Flash Card Review topics for Biochemistry and Evolution
AP BIO 9/2011
1. Describe an example of a structure-function relationship at the molecular level in animals.
Proteins
The function of a protein is determined by its shape. Also, the shape of a protein is determined by its sequence of amino
acids. The function of a protein is directly dependent on its three dimensional structure.
Examples of this:
Structural proteins have to be large. They also must be insoluble in water so the side groups on the amino acids
that are used are generally non polar.
However, things like enzymes, carriers and antibodies, are a little bit smaller than structural proteins. In order
for them to move through the blood and cell fluids, they must have polar side groups to allow them to be more
soluble.
The tertiary structure or the quaternary structure of a protein can provide important clues about how the protein
performs its function. The sequence of amino acids may determine whether the protein functions as an antibody,
enzyme, hormone, structural, storage, transport or other types of proteins.
Explanations:
Antibodies are specialized proteins involved in defending the body from “foreign invaders.
Enzymes are proteins that speed up chemical reactions in the body, etc.
Hormonal Proteins are messenger proteins which help to coordinate certain activities in the body.
Structural Proteins are fibrous and stringy. They provide support. (ex: in connective tissues such as tendons and
ligaments)
Storage Proteins store amino acids.
Transport proteins move molecules from one place to another around the body.
Each of these different types of proteins above has a different structure which gives them a different function.
2.
Co-evolution: A scenario where two organisms trigger evolution in each other by selecting for traits
that allow them to interact. For example: a flower that lives in the same area as a hummingbird is
selected to have color that a hummingbird can see well, as well as nectar that a hummingbird can eat,
and a shape that allows the bird to drink the nectar. At the same time, a hummingbird evolves a beak to
reach into the flower and drink nectar, and the ability to position itself in such a way that it can drink
the nectar in mid air. The two organisms evolve together.
3. Cohesion: A property of certain molecules to stick to other molecules of the same type. Water is
strongly cohesive because water molecules form up to four hydrogen bonds with other water molecules.
This relates to biochemistry because it is responsible for many of the properties of water. This is the
reason water beads. It is also the reason for surface tension and it aids in the transfer of water up the
stems of plants (along with adhesion.)
4.
hydrophilic- when a substance has an affinity for water because of it's polarity.
5. Discuss the difference in structure between cellulose and starch and how that affects
digestion in animals.
-Starch is a storage polysaccharide with 1-4 linkages of alpha glucose monomers and cellulose is a
structural polysaccharide with 1-4 linkages of beta glucose monomers.. Enzymes that digest starch by
hydrolyzing its alpha linkages can't hydrolyze the beta linkages in cellulose, and vice versa. So very few
organisms can digest cellulose.
6. Q: Explain how pesticide resistence occurs in insects.
A: When pests reproduce, the usually produce a huge number of offspring. That cause chances for random
mutations to increase. Therefore, this leads to differential reproductive success, meaning that individuals who
have the necessary traits to reproduce will tend to leave more offspring. Since the pests who aren't able to resist
the pesticides will die, that will leave the next generation with more pesticide-resistant pests. Over time, the
match between pests with favorable adaptations and their environment will increase.
7. Explain the difference between Darwin and Lamarck's theories.
Darwin
Darwin's theory of natural selection (better known as "survival of the fittest") is the basis of Darwinism. Darwin's
theory proposes that evolution progresses through natural selection, which is the differences in survival and
reproduction among individuals in a population as a result of their interaction with the environment.
Lamarck
Lamarck's theory for evolution included three major ideas 1) Use and disuse: describes how body parts of organisms can develop with increased usage, while unused parts
weaken. This idea is the only one that is actually correct. Ex: This theory is observed among athletes who train for
competitions.
2) Inheritance of acquired characteristics: describes how body features acquired during the lifetime of an organism
could be passed on to offspring. But this idea is incorrect because only changes in the genetic material of cells can be
passed on to offspring.
3) Natural transformation of of species: describes how organisms produce offspring with changes, transforming each
subsequent generation into a slightly different form toward a higher order of complexity. Species do not become extinct or
split and change into two or more species. This idea is incorrect.
8. Discuss the levels of protein structure and the role of specific bonds at each level:
The Primary structure of a protein is its unique sequence of amino acids. One of twenty different amino acids is
linked together via peptide bonds (covalent bond between NH2 of one amino acid and COOH of another) to form long
chains. The sequence is determined by genes (DNA) and a slight change could affect the protein’s structure and function.
The Secondary Structure of a protein is the repeated folding and coiling of the polypeptide chains that add to the
protein’s overall shape. The folding is caused by hydrogen bonds between the polypeptide backbones. The slightly
positive hydrogen atom attached to the nitrogen is attracted to the oxygen of a nearby peptide bond. Although these bonds
are weak, the vast numbers of them in a polypeptide chain are able to hold the shape. There are two secondary structures:
 α helix: Helical shape held together by hydrogen bonding between every fourth amino acid.
 β pleated sheet: Two or more regions of polypeptide chain lying side by side connected by hydrogen
bonds between parts of two parallel polypeptide backbones.
The Tertiary Structure of a protein is the overall shape of a polypeptide resulting from interactions between side
chains (R groups) of the various amino acids. They are held in place by:
 Hydrophobic interactions: As a polypeptide folds into its shape, amino acids with hydrophobic side
chains end up in a cluster at the core of the protein, out of contact with water. When they are clustered
Van Der Waals interactions help hold them together. At the same time hydrogen bonds between polar
side chains and ionic bonds between +/- side chains stabilize the structure.
 Disulfide bridges: These form when amino acids with sulfhydryl groups on their side chains are brought
closer together by the forming of a protein. The sulfur of one covalently bonds to the sulfur of another,
anchoring the 3d shape.
The Quaternary Structure of a protein is the overall protein structure that results from combination of
polypeptide subunits. Only then does the polypeptide become a functional protein. This structure is held in place by
Hydrophobic Interactions.
9. Hydrolysis: the reverse of dehydration synthesis. H2O is split into H+ and OH- where it is then attached to the
ends of a now split polymer. This action requires enzymes and releases energy.
10. Explain convergent evolution. Give an example.
A: Convergent evolution is when organisms that are not even closely related to one another gain traits that are
similar because of how they adapt to their environment. An example of convergent evolution is shown with
dolphins and sharks. They have similar effects yet they are not even the same species.
11. Describe how the physical properties of water contribute to transpiration.
Answer: Transpiration is when water molecules evaporate out of the pores of plant leaves and other
parts. Water's many bonding properties allows this to happen. First, the water seeps through the
ground and is sucked up through the roots of the plant using the property of adhesion, water
molecules attracting to non-water substances. Once the water is in the plant's systems, it is
transported up the stem using adhesion to get up the pipes, but also cohesion, water molecules
attracting to other water molecules, to keep the water moving in one unit. When water evaporates out
of the pores, more water moves up the stem and takes its place.
12. "Explain how reproductive (sympatric) isolation leads to speciation."
Reproductive isolation can be defined as "the existence of biological factors (barriers) that impede members of
2 species from producing viable, fertile offspring." Speciation, can be defined as "the process by which one
species splits into two or more species." The uniqueness about sympatric speciation is that it occurs in
populations that live in the same geographic area. How can a species split, though, if the populations live in
close proximity and interbreed constantly? There are three methods that allow reproductive isolation to occur in
sympatric speciation.
First, polyploidy is when an accident occurs during cell division and a cell is given an extra set
of chromosomes. This mutation causes a cell to be genetically different from the parent species, even though
they live in close range, and therefore creates a different species all together.
Second, habitat differentiation is when a sub-population exploits a habitat or resource that is not used by that
parent population. The sub-population starts using a resource or living in a habitat that the parent population
doesn't use or live in, and through natural selection the sub-population evolves and adapts to this
new environment or use of resources, creating a new species.
Third, sexual selection occurs when, most often, females choose males based on certain physical characteristics.
The selectivity of females in choosing mates can keep the gene pools separate where they would otherwise
merge and form hybrids.
Summary: Reproductive (sympatric) isolation leads to speciation through the methods of polyploidy,
habitat differentiation, and sexual selection.
13. Continuity and Change
List and describe pre-reproduction barriers that lead to speciation
Habitat Isolation: Two species that occupy different habitats within the same area may
encounter each other rarely
Temporal: Species that only breed during different times of the day, season, or year cannot
mix their gametes
Behavioral: Courtship rituals that attract mates and other behaviors are unique to each species
Mechanical: Mating is attempted, but morphological differences prevent its successful
completion
Gametic: Sperm of one species may not be able to fertilize the eggs of another species
14. Discuss how the structure of a protein affects enzyme activity
A protein needs to be properly folded in order to function effectively. Since there are 20 different types of
amino acids, each with its own properties, it is important to have them in the correct order in the primary
structure in order for the enzyme to function. If the amino acids are in the wrong order or if even one amino
acid is switched to another the structure can change in the tertiary structure. For example in sickle cell anemia a
single hydrophilic amino acid is switched to a hydrophobic amino acid, and the entire shape of the protein
changes. This change can cause major health problems in the subject. So the proteins structure has to be precise
otherwise it could possibly not function.
15. Explain how the anatomical record supports evolution. Give an example.
Many related species have similar, underlying characteristics and structures. These similarities from a common
ancestor are known as homologies. These homologies support evolution because they prove the existence of a common
ancestor, confirming that all “children specie” have evolved from that ancestor. Particularly, anatomical homologies are
easy to identify. Closely-related species not only have similar looks and habits but also very similar anatomies. These
homologies may be distorted by time, but the base features are the same. For example, the forelimbs of all mammals,
from the fins of whales to the wings of bats, share the same bone arrangement.
16. Define “hydrocarbon” and explain its relationship to biochemistry.
Hydrocarbons are compounds made only of carbon and hydrocarbon atoms; they form the basis of organic
chemistry. Hydrocarbons are a line or ring of carbon atoms with hydrogen atoms or hydrocarbon chains attached to
every bonding point not bonded to by another carbon. These hydrocarbons are very important in chemistry, specifically
biochemistry, because they form the base structure of more complicated organic compounds that are very vital to the
functioning of plants and animals. In fact, these carbon compounds are present and important in almost every body
process and take up 25% of the body’s composition.
17. Describe an example of a structure-function relationship at the tissue level in animals.
In epithelial tissue, some cells have microvilli, small projections, which increase the surface area for greater
absorption. Other cells have cilia, which move mucus and trapped particles from the trachea to the mouth.
In connective tissue, fibrous connective tissue is made of fibers in parallel bundles. These parallel bundles give
the tissue non-elastic strength. Such tissue securely connects muscles to bones or bones to joints.
18. Describe how the physical properties of water contribute to plasma membrane structure.
Plasma membranes are composed of a phospholipid bilayer. Each individual phospholipid is
composed of two nonpolar fatty acid chains (the "tails") attached to a polar "head" (containing choline,
phosphate, and glycerol). Water is a polar molecule--it dissolves polar substances by surrounding charged
particles and "pulling" them into solution. This causes the tails of each phospholipid to be hydrophobic while
the head to be hydrophilic. Thus, the "water-fearing" fatty acid tails align inwards (away from water) and the
"water-loving" heads face outward (in contact with the water). The phospholipids form a bilayer, with the tails
facing each other on the inside and the heads facing the water--this is the plasma membrane.
19. Explain the 5 principles of natural selection.
-- 1. An important motive for species is to survive and reproduce, to pass on the genetic information. Because
this is such a prime motive, most species tend to over produce, too much for the environment.
2. Due to the sudden overpopulation, the environment does not have enough resources for the species, which
increases competition within the population. This increased competition leads to the death of many organisms.
3. The organisms that survived this competition were found to be more suited for their environment.
4. This is where the phrase "survival of the fittest" comes into play. The organisms that were better suited to
their environment were more likely to survive.
5. Those that exhibited more desirable characteristics will reproduce and pass those characteristics onto their
offspring.
20. List and describe post-reproductive barriers that lead to speciation.
--Reduced Hybrid Variability: The genes of different parent species may interact in ways that impair the hybrid's
development or survival in its environment.
Reduced Hybrid Fertility: Even if hybrids are vigorous, they may be sterile. If the chromosomes of the two
parent species differ in number or structure, meiosis in the hybrids may fail to produce normal gametes. Since
the infertile hybrids cannot produce offspring when they mate with either parent species, genes cannot flow
freely between the species.
Hybrid Breakdown: Some first-generation hybrids are viable and fertile, but when they mate with one another
or with either parent species, offspring of the next generation are feeble or sterile.
21. Describe a function that requires the conformational change of a protein.
A) The cooperative process in which hemoglobin maximizes its ability to transport oxygen is a conformational
change of the protein. This conformational change is classified by the functional group, or ligand, that attaches
to the metal ion, iron.
22. Glucose
A) Glucose is a very abundant, important monosaccharide (simple sugar) or carbohydrate in biochemistry. It
has a chemical make up of 6 carbons, 12 hydrogen, and 6 oxygen. It is also the base for many disaccharides and
polysaccharides.
23. Explain Ernst Mayr biological species concept
A: The Ernst Mayr biological species concept defines a specie as a group of individuals who can interbreed and
produce offspring who are also able to produce offspring, but cannot produce fertile offspring among other
groups. Cockatoos are a different species from humans since they can't produce fertile offspring, despite
anyone's best efforts. A horse and donkey CAN produce a mule as an offspring, but mules are not separate
species due to their general sterility.
24. 5 main principles of natural selection:
1. Concept of Variation. (different physical features like fur, eyes, height, etc.)
2. Outcomes of Variation- variations will increase the likelihood of an organism surviving. (green beetles in grass
might survive better than brown beetles in same environment), when organisms survive, they tend to reproduce
more
3. Individuals that are better suited to their environment tend to overproduce. This leads to competition
among the population (fight for water, food)
4. Individuals that survive will tend to pass their successful traits to offspring and future generations will benefit
from them.
5. Over time, advantageous traits will accumulate and eventually all individuals of the future population will
benefit from the variations.
25. Hydrophobic:
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Greek hydro- for water and phobos for fear.
Water-fearing molecules or particles.
Anything that is hydrophobic lacks an affinity for water.
It moves away from or can be repelled by water.
They also have a difficult time dissolving in water (if the molecule can dissolve at all).
Usually the molecule is non-polar.
Examples: waxes, oils, fats, steroids and most other greasy substances
26. Describe the 5 agents of evolutionary change acting on a population:
Natural Selection: results in alleles being passed to the next generation in proportions different from their
relative frequencies in the present generation. Individuals with variations that are better suited to their environment
tend to produce more offspring than those with variations that are less suited.
Genetic drift: is the unpredictable fluctuation in allelic frequencies from one generation to the next. The
smaller the population, the greater the chance is for genetic drift. This is a random, nonadaptive change in allelic
frequencies. Two examples are: founder effect and bottleneck effect
Founder effect: a few individuals become isolated from a larger population and establish a new population
whose gene pool is not reflective of the source population.
Bottleneck effect: a sudden change in the environment (for example, an earthquake, flood, or fire) drastically
reduces the size of a population. The few survivors that pass through the restrictive bottleneck may have a gene pool
that no longer reflects the original population’s gene pool. Example: The population of California condors was reduced
to nine individuals. This represents a bottlenecking event.
Gene flow: occurs when a populations gains or loses alleles by genetic additions to and/or subtractions from the
population. This results from the movement of fertile individuals or gametes. Gene flow tends to reduce the genetic
differences between populations, thus making populations more similar.
27. Geographic isolation:
is a phenomena wherein a population is split and isolated from itself, separating the population into two.
The different populations are subject to different environments and, as such, evolve in different ways.
Eventually the original population is now two different populations of different species.