Final Review Part I: Lectures 1-10

Question 1

What is? Inductive Reasoning

Answer 1

Predictive generalizations that are based on a large number of observations. EX: We predict that the sun will rise in the east tomorrow morning based on past experiences of the sun doing just that.

Question 2

What is? Induction Based Science

Answer 2

makes predictions based on past
experience; an example of induction-based science is the development of “Cell
Theory”, a series of generalizations about cells based on observing many cells

Question 3

Hypothesis Based Science

Answer 3

uses deductive reasoning (maybe; there is some
controversy about this); hypothesis-based science gets most of the attention from
philosophers of science

Question 4

Deductive Reasoning

Answer 4

reasoning from more general statements to a
conclusion that must be true; e.g. (from Wikipedia)
1) All men are mortal.
2) Socrates is a man.
3) Therefore, Socrates is mortal.

Question 5

Hypothesis

Answer 5

tentative explanation for an observation

Question 6

Hypothetico-Deductive Method

Answer 6

one possible description of the method of
hypothesis-based science; hypotheses are tested by the use of experiments; the
outcome of the experiments is predictable based on the hypotheses; if the
outcomes of the experiments are inconsistent with the predictions, then the
hypothesis is rejected (it is wrong/incorrect/refuted/rejected); alternatively, if the
outcome of the experiments are consistent with the predictions for the outcomes,
then we have support for the hypothesis (but support ≠ “proof”)

Question 7

Testable Hypothesis

Answer 7

a hypothesis which can provide testable predictions for

outcomes of experiments

Question 8

Non-Testable Hypothesis -

Answer 8

a hypothesis which cannot provide testable predictions;
such a hypothesis is not necessarily incorrect, the scientific method simply can’t
deal with it

Question 9

Occam’s (Ockham’s) Razor

Answer 9

– If several explanations are compatible with the evidence
at hand, the simplest should be considered the most likely; alternative version:
explanations should be no more complicated than necessary; named after William
of Occam (who was not the inventor of the idea, but who popularized it)

Question 10

Importance of the “Control”

Answer 10

all scientific experiments must have “controls”, which
act as comparisons for “treatments”; without controls it is impossible to know
whether the treatments have had an effect (e.g. would the observed outcome have
occurred even in the absence of the treatment?)

Question 11

Negative and Positive Controls

Answer 11

this difference was not discussed in lecture (i.e. this is
for interest only); negative controls are experiments in which nothing is done or
added (there is no “treatment”); positive controls are controls in which a certain
treatment has a known effect, and this known effect is used to compare with
treatments of unknown effect; almost all experiments have negative controls;
depending on the type of experiment, there may or may not be positive controls
incorporated into the overall design of the experiment

Question 12

Composition of an Atom

Answer 12

nucleus composed of protons (+1 charge) and neutrons (no
charge); electrons (-1 charge) in orbitals around the atom; electrons are much
smaller than protons or neutrons; there are many ways of indicating orbitals in
diagrams; we will diagram orbitals simply as circles around the nucleus

Question 13

The Number of Protons Defines the Type of Atom

Answer 13

e.g. hydrogen (H )atoms have one
proton, helium (He) atoms have two protons, carbon (C) atoms have 6 protons,
oxygen atoms (O) have 8 protons

Question 14

Bonds between Atoms are Based on Electrons

Answer 14

there are possibly single, double or
triple bonds between two atoms; quadruple bonds do not exist; a chemical bond is
based on a pair of electrons, one electron provided by each atom

Question 15

Hydrogen (H)

Answer 15

smallest atom, composed of one electron and one proton; if a H atom
loses an electron, only the proton remains – this is shown as H+
(i.e. “H+” and
“proton” are synonymous; protons are very important in later discussions of
respiration and photosynthesis).

Question 16

Ions

Answer 16

atoms or molecules in which the number of protons ≠ the number of electrons

Question 17

Cations

Answer 17

positively charged ions, in which there are more protons than electrons

Question 18

Anions

Answer 18

negatively charged ions in which there are fewer protons than electrons

Question 19

Hydrogen Bonds (H bonds)

Answer 19

are weak, transient (constantly breaking and re-forming)
bonds, and are a consequence of polar covalent bonds containing H. Liquid water is
the classic example used to illustrate H bonding. Water is a small molecule, and almost
all other molecules of similar size are gases at room temperature. Water is a liquid at
room temperature because of H bonding: the δ+ of the H atoms (δ+ because they are
in polar covalent bonds with O) on water molecule are attracted to the δ- on the O
atoms of other water molecules. Although H bonds are weak and transient, at any
instant in time there are a lot of them. See diagram next page.

Question 20

Electronegativity

Answer 20

the ability of an atom to attract electrons to itself; a fixed property
of atoms

Question 21

Non-Polar Covalent Bond

Answer 21

a chemical bond between two atoms in which electrons in
the bond are shared equally between the atoms; occurs when there are bonds
between like atoms, e.g. O=O, H-H, or between atoms that have very similar
electronegativity e.g. C-H bonds; there are no partial charges associated with
these bonds

Question 22

Polar Covalent Bond

Answer 22

a chemical bond between atoms of moderately different
electronegativity; results in unequal sharing of electrons in the bond, with the
electron air displaced towards the atom with higher electronegativity; results in
partial charges (δ+, δ-
); important polar covalent bonds in biology include: O-H,
N-H, O-C, N-C

Question 23

Ionic Bond

Answer 23

a chemical bond between atoms of greatly differing electronegativity;
electrons in the bond are not shared, but rather the atom with higher
electronegativity takes an electron from the atom with lower electronegativity

Question 24

Polar Molecules

Answer 24

have many polar covalent bonds, and thus have partial charges;
there are degrees of polarity, with the number of polar covalent bonds compared
to other types of bonds determining the degree of polarity; small polar molecules
tend to be highly water soluble

Question 25

Polar Covalent Bonds Containing H

Answer 25

will lead to the possibility for H-bonding – water is | a standard example of H-bonding, with the δ+ of the H atoms is attracted to the δof O atoms on nearby water molecules

Question 26

Hydrogen (H) Bonds

Answer 26

weak transient bonds caused by polar covalent bonds | containing H

Question 27

Water Molecule

Answer 27

polar covalent bonds containing H lead to partial charges, and thus to the possibility for H-bonding; the extensive H-bonding in water causes it to be a liquid at room temperature; other molecules of similar (low) molecular mass all are gases at room temperature (note that molecules other than water can exhibit Hbonding as well; H-bonding is not restricted to water)

Question 28

Water Exhibits Cohesion

Answer 28

due to H-bonding, water molecules are attracted to each other; they stick to each other; this explains the liquid nature of water at room temperature; also explains surface tension

Question 29

Water Exhibits Adhesion

Answer 29

water is attracted to large polar/charged molecules; water is attracted to those molecules, even though the molecules are too large to be dissolved; explains the “meniscus curve” of a graduated cylinder or other glassware

Question 30

Hydrophilic

Answer 30

literally means “water-liking”; hydrophilic molecules are polar and/or charged, and exhibit mutual attraction with water molecules

Question 31

Hydrophobic

Answer 31

literally means “water-fearing”; hydrophobic molecules are composed largely of non-polar covalent bonds (e.g. as fats); hydrophobic molecules exhibit mutual repulsion with water

Question 32

Dissociation of Water

Answer 32

H2O H+ + OHThe dissociation can also be thought of as: 2 H2O H3O+ + OH- (H3O+ = the hydronium ion) Acidity – think of acidity as H+s (protons); high acidity = high [H+] pH – measure of acidity; pH = -log[H+]; pH 7 is considered to be “neutral”, pH < 7 is “acidic”, and pH > 7 is “basic” pH of pure water (no dissolved gases) = 7 pH of lemon juice ~2 pH of household bleach ~12 Hydrochloric Acid – a strong acid; shows complete dissociation, unlike the equilibrium for the dissociation of water: HCl H+ + ClEffect of atmospheric CO2 on the pH of water – CO2 reacts with water to produce carbonic acid, which causes the water to acidify (increase in [H+]): CO2 + H2O H2CO3 H+ + HCO3 - carbonic bicarbonate ion acid

Question 33

Water PH

Answer 33

The pH scale measures the concentration of hydrogen ions (H+) in a solution. (credit: modification of work by Edward Stevens). From OpenStax Biology. Note: the pH of distilled water (= pure water) is 7 only if it is completely pure water. Contact with air, which contains CO2, will cause the water to acidify due to carbonic acid formation.

Question 34

Water Hydrogen Bonding

Answer 34

Cyclic dimer of acetic acid; dashed green lines represent hydrogen bonds. That is, H bonds don’t occur only in water. H bonds are very common, and crop up numerous times in biology, e.g. in the structure of the DNA double helix.

Question 35

Water as a Solvent

Answer 35

the polar covalent bonds of water, which lead to a δ- on the O and a δ+ on the H, cause water to be a polar molecule; as such, water is a good solvent for small polar and charged molecules (which are hydrophilic)

Question 36

Effect of Molecule Size on Water Solubility

Answer 36

the solubility of polar molecules decreases as the molecules get larger; the reasons for the decrease in solubility with larger size are complex and only partially understood

Question 37

Molecules with Mainly C-H and C-C Bonds are not Water Soluble

Answer 37

these molecules do not have partial or full charges, and do not interact with water, i.e. they are hydrophobic and are not water soluble; a common example is vegetable oil, which does not mix with water; water is not a universal solvent

Question 38

Life is Carbon-Based

Answer 38

if you remove the water from an organism, what’s left is mainly carbon; all biological molecules are C-based (although different types of atoms are may be attached to the C-based molecules); the key to understanding the C basis of life is that C is extremely versatile; think of it as a Lego block

Question 39

Carbon atoms always have four bonds

Answer 39

could be four single bonds, two singles and a | double, two double bonds, or a single and a triple bond

Question 40

Carbon Electronegativity

Answer 40

C has a moderate to low electronegativity

Question 41

Non-Polar Covalent Bonds

Answer 41

C-C and C-H bonds are non-polar covalent; C and H have | virtually the same electronegativity

Question 42

Polar Covalent Bonds

Answer 42

C-O, C-N bonds are polar covalent; O and N have higher | electronegativity than C, therefore C will have a δ+ charge while O or N will have a δcharge

Question 43

Carbon-Based Molecules May Exhibit Isomerism

Answer 43

there are three main types of isomerism, listed below (molecules that are isomers have the same molecular formula but different structures)

Question 44

Structural Isomerism

Answer 44

when different molecules have the same molecular formula | but differ in how C atoms are arranged, e.g. C4H10 may be assembled in two ways

Question 45

Cis/Trans Isomerism (part of Geometric Isomerism)

Answer 45

when different molecules have the same molecular formula, but differ in how parts of the molecule are assembled around a C=C bond; based on the fact that C=C bonds are inflexible and do not allow rotation

Question 46

Enantiomers

Answer 46

occur when a C atom has 4 different things attached; this C atom is termed as being “asymmetric” or “chiral”; molecules that are enantiomers have the same molecular formula but are mirror images of each other; a common analogy is that the left and right hands of humans are mirror images of each other

Question 47

Bonds with Carbon can be arranged in three dimensions

Answer 47

if there are four single bonds, the bonds are definitely in three dimensions. Consider methane (largest single component of natural gas), which has the molecular formula CH4. Methane is often drawn as a flat molecule:

Question 48

Structural Isomers

Answer 48

have the same molecular formula but differ in the arrangement of the C atoms. Both molecules shown below have the formula C4H10 (images from Wikipedia).

Question 49

Cis/Trans Isomers (which are a subset of Geometric Isomers)

Answer 49

occur when there is variation in arrangement around a C=C bond. But for cis/trans isomers, both of the isomers have exactly the same atoms joined up in exactly the same order. C=C bonds cannot rotate, thus the two molecules shown below are different molecules with slightly different chemical properties (images from Wikipedia).

Question 50

Enantiomers

Answer 50

occur when there are C atoms with 4 different things attached. These C atoms are called “chiral” or “asymmetrical”. In the example below, the central (chiral/asymmterical) carbon has 4 different things attached to it, and there are two ways to do the attachment. This leads to different molecules that are nonsuperimposable mirror images of each other. Two forms of lactic acid are shown below (image from Wikipedia).

Question 51

Isomerism of Carbon-Based | Molecules

Answer 51

``` Molecules that have the same number and type of atoms arranged differently are called isomers. (a) Structural isomers have a different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c) Enantiomers are mirror images of each other. ```

Question 52

Macromolecules

Answer 52

very large biological molecules; polymers composed of many monomer subunits; synthesized by condensation synthesis (= dehydration synthesis); carbohydrates, proteins and nucleic acids are macromolecules

Question 53

Large Biological Molecules

Answer 53

biological molecules not quite as big as macromolecules, | e.g. lipids are considered to large biological molecules rather than macromolecules

Question 54

Monomer

Answer 54

``` building block (subunit) of a polymer, e.g. monosaccharides are the monomers that are linked together to produce polysaccharides (a polymer) ```

Question 55

Polymer

Answer 55

a large molecule composed of numerous linked monomers; the monomers are linked by covalent bonds

Question 56

Condensation Reaction/Dehydration Reaction –

Answer 56

formation of a covalent bond with the | loss of a water molecule

Question 57

Condensation Synthesis/Dehydration Synthesis

Answer 57

several to many rounds of condensation reactions, leading to the formation of large biological molecules or macromolecules

Question 58

Hydrolysis

Answer 58

break apart with water; opposite of a condensation reaction

Question 59

Hydrolysis of Macromolecules

Answer 59

Why do it? – to remove damaged macromolecules or macromolecules that are no longer needed; the monomer subunits of the macromolecules can be recycled to produce new macromolecules

Question 60

Carbohydrates

Answer 60

sugars or sugar-derived molecules; include monosaccharides (which are monomers), oligosaccharides (2+ linked sugar monomers, but smaller than a polysaccharide), and polysaccharides (100s to 1000s of linked sugar monomers); carbohydrates contain many polar covalent bonds (O-H, O-C) and are thus hydrophilic; smaller carbohydrates are easily water soluble

Question 61

Starch Versus Cellulose

Answer 61

both are glucose polymers; starch is held together by α-1,4 bonds, which the human digestive can break apart and thus access the glucose as an energy source; cellulose is held together by β-1,4 bonds which the human digestive system cannot break apart, hence cellulose (which is a major component of plant cells) is not an energy source for humans

Question 62

Lipids

Answer 62

large biological molecules that mix poorly with water, if at all; fats (which include oils), phospholipids, steroids; fats and steroids are hydrophobic and do not mix with water at all

Question 63

Fats (= Triglycerides)

Answer 63

three fatty acids attached to glycerol (3C molecule); extremely hydrophobic; used as energy storage molecule

Question 64

Saturated Fat

Answer 64

has only C-C bonds in the fatty acids

Question 65

Unsaturated Fat

Answer 65

has a C=C bond in the fatty acids

Question 66

Polyunsaturated Fat

Answer 66

has 2+ C=C bonds in the fatty acids; but the majority of the | bonds are C-C

Question 67

Oil

Answer 67

a fat that is liquid at room temperature (due to C=C bonds in the fatty acids, which introduce kinks/bends and thereby prevent close packing of the molecules)

Question 68

Phospholipids

Answer 68

composed of glycerol (3C molecule) + 2 fatty acids and a head group; the head group contains phosphate (PO4 3- ) plus an “R” group; the R group is either charged or polar; because of this structure, phospholipids are partly hydrophobic (the fatty acids) and partly hydrophilic (the head group) – thus phospholipids are amphipathic molecules (part of the molecule is hydrophobic and part of the molecule is hydrophilic)

Question 69

Phospholipid Bilayers

Answer 69

form the basis for biological membranes; they have a hydrophobic core, and water molecules are associated with the hydrophilic head groups

Question 70

Steroids

Answer 70

non-fatty acid-based lipids; have 4 carbon-based rings; are hydrophobic; there are many types of steroids, but all have similar structures; are components of membranes, and are also hormones (e.g. progesterone, testosterone)

Question 71

Proteins

Answer 71

polymers of amino acid monomers; have various levels of structure

Question 72

Amino Acids

Answer 72

most amino acids have the same basic structure; the individual amino acids are defined by their “side chains” or “R groups”

Question 73

Protein Amino Acids

Answer 73

there are 20 protein amino acids; plants can synthesize all 20 of these amino acids; animals cannot synthesize all of the amino acids; for animals, amino acids that cannot be synthesized must be provided in the diet – these are known as “essential amino acids”

Question 74

Nucleic Acids

Answer 74

polymers of nucleotide monomers; DNA and RNA; DNA is composed of DNA nucleotides (containing the 5C sugar deoxyribose), RNA is composed of RNA nucleotides (containing the 5C sugar ribose)

Question 75

Nucleotide

Answer 75

nucleic acid monomer; contains a 5C sugar, a nitrogenous base and a phosphate group

Question 76

Nucleotide Nitrogenous Base

Answer 76

defines the type of nucleotide; both DNA and RNA are composed of 4 types of nucleotides; DNA is composed of A, T, C, G; RNA is composed of A, U, C, G

Question 77

DNA is present as a double-stranded helix

Answer 77

the “double strand” is due to complementary pairing of nitrogenous bases; A has double H-bonds with T (A=T), and G has triple H-bonds with C (G≡C)

Question 78

DNA Represents Information

Answer 78

genes” are mostly sequences of DNA nucleotides that | define the primary structure of proteins

Question 79

Genetic information flow involves three types of macromolecules:

Answer 79

DNA RNA Protein transcription translation The above diagram shows the flow of information, not the flow of matter. In other words, the information represented by DNA is transcribed into the information represented by RNA, and the information represented by RNA is used to determine the primary structure (amino acid sequence) of a protein. Keep in mind that the information of DNA is in the form of a linear sequence of DNA nucleotides, that RNA’s information is in the form of a linear sequence of RNA nucleotides, and in the end, what we have is a sequence of amino acids (a protein). So, we are talking about three different types of macromolecule, all of which are composed of different types of monomer subunits. Polymers and Monomer subunits Associated with Genetic Information Flow: DNA (= a macromolecule/polymer) subunits are DNA nucleotides (monomer) RNA (= a macromolecule/polymer) subunits are RNA nucleotides (monomer) Protein (= a macromolecule/polymer) subunits are amino acids (monomer)

Question 80

Hydrolysis

Answer 80

• Macromolecules and large biological molecules are polymers composed of monomer subunits. • Condensation reactions (= dehydration reactions) link monomer subunits together. • A condensation reaction involves the removal of a water molecule from the two monomers, resulting in a covalent bond. • In a macromolecule, there are many monomer subunits linked together, and every monomer was added via an individual condensation reaction. Thus, there are many condensation reactions needed in order to produce a macromolecule. This process of repeated condensation reactions is known as condensation synthesis (= dehydration synthesis). • Macromolecules can also be broken down, via the process of hydrolysis. • Hydrolysis, in a simple sense, is the opposite of condensation synthesis. Hydrolysis literally means to “break apart with water”, and involves the re-addition of water molecule to break a covalent bond. • Both condensation synthesis and hydrolysis are tightly regulated by cells, and are catalyzed by enzymes (enzymes are discussed later in the course). • Macromolecules may be hydrolyzed because: 1) they are damaged, or 2) they are no longer needed. The monomer subunits resulting from hydrolysis can be recycled to produce other macromolecules

Question 81

Carbohydrates

Answer 81

* simple sugars or polymers of sugar units | * probably the single most abundant group of biological molecules

Question 82

Monosaccharides

Answer 82

simply a sugar monomer, e.g. glucose or fructose • C-based; the most common ones have 5 or 6 C atoms as a "backbone“; may contain from 3 - 7 C atoms • names typically end in “-ose” (also true for many oligosaccharides and polysaccharides) • highly H2O soluble (are small polar molecules) • most have a sweet taste • contain 2 or more -OH groups

Question 83

Oligosaccharides

Answer 83

short chain of 2 or more sugar monomers • chain is formed by condensation synthesis between monosaccharide monomers • "disaccharides" are oligosaccharides composed of only 2 subunits; e.g. sucrose (table sugar) is composed of glucose-fructose • also includes trisaccharides and longer chains, up to perhaps 16 to 18 carbon atoms • the shorter chain oligosaccharides are highly water soluble, whole the longer chain oligosaccharides are less soluble and are typically found attached to proteins or lipids

Question 84

Glucose

Answer 84

is a 6 carbon sugar, a monosaccharide, and an important source of energy in cells; in mammals it is “blood sugar”. Glucose is a small polar molecule and is highly water-soluble (due to the combination of partial charges and the relatively small size of the molecule). The partial charges of the molecule are due to the many O-H and O-C bonds (which are polar covalent bonds). Glucose is also the monomer subunit of polysaccharides such as starch and cellulose. In starch and cellulose the carbon #1 of one glucose molecule is attached to the carbon #4 of the adjacent glucose molecule via a condensation (dehydration) reaction.

Question 85

Polysaccharides

Answer 85

the true macromolecules among the carbohydrates • extremely long chains of sugar monomers; typically 1000's of linked monomers • form as a result of many condensation reactions • generally only poorly water soluble, but do attract water (they are hydrophilic); are hydrophilic because of the many polar covalent bonds • polysaccharides that are glucose polymers are starch, glycogen and cellulose; starch is an important plant C storage compound, and glycogen serves that function in animals; cellulose is an important component of plant cell walls • starch/glycogen have α-1, 4 linkages between the C atoms of adjacent glucose units; these are easily hydrolyzed by mammals (including humans); hydrolytic breakdown of starch/glycogen yields glucose (= an energy source); the hydrolysis is done by specific enzymes • cellulose has β-1,4 linkages ; not easily hydrolyzed by mammals; mammals such as cattle have microbes in their digestive systems that are able to hydrolyze β-1,4 linkages; humans are not able to hydrolyze β-1,4 linkages, therefore cellulose is not an energy source for humans (acts only as a component of “dietary fibre”)

Question 86

Lipids

Answer 86

• Are often classified as large biological molecules rather than macromolecules. • Three sub-types of lipids: fats, phospholipids and steroids; fats and steroids are hydrophobic, while phospholipids are amphipathic.

Question 87

Fats

Answer 87

are composed of a three carbon (3C) backbone (glycerol) with three fatty acids attached (via condensation/dehydration synthesis).

Question 88

Fats versus Oils

Answer 88

oils are simply fats that are liquids at room temperature; same basic structure of glycerol + 3 fatty acids; difference is that fats have saturated fatty acids while oils have unsaturated or polyunsaturated fatty acids; the kinks/bends introduced by the C=C bonds hinders close packing of the oil molecules, and they remain liquid at room temperature (they will solidify if the temperature is lowered sufficiently); fats, with saturated fatty acids, exhibit close packing at room temperature

Question 89

Phospholipids

Answer 89

similar, but not identical structure to fats; composed of glycerol plus two (not three) fatty acids; the third fatty acid is replaced by a hydrophilic head group • the head group contains phosphate (which is charged); the phosphate is attached to the glycerol; as well, there is another group (the “R group”) that is attached to the phosphate; the R group varies among different phospholipids, but is always either polar or charged • thus phospholipids have a hydrophobic portion of the molecule (the fatty acids) and a hydrophilic portion (the head group); molecules that are partly hydrophobic and partly hydrophilic are called amphipathic • in contrast to fats, phospholipids play a structural role in cells; biological membranes are composed of a phospholipid bilayer with associated proteins

Question 90

Steroids

Answer 90

• hydrophobic, non-fatty acid-based lipids • there are many types of steroids, but all have the same basic structure (four Cbased rings); different steroids have different atoms attached to various parts of the basic steroid structure • play two major roles: hormones (there are many steroid-based hormones, e.g. estrogen and testosterone) and structural (steroids are components of biological membrane, and influence the “fluidity” of the membranes)