protein synthesis.  Finally, the function of fatty acids are energy storage and  structural elements of cell membranes.  Lecture 2:  1. What is the ultimate source of energy for nutrients on the  earth? The sun 2. What is a nucleotide? How is its structure? Through which bond  does nucleotide bond together to make a DNA strand? What is  a “DNA double helix”? What are the largest molecules in living  cells? A nucleotide is a compound that is a structural  component of DNA and RNA. It has three components: 1.) a  base ring structure that has ATCG, which are specific  nucleotides 2.) cyclic 5 carbon sugar ribose, and 3.) a  phosphate group. Nucleotides bond together to make a DNA  double helix through a phosphate group binding ribose at two  different positions; this is called a phosphodiester bond. A DNA  ‘double helix” describes the appearance of a double-stranded  DNA; it is composed of two linear strands that run opposite to  each other and twist. Each strand within the double helix is  made of smaller units (nucleotides) that form a chain. The  backbone of the helix are made of sugar and phosphate  molecules. The two strands are connected into the double helix through interactions between pars of nucleotides (AT, CG) 3. What is isotonic, hypotonic, hypertonic solution (environment)?  Isotonic: the salt concentration outside the cell is equal to inside the cell. Hypotonic: the salt concentration outside the  cell is less than inside the cell (cell bursts). Hypertonic: salt  concentration outside the cell is greater than inside the cell  (cell will deflate)  4. Are covalent bonds strong bonds? How do they compare with  electrostatic interactions? Covalent bonds are strong bonds,  and isoelectronic bonds are weaker than covalent bonds  5. What are the most abundant polymer in the biosphere?  Polysaccharides  6. When we eat where does the conversion of  polymers→monomers take place? Stomach and small intestine 7. What is this process called, does it use water? Where do the  monomers go? Why do we need to break down the polymers?  The process of cutting proteins into individual amino acids is  called hydrolysis, and it must use water. The cut amino acid  monomers are taken up by the blood and brought to tissues  where they serve as building blocks to be converted from  monomer AA to polymer proteins that our DNA base code calls  for. We must break down polymers because meet has the AA  sequence of the starting material; the deer, pig, etc. We must  resynthesize the AA sequence to have OUR sequence that is  determined by our DNA to use the proteins as building blocks.  8. Where does the Conversion of Monomers back to Biopolymers  take place? The conversion of monomers back to polymers  occurs in the tissues of the body that is supplied by blood after  the nutrients have been transported across the cell membrane. 9. What is the difference between Organic Chemistry and  Biochemistry reactions in cells? What makes the reactions  within the cell go so fast and accurate? Why are reactions in  organic chemistry often slow with “side reactions”? Reactions  in organic chemistry often have smelly solvents, have high  concentrations of solutes, do not use a catalyst, are slower  reactions, use high temperatures, yields are poor, there are  often side chain reactions, little internal control during the  reaction, polymers as a product do not usually occur, bond  strength is high, there is no compartmentalization within  organic chemistry reactions, and finally, there is only one  reaction possible in organic chemistry. In biochemical reactions, the solvent is water, the concentration of a solute is low, catalysts are almost always used, reaction speed is high, the  temperature is much lower relative to organic chemistry  reactions, there are never side reactions, the yield of the  reaction is high, there is high internal control, polymers as  products are common, bond strength can be high (covalent) or  weak (noncovalent: isoelectronic), reactions are  compartmentalized (organelles) and there are pathways of  reactions (choices). Reactions within the cell are fast and  accurate is through the use of catalysts. Reactions in organic  chemistry are often slow with “side reactions” because speed is determined by the number of collisions of 2 molecules. A  reaction is deemed complete when the correct orientation has  been met. It may take many tries to meet the correct  orientation, and it is dependent on amount of reactant. Side  chains occur when the wrong collusion occurs, and this results  in an undesired “side” product.  10. What are Valance electron, bonding electron, nonbonding  electron? Use hydrogen as an example. A valence electron is an electron on the outermost shell. A bonding electron is an  electron that forms covalent bonds (shared electrons) or  nonbonding, where no covalent bond is formed (no shared  electrons). Hydrogen has one valence electron, is a bonding  electron (can form a max of 2).  11. What makes carbon so unique within biological compounds?  Carbon can share each of its valence electrons with a valence  electron from another atom to make covalent bonds between  the atoms and of carbon Lecture 3: 1. Why do we need to know that nitrogen and oxygen atoms have nonbonding valence electrons? What are they used for? We  need to know that Nitrogen and Oxygen atoms have  nonbonding valence electrons because N and O can be used for hydrogen bonding which is important for how water bonds with  itself, with other functional groups on proteins, and how  proteins fold  2. How is the geometry of a “saturated” carbon compound such  as CH4? Carbon with 4 Hydrogens bonded to it has four  bonding electrons capable of being shared to form four covalent single bonds in tetrahedral arrangement, 109.5  degree angles  3. What is “cis”, “trans” geometry of C=C double bonds? Which is  more preferred by Mother Nature (MN)? Cis geometry means  that substituents are on the same side of the double bond.  Trans geometry means that substituents are on opposite sides  of the double bond GO BACK 4. What is the meaning of an “R” group? An “R” group indicates a  carbon length of a chain of unspecified length , and the  properties of an organic molecule are determined by their  functional group  5. What is a carbonyl group? What is the properties of it? Are  electrons shared equally? Why? Why does Mother Nature “love” carbonyl groups? A carbonyl is a C double bonded to an O,  where bonding of electron of Carbon and O are shared, but  they are not shared equally. They are not shared equally  because oxygen has a higher electronegativity than carbon;  meaning oxygen draws carbons electrons away from it causing  the electrons to be more attracted to oxygen than carbon.  Mother nature “loves” carbon of carbonyl group because it is  easy to attack with a hydroxide ion (H-)  6. Based on what we learned, what functions groups and  chemicals/molecules have carbonyl group? Aldehydes and  Ketones, Carboxylic Acids and Esters  7. What is aldehyde? What is ketone? An aldehyde has an  external carbonyl group at the end of a chain . A ketone has an  internal carbonyl on the inside of a carbon chain  8. How is the general structure of glucose and fructose? Is glucose an aldehyde? Is fructose a ketone? Glucose and Fructose both  carbonyl groups. GLUCOSE has an aldehyde group, and  FRUCTOSE has a ketone group (both have alcohol groups as  well). 9. What is carboxylic acid group? Does fatty acid belong to  carboxylic acid? A carboxylic acid group is always at the end of  a carbon chain; it is a carbon double bonded to an oxygen, with an OH group at the end. Fatty acids belong to carboxylic acids  10. What is a carbon ester group (bond)? How do carbon ester  and carboxylic acid convert to each other? And the general  mechanism of hydrolysis of carbon esters? A carbon ester  group bond is a carbonyl group bonded to an O bonded to and  R. Esters are derivatives of carboxylic acids; the OH of the  COOH is substituted by an OR. The general mechanism of  hydrolysis of carbon esters are: a carbon ester + water carboxylic acid and alcohol. 1.) mother nature splits water  through hydrolysis, clipping hydrogens bond e- in OH. Since OH has an extra electron, it becomes and OH ion. 2.) OH- ion is the  neg charged “attacking ion” seeking positive carbonyl carbon.  3.) the group “kicked out” is the OR, along with its bonding  electron to the carbonyl carbon. The extra electron makes the  OR group negatively charged, which then unites with the  hydrogen of the split water molecule to make an alcohol 4.) the OH group takes place of the OR to form a carboxylic acid  11. Why do people say “ethanol masquerading as an ester”?  12. How is the structure of triacylglycerol (fat in our adipose  tissue)? What are its components? What does it produce when  hydrolyzed? The fat in adipose tissue is stored as a tri-ester of  glycerol. It is composed of a glycerol backbone, 3 long chain  fatty acids, and 3 carbon ester bonds. When hydrolyzed,  triacylglycerol forms 3 long chain fatty acids and one molecule  of glycerol.  13. What is alcohol and what are the 3 different classes of  alcohols? Is glucose an alcohol? Alcohols are carbon chains with an OH group bonded as a substituent. There are three classes  of alcohols. The first is a primary alcohol, which has a carbon, 2 bonding hydrogens, and one R group. A secondary alcohol has  a carbon, one bonding hydrogen, and two R groups. A tertiary  alcohol is a carbon with three bonding R groups. Glucose is not  an alcohol  14. What is the common structure of an amino acid? What are its three functional groups? Where is alpha-carbon located? What  elements does amino acids use? The primary structure of an amino acid is a primary amine group (RNH2), a carboxylic acid  group, and an R group that distinguishes one amino acid from  another. An alpha carbon is the carbon next to the carbonyl  group. Amino acids have 4 elements. They are C, H,O,N and  there are 2 amino acids that have S,C,O,N Lecture 4:  1. How does amine group react with carboxyl group? What is the  new bond called? The product is an amide bond. It produces  chains of amino acids (proteins). OH is replaced with NHR.  Carboxylic Acid+Amine- Amide Bond + Water 2. When amide goes through hydrolysis, what does it produce?  (products) (Reverse rxn) It produces a carboxylic acid and an  amine  3. What is peptide bond? Where do the peptide bonds in proteins  we eat get hydrolyzed and what does the hydrolysis release? A  peptide bond is an amide bond. Peptide bonds in proteins we  get get hydrolyzed in our stomachs and small intestines.  Hydrolysis of peptide bonds release amino acids.  4. How can amino acids bond to form long chains of protein or  peptide? Amino Acids are bonded to each other through amide  bonds from the carboxylic acid group of one amino acid and the amine group of another amino acid.  5. What does the first amino acid in a peptide have, a free amino  group or a free carboxylic acid group? Free amino acid group 6. How is sulfur similar to oxygen element? (valence electron and  bonding electron numbers). What is thiol? What is Sulfhydryl  group? What is sulfide? Sulfur is similar to oxygen because they both have 6 valence electrons, 2 bonding electrons and 4  nonbonding electrons. A thiol is a molecule that contains a  sulfhydryl group instead of a hydroxyl group (CH3CH2SH) A  sulfhydryl group is a hydrogen bonded to a sulfur. A sulfide is a  sulfur in the middle with two R groups attached.  7. What are the two amino acids that contain sulfur? The two  amino acids that contain sulfur and cysteine and methionine. 8. What is Thioester? What are the reactants to form a thioester,  and what does a thioester produce when hydrolyzed? A  thioester is similar to an oxygen ester. They are produced by  the rxn of a carboxylic acid with a thiol. O is replaced with S.  RCOOH + HS-R-RCO-SR + H2O  9. The hydrolysis of an ester, the hydrolysis of an amide, and the  hydrolysis of a thioester all share a common product. What is  this common product? Carboxylic Acid.  10. Is “Phosphoryl group” (P=O) analogous to the “carbonyl  group” (C=O)? What are the structures of a  phosphor(mono)ester, phosphodiester, phosphoanhydride, respectively? Yes, a phosphoryl group is analogous to carbonyl group. A phosphomonoester has one one ester linkage. (POR) (IMAGE ONE) A phosphodiester has two ester linkages (OPO) (IMAGE TWO). A phosphoanhydride has three ester linkages (POP) (IMAGE THREE) 11. How is Phospho(mono)ester and phosphodiester synthesis?  How is Phospho(mono)ester synthesis? Phosphoric acid+alcohol-phosphomonoester. A Phospomonoester+ another alcohol-phosphodiester.  12. How do nucleotides form a DNA chain? What bonds do they form? Nucleotides form DNA chains through phosphodiester bonds that link each nucleotide with the next on one “strand” of DNA.  13. How is Phosphoanhydride synthesized? Where are the two Phosphoanhydride bonds in ATP that contain high energy? There is another phosphorous-containing bond in ATP, what is that bond? Does it contain high energy too? Phosphoanhydrides are synthesized by the rxn of 2 phosphoric acids. There is another phosphorous containing bond in ATP. It is a phosphomonoester.  14. Are you able to draw or recognize: (regular) ester bond /  Amide (peptide) bond /Thioester bond / Phospho(mono)ester  bond / Phosphodiester bond / Phosphoanhydride bond? Ester:  Amide Bond:  Thioester Bond:  15. What are the products of complete oxidation of glucose?  What is oxidation? Carbon Dioxide and Water. Oxidation rxns  are the main source of energyin BCH reactions. Oxidation is the removal of electrons from a molecule (More C-O bonds, less C H bonds) 16. What are the 3 electronic species of hydrogen? Which one is  The three electronic species of hydrogen are an H+ (H ion,  proton), H∙, (an electron, charge 0) and H: or H- (hydride ion,  charge -1)  17. When an hydride ion is taken away from a C-H bond (and the C-H bond breaks), what happens to the bond energy? (where  does it go) energy produced comes from breakage of C-H bond. The bond and its energy are removed and released as heat.  18. What are the products of primary alcohol, secondary alcohol  and aldehyde oxidation, respectively? The products of primary  oxidation are aldehydecarboxylic acid. The product of  secondary alcohol is a ketone 19. When a hydride ion is removed from carbon atom being  oxidized, where does it go? What is the common electron (or  hydride ion) receptor in cells? When a hydride ion is removed  from a carbon atom being oxidized, it is transferred to an  hydride ion acceptor. (Like NAD+ which is reduced to NADH) 20. What is a reduction reaction? How are the products when  ketones and aldehydes get reduced? A reduction reaction at  carbon occurs when electrons are added to the carbon atom. When a ketone is reduced, it forms a secondary alcohol. When  an aldehyde is reduced, it forms a primary alcohol.  21. When you are given an oxidation/reduction reaction, are you  able to find: the hydride ion donor, the hydride ion acceptor,  the oxidizing agent, the reducing agent? Hydride ion donor:  molecule that gives up hydride. Hydride ion acceptor: molecule gaining hydride ion. (NAD+). Oxidizing agent: molecule that will accept H in the products (NAD+). Reducing agent: molecule  that accepts H (NADH)  22. Pyruvate to lactate in muscles is a very important reaction.  When does it happen? What is oxidized in this reaction? During  hard exercise, pyruvate is reduced to lactate by muscle. When  lactate levels rise to high levels in the blood, it indicates  overtraining and results in muscle soreness. NADH is oxidized to NAD+, it is the hydride ion donor. NADH is  reducing agent  Lecture 5:  1. When you are given an oxidation/reduction reaction, are you  able to find the molecule that is being oxidized? Also the  molecule that is being reduced? The molecule that is being  oxidized is losing an H in a C-H bond. The molecule that is  being reduced is gaining an H in a C-H bond.  2. When you are given different molecules, are you able to find  which one is more oxidized or reduced? Molecules being  oxidized have more C-O bonds and less C-H bonds. Molecules  being reduced have more C-H bonds and less C-O bonds.  3. What is the product when two thiols are oxidized? What is a  disulfide? The product of two thiols being oxidized is a disulfide. A disulfide is R-S-S-R. 4. Which amino acids is a thiol, and why it is important for protein  structure? Cysteine is a thiol (R-SH) and it is important in  protein folding. 5. What is thermodynamics? What is high energy bond? (in terms  of energy released and in terms of reaction equilibrium). What  is the high energy bond that we learned? What molecules have  it? Thermodynamics is the study of energy transformations that accompany physical/chemical changes in matter. A high energy bond is a chemical bond which is easily hydrolyzed by a  catalyst and releases a large amount of energy. A high energy  bond that we learned is a phosphoanhydride bond. ATP has it.  6. What is ΔG of a reaction? How do we describe a reaction when  the ΔG is negative? And when the ΔG is positive?  (Spontaneous? Favorable? Exothermic? Endothermic?) What are the examples of ΔG positive and negative reactions that we  discussed in class? Change is G (Gibbs Free Energy) is energy  associated with chemical rxn to be used to do workheat  released. When change in G is negative, the rxn is  spontaneous, exothermic (energy released) and the rxn is  favorable. ATP falls down the energy hill to form ADP +  Pi+energy. There are more reactants than products. A positive  change in G is when the rxn is nonspontaneous, is endothermic (energy needed) and is unfavorable. The reaction is moving up  the energy hill to form ATP. There is more reactants than  products.  7. Which reactions is more favorable, a reaction with a ΔG of -2 or a reaction with a ΔG of -20? Which reactions is more  unfavorable, a reaction with a ΔG of +2 or a reaction with a ΔG of +20? A reaction with a delta G of -20 is more favorable. A  more unfavorable reaction would have a delta G of +20.  8. What is the First Law of Thermodynamics? How do you apply it  to life? When nutrients are oxidized, where does the energy go? The first law of thermodynamics states that energy cannot be  created or destroyed, but it can be changed from one form to  another. (One type of bond to another). It can be applied to life  in the following way: all energy comes from the sun, which is  captured by plants, and photosynthesis changes the energy  into sugars (from carbon dioxide) and water. When nutrients  are oxidized, energy is released as heat.  9. What are the 6 types of chemical reactions that are important  for life? When you see a reaction, are you able to tell which  type it belongs to? Oxidation:  Oxidation of a thioldithiol 2R-SH +O2- RS-SR Dehydration Rxn: loss of water molecule from reacting molecule Addition Rxn: adding H2O to a double bond Isomerization Rxn: process by which one molecule is transformed into its isomer Substitution Rxn: rxn during which one functional group in a chemical rxn is replaced by  another functional groupHydrolysis: breaking of a bond in a molecule involving water. Hydrolysis of ATP is a  nucleophlic substitution. Oxygen of H2O attacks electropositive third phosphate 10. Is hydrolysis of ATP an example of a nucleophilic (“+ charge  loving”) substitution reaction? Why? Hydrolysis of ATP is an  example of a nucleophilic sub rxn because nonbonding  electrons on water are nucleophilic  Lecture 6: 1. How is isomerization reaction related to oxidation/reduction  reaction? How is ATP hydrolysis related to substitution reaction? Isomerization reactions are related to oxidation/reduction  because isomerization is an internal oxidation/reduction rxn.  ATP hydrolysis is related to substitution. This is because the  nonbonding pairs of electrons on the oxygen from water or  nucleophilic (+ charge loving). The oxygen of water attacks  electropositive third phosphate of ATP to set free the inorganic  phosphate (the one that doesn’t have carbon). The group that  leaves or is kicked out is the ADP. Entering hydroxide is  substituted for ADP. Hydrolysis cleaves a high energy  phosphoanhydride bond, whose breakdown by water  (hydrolysis) is accompanied by a large decrease in free energy.  2. What is “cellular organelle” of eukaryotic cells? What are the  important organelles and their general structure and functions? (including plasma membrane, ER, Lysosome, nucleus,  mitochondrion, Golgi apparatus). Which is involved in  exocytosis? What are the special features of mitochondrion? A  cellular organelle is a membrane enclosed structure in the cytoplasm that allows enzyme biochemistry to occur away from other structures in the cell. Organelles and their functions are  as follows:  Plasma Membrane: barrier to extracellular medium; charged  molecules cannot pass through Nucleus: location of main genome; site of most DNA and RNA  synthesis  Endoplasmic Reticulum: network of membraneous tubes that are  continuous with the cell membrane. The ROUGH ER contains  ribosomes, and is used for protein synthesis. Protein is  synthesized on the ribosome, passes through the ER, gets  cut/modified/folded/held in shape. Its additional jobs include  addition/processing of carbs, formation of disulfide bond,  proteolytic cleavages, folding/assembly of protein. The  endoplasmic reticulum incudes a sugar residue that are put on  protein that go to the cell membrane for communication. The ER  is involved in crosslinking folded strands through cysteine  residues that are oxidized. Alcohol and drugs are metabolized by  enzymes within the ER of the liver.  Golgi Apparatus: packages proteins into membrane-bound  vesicles before vesicle is sent to destination. Golgi is important in  the processing of proteins used for secretion; they contain a set of glycosylation enzymes that attack sugar monomers to proteins as the proteins move through.  Lysosome: membrane-enclosed organ that contains enzymes that break down biological polymers---protein, nucleic acids,  carbohydrates, lipids. Within the cell there is degradation. Outside the cell there are components of lysosomes “secretory  lysosomes” that remodel bones through reabsorption—deposition Mitochondrion: site of aerobic metabolism---food is oxidized for  oxygen dependent ATP synthesis, releasing CO2---regulates  apoptosis (cell death)---normal turnover of old/birth new cells  After synthesis and processing in the ER, the insulin  molecule goes to the GOLGI APPARATUS. The vesicle buds off  from the golgi and goes to the plasma membrane, fuses with it, dumps insulin extracellularly and into the blood. Special  features of the mitochondrion are: the mitochondrion have a  double layer that separates an inner compartment (matrix)  with folds (cristae) and an outer compartment (intermembrane space). Enzymes are packed in “lakes”--- matrix/intermembrane space. Membrane-bound enzymes are  found in the inner mitochondrial membrane. There is DNA in the  matrix of a mitochondrion. Mitochondrion can replicate without  muscle cell dividing  3. What is “Extracellular Matrix” (ECM)? The ECM is a collection of  cells that provide structural/biochemical support to surrounding cells. The ECM is made of fibroblasts (rope like insoluble protein called collagen).  4. What is covalent bond and non-covalent bond? How is the  Hydrogen bond network of water molecules? Nonovalent Bond:  no sharing of electrons---instead often isoelectronic b/w  oppositely charged ions. Covalent Bond: sharing of electrons.  Hydrogen bonds (noncovalent bonds) hold water together in a  network through a network of hydrogen bonds.  5. Is water a dipole? Why? Yes, water is a dipole of partial  electrical charges. A dipole occurs in this case when an O of a  covalent bond between H---O draws and electron away from  the H.  6. How does two water molecules form an Hydrogen bond? When  given an Hydrogen bond, are you able to tell which is the  Hydrogen bond acceptor and which is the Hydrogen bond  donor? Hydrogen bonds form when the electron deficient H on  one water molecule interacts with another molecule of water. A H bond donor is where a H is donated from and OH covalent  bond of one water molecule to the nonbonding electron pair on  O of another molecule. A H bond acceptor is where the  nonbonding pair of electrons on O of one water molecule  accepts in the interaction with H from the other O---H covalent  bond of another water molecule.) 7. How many molecules can one water molecule interact with?  Why water is packed so tight and has a high boiling point? One  water molecule can react with 4 other molecules. Water can  pack so tight because each water molecule is linked to the  others by hydrogen bonds. The tight packing, along with strong hydrogen bonds, makes water network have a high boiling  point; more energy is needed to break bonds. 8. Is Hydrogen bond a covalent bond? Is it stronger or weaker  than a covalent bond? A Hydrogen bond is a noncovalent bond. It is weaker than a covalent bond.  9. What are the types of non-covalent bonding important in  Biochemistry? Electrostatic interaction (b/w an ion and a dipole, or between fully charged opposite ions. Hydrogen Bonds, and  hydrophobic interations are also important in BCH.  What are polar and non-polar groups? Polar: molecules or atoms that pull  electrons away from H. Nonpolar: no pulling of electrons.  Lecture 7:  1. What are the two types of Electrostatic interactions? 2. What is the example of Ion:dipole interaction we learned?  Example of ION:ION interaction? What is protein “salt bridge”  and why is it important? Does the salt bridge form on protein  surfaces? Why? 3. What are the three kinds of hydrogen bond? Where do they  exist? Which are the hydrogen bond donors and acceptors,  respectively? 4. How do hydrogen bonds form in proteins, nucleic acids, and in  glucose solution? 5. What is Dipole’ Induced dipole Interaction? What is hydrophobic interaction? What are the examples of hydrophobic interaction? 6. Are nucleotide bases polar or non-polar? Why are they put in  the center of the DNA double-stranded molecule? 7. What is Long Chain Fatty Acids and what can they form in  water? Why? 8. Why cell Membrane is called a “lipid bilayer”? How is its  structure? How is the structure related to hydrophobic  interaction? 9. Why is the cell membrane semipermeable? What does it allow  to pass (without usage of membrane transporters)? What other  components does a cell membrane have? 10. What is the Ionization of water? What is pH? How is pH  calculated and what is its range? Lecture 8: 1. If Solution-A has a pH of 1, Solution-B has a pH of 4, what are  their proton concentrations, respectively? 2. What is Kd, Kw and what is the value of Kw?3. What are strong acid, strong base, weak acid and weak base?  What are the common examples that we learned? 4. (For a weak acid) What is Ka and what is pKa? What is the pH  value of a solution when [conj base] = [weak acid]? 5. What is buffer, buffer range, and what’s the relationship  between buffer range and pKa? 6. What is Henderson Hasselbalch Equation?  7. What is “buffer pair” (conjugate base and acid pair)?  8. Which buffer is the principal buffer in cells and blood,  respectively? What are their pKa values? What are the two  “buffer pairs” (one pair for each buffer), respectively? 9. How many pKas does Phosphoric acid have? 10. In a weak acid dissociation reaction, when you increase pH  (decrease proton), which direction does the reaction go? How  about when you decrease pH (increase proton)? 11. How we breathe using the blood buffer pair H2CO3 and HCO3- 1?  12. Why do some Olympic sprinters hyperventilate at the  starting blocks before the 100m race? (what is the benefit?) 13. Taken Ibuprofen as an example of a weak acid, if it goes  through dissociation, which is the uncharged form? Which is the charged form? Which form can across the cell membrane  without membrane transporters? Which direction of the  dissociation reaction will low pH drive to?

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