Ap Bio Ch 1-3, 55
13. Why do atoms bond?
to become more stable and fill their outer energy levels (octet rule - to be like the nobles)
44. How can you tell a biological molecule is a lipid?
Lipids are insoluble in water and have a high proportion of nonpolar carbon-hydrogen bonds. They are composed of glycerol and fatty acids.
1. How does organismal behavior demonstrate an emergent property of an organism's physiology (normal functions - influenced by hormones, nerve cells, and other internal factors)?
The physiology of an organism is the normal daily functions that the organism does. Like, breathing and eating. Behavior shows emergent properties of physiology because it comes as a result of physiology. Ex: Humans who don't ordinarily kill, will kill animals or even other humans of they are hungry and need energy. Also, back in the day, people followed herds for food and they made fire when they were cold.
47. Chemical differences between carbohydrates and lipids
The ratio of Carbon atoms to Hydrogen atoms in fats is twice the ratio in carbohydrates, making lipids, much more efficient for storing chemical energy lipids- nonpolar, hydrophobic, insoluble in water, no monomer, glcyerol backbone bonded to fatty acid chains carbohydrates - made up of sugars
29. Explain the relationship between the dissociation of water and the pH of a particular aqueous solution.
The stronger the acid or base, the more it dissociates in water.
52. How does the structure of the "R" group affect the properties of a particular amino acid?
The structure of the R group determines the unique properties of amino acids. The 20 amino acids are grouped into 5 chemical classes, based on their R group: 1. Nonpolar amino acids often have R groups containing CH2 or CH3 2. Polar uncharged amino acids often have R groups with oxygen or -OH 3. Charged amino acids have R groups that contain acids or bases that ionize. 4. Aromatic amino acids have R groups that contain an organic (carbon) ring with alternating single and double bonds. Also nonpolar 5. Amino acids that have special functions have unique properties. Ex: Methionine is usually the 1st amino acid in a chain. Proline causes kinks in chains. Cysteine links chains together.
High heat of vaporization
Many hydrogen bonds must be broken for water to evaporate and when hydrogen bonds break they absorb heat. Therefore, water cools as it evaporates and it can cool body surfaces
35. Why are molecules that contain carboxyl groups acidic?
Molecules containing carboxyl groups (COOH) are acidic because when carboxyl groups ionize, they release/donate hydrogen ions (H+) making them acids.
41. Explain the relationship between monosaccharides, disaccharides, and polysaccharides.
Monosaccharides are simple sugars and are composed of one sugar. They are often used to form larger molecules. Disaccharides are formed by linking two monosaccharides together. Polysaccharides are longer polymers made up of three or more monosaccharides that have been joined through dehydration synthesis.
17. How do the properties of a compound like NaCl illustrate the concept of emergent properties?
Na - metal Cl - poisonous gas NaCl - cyrstaline solid that is edible
Cognitive behavior
Thinking, analyzing situations and problem solving
Tertiary Structure and bonds involved
""whole molecule folding" final 3D shape of the polypeptide. Determines how regions of secondary structure are further folded in space to form the final shape of the protein. Driven by: hydrophobic exclusion, ionic bonds between R groups, and disulfide bonds (covalent bonds between two cysteine R groups) lock particular regions together. Final folding is determined by primary structure and the chemical nature of its side groups Stabilized by: hydrogen bonding between R groups of different amino acids, electrostatic attraction between R groups of different charges (also called salt bridges), hydrophobic exclusion of nonpolar R groups, and covalent bonds in the form of disulfides. No holes in interior of proteins. unique shapes of R groups allow them to fit precisely. Van der Waals forces help stability
Secondary structure of proteins and bonds involved
"local folding" The peptides (amino acids) from hydrogen bonds with each other. The CO group of one and HN group of another (groups come from the peptide backbone) form weak hydrogen bonds that help to support the structure of the peptide chain. These bonds/interactions determine whether the secondary structure. There are 2 kinds: a helix (coils, cylindrical) and B pleated sheets (planar). There can be a mix of these in one protein.
23. Describe how to identify if a molecule is polar or nonpolar.
Polar molecules have large differences in electronegativity in the atoms that are sharing electrons, so the electrons are shared unequally and the sides of the molecule have slight charges. They dissolve in water. Nonpolar molecules contain relatively similar electronegativities, so the electrons are shared equal, and there is no charge.
Water as a good solvent
Polar water molecules are attracted to ions and polar compounds, making these soluble. Water's polarity also causes hydrophobic exclusion. Important for life because many molecules (polar, ions) can move freely in cells, permitting a diverse array of chemical reactions. Also important, because it helps shape proteins.
19. Describe the periodic location, atomic number, number of valence electrons, and biological utility of S,P,O,N,C,H, Ca, K, Na, & Cl.
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56. Explain how the structure of proteins and nucleic acids allow for their biological functions.
Proteins: Because there are 20 different amino acids that can be assembled in any order, there are so many different shapes proteins can have. The shape of the protein determines its function. Example: The shape of hemoglobin enables it to move through human veins and arteries transporting oxygen and carbon dioxide. Nucleic Acids: The weak hydrogen bonds between nitrogen bases in DNA make it easy to separate strands and replicate them. The fact that DNA strands are complementary also helps for reproduction of cells. (mitosis and meiosis)
2. Explain the difference between proximate and ultimate explanations for a particular behavior.
Proximate - immediate mechanisms that enable a specific behavior to occur. How? What? Ex: a male songbird sings during the breeding season because of an increased level of testosterone, which binds to receptors in the brain and triggers the production of song. Ultimate - evolutionary reason for the behavior. Why? Ex: a male songbird sings during the breeding season to defend territory from other males and to attract a female for reproduction.
18. Why are radioactive elements useful for the study of biological systems?
Radioactive isotopes can be used to label or tag a specific molecule and follow its progress either in a chemical reaction or in living cells and tissues. When a patient is injected with a radioactive element, a special camera can take pictures of the internal workings of the organ. They can be used to identify abnormal bodily processes. This is possible because some natural elements tend to concentrate in certains parts of the body; iodine in the thyroid, phosphorus in the bones, potassium in the muscles.
37. How large of a change to the structure of an organic molecule has to be made for that molecule to have a major difference in its effect on a living system?
A very small change can completely change the function of a molecule, thus changing its effect on a living system. So basically, any change at all
10. Describe the evolutionary explanation for the emergence of agnostic and altruistic behaviors.
Agnostic - organisms have to be able to protect themselves against competition and prey in order to survive. Altruistic -some genetically unrelated individuals may form "partnerships" in which mutual exchanges of altruistic acts occur because they benefit both participants => partners are willing to give aid at one time and delay "repayment" for the good deed to a time in the future when they themselves are in need => partnerships are stable because "cheaters" (nonreciprocaters) are discriminated against and do not receive future aid => known as reciprocal altruism For kin selection, if an organism sacrifices themselves for a kin member, their genes can still be passed down through their families.
12. Explain the relationship between matter and energy.
Any substance in the universe that has mass and occupies space is defined as matter. Energy is a property of matter and all matter has it. Energy is the ability to do work. The mass of an object, a key characteristic of matter, is really a measure of its energy. Matter can be converted to energy and vice versa. For example, plants use sunlight to perform photosynthesis, which converts light energy into matter.
57. Explain why directionality and sequence are crucial for the structure and function of proteins and nucleic acids.
Sequence - In nucleic acids, the specific sequence of nucleotide bases determines the genetic information that DNA stores. For RNA, the sequence directs protein synthesis. In proteins, the sequence of amino acids ultimately determines the overall shape of the protein and therefore the function. Directionality -Nucleic acids have ends: the 5' phosphate end and the 3' hydroxyl end direct which nucleotides will be added during DNA synthesis and the direction in which the process occurs. .....
46. How are triglycerides, phospholipids, and steroids similar? How do they differ?
Similarities - hydrophobic, lipids, nonpolar molecules, insoluble in water Triglyceride - molecule with 3 fatty acids bonded to a glycerol backbone; main function = long term energy storage Phospholipids - molecule with 2 fatty acids and a phosphate attached to a glycerol backbone. (often with another molecule on the phosphate) important for cell membranes, (polar head + nonpolar tails = phospholipid bilayer) Steroids - composed of 4 carbon rings and a functional group, serve as hormones, are in most animal cell membranes
42. Why are starch and glycogen useful as energy storage molecules, while cellulose is useful for structure and support? Why isn't cellulose easily broken down?
Starch and glycogen are useful for energy storage because their structure allows them to be easily digested by organisms. As the bonds between the α-glucose units are broken with the help of starch-hydrolyzing enzymes, energy is released. The structure of cellulose makes it good for structure and support. The β-glucose units that make up cellulose make tough fibers when linked. Most organisms do not have enzymes that can break the bonds between two β-glucose units because they only recognize α linkages.
Nucleotide polymer (nucleic acid) structure
Backbone = bonds between pentose sugar of one nucleotide and a phosphate group of another. Bond is formed through dehydration synthesis and is called a phosphodiester bond. Nitrogen bases hang off the backbone and bond between strands/backbones. A::T or A::U (2 H bonds) and G::C (3 H bonds)
3. Why does behavior require communication?
Because organisms rely on each other and the environment to survive. Reproduction can only occur when organisms communicate through the release of hormones or a certain behavior. Organisms of the same species communicate to help each other find food and necessities or to mark their territory.
49. Why are proteins the most complex biological molecules?
Because they have many different functions based on their structure. The structure of a protein depends on the sequence of amino acids and there are 20 different amino acids, which can be assembled in any order, so there are a lot of ways a protein can be folded. This is why proteins have many functions which are categorized into 7 main functions: defense, transport, support, enzyme catalysis, motion, regulation, and storage
25. Why are living things mostly made of water?
Because vital chemical reactions take place in water, and water is necessary to sustain life because of the important properties, like adhesion, and evaporative cooling. Water is a good solvent, so many molecules can move freely and interact in water.
48. Explain the roles of carbohydrates and lipids in biological systems.
Carbohydrates are well suited for short term energy storage. In humans, glucose circulates in blood as a monosaccharide. Disaccharides serve as transport molecules in plants and provide nutrition to animals. Polysaccharides provide energy storage and structural components. Chitin in arthropods and insects provides an exoskeleton. Cellulose gives support in plant cell walls. (1. quick energy-> short term energy storage, 2. raw materials -> structural materials) Lipids provide long term energy storage. The have large numbers of C-H bonds which are strong covalent bonds and release a lot of energy when broken. They are also useful in the formation of cell membranes (phospholipids) and they act as chemical messengers in the body (hormones=cholesterol and sex hormones).
40. How can you tell a biological molecule is a carbohydrate?
Carbohydrates contain carbon, hydrogen, and oxygen in the molar ratio 1:2:1. The empirical formula for carbohydrates is CH2O. The monomers of carbohydrates are sugars.
32. Why is carbon central to the structure of all biological molecules?
Carbon can form up to 4 covalent bonds with other carbons atoms, phosphorus, oxygen, nitrogen, and sulfur. It can make many different shapes, such as straight chains, branches, rings, coils, tubes, and balls.
58. Explain how nucleic acids and proteins function in storage and expression of biological information.
Certain proteins, such as ferritin, casein, and calmodulin, have the function of ion-binding. They bind and store various ions, including iron and calcium. Proteins are responsible for most of our appearances and bodily functions. Nucleic acids store information in the sequences of nucleotides. DNA encodes the genetic info and uses it to make proteins.
27-28. Special Properties of Water (the following 6 cards also come from these two questions - structure and usefulness)
Cohesion and Adhesion Good solvent Lower density as a solid high specific heat high heat of vaporization dissociation of water molecules (ions)
7. How can natural selection act on innate and learned behaviors?
The innate and learned behaviors that are beneficial to an organism's survival will most likely be passed down to future generations. The behaviors that are harmful will not be passed down because the organism will not be able to survive long enough to reproduce.
55. Explain the three major structural differences between DNA and RNA.
DNA - double helix, pentose sugar = deoxyribose, uses thymine (T) RNA - single helix, pentose sugar = ribose, replaces T (thymine) with U (uracil)
20. Describe how energy interacts with atoms.
Energy holds electrons to the nucleus. When atoms gain energy, electrons are moved to a higher energy level. When the electrons move back down, they release the same amount of energy in a photon.
Types of innate behavior
Fixed action patterns - stereotypical behaviors that are triggered by a stimuli. Ex: goose rolling egg Imprinting- forming of social attachments to other individuals or develop preferences that incline behavior later in life. Ex: goslings follow the first thing the see after hatching.
43. How do herbivores solve the problem of cellulose digestion?
Herbivores have evolved a mechanism to digest cellulose. These organisms have symbiotic bacteria and protists in their digestive tracts that provide the necessary enzymes for breaking the β linkages in cellulose, enabling access to energy.
30. Describe how the properties of water demonstrate the concept of emergence.
Hydrogen and Oxygen are gases at room temperature when they are separate. When together, they become liquid at room temperature and have all of the social qualities of water.
54. How can the structure of a protein be changed/denatured?
If a protein's environment changes, the protein can change shape or unfold completely. These are changes in pH, temperature, or ionic concentration of the surrounding solution. Denatured proteins are usually biologically inactive, particularly in enzymes.
45. Chemically, what is the difference between a saturated fat and an unsaturated fat? How does this difference affect the properties of the molecules?
In a saturated fat, all of the carbons are bonded to two or more hydrogens. In an unsaturated fat, there is at least one double bond between carbons, meaning that one or more carbons are only bonded to 1 hydrogen. Having double bonds changes the behavior of the molecule because free rotation cannot occur about a C=C double bond as it can with a C-C single bond. This mainly affects melting point: saturated are solid, while unsaturated are liquid at room temperature.
4. Explain the difference between innate and learned behaviors.
Innate behaviors are instinctive and automatic. They are controlled by genes and are inherited. Learned behaviors require interaction with the environment or with other organisms to occur.
21. Describe the differences between ionic and covalent bonds.
Ionic bonds involve the transfer of electrons (oxidation and reduction). Form between a nonmetal and a metal. Covalent bonds involve the sharing of electrons between two or more atoms. Form between nonmetals
22. Describe how to identify if a substance is covalent (molecular) or ionic. What are the basic differences between these substances.
Ionic compounds form crystalline solids at room temp. They dissolve in water, have high melting and boiling points. They are hard and brittle. They have strong bonds, are electrically reactive (conducts electricity), and electron orbitals are separate. Covalent -liquid or gas at room temp, insoluble in water, low melting and boiling points, bad conductors, relatively soft, weak bonds, shared electrons, orbitals overlap
33. Explain the concept of an isomer. As the number of carbon atoms in a molecule increases, what happens to the number of possible isomers of that molecule?
Isomers are organic molecules that have the same molecular or empirical formula and exist in different forms. For example: glucose and fructose have the formula C6H12O6, but their structures are different making them structural isomers. As the number of carbon atoms increases, the number of possible isomers also increases because there are more possible places to fill with other molecules.
Primary structure of Protein and bonds involved
It's the sequence of amino acids. Dehydration synthesis creates peptide bonds (which are covalent btw) between two amino acids. The peptide bonds act as a partial double bond and inhibit free rotation, which affects the structural character of the coils and other shapes formed by chains of amino acids.
Carbohydrates - basic skeleton (empirical formula), monomer, overall function, main 4 examples in bio and specific functions
empirical formula - CH2O monomer - sugar (glucose) function - quick energy, structure starch - energy storage in plants glycogen - energy storage in animals cellulose - structure, plant cell walls chitin - structure in anthropods and fungi; exoskeleton of insects and crustaceans
Proteins - function (at least 4), monomer, examples
function - enzyme catalysis, transport, signals, defense, structure, receptors, storage, motion, regulation (signals and receptors) monomer - amino acids examples - hemoglobin carries O2 and CO2 in blood, keratin forms hair and nails, insulin regulates levels of blood sugar, proteases is an enzyme that breaks down proteins
Nucleic Acids - types, function, monomer
function - information storage, transfer DNA - encodes genes RNA - gene expression, transfer monomer - nucleotide
Lipids - monomer, structure,function, examples
monomer - n/a structure - made up of a glycerol and fatty acid chain (lots of H-C bonds) function - long term energy storage, membranes, hormones (cholesterol and sex) examples - steroids, sex hormones, phospholipids, cholesterol
36. Why are molecules that contain amino groups basic?
because amino groups (NH2) accept hydrogen ions (H+) making the whole molecule basic
38. Why is Carbon such a versatile atom?
because it can form up to 4 covalent bonds even with itself, making it able to form chains, balls, coils, tubes, branches, etc.
34. Why is it significant that all biological systems use L-amino acids and D-sugars?
because these two molecules are important for life. The structure of these molecules allow them to perform certain functions that are essential for living systems. If the the other forms are in a living system, then they do not perform the correct function, and life could be harmed or destroyed.
14. What is the cause of molecular polarity?
Unequal sharing of electrons cause by large differences in electronegativity.
24. What is the cause of radioactivity?
Unstable atoms give up energy in the form of radiation. The nucleus breaks up into elements with smaller atomic numbers which causes the nucleus to have an excess of energy, which it shoots off.
Cohesion and Adhesion (water's structure and usefulness)
cohesion - the polarity of water molecules allows them to be attracted to each other (hydrogen bonding). Cohesion holds water molecules together. Responsible for making water a liquid at moderate temperatures and for water's surface tension. adhesion - the polarity of water molecules accounts for attractions with other polar molecules. Water adheres to any substance with which it can form hydrogen bonds. Responsible for capillary action and for transpiration.
Dissociation of Water
Water can form ions. Sometimes, water spontaneously ionizes, and an H+ separates from OH-. The concentration of these affects pH.
High specific heat
Water resists temperature change because it hydrogen bonds absorb heat when they break and release heat when they form. Important for life because water moderates temperature in cells and in the outside world
Nucleotide Structure
pentose sugar (5C), phosphate group (negatively charged, polar), nitrogen base (C-N) ring with either a purine (A,G) or a pyrimidine (T,C,U)
Quaternary Structure
The arrangement of polypeptide subunits. Only found in proteins with multiple polypeptides. Interfaces where the subunits touch our often nonpolar and are important for transmitting information between the subunits about individual subunit activities. There are hydrophobic interactions that also help to determine structure.
Types of learned behavior
Habituation - non-harmful stimulus is repeated and organism learns to ignore it Conditioning- type of learning in which a stimulus is associated with a particular behavior Classical conditioning- when two stimuli are displayed together repeatedly, and organism starts to associate them together (Pavlov's dogs) Operant conditioning - associating a behavior with a reward or punishment (rats pushing levers to get food pellets)
Lower density as a solid
Ice floats! Water forms crystals when frozen which are relatively far apart. Water freezes from the top down not the down up. Important because it enables life to survive in lakes and oceans during the winter.
39. How are macromolecule polymers assembled from monomers? How are they broken down?
Macromolecule polymers are assembled by the bonding of monomers. For monomers to bond, an -OH group is removed from one monomer and a hydrogen atom is removed from another in a process called dehydration synthesis. For every subunit added to a macromolecule, one water molecule is removed. Macromolecule polymers are broken down by breaking bonds between subunits. This process is called hydrolysis and is the reverse of dehydration. During hydrolysis, a hydrogen atom is added to one monomer and a hydroxyl group to the other, breaking the covalent bond between the monomers.
11. How common are the elements that living systems are made out of?
carbon, nitrogen, oxygen, phosphorous, sulfur, hydrogen all highly common hydrogen is the most common element in the universe oxygen makes up 20% of the atmosphere phosphorous is the most common component of dirt (which is everywhere) nitrogen makes up more than 79% of the atmosphere sulfur has been playing a major role in all volcanic activity for million of years they didn't give an example for carbon but its everywhere people