Chapter 2 Vocabulary:
Amphiatic: having both hydrophilic and hydrophobic parts
Anabolic reactions: metabolic reaction where energy is stored in chemical bonds following the
law of conservation of matter
Anions: negative ion that has gained electrons
Atomic number: number of protons in an element; sorting factor on the periodic table
Atoms: building blocks of all matter; reaction determined by electrons
Bilayer: made of lipids and composition of all biological membranes
Bohr model: diagram of how bonds connect by showing the electrons in the electron shells
Carbohydrates: general formula of Cn(H20)n; function to store energy, transport stored energy,
structural molecules and recognition or signaling molecules
Catabolic reactions: metabolic reaction where energy is released from chemical bonds; follows
law of conservation of matter
Cations: positive ion that has lost electrons
Chemical bond: three types; ionic, covalent, and hydrogen bonds (in order of
Chemical reaction: requires ENERGY
Cohesion: attraction between molecules of the same substance
Condensation reaction: combining of two molecules with the byproduct of H20
Covalent bond: consist of shared pairs of electrons between 2 atoms; not always equal (polar
covalent bonds)
Disaccharide: two monosaccharide (simple sugars) connected in a dehydration reaction
Electron shells: the "rings" around the nucleus in an atom
Electronegativity: tendency of an atom or radical to attract electrons to form an ionic bond
Electrons: one of three main subatomic particles inside an atom; the protons and neutrons reside
in the nucleus and the electrons reside in the electron shells around the nucleus
Chapter 2 Questions:
1. Why is the search for water important in the search for life?
Every organism needs water to survive. In fact, without water, life on Earth would have never
begun. Acting as a medium in which organic compounds could mix with one another, water
facilitated the formation of the planet's first life forms, possibly even protecting them from the
sun's radiation. From those simple starter organisms to the most complex plants and animals,
water has played a critical role in survival ever since. In humans, it acts as both a solvent and a
delivery mechanism, dissolving essential vitamins and nutrients from food and delivering them
to cells. Our bodies also use water to flush out toxins, regulate body temperature and aid our
metabolism. No wonder, then, that water makes up nearly 60 percent of our bodies or that we
can't go for more than a few days without it. Besides being essential for our bodies to function,
water also promotes life in numerous other ways. Without it, we couldn't grow crops, keep
livestock or wash our food. Water has also advanced civilization, providing a means for travel
for entire parts of the world and a source of power for factories. Because water can also exist as a
vapor, it can be stored in the atmosphere and be delivered as rain across the planet. Earth's
oceans also help regulate the planet's climate, absorbing heat in the summer and releasing it
during the winter. And of course, those same oceans serve as a home for countless plants and
animals.
2. Why are the electrons the most important part of atoms when it comes to
chemical interactions?
The fullness of the outermost orbit of an atom is where that atom's chemistry comes from: those
outermost electrons interact with the outermost electrons of other atoms to produce chemical
reactions. A simple rule about atom chemistry: usually, a full outer orbit makes for a chemically
stable atom. An atom with equal numbers of protons in the nucleus and electrons buzzing around
has no overall charge. However, if the outer orbital is not full, that atom will be unstable, ready
to react in a way that will give it a full outer shell. If an atom with a nearly-full outer orbital can
grab free electrons, it will trap them and fill that layer. Each extra electron brings in its negative
charge, and the atom is now a negatively-charged ion. If the outer orbital has only one or two
electrons and needs eight to be full, those outer electrons may be dumped off, leaving
unbalanced proton charges and producing a positively-charged ion. Ions are often much more
stable than radicals: the chloride in table salt is a benign ion, while the chlorine in bleach is a
very reactive radical, but they are both the same element.
3. What is the octet rule and why is it important?
Octect Rule: In chemistry, the statement that when atoms combine to form molecules they
generally each lose, gain, or share valance electrons until they attain or share eight; also called
the Lewis rule of eight. This is important because this is where a atom is most stable and least
likely to chemically react.
4. Describe the three different types of chemical bonds and the attributes of each.
Ionic Bonds: Ionic bonds form when two atoms have a large difference in electro negativity.
(Electro negativity is the quantitative representation of an atom’s ability to attract an electron to
itself). Although scientists do not have an exact value to signal an ionic bond, the amount is
generally accepted as 1.7 and over to qualify a bond as ionic. Ionic bonds often occur between
metals and salts; chloride is often the bonding salt. Compounds displaying ionic bonds form
ionic crystals in which ions of positive and negative charges hover near each other, but there is
not always a direct 1-1 correlation between positive and negative ions. Ionic bonds can typically
be broken through hydrogenation or the addition of water to a compound.
Covalent Bonds: Covalent bonds form when two atoms have a very small (nearly insignificant)
difference in electro negativity. The value of difference in electro negativity between two atoms
in a covalent bond is less than 1.7. Covalent bonds often form between similar atoms, nonmetal
to nonmetal or metal to metal. Covalent bonding signals a complete sharing of electrons. There is
usually a direct correlation between positive and negative ions, meaning that because they share
electrons, the atoms balance. Covalent bonds are usually strong because of this direct bonding.
Polar Covalent Bonds: Polar covalent bonds fall between ionic and covalent bonds. They result
when two elements bond with a moderate difference in electronegativity moderately to greatly,
but they do not surpass 1.7 in electronegativity difference. Although polar covalent bonds are
classified as covalent, they do have significant ionic properties. They also induce dipole-dipole
interactions, where one atom becomes slightly negative and the other atom becomes slightly
positive. However, the slight change in charge is not large enough to classify it entirely as an ion;
they are simply considered slightly positive or slightly negative. Polar covalent bonds often
indicate polar molecules, which are likely to bond with other polar molecules but are unlikely to
bond with non-polar molecules.
Hydrogen Bonds: Hydrogen bonds only form between hydrogen and oxygen (O), nitrogen (N)
or fluorine (F). Hydrogen bonds are very specific and lead to certain molecules having special
properties due to these types of bonds. Hydrogen bonding sometimes results in the element that
is not hydrogen (oxygen, for example) having a lone pair of electrons on the atom, making it
polar. Lone pairs of electrons are non-bonding electrons that sit in twos (pairs) on the central
atom of the compound. Water, for example, exhibits hydrogen bonding and polarity as a result of
the bonding. This is shown in the diagram below.
Because of this polarity, the oxygen end of the molecule would repel negative atoms like
itself, while attracting positive atoms, like hydrogen. Hydrogen, which becomes slightly
positive, would repel positive atoms (like other hydrogen atoms) and attract negative atoms
(such as oxygen atoms). This positive and negative attraction system helps water molecules
stick together, which is what makes the boiling point of water high (as it takes more energy
to break these bonds between water molecules). In addition to the four types of chemical
bonds, there are also three categories bonds fit into: single, double, and triple. Single bonds
involve one pair of shared electrons between two atoms. Double bonds involve two pairs of
shared electrons between two atoms, and triple bonds involve three pairs of shared electrons
between two atoms. These bonds take on different natures due to the differing amounts of
electrons needed and able to be given up.
(http://www.wyzant.com/resources/lessons/science/chemistry/bonds)
5. Describe the properties of water and why they occur.
6. Explain the difference between hydrophobic and hydrophilic.
From etymology, the word “hydro-” means “water.” Thus, studying hydrophobic and hydrophilic
molecules concerns the solubility and other reaction of particles as they interact with water. The
term “–phobic” originating from “phobia” would translate into the repulsion to water.
Hydrophobic molecules and particles, therefore, can be defined as those who are insoluble to
water. On the other hand, hydrophilic molecules are those that interact well with H2O. In other
words, the distinction between hydrophobic and hydrophilic molecules is drawn by observance
of the hydrophobic particles’ repulsion to water and hydrophilic molecules’ attraction to water.
7. What is dehydration synthesis?
Dehydration synthesis: A chemical reaction that builds up molecules by losing water molecules.
It is a type of condensation reaction in which monomers join together into polymers while
losing water molecules. This process is carried out by losing (-OH) from one of
the monomers and (H) from another monomer. The two unstable monomers join together, and
the (-OH) and (H) combine forming water (H2O).
8. Why are sugars like legos?
Sugars are like legos because they have monosaccharide, or the basic building block of
carbohydrates, which allow two monosaccharides to be combined to form a disaccharide.
9. Compare and contrast the branching of cellulose, glycogen, and starch. Explain
how this branching affects their role in living organisms.
Cellulose is found in numerous rows of parallel molecules that form hydrogen bonds with other
rows to form sheets. Starches branch off at odd angles making starch less compact than cellulose.
And glycogen has many branches whose offshoots are more compacted that starch branching.
Glycogen is easily digested by humans because the numerous branches provide for many
accessible access points for the enzymes to latch on and begin eating away at the molecules.
With starch, this process is slightly slower because there are fewer offshoots. Cellulose’s process
is too slow. The enzymes have difficulty entering the structure of the cellulose sheets so they
can't digest cellulose.
10. Explain the difference between a saturated and unsaturated fatty acid and the
metabolism of each.
Fatty acids that have carbon–carbon
double bonds are known as
unsaturated. Fatty acids without double
bonds are known as saturated. They
differ in length as well. Unsaturated
fatty acids are much easier to break
down because of the kink in their
structure at each double bond. Because of this, they also take up more space.
11. Explain the two laws of thermodynamics and how each affect metabolism.
Metabolism in humans is the conversion of food into energy, which is then used by the body to
perform activities. It is an example of the first law of thermodynamics in action. Considering the
body as the system of interest, we can use the first law to examine heat transfer, doing work, and
internal energy in activities ranging from sleep to heavy exercise.
The body provides us with an excellent indication that many thermodynamic processes are
irreversible. An irreversible process can go in one direction but not the reverse, under a given set
of conditions. For example, although body fat can be converted to do work and produce heat
transfer, work done on the body and heat transfer into it cannot be converted to body fat.
(https://www.boundless.com/physics/textbooks/boundless-physics-textbook/thermodynamics14/the-first-law-of-thermodynamics-117/human-metabolism-410-6345/)
Chapter 3 Vocabulary:
Activation energy (Ea): the energy barrier that blocks a tendency for a chemical reaction to
occur
Active site: region on surface of enzyme or ribosome where the substance binds, and where
catalysis occurs
Adenine (A): part of a nucleotide; pairs with thymine in DNA and uracil in RNA
Allosteric regulation: regulation of an enzyme or other protein by binding an effector molecule
at the protein's allosteric site (not the active site) so the enzyme must change shape;
regulates enzymes by changing their shape!
Alpha helix: shape a protein makes when it folds into a spiral
Amino acids: monomers of proteins
Beta pleated sheet: shape a protein makes when it folds into a zig zag
Base: a nitrogenous base is either adenine, cytosine, guanine, thymine, or uracil and it is an
essential part of the nucleutide
Catalyst: making a biological reaction faster and in biological conditions
Competative inhibitor: a nonsubstrate that binds to the active site of an enzyme and thereby
inhibits binding of its substrate
Complementary base pairing: adenine pairs with thymine in DNA or uracil in RNA; guanine
and cytosine always base pair; a purine must be paired with a pyramidine
Cytosine (C): part of a nucleotide; pairs with guanine
Denatured: when the proteins structure is disturbed and its function is therefore corrupted.
Deoxyribose: the sugar that makes up DNA, has a hydroxyl attached to the pentose ring
Disulfide bridge: connection between two sulfhydrils that underwent a denhydration reaction
Deoxyribonucleic acid (DNA): a nucleic acid in a double helix shape that carries genetic
information and can self replicate.
Enzyme-substrate complex (ES): an intermediate in an enzyme-catalyzed reaction; consists of
the enzyme bound to its substrate
Feedback mechanism: the end-product will bind to the active site on the enzyme; wrong step so
it inactivates the enzyme
Genes: DNA that codes for building proteins
Genome: all of the genes in an organism
Guanine (G): part of a nucleotide; pairs with cytosine
Noncompetitive inhibitor: a non-substrate that inhibits the activity of an enzyme by binding to
a site other than its active site
Nucleic acids: DNA and RNA
Nucleotide: building blocks of nucleic acids; pentose sugar, phosphate group and a nitrogenous
base.
Peptide linkage: bonding between amino acids that connect to make a long chain (polypeptide
chain), or a protein
Phosphodiester linkage: how nucleic acids bond through condenstation reaction to form DNA
and RNA
Primary structure: initial folding for proteins; connection of amino acids
Purine: a hexagon and pentagon shaped nucleotide; adenine and guanine
Pyrimidine: only a hexagon shaped nucleotide; thymine/uracil and cytosine
Quaternary structure: folding pattern for multiple proteins; after tertiary to form complex
proteins.
R group: part of the amino acid structure that determines the identity of the aa
Ribose: sugar of RNA; doesn't have a hydroxyl group attached to the pentose
RNA: ribonucleic acid; can catalyze biological reactions, control gene expression, or sense and
communicate responses to cellular signals; unlike DNA, it is single stranded, very short
in nucleotide length, contains ribose, and is less stable because RNA is more prone to
hydrosis.
Secondary structure: folding pattern for proteins; bonds form to pull the amino acids into a 3-D
shape
Substrates: molecule on which an enzyme exerts catalytic action; the reactant
Tertiary structure: folding pattern for proteins; bonds form to pull the amino acids into a 3-D
shape; after secondary folding
Thymine (T): part of a nucleotide; pairs with adenine in DNA
Transition state: in an enzyme-catalyzed reaction, the reactive condition of the substrate after
there has been sufficient input of energy (Ea) to initiate a reaction
Uracil (U): replaces thymine in RNA; part of a nucleotide that pairs with adenine in RNA
Chapter 3 Questions:
1. No question
2. Fully describe the four levels of protein structure and explain what types of
interactions are responsible for each level.
Above all the wide variety of conformations is due to the huge amount of different sequences of
amino acid residues. The primary structure is the sequence of residues in the polypeptide chain.
Secondary structure is a local regularly occurring structure in proteins and is mainly formed
through hydrogen bonds between backbone atoms. So-called random coils, loops or turns don't
have a stable secondary structure. There are two types of stable secondary structures: Alpha
helices and beta-sheets. Alpha-helices and beta-sheets are preferably located at the core of the
protein, whereat loops prefer to reside in outer regions. Tertiary structure describes the packing
of alpha-helices, beta-sheets and random coils with respect to each other on the level of one
whole polypeptide chain. Figure 5 shows the tertiary structure of Chain B of Protein Kinase C
Interacting Protein. Quaternary structure only exists, if there is more than one polypeptide chain
present in a complex protein. Then quaternary structure describes the spatial organization of the
chains. Figure 6 shows both, Chain A and Chain B of Protein Kinase C Interacting Protein
forming the quaternary structure.
3. What kinds of factors cause denaturation of the protein and how this might affect
the protein’s ability to function?
If the temperature reaches the melting point of a protein, then the protein will denature. Factors
other than heat can also denature proteins. Changes in pH affect the chemistry of amino acid
residues and can lead to denaturation. Hydrogen bonding often involves these side
changes. Protonation of the amino acid residues (when an acidic proton H + attaches to a lone
pair of electrons on a nitrogen) changes whether or not they participate in hydrogen bonding, so
a change in the pH can denature a protein. The factor causes the folded protein (the tertiary
structure) to unfold, to unravel. If the protein functioned as an enzyme, then denaturation causes
it to lose its enzymatic activity. If the protein was embedded in a cell membrane where it
transported ions or molecules through the membrane, then denaturation destroys that ability. If
the protein was an antibody, responsible for recognizing an infectious agent, denaturation will
destroy that protective ability.
4. Research and describe with drawing or picture the feedback mechanism involving
insulin and gluconeogenesis. Explain what happens to the body when this pathway
gets disrupted with insulin resistance.
Insulin resistance is a condition in which the body produces insulin but does not use it
effectively. When people have insulin resistance, glucose builds up in the blood instead of being
absorbed by the cells, leading to type 2 diabetes or pre-diabetes. In insulin resistance, muscle, fat,
and liver cells do not respond properly to insulin and thus cannot easily absorb glucose from the
bloodstream. As a result, the body needs higher levels of insulin to help glucose enter cells.
The beta cells in the pancreas try to keep up with this increased demand for insulin by producing
more. As long as the beta cells are able to produce enough insulin to overcome the insulin
resistance, blood glucose levels stay in the healthy range.
Over time, insulin resistance can lead to type 2 diabetes and pre-diabetes because the beta cells
fail to keep up with the body’s increased need for insulin. Without enough insulin, excess
glucose builds up in the bloodstream, leading to diabetes, pre-diabetes, and other serious health
disorders.
5. Explain what is happening in this animation. Redraw this animation to show an
endergonic reaction.
The reaction in the packet is exergonic. The free energy is negative. In an endergonic reaction,
the standard change in free energy is positive, and energy is absorbed. The total energy is a
negative net result.