Final Review Part I: Lectures 1-10 Flashcards
What is? Inductive Reasoning
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.
What is? Induction Based Science
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
Hypothesis Based Science
uses deductive reasoning (maybe; there is some
controversy about this); hypothesis-based science gets most of the attention from
philosophers of science
Deductive Reasoning
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.
Hypothesis
tentative explanation for an observation
Hypothetico-Deductive Method
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”)
Testable Hypothesis
a hypothesis which can provide testable predictions for
outcomes of experiments
Non-Testable Hypothesis -
a hypothesis which cannot provide testable predictions;
such a hypothesis is not necessarily incorrect, the scientific method simply can’t
deal with it
Occam’s (Ockham’s) Razor
– 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)
Importance of the “Control”
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?)
Negative and Positive Controls
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
Composition of an Atom
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
The Number of Protons Defines the Type of Atom
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
Bonds between Atoms are Based on Electrons
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
Hydrogen (H)
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).
Ions
atoms or molecules in which the number of protons ≠ the number of electrons
Cations
positively charged ions, in which there are more protons than electrons
Anions
negatively charged ions in which there are fewer protons than electrons
Hydrogen Bonds (H bonds)
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.
Electronegativity
the ability of an atom to attract electrons to itself; a fixed property
of atoms
Non-Polar Covalent Bond
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
Polar Covalent Bond
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
Ionic Bond
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
Polar Molecules
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
Polar Covalent Bonds Containing H
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
Hydrogen (H) Bonds
weak transient bonds caused by polar covalent bonds
containing H
Water Molecule
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)
Water Exhibits Cohesion
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
Water Exhibits Adhesion
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
Hydrophilic
literally means “water-liking”; hydrophilic molecules are polar and/or
charged, and exhibit mutual attraction with water molecules
Hydrophobic
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
Dissociation of Water
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
Water PH
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.
Water Hydrogen Bonding
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.
Water as a Solvent
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)
Effect of Molecule Size on Water Solubility
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
Molecules with Mainly C-H and C-C Bonds are not Water Soluble
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
Life is Carbon-Based
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
Carbon atoms always have four bonds
could be four single bonds, two singles and a
double, two double bonds, or a single and a triple bond
Carbon Electronegativity
C has a moderate to low electronegativity
Non-Polar Covalent Bonds
C-C and C-H bonds are non-polar covalent; C and H have
virtually the same electronegativity
Polar Covalent Bonds
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
Carbon-Based Molecules May Exhibit Isomerism
there are three main types of
isomerism, listed below (molecules that are isomers have the same molecular
formula but different structures)
Structural Isomerism
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
Cis/Trans Isomerism (part of Geometric Isomerism)
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
Enantiomers
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
Bonds with Carbon can be arranged in three dimensions
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:
Structural Isomers
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).
Cis/Trans Isomers (which are a subset of Geometric Isomers)
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).
Enantiomers
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).
Isomerism of Carbon-Based
Molecules
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.
Macromolecules
very large biological molecules; polymers composed of many
monomer subunits; synthesized by condensation synthesis (= dehydration
synthesis); carbohydrates, proteins and nucleic acids are macromolecules
Large Biological Molecules
biological molecules not quite as big as macromolecules,
e.g. lipids are considered to large biological molecules rather than macromolecules
Monomer
building block (subunit) of a polymer, e.g. monosaccharides are the monomers that are linked together to produce polysaccharides (a polymer)
Polymer
a large molecule composed of numerous linked monomers; the monomers
are linked by covalent bonds
Condensation Reaction/Dehydration Reaction –
formation of a covalent bond with the
loss of a water molecule
Condensation Synthesis/Dehydration Synthesis
several to many rounds of
condensation reactions, leading to the formation of large biological molecules or
macromolecules
Hydrolysis
break apart with water; opposite of a condensation reaction
Hydrolysis of Macromolecules
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
Carbohydrates
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
Starch Versus Cellulose
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
Lipids
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
Fats (= Triglycerides)
three fatty acids attached to glycerol (3C molecule); extremely
hydrophobic; used as energy storage molecule
Saturated Fat
has only C-C bonds in the fatty acids
Unsaturated Fat
has a C=C bond in the fatty acids
Polyunsaturated Fat
has 2+ C=C bonds in the fatty acids; but the majority of the
bonds are C-C
Oil
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)
Phospholipids
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)
Phospholipid Bilayers
form the basis for biological membranes; they have a
hydrophobic core, and water molecules are associated with the hydrophilic head
groups
Steroids
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)
Proteins
polymers of amino acid monomers; have various levels of structure
Amino Acids
most amino acids have the same basic structure; the individual amino
acids are defined by their “side chains” or “R groups”
Protein Amino Acids
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”
Nucleic Acids
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)
Nucleotide
nucleic acid monomer; contains a 5C sugar, a nitrogenous base and a
phosphate group
Nucleotide Nitrogenous Base
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
DNA is present as a double-stranded helix
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)
DNA Represents Information
genes” are mostly sequences of DNA nucleotides that
define the primary structure of proteins
Genetic information flow involves three types of macromolecules:
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)
Hydrolysis
• 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
Carbohydrates
- simple sugars or polymers of sugar units
* probably the single most abundant group of biological molecules
Monosaccharides
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
Oligosaccharides
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
Glucose
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.
Polysaccharides
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”)
Lipids
• 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.
Fats
are composed of a three carbon (3C) backbone (glycerol) with three fatty acids
attached (via condensation/dehydration synthesis).
Fats versus Oils
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
Phospholipids
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
Steroids
• 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)
