Module 2: The Macromolecules of Life Flashcards
What are the 2 model systems for investigating chemical evolution?
Prebiotic soup model: proposes that certain molecules were synthesized from gases in the atmosphere or arrived via meteorites.
-They would condense with rain and accumulate in the ocean, resulting in an organic “soup”.
Surface metabolism model: suggests that dissolved gases came in contact with minerals lining the walls of deep-sea vents, forming increasingly complex organic molecules.
Alexander I Oparin
JBS Haldane
Stanley Miller
Alexander I Oparin: first proposed chemical evolution in 1924.
JBS Haldane: re-published Oparin’s proposal 5 years later.
Stanley Miller: American graduate student who tested the Oparin-Haldane hypothesis in 1953.
Photon
A discrete packet of light energy; a particle of light.
What are the 6 major functions of proteins?
- Defense
- Movement
- Catalysis
- Signalling
- Structure
- Transport
What 4 groups are present in all 20 amino acids?
- Hydrogen atom
- Amino group (NH2)
- Carboxyl group (COOH)
- R-group (side chain)
What are 3 questions you can ask to determine what type of amino acid an R-group is?
- Does it have a negative charge?
- If so, it is acidic and will lose a proton. - Does it have a positive charge?
- If so, it is basic and will gain a proton. - If it is uncharged, does it have an oxygen atom?
- If so, the electronegative oxygen will form a polar covalent bond in the R-group, making it uncharged polar.
Polymerization
The process of linking monomers together to form polymers.
Peptide bond
The covalent bond formed by a condensation reaction between 2 amino acids.
Oligopeptide
Polypeptide
Oligopeptide: a polymer consisting of 50 or fewer amino acids.
Polypeptide: polymers of 50 or more amino acids.
What are the 4 levels of protein structure?
- Primary - the sequences of amino acids in a polypeptide, stabilized by peptide bonds.
- Secondary - formation of alpha-helixes and beta-pleated sheets, stabilized by hydrogen bonding.
- Tertiary - overall 3-dimensional shape.
- Quaternary - shape produced by combinations of polypeptides.
Macromolecular machine
A group of proteins and possibly other macromolecules that assemble to carry out a particular function.
Substrate
A reactant that interacts with a catalyst, such as an enzyme, in a chemical reaction.
Active site
Location of the enzyme where substrates bind and react, causing catalysis.
Why are origin-of-life researchers skeptical that life began with a protein?
It would have needed to possess information, replicate and evolve. If they cannot replicate themselves, they cannot evolve on their own.
RNA world hypothesis
Proposal that at a particular stage in the evolution of life, RNA stored both genetic information and catalyzed its own replication.
Nucleoside
Nucleotide
Nucleoside: A molecule consisting of a 5-carbon sugar and one of several nitrogen-containing bases.
Nucleotide: Same as a nucleoside, plus one or more phosphate groups.
Phosphodiester bond
Chemical linkage between adjacent nucleotide residues in DNA and RNA.
Phosphodiester bonds between ribonucleotides produce the polymer RNA, bonds between deoxynucleotides produce DNA.
What are the 3 basic units that make up a nucleotide?
- A sugar
- At least one phosphate group
- A nitrogenous base
X-ray Crystallography
A technique for determining the 3D structure of macromolecules by analyzing the diffraction patterns produced by X-rays beamed at crystals of the molecule.
It found that DNA had a regular and repeating structure.
What are Chargoff’s 2 rules?
- The number of purines in a given DNA molecule is equal to the number of pyrimidines.
- The DNA molecule has an equal number of T’s and A’s, and an equal number of G’s and C’s.
Complimentary base pairing
The association between specific nitrogenous bases of nucleic acids stabilized in hydrogen bonding.
-Example: A+T/U, G+C.
Also known as Watson-Crick pairing.
What are the purines?
What are the pyrimidines?
Purines: Adenine, Guanine.
Pyrimidines: Cytosine, Urasil, Thymine.
Viroid
A pathogenic RNA molecule.
Ribozyme
Any RNA molecule that can act as a catalyst to increase the rate of a chemical reaction.
Carbohydrate polymers are made of __________ monomers.
Nucleic acid polymers are made of __________ monomers.
Protein polymers are made of __________ monomers.
Carbohydrate polymers are made of simple sugar monomers.
Nucleic acid polymers are made of nucleotide monomers.
Protein polymers are made of amino acid monomers.
Carbohydrate
Any class of molecules that contain:
- A carbonyl group (C=O)
- Several hydroxyl groups (-OH)
- Multiple carbon-hydrogen bonds (C-H)
Triose
Pentose
Hexose
Triose: a monosaccharide containing 3 carbon atoms.
Pentose: a monosaccharide containing 5 carbon atoms (ribose).
Hexose: a monosaccharide containing 6 carbon atoms (glucose).
Simple sugars differ from each other in what 3 ways?
- The location of their carbonyl group (C=O).
- The number of carbon atoms present.
- The spatial arrangement of their atoms (particularly the relative positions of their hydroxyl groups).
Glycosidic linkage
The covalent bond formed by a condensation reaction between two sugar monomers.
Also called glycosidic bond.
Starch
A mixture of 2 storage polysaccharides, both formed from α-glucose monomers.
Glycogen
A highly-branched storage polysaccharide composed of glucose monomers joined by α-1,4- and α1,6- glycosidic linkages.
Cellulose
Structural polysaccharide composed of glucose monomers joined by β-1,4- glycosidic linkages.
Chitlin
Structural polysaccharide composed of glucose monomers joined by β1,4- glycosidic linkages.
Peptidoglycan
A complex structural polysaccharide found in bacterial cell walls.
Polysaccharide
Oligosaccharide
Polysaccharide: a linear or branched carbohydrate chain consisting of many (>50) monosaccharides.
-Long chain of simple sugars.
Oligosaccharide: a linear or branched carbohydrate chain consisting of fewer than 50 monosaccharides (typically 3-10).
-Short chain of simple sugars.
What are 4 functions of carbohydrates?
- Serve as precursors to larger molecules.
- Provide fibrous structural materials.
- Indicate cell identity.
4 Store chemical energy.
Glycolipid
Glycoprotein
Glycolipid: a lipid that has one of more covalently bonded carbohydrate (it is glycosolated).
Glycoprotein: a protein that has one or more covalently bonded carbohydrates.
Define antigens. What are the 4 types?
Antigens are oligosaccharides that can potentially provoke an immune system response.
- A antigen
- B antigen
- C antigen
Photosynthesis
The complex biological process that converts light energy to chemical energy.
CO2 + H2O = sunlight»_space; (CH2O)n + O2
Phosphorylase
Amylase
Phosphorylase: An enzyme that can break down glycogen by catalyzing hydrolysis of the α-glycosidic linkages between the glucose residues.
Amylase: Any enzyme that can break down starch by catalyzing hydrolysis of the α-glycosidic linkages between glucose residues.
Lipid
Any organic compound that are nonpolar and hydrophobic.
Hydrocarbons
Molecules that contain only carbon and hydrogen.
They are nonpolar because electrons are shared equally in C-H bonds.
Fatty acid
A simple lipid consisting of a hydrocarbon chain bonded to a carboxyl functional group.
Saturated fatty acid
Unsaturated fatty acid
Saturated fatty acid: hydrocarbon chains consisting of only single bonds between carbons.
Unsaturated fatty acid: hydrocarbon chains with one or more double carbon bonds.
Steroid
Class of lipid with a characteristic 4-ring hydrocarbon structure.
Fat
Class of lipid consisting of 3 fatty acid molecules joined by ester linkages to a glycerol molecule.
Also called a trigliceride.
Ester linkage
The covalent bond formed by a condensation reaction between a carboxyl group and a hydroxyl group.
They join fatty acids to glycerol to form a fat or phospholipid.
Phospholipid
A class of lipid having a hydrophilic head and hydrophobic tail.
Amphipathic
Substances that contain both hydrophobic and hydrophilic regions.
Instead of dissolving in water, amphipathic liquids can form one of which two structures?
- Micelles - tiny clusters created when the heads face the water and form hydrogen bonds while the tails interact with each other in the middle, away from the water.
- Lipid bilayer - lipid molecules arranged in paired sheets.
Today, high-energy photons are unable to reach Earth’s surface due to the presence of __________ in the atmosphere. This same gas was not present in appreciable amounts during early chemical evolution.
Ozone (O₃)
In the following reaction, the formation of acetic acid from carbon dioxide and hydrogen was most likely catalyzed by vent minerals: 2 CO2 (aq) + 4 H2 (aq) CH3COOH (aq) + 2 H2O (l). The reaction appears to be a nonspontaneous reaction because __________.
The total number of reactants (6) is greater than the total number of products (3), suggesting a decrease in entropy.
When the products of a chemical reaction are less ordered than the reactant molecules are, entropy increases, and the reaction tends to be spontaneous.
Six main functional groups in organic compounds dictate the function of molecules based on their chemistry. Functional groups containing oxygen and nitrogen are good at __________.
Gaining or losing protons in molecular reactions.
Specifically, amino (nitrogen) and carboxyl (oxygen) functional groups tend to attract or drop a proton, respectively, when in a solution.
A radioactive isotope of an element refers to an unstable form of an element that will __________ and be converted into a more stable isotope of the same element.
Release energy.
Free radicals are extremely reactive and are formed when __________ strike molecules of hydrogen or carbon dioxide.
High-energy photons.
High-energy photons or pulses of intense electrical energy, such as lightning, are able to knock apart the shared electrons within the shells of hydrogen and carbon dioxide molecules to create free radicals.
What feature of mononucleotides provides the energy needed for polymerization when nucleic acids are formed?
a. Their methyl groups
b. Their sugar groups
c. Their nitrogenous bases
d. Their phosphate groups
d. Their phosphate groups
Which of the following best describes DNA’s secondary structure?
a. Beta-pleated sheet
b. Double parallel helical strands
c. Turn-loop-turn
d. Double antiparallel helical strands
d. Double antiparallel helical strands
Which of the following best explains why “carbs” (carbohydrates) are advertised by manufacturers of candy bars and sports drinks as a “quick energy boost”?
a. The energy in them can be stored as fat, which has high energy per unit weight.
b. The carbons in carbs are rich in energy because they are highly oxidized.
c. Carbs are reduced molecules that have high-energy electrons.
d. This is an advertising gimmick that has no scientific evidence to support it.
c. Carbs are reduced molecules that have high-energy electrons.
Which of the following can vary among monosaccharides?
a. The number of carbon atoms
b. The presence of a carbonyl group
c. The presence of hydroxyl groups
d. All of the above
a. The number of carbon atoms
Although DNA is the main hereditary material in all life-forms, it lacks one important characteristic of being a candidate for the first life-form. Why have researchers rejected the idea that DNA was found in the first life-form?
It does not function as a catalyst.
An enzyme has a total of four active sites. When you denature the molecule and study its composition, you find that each active site occurs on a different polypeptide. Which of the following hypotheses does this observation support?
a. The enzyme is subject to allosteric regulation.
b. The enzyme requires a cofactor to function normally.
c. The protein’s structure is affected by temperature and pH.
d. The protein has quaternary structure.
The protein has quaternary structure.
A nucleotide is made up of which of the following subunits?
A 5-carbon sugar, a phosphate group, and a nitrogenous base
At the pH found in cells (about 7.0), what happens to the carboxyl group on an amino acid?
a. It acts as a base and gains a proton, giving it a positive charge.
b. It acts as an acid and loses a proton, giving it a negative charge.
c. It is oxidized, and tends to act as an electron acceptor in redox reactions.
d. It remains neutral, like water, and does not have a charge.
b. It acts as an acid and loses a proton, giving it a negative charge.
Enzymes that readily break starch apart cannot hydrolyze the glycosidic linkages found in cellulose. Why is this logical?
The geometry of the bonds is different, and the shapes of enzyme active sites are highly specific.
Hairpins and stem-and-loop patterns make up what part of RNA’s structure?
Secondary.
How does the structure of an amino acid enable it to play its most important roles in cells?
The presence of carboxyl and amino groups gives it the ability to form peptide bonds, and its side chain gives it unique chemical properties.
In animals the role of carbohydrate polymers is primarily:
Energy storage
In the context of chemical evolution, DNA’s structure is interesting because it suggests a possible copying mechanism. What about DNA’s structure facilitates copying?
The strands of the double helix are complementary.
The term ribozyme describes what property of RNA molecules?
a. Single-stranded
b. Catalytic
c. Its shape
d. The fact that part of RNA molecules can be double-stranded similar to DNA
b. Catalytic
What is the difference between a ribonucleotide and a deoxyribonucleotide?
Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit.
Which of the following best describes primary structure in proteins?
a. It is the number of amino acids present in the complete protein.
b. It is the number of peptide bonds in the complete protein.
c. It is the sequence of amino acids in the complete protein.
d. It is the number of α-helices and ²-pleated sheets in the complete protein.
c. It is the sequence of amino acids in the complete protein.
Which of the following nitrogenous bases is found in RNA, but not DNA?
a. Thymine
b. Adenine
c. Uracil
d. Guanine
c. Uracil
Which of the following sugars might have the formula C6H12O6?
a. Triose
b. Pentose
c. Hexose
d. Heptose
c. Hexose
