Exam 1 Practice Questions Review
Exam 1 Practice Questions: Detailed Study Notes
Atomic Structure and Chemical Bonding
Atomic Composition of an Isotope:
For Titanium (Ti) with atomic number 22:
Protons (p): The atomic number directly equals the number of protons. Thus, p = 22.
Electrons (e): In a neutral atom, the number of electrons equals the number of protons. Thus, e = 22.
Neutrons (n): The mass number (A) is the sum of protons and neutrons (A = p + n). For an isotope with a mass number of 48, the number of neutrons is n = A - p = 48 - 22 = 26.
Answer: p = 22, n = 26, e = 22.
Balancing Chemical Equations (Conservation of Matter):
To balance the reaction Fe3O4 + __C \rightarrow __Fe + __CO, coefficients must be chosen to ensure the same number of each type of atom on both sides.
The balanced equation is Fe3O4 + 4C \rightarrow 3Fe + 4CO.
Coefficients: The blanks correspond to C, Fe, and CO, so the coefficients are 4; 3; 4.
Determinants of Atomic Bonds:
Electrons, specifically the valence electrons (those in the outermost shell), indirectly determine the bonds an atom can form. These electrons are involved in sharing (covalent bonds) or transferring (ionic bonds) to achieve a stable electron configuration.
Commonalities of Elements Based on Atomic Number:
Elements with atomic numbers 6 (Carbon), 14 (Silicon), and 22 (Titanium) are all in the same group (Group 14 or Group IVA) of the periodic table.
This means they have the same number of valence electrons (four) and will tend to form the same number of covalent bonds (four).
Electron Shell Configuration:
For Oxygen with an atomic number of 8
The first electron shell can hold a maximum of 2 electrons.
The second electron shell can hold up to 8 electrons. After filling the first shell, the remaining 8 - 2 = 6 electrons go into the second shell.
Thus, the electron distribution is 2, 6, 0 for the first, second, and third shells, respectively.
Properties of Water and Biological Molecules
Lipid Properties and Bond Types:
Nonpolar covalent bonds (especially C-H bonds) are highly prevalent in lipids.
These nonpolar bonds lead to an even distribution of charge, making lipids hydrophobic (water-fearing) and insoluble in water.
Effect of Reducing Water Surface Tension:
Surface tension in water is caused by the strong cohesive forces (hydrogen bonds) between water molecules.
Reducing surface tension would decrease water's cohesion, leading to:
Water spreading out into a thin film instead of forming beads.
Water forming smaller droplets or failing to form droplets.
Organisms that rely on surface tension for support, like water striders, would sink.
Answer: All of the above would occur.
Water Expansion and Frost Wedging:
A unique property of water is its expansion upon freezing.
When water infiltrates cracks in rocks and freezes, its expansion exerts significant pressure, which can cause boulders to crack (a process known as frost wedging or freeze-thaw weathering).
High Specific Heat of Water:
Water has an unusually high specific heat capacity (approx. 4.18 \ \text{J/(g} \cdot \text{°C)}).
This means that a large amount of heat energy is required to raise the temperature of water by a given amount. This property helps to moderate temperatures in living organisms and environments.
pH Scale and Hydrogen Ion Concentration:
The pH scale is logarithmic, meaning each unit change in pH represents a tenfold change in hydrogen ion concentration ([H^+]).
A solution at pH 8 is basic, and a solution at pH 5 is acidic.
The difference in pH is 8 - 5 = 3 units.
Since pH 8 is more basic, it has fewer H^+ ions than pH 5. Specifically, it has 10^3 or 1,000 times fewer hydrogen ions ([H^+]).
Calculating Hydrogen and Hydroxide Ion Concentrations:
Given pH = 4.0
Hydrogen ion concentration: [H^+] = 10^{-pH} = 10^{-4} \ \text{M}.
Hydroxide ion concentration: In aqueous solutions, the ion product of water (K_w) is constant at 25°C: [H^+][OH^-] = 10^{-14}.
Therefore, [OH^-] = \frac{10^{-14}}{[H^+]} = \frac{10^{-14}}{10^{-4}} = 10^{-10} \ \text{M}.
Answer: hydrogen ion = 10^{-4} \ \text{M} and hydroxide ion = 10^{-10} \ \text{M}.
pH Buffers in Blood:
The human blood's pH is maintained within a narrow range (7.35-7.45) by buffer systems.
The most important buffer system in blood is the carbonic acid-bicarbonate buffer system, which involves both carbonic acid (H2CO3) and the bicarbonate ion (HCO_3^-). They act as a weak acid and its conjugate base, respectively, to resist pH changes.
Importance of Buffers for Protein Function:
Proteins are highly sensitive to pH changes because their three-dimensional structure and thus their function depend on specific ionic interactions and hydrogen bonds, which are affected by [H^+].
Therefore, a buffer is essential in a solution containing a protein to maintain a stable pH and ensure the protein's proper activity.
Hydrophobic Nature of Lipids (Meat Juices):
Small circles observed in aqueous meat juices are lipid (fat) droplets.
Lipids are hydrophobic, meaning they do not mix with water and tend to coalesce to minimize their surface area contact with the aqueous environment, forming spherical droplets.
Planarity and Hybridization of Bonds:
A completely flat section in a biological molecule suggests the presence of double or triple bonds.
Double bonds involve sp^2 hybridization and triple bonds involve sp hybridization, both of which result in planar or linear geometries around the bonded atoms, restricting rotation and creating rigid, flat regions.
Organic Chemistry and Macromolecules
Isomers (General):
Structural isomers have the same molecular formula but different connectivity of atoms.
Cis-trans isomers (geometric isomers) have the same connectivity but different spatial arrangements around a rigid structure like a double bond or ring.
Enantiomers are mirror-image isomers that are non-superimposable (chiral).
Isotopes are atoms of the same element with different numbers of neutrons. (This is not an isomer description).
Hydrocarbons with Double Bonds:
To determine if a hydrocarbon has a double bond, compare its formula to the general formulas for alkanes (CnH{2n+2}), alkenes (CnH{2n}), and alkynes (CnH{2n-2}).
C3H8 (propane) is an alkane (single bonds).
C2H6 (ethane) is an alkane (single bonds).
C2H4 (ethene) is an alkene and contains a double bond.
C2H2 (ethyne) is an alkyne (triple bond).
Impact of Methyl Group Substitution in DNA:
Phosphate groups are integral to the backbone of DNA, linking sugars via phosphodiester bonds and carrying a negative charge crucial for DNA's structure and interaction with proteins.
Substituting phosphate groups with methyl groups (-CH_3), which are nonpolar and lack the ability to form phosphodiester linkages, would cause the DNA molecule to fall apart as its structural integrity would be destroyed.
Basic Functional Group in Organic Molecules:
The amino group (-NH2 or protonated form -NH3^+) behaves as a base because it can accept a proton (H^+) from the surrounding solution, thereby raising pH.
Acidic Functional Group in Organic Molecules:
The carboxyl group (-COOH or deprotonated form -COO^-) behaves as an acid because it can donate a proton (H^+) to the surrounding solution, thereby lowering pH.
Bond Linking Functional Groups to Carbon Skeleton:
Functional groups are typically joined to the carbon skeleton of large molecules by stable covalent bonds.
Structural Isomers (Propanal vs. Acetone):
Propanal (an aldehyde, CH3CH2CHO) and acetone (a ketone, CH3COCH3) both have the molecular formula C3H6O.
However, their atoms are connected differently (one has a carbonyl group at the end, the other in the middle).
Thus, propanal and acetone are structural isomers.
Functional Group Critical for Protein Shape:
The sulfhydryl group (-SH) is crucial because the reaction of two sulfhydryl groups forms a disulfide bond (-S-S-).
Disulfide bonds are strong covalent bonds that play a significant role in stabilizing the tertiary and quaternary structures of many proteins, particularly in extracellular environments.
Formation of Polymer Linkages (Monomers):
All biological monomers are connected to form polymers through a dehydration reaction (also known as a condensation reaction).
In this reaction, a molecule of water is removed as a covalent bond is formed between two monomers.
Defining Hydrocarbons:
If all functional groups are removed from an organic molecule, leaving only carbon and hydrogen atoms, the resulting molecule is a hydrocarbon.
Levels of Protein Structure:
Proteins exhibit four levels of structure:
Primary: Linear sequence of amino acids.
Secondary: Local folding patterns (e.g., \alpha-helix, \beta-pleated sheet) stabilized by hydrogen bonds.
Tertiary: Overall three-dimensional shape of a single polypeptide chain, stabilized by various interactions (hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges).
Quaternary: The most complex level, involving the arrangement and interaction of multiple polypeptide subunits (if a protein has more than one).
Nucleic Acid Backbone Linkages:
Nucleic acids (DNA and RNA) are polymers where 5-carbon sugars are linked together by phosphodiester bonds.
These bonds connect the 5' carbon of one sugar to the 3' carbon of the next sugar via a phosphate group, forming the sugar-phosphate backbone.
Double Helix Structure:
The double helix describes the characteristic three-dimensional structure of a DNA molecule, consisting of two strands wound around each other.
Bonds Holding DNA Nitrogenous Bases Together:
In a DNA molecule, the nitrogenous bases from the two complementary polymer chains are held together by hydrogen bonds.
Adenine (A) forms two hydrogen bonds with Thymine (T), and Guanine (G) forms three hydrogen bonds with Cytosine (C).
Number of C-H Bonds and Saturation:
Among molecules with the same number of carbon atoms, a saturated fat will have the most C-H bonds.
Saturated fats contain only single C-C bonds, allowing each carbon to be bonded to as many hydrogen atoms as possible. Unsaturated fats contain double or triple C-C bonds, which reduce the number of C-H bonds.
Nitrogenous Bases in DNA vs. RNA:
DNA contains the nitrogenous bases Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).
RNA contains Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).
Therefore, Thymine is found in DNA but not in RNA. Uracil is found in RNA but not in DNA.
Impact of Amino Acid Substitution (Alanine for Glycine):
Alanine (side chain -CH_3) and Glycine (side chain -H) are both relatively small, nonpolar, hydrophobic amino acids.
Replacing Glycine with Alanine is generally considered a conservative substitution.
While Glycine's very small side chain provides unique flexibility, substituting it with Alanine, another hydrophobic amino acid, would likely result in little change to the overall protein structure, especially compared to substitutions involving charges or polarity.
Identifying N-terminus and C-terminus:
Polypeptides are synthesized and typically written from the N-terminus (the end with a free amino group) to the C-terminus (the end with a free carboxyl group).
In the polypeptide Gly-Ser-Phe-Ala-Tyr-His, Gly is at the N-terminus and His is at the C-terminus.
Indigestible Polysaccharide (Cellulose):
Cellulose is a polysaccharide composed of unbranched chains of \beta-glucose monomers linked by \beta-1,4 glycosidic bonds.
Humans lack the enzymes necessary to hydrolyze these \beta-linkages, making cellulose an indigestible dietary fiber.
DNA Complementary Strand (Antiparallel Pairing):
DNA strands are complementary and antiparallel.
The pairing rules are Adenine (A) with Thymine (T) and Guanine (G) with Cytosine (C).
Given the sequence 5' -TAGGCCT-3':
The complementary bases would be A-T, T-A, G-C, G-C, C-G, C-G, T-A.
The complementary strand would run in the antiparallel direction, so if the original is 5' \rightarrow 3', the new one is 3' \rightarrow 5'.
Therefore, the complementary strand is 3' -ATCCGGA-5'.
Phospholipid Hydrophilic and Hydrophobic Parts:
A phospholipid consists of a hydrophilic head and hydrophobic tails.
The hydrophilic head is composed of glycerol and a phosphate group (often with an additional polar molecule).
The hydrophobic tails are made up of two fatty acid chains.
Unsaturated Lipids and Packing Density:
Unsaturated fatty acids contain one or more double bonds, which introduce kinks into their hydrocarbon chains.
These kinks prevent the chains from packing together tightly.
As a result, unsaturated lipids are loosely packed because of their double bonds, making them liquid at room temperature.
Cell Structure and Organelles
Structures Common to All Three Domains of Life:
All known life forms, across all three domains (Bacteria, Archaea, Eukarya), possess a phospholipid bilayer cell membrane (also known as the plasma membrane).
Other options like nucleus, ER, mitochondria, and endocytotic vesicles are exclusive to eukaryotes.
Hierarchy of Biological Sizes:
The correct order from largest to smallest is: human body (macroscale), frog egg (visible to the naked eye, mm), mitochondrion (organelle, \mu m), lipid (molecule, nm/Å).
Alcohol Detoxification Site:
The peroxisome is an organelle involved in various metabolic processes, including the detoxification of alcohol and other harmful compounds by removing hydrogen atoms (oxidation), often producing hydrogen peroxide as a byproduct.
The smooth ER also plays a role, but peroxisomes are central to this specific mechanism.
Components of Chromosomes:
Eukaryotic chromosomes are complex structures composed of tightly coiled DNA (deoxyribonucleic acid) wrapped around specialized proteins called histone proteins.
Location of Ribosomal RNA (rRNA) Synthesis:
Ribosomal RNA (rRNA), a key component of ribosomes, is synthesized in the nucleolus, a dense region within the eukaryotic nucleus.
Composition of Ribosomes:
Ribosomes, the cellular machinery for protein synthesis, are complex molecular structures composed of both ribosomal RNA (rRNA) and proteins.
Organelle for Protein Synthesis:
Ribosomes are the organelles responsible for carrying out protein synthesis (translation) by reading messenger RNA (mRNA) and assembling amino acids into polypeptide chains.
Mitochondrial Inner Membrane Folds:
The inner mitochondrial membrane has numerous folds or invaginations called cristae.
These cristae dramatically increase the surface area for the reactions of the electron transport chain and ATP synthesis.
Structures Common to Plant and Animal Cells:
Both plant and animal cells are eukaryotic and therefore contain membrane-bound organelles like the mitochondrion, which is essential for cellular respiration in both cell types.
Chloroplasts and central vacuoles are specific to plant cells, while centrioles are primarily found in animal cells.
Cyanide's Target in a Cell:
Cyanide is a potent poison that interferes with cellular respiration by binding to molecules involved in the electron transport chain, specifically cytochrome c oxidase.
The electron transport chain and ATP production occur primarily in the mitochondria. Thus, cyanide would accumulate and exert its effects mainly in the mitochondria.
Common Traits of Chloroplasts and Mitochondria:
Both chloroplasts and mitochondria are unique among organelles in that they contain their own circular DNA (similar to prokaryotic DNA) and their own ribosomes.
This supports the endosymbiotic theory, which posits that these organelles originated from free-living prokaryotes engulfed by ancestral eukaryotic cells.
Fatty Acid to Sugar Conversion in Plants:
In plants, specialized peroxisomes called glyoxysomes contain enzymes that can convert fatty acids into sugars.
This is particularly important in germinating seeds, allowing them to use stored fats as an energy source for growth until photosynthesis can begin.
Composition of Plasma Membrane:
The plasma membrane, which encloses all cells, is primarily composed of a phospholipid bilayer.
Proteins are embedded within or associated with this bilayer, and carbohydrates are often attached to the outer surface of lipids (glycolipids) and proteins (glycoproteins).
DNA Location in Eukaryotes vs. Prokaryotes:
In eukaryotic cells, the main genetic material (DNA) is housed within a membrane-bound organelle called the nucleus.
In prokaryotic cells, DNA is typically located in an irregularly shaped region in the cytoplasm called the nucleoid, which lacks a membrane enclosure.