Lecture 1: Foundation of Biochemistry: Water, Molecular Interactions Flashcards
What are the 6 kingdoms of life
Archaea, Bacteria, Protista, Fungi, Plantae, Animalia
Nucleolus
single, circular DNA molecule; ribosomal synthesis
Pili
Points of adhesion to surface
Flagella
Propels to surroundings
Ribosomes
Smaller than eukaryotic ribosomes; Protein Synthesis
Cell Envelope
Surrounds cell
Nucleus
Contains chromatin
Nuclear Envelope
Separates chromatin from cytoplasm
Nucleolus
Site of ribosomal RNA synthesis
Plasma Membrane
regulates movement of materials in and out of cell
Mitochondrion
ATP production
Rough ER
protein synthesis
Smooth ER
lipid synthesis & drug metabolism
Golgi Complex
Processes, packages and targets proteins to other organelles for export
Transport Vesicles
shuttles lipids and proteins between ER, Golgi and PM
Lysosome
degrades intracellular debris
Cytoskeleton
supports cell; aids in movement of organelles
Peroxisome
oxidizes Fatty Acids
Ribosomes
Protein Synthesizing machines
Chloroplast
harvests sunlight, produces ATP and carbs
Starch granules
temporarily stores carb products of photosynthesis
Thylakoids
site of light-driven ATP synthesis
Cell Wall
provides shape and rigidity; protects cell from osmotic swelling
Vacuole
degrades and recycles macromolecules, stores metabolites
Plasmodesma
provides path between two plant cells
Glyoxysome
contains enzymes of the glyoxylate cycle
Which is NOT a feature of Bacteria?
Pili Flagella Cell Envelope Ribosomes
Ribosomes
Nucleoid
Bacterial structure; contains DNA
Difference between Gram (+)/ Gram (-)
Gram (-) has a cellular envelope with an outer membrane; Gram (+) has a cellular envelope without an outer membrane
Phototrophs
energy from light
Chemotrophs
energy from oxidation of chemical fuels
True of false; Biomolecules are Carbon based
True
What are stereoisomers?
Molecules with the same chemical bonds but different configurations.
What are geometric isomers?
Differ in the arrangement of their substituent groups with respect to a non rotating double bond.
What are isomers with mirror images of each other?
Enantiomers
What are isomers that are NOT mirror images of each other?
Diastereomers
What are two ways that enzymes speed up reactions
Couple to a fast one; Lower activation energy
Metabolic reactions require energy? True or False
If true, is it Endergonic or Exergonic
True
Endergonic
Do endergonic Reactions have a (+) or (-) DeltaG?
(+)
Do exergonic Reactions have a (+) or (-) DeltaG?
(-)
True or False; Catalysts alter the Delta G?
False; catalysts do NOT alter DeltaG
Endergonic. Favorable or Unfavorable
unfavorable
Exergonic. Favorable or Unfavorable
favorable
What are the (4) types of non-covalent interactions?
(HI-DV= Hi Devon)
Hydrophobic Effect- Ionic (Coulombic)
Dipole Interactions - Van der Waals
Hydrophobic Effect
Ordering of water molecules around non-polar substances
Ionic (Coulombic)
Electrostatic interactions bt. permanently charges species or between the ion and a permanent dipole
Dipole Interactions
Electrostatic Interactions bt. uncharged- polar molecules
Van der Waals
weak interactions bt. all atoms; Attractive= dispersion and repulsive= steric
True or False
Hydrogen Bonds are WEAKEST when the bonded molecules are oriented to maximize electrostatic interactions.
False; STRONGEST
What type of interaction are London Dispersions and what do they depend on?
Van der Waals Interactions; polarizability
What type of interaction are Steric Repulsion and what do they depend on?
Van der Waals Interactions; size of atoms
True or false
Van der Waals attraction dominates at long distances?
True
True or false
Van der Waals Interactions are hard to break and irreversible?
False; they are easily broken and reversible
True or False; Hydrophobic Effect refers to the interaction of non-polar substances in aqueous solution?
True
True or False; Hydrophobic solutes have high solutbility
False; Hydrophobic Solutes have low solubility
True of False; Hydrophobic Effect; High entropy is thermodynamically favorable
True
True or False; Micelles; Micelle will spontaneously form through phospholipids in an aqueous solution
True
True or False; Micelles; Micelle is simply a cellular membrane with a vacuous interior
False
True or False; Micelles; The hydrophobic effect is the driving force for the formation of a micelle
True
True or False: Micelles; When a micelle forms there is an overall INCREASE in Gibbs Free Energy
False; there is a decrease in Gibbs free energy
Are binding sites in enzymes or receptors hydrophobic?
Yes
Where are ribosomes produced?
Nucleolus
In a bacterial cell, the DNA is in the:
Nucleoid
A major change occurring in the evolution of eukaryotes from prokaryotes was the development of:
Nucleus
In eukaryotes, the nucleus is enclosed by a double membrane called the:
Nuclear Envelope
Which group of single-celled micro-organisms has many members found growing in extreme environments?
Archaea
Which one of the following has the cellular components arranged in order of increasing size?
A) Amino acid < protein < mitochondrion < ribosome
B) Amino acid < protein < ribosome < mitochondrion
C) Amino acid < ribosome < protein < mitochondrion
D) Protein < amino acid < mitochondrion < ribosome
E) Protein < ribosome < mitochondrion < amino acid
B
The three-dimensional structure of macromolecules is formed and maintained primarily through noncovalent interactions. Which one of the following is not considered a noncovalent interaction?
A) carbon-carbon bonds B) hydrogen bonds C) hydrophobic interactions D) ionic interactions E) van der Waals interactions
A
Which one of the following is not among the four most abundant elements in living organisms?
A) Carbon B) Hydrogen C) Nitrogen D) Oxygen E) Phosphorus
E
The four covalent bonds in methane (CH4) are arranged around carbon to give which one of the following geometries?
A) linear B) tetrahedral C) trigonal bipyramidal D) trigonal planar E) trigonal pyramidal
B
The macromolecules that serve in the storage and transmission of genetic information are:
Nucleic Acids
Stereoisomers that are nonsuperimposable mirror images of each other are known as:
Enantiomers
The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid, the cis isomer of fumaric acid. This is an example of:
Stereospecificity
Energy requiring metabolic pathways that yield complex molecules from simpler precursors are:
Anabolic
The three-dimensional structure of a protein is determined primarily by:
the sequence of amino acids in the protein
________denotes the spatial arrangement of a molecule that is determined by the presence of either double bonds or chiral centers. _________refers to the spatial arrangement of substituted groups that are free to assume different positions in space.
Configuration; Conformation
T/F: Freedom of bond rotation is possible for both carbon-carbon single bonds and carbon-carbon double bonds.
False
T/F: Enzymes catalyze stereospecific reactions.
True
T/F: Metabolism is all the ordered reaction pathways by which cellular chemistry proceeds and biological energy transformation occurs.
True
An atom whose substituents are arranged such that it can be superimposed on its mirror image:
achiral center
The reactions by which biomolecules are synthesized from simpler components:
Anabolism
An organism that can synthesize all its cellular components from simple molecules, such as carbon dioxide and ammonia
Autotroph
The degradative metabolic reactions in which nutrients and cell constituents are broken down for energy and raw materials
Catabolism
An organism that obtains energy by oxidizing a chemical fuel
Chemotroph
An atom whose substituents are arranged such that it is not superimposable on its mirror image; also called an asymmetric center
Chiral Center
Spatial arrangement of an organic molecule that is conferred by the presence of either i) double bonds or ii) chiral centers. These isomers cannot be interconverted without breaking one or more covalent bonds
Configuration
Spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of freedom of bond rotation
Conformation
Stereoisomer of a compound having two or more chiral centers that is not a mirror image of another stereoisomer of the same compound
Diastereomers
Molecules that are nonsuperimposable mirror images of one another; a type of stereoiosomer
Enantiomers
Exergonic/Endergonic vs Exothermic/Endothermic
Exergonic = a negative free energy change, G < 0 (spontaneous)/Endergonic = a positive free energy change, G > 0 (nonspontaneous)
Exothermic = heat is released, H < 0/ Endothermic = heat is absorbed, H > 0
The inhibition of an early step in a reaction sequence by the product of a later step
Feedback Inhibition
Isomers related by rotation about a double bond; also called cis and trans isomers
Geometric Isomers
An organism that requires complex nutrient molecules, such as glucose, as a source of energy and carbon
Heterotroph
Chiral molecules with different configurations about at least one of their asymmetric centers but which are otherwise identical
Stereoisomers
Molecular assembly at the point of maximal free energy in the reaction coordinate diagram of a chemical reaction
Transition State
Prokaryote vs Eukaryote:
Prokaryotes DO NOT have a membrane bound nucleus, Eukaryotes DO
Which of these statements about hydrogen bonds is not true?
A) Hydrogen bonds account for the anomalously high boiling point of water.
B) In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules.
C) Individual hydrogen bonds are much weaker than covalent bonds.
D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.
E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond.
D
A true statement about hydrophobic interactions is that they:
A) are the driving force in the formation of micelles of amphipathic compounds in water.
B) do not contribute to the structure of water-soluble proteins.
C) have bonding energies of approximately 20-40 Kjoule per mole.
D) involve the ability of water to denature proteins.
E) primarily involve the effect of polar solutes on the entropy of aqueous systems.
A
Hydrophobic interactions make important energetic contributions to:
A) binding of a hormone to its receptor protein.
B) enzyme-substrate interactions.
C) membrane structure.
D) three-dimensional folding of a polypeptide chain.
E) all of the above are true.
E
Dissolved solutes alter some physical (colligative) properties of the solvent water because they change the: A) concentration of the water. B) hydrogen bonding of the water. C) ionic bonding of the water. D) pH of the water. E) temperature of the water.
A
Osmosis is movement of a:
A) charged solute molecule (ion) across a membrane.
B) gas molecule across a membrane.
C) nonpolar solute molecule across a membrane.
D) polar solute molecule across a membrane.
E) water molecule across a membrane.
E
A hydronium ion: A) has the structure H3O+. B) is a hydrated hydrogen ion. C) is a hydrated proton. D) is the usual form of one of the dissociation products of water in solution. E) all of the above are true.
E
The pH of a solution of 1 M HCl is: A) 0 B) 0.1 C) 1 D) 10 E) -1
A
The pH of a solution of 0.1 M NaOH is: A) 0.1 B) 1.0 C) 12.8 D) 13 E) 14
D
Which of the following is true about the properties of aqueous solutions?
A) A pH change from 5.0 to 6.0 reflects an increase in the hydroxide ion concentration ([OH-]) of 20%.
B) A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100.
C) Charged molecules are generally insoluble in water.
D) Hydrogen bonds form readily in aqueous solutions.
E) The pH can be calculated by adding 7 to the value of the pOH
D
The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has:
A) 0.189 times the [H+] as the gastric juice.
B) 5.29 times lower [H+] than the gastric juice.
C) 6 times lower [H+] than the gastric juice.
D) 6,000 times lower [H+] than the gastric juice.
E) a million times lower [H+] than the gastric juice.
E
The aqueous solution with the lowest pH is: A) 0.01 M HCl. B) 0.1 M acetic acid (pKa = 4.86). C) 0.1 M formic acid (pKa = 3.75). D) 0.1 M HCl. E) 10-12 M NaOH.
D
The aqueous solution with the highest pH is: A) 1 M HCl. B) 1 M NH3 (pKa = 9.25). C) 0.5 M NaHCO3 (pKa = 3.77). D) 0.1 M NaOH. E) 0.001 M NaOH.
D
Phosphoric acid is tribasic, with pKa's of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is: A) H3PO4. B) H2PO4-. C) HPO42-. D) PO43-. E) none of the above.
B
Which of the following statements about buffers is true?
A) A buffer composed of a weak acid of pKa = 5 is stronger at pH 4 than at pH 6.
B) At pH values lower than the pKa, the salt concentration is higher than that of the acid.
C) The pH of a buffered solution remains constant no matter how much acid or base is added to the solution.
D) The strongest buffers are those composed of strong acids and strong bases.
E) When pH = pKa, the weak acid and salt concentrations in a buffer are equal.
E
A compound has a pKa of 7.4. To 100 mL of a 1.0 M solution of this compound at pH 8.0 is added 30 mL of 1.0 M hydrochloric acid. The resulting solution is pH: A) 6.5 B) 6.8 C) 7.2 D) 7.4 E) 7.5
D
The Henderson-Hasselbalch equation:
A) allows the graphic determination of the molecular weight of a weak acid from its pH alone.
B) does not explain the behavior of di- or tri-basic weak acids
C) employs the same value for pKa for all weak acids.
D) is equally useful with solutions of acetic acid and of hydrochloric acid.
E) relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.
E
Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:
A) pH remains constant.
B) pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76.
C) pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76.
D) ratio of acetic acid to sodium acetate in the buffer falls.
E) sodium acetate formed precipitates because it is less soluble than acetic acid.
D
A compound is known to have a free amino group with a pKa of 8.8, and one other ionizable group with a pKa between 5 and 7. To 100 mL of a 0.2 M solution of this compound at pH 8.2 was added 40 mL of a solution of 0.2 M hydrochloric acid. The pH changed to 6.2. The pKa of the second ionizable group is:
A) The pH cannot be determined from this information.
B) 5.4
C) 5.6
D) 6.0
E) 6.2
C
Which of these statements is true of the resulting buffers?
A) pH of buffer 1 < pH of buffer 2 < pH of buffer 3
B) pH of buffer 1 = pH of buffer 2 = pH of buffer 3
C) pH of buffer 1 > pH of buffer 2 > pH of buffer 3
D) The problem cannot be solved without knowing the value of pKa.
E) None of the above.
C
A 1.0 M solution of a compound with 2 ionizable groups (pKa’s = 6.2 and 9.5; 100 mL total) has a pH of 6.8. If a biochemist adds 60 mL of 1.0 M HCl to this solution, the solution will change to pH:
A) 5.60
B) 8.90
C) 9.13
D) 9.32
E) The pH cannot be determined from this information.
A
In which reaction below does water not participate as a reactant (rather than as a product)?
A) Conversion of an acid anhydride to two acids.
B) Conversion of an ester to an acid and an alcohol.
C) Conversion of ATP to ADP.
D) Photosynthesis
E) Production of gaseous carbon dioxide from bicarbonate.
E
Which of the following properties of water does not contribute to the fitness of the aqueous environment for living organisms?
A) Cohesion of liquid water due to hydrogen bonding.
B) High heat of vaporization.
C) High specific heat.
D) The density of water is greater than the density of ice.
E) The very low molecular weight of water.
E
