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/thermodynamics-

14/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.