Biology Review- Chapter 4

4.1-Organic Chemistry

Carbon: makes up various living organisms through chemicals mostly based on carbon (ex. Plants, trilo
beetle). Enters atmosphere through action of plants that use solar energy to transform atmospheric CO2
into the molecules of life which are passed on to animals that feed off plants etc.

Unique: of all living elements unparalleled in ability to form molecules that are large and diverse. Ex.
Proteins, DNA, carbohydrates etc. and distinguish living matter from inanimate material are composed
of carbon.

Organic Chemistry: the branch of chemistry that specializes in the study of carbon compounds.

Organic Compounds: compounds containing carbon. Range from simple (methane-CH 4) to colossal
(proteins with thousands of atoms.

4.2 Carbon atoms can form diverse molecules by bonding to four other atoms

Chemical characteristics: key to this is its electron configuration which determines the kinds of bonds an
atom will form with other atoms.

Carbon tetra valence: is one facet of carbon’s versatility that makes large, complex molecules possible.
Because each carbon atom acts as an intersection point from which a molecule can branch off in as
many as four directions (due to the fact that it has 4 valence electrons). When it forms four single
covalent bonds, the arrangement of its four hybrid orbitals causes the bonds to angle toward the
corners of an imaginary tetrahedron.

Every grouping of a carbon bonded to four other atoms has a tetrahedral shape

Exception=when carbon atoms are joined by a double bond they are in the same plane (flat)

We write them as if they were flat, but must keep in mind that they are not and that their 3D shapes
determine their properties.

Hydrocarbons: organic molecules consisting of only carbon and hydrogen. Main components in
petroleum which is a fossil fuel. Not prevalent in living organisms. Many of cell’s organic molecules have
regions consisting of only hydrogen and carbon (ex. Fats have long hydrocarbon tails attached to a non-
hydrocarbon component)

Hydrocarbon are: mostly hydrophobic (ex. Petroleum nor fat dissolves in water) because most rely on
nonpolar carbon-to-hydrogen linkages.

-can undergoe reactions that release relatively large amounts of energy. Ex. Gasoline that fuels a car
consists of hydrocarbons
Isomers: variation in architecture of organic molecules (same numbers of atoms of the same elements,
but different structures and hence different properties).

Structural Isomers: differ in the covalent arrangements of their atoms (possible number of isomers
increases tremendously as carbon skeletons increase in size). Three forms of C 5H12 but 18 variations of
C8H18 .

Drawing of structural isomers C5H12

Geometric Isomers: have the same covalent partnerships but differ in spatial arrangements which arise
from inflexibility of double bonds.

Single bonds=allow atoms they join to rotate freely about the bond axis without changing the compound

Double bonds=do not permit such rotation therefore possibility of geometric isomers

Cis isomer: trans isomer:

Can dramatically affect: ex. Biochemistry of vision involves a light-induced change of rhodopsin from the
cis isomer to the trans isomer

Enantiomers: can both be asymmetric carbons, but arranged in different ways. Left handed-right
handed versions of each other. Usually one is active and the other isn’t.

Useful in pharmaceutical because one version may be useful and the other may not be. One may
produce harmful effects. Ex. Thalidomide pregnant women drug (mixture of two antiomers where one
prevented morning sickeness but the other one caused severe birth defects).

4.3 A small number of chemical groups are key to the functioning of biological molecules

Dependent not only on structure but on what is attached onto the skeleton

Number of arrangements give unique properties

Ex. Sex Hormones: male and female (testosterone and estadiol) differ only between the group attached
at the end which differ their reactions with other bodily functions and chemical thus altering shapes.
Functional Groups: different attached elements at the ends, therefore differ in chemical reactions.

Biology Review- Chapter 5

Macromolecules: carbohydrates, lipids, proteins and nucleic acids. They are the critically important
large molecules of all living things. They are giant molecules made up of polymers (which are chains of
monomers).

“While they have different structures and functions, they are all composed of long complex
chains of molecules (polymers) made up of simpler, smaller subunits (monomers).”

-architecture of large biological molecules help explain how it works and exhibit unique properties arisin
from the orderly arrangement of their atoms.

5.1 Macromolecules are polymers built from monomers

Polymer: long molecule consisting of many similar building blocks linked by covalent bonds
(carbohydrates, proteins etc. are polymers).

Monomers: repeating units of that serve as building blocks to polymers.

Condensation Reaction (dehydration reaction): monomers are connected by reaction in which two
molecules are covalently bonded to each other through the loss of a water molecule.

One contributes to hydroxyl group, and other contributes to hydrogen.

Enzymes: specialized macromolecules that speed up chemical reactions in cells.

Hydrolysis: the way the polymers are disassembled. Ex. Digestion. Bulk of organic material in our food is
in the form of polymers that are much too large to enter our cells therefore various enzymes attack
polymers speeding up hydrolysis.

-cells have thousands of different macromolecules

5.2 Carbohydrates serve as fuel and building material

Carbohydrates: include both sugars and polymers of sugar. Include monosacharides (simple sugars),
disaccharides (double sugars covalently bonded), and polysaccharides (polymers composed of many
sugar building blocks-carbohydrates).

Sugars

Monosaccharide’s: generally have molecular formula that is some multiple of the unit (ex. Glucose most
common monosaccharide= C6H12O6)

Trademarks: has a carbonyl group, and multiple hydroxyl groups. Depending on location can either de
an aldose(aldehyde sugar) or a ketose(ketone sugar).
Glucose=aldose fructose=ketose

-often names end in “ose” and often have skeleton ranging ranging from 3 to 7 carbons long. Ex.
Glucose, fructose are hexoses because they are six sugars long

Trioses and pentoses are also common

-diversity for simple sugars is in the spatial arrangement of their parts around asymmetric carbons. Ex.
Glucose and galactose differ only in the placement of parts around one asymmetric carbon, but this is
significant enough to give the two sugars distinctive shapes and behaviors.

-often form rings, even though writing them as linear skeletons is practical

Purpose: Major nutrition for cells (particularly glucose) in the process of cellular respiration where cells
extract energy in a series of reactions starting with glucose molecules. Therefore are major fuel for
cellular work. Can also serve as raw material for the synthesis of other types of small organic molecules
such as amino acids or fatty acids, and if not used for this, are generally incorporated in….

Disaccharide: Consists of two monosaccharide’s joined by a glycosidic linkage (covalent bond formed
between two monosaccharides by dehydration reaction). Ex. Maltose= link of two glucose(malt sugar in
beer)

Ex.sucrose=glucose and fructose (table sugar)

Ex.lactose= glucose joined to galactose molecule (sugar present in milk)

Polysaccharides

are macromolecules, polymers with a few hundred to few thousand monosaccharides joined by
glycosidic linkages. Some serve as building material for protection for cells, others as storage matieral.
Determined by its sugar monomers and position of glycosidic linkages.

Storage: both plants and animals store sugars for later use in form of storage polysaccharides. Plants
store starch (chain –polymer of glucose) which helps plant to stockpile surplus glucose when
synthesizing (glucose=energy). Most humans and animals have enzymes that can hydrolyze plant starch
(ex. Why pasta is such good fuel for athletes-comes from wheat).

Most glucose monomers in starch joined by 1-4 linkages (number 1 carbon linked to number 4 carbon)

Amylose: simplest form of starch and is unbranched

Glycogen: is an amyloceptin but more extensively branched in which animals and humans store mainly
in the liver and muscle cells. Hydrolisis of glycogen in these cells release glucose when the demand for
sugar increases, although this fuel cannot sustain animal for long. Ex. In humans glycogen stores are
depleted in about a day unless they are replenished by consumption of food.

Structural Polysaccharides: organisms build strong materials from structural polysaccharides.

Cellulose: is a major component of the tough walls that enclose plant cells. Plants produce almost 10 14kg
of cellulose per year and is the most abundant organic compound on earth. It is composed of glucose,
but the glycosidic linkages differ.

Glucose is an alpha and cellulose is a beta (making every glucose monomer upside down with respect to
its neighbor).

Different linkages give different shapes as well: a starch molecule is rather helical and a cellulose is
straight.

Microfribrils: cellulose is never branched, but some hydroxyl groups, hydrogen bond with others lying
parallel to it. They are held together this way and are grouped into units called microfribrils. They are
strog building materials for plants and important for humans because it is the major constituent for
paper and cotton.

Digestion of beta: beta linkages cannot be digested because they are unable to hydrolyze it because of
its distinct shapes. Can digest the alpha, but cannot digest the beta linkages, therefore when cellulose in
our food passes through the digestive tract it is eliminated by feces, and along the way the cellulose
abrades the digestive tract wall which aids in the smooth passage of food. Therefore, even though it is
not a nutritient for humans, it is important in our diet (ex. Fruits and vegetables are rich in cellulose).

Prokaryotes: cow produces this cellulose digesting element that hydrolyzes the cellulose of hay and
grass to convert the glucose into other nutrients that nourish the cow.

Chitin: another important polysaccharide which is a carbohydrate used by arthropods (insects, spiders,
crustaceans etc.) to build their exoskeletons (hard case that surrounds the soft parts of the animal). Also
found in many fungi, which use this fungi rather than cellulose in building material for their cell walls.
Similar to glucose except has a nitrogen containing appendage.
5.3 lipids are a diverse group of hydrophobic molecules

Lipids: Do not include true polymers and are generally not big enough to be considered
macromolecules. Are generally grouped together because they share one important trait: they mix
poorly if at all with water which is based on their molecular structure (have some polar bonds associated
with oxygen, but consist mostly of hydrocarbon regions).

Fats: not polymers but are assembled from few smaller molecules by dehydration reactions, and are
constructed from two kinds of smaller molecules (glycerol and fatty acids). The relatively non-polar C-H
bonds in the hydrocarbon chain are the reason why fats are hydrophobic (fats separate from water
because the water molecules hydrogen bond to one another and exclude the fats.

Major function of fats is energy storage (gram of fat stores twice as much energy as a gram of a
polysaccharide such as starch). Because plants don’t move, they can use energy storage through bulk
starch, but animals must carry their energy stores, so fat is more compact fuel.

Glycerol: an alcohol with 3 carbons each bearing a hydroxyl group

Fatty acid: long carbon skeleton usually 16 or 18 carbons in length. Carbon at one end is a part of the
carboxyl group (which gives the name hence acid) and attached to this group is a large hydrocarbon
chain.

Triacyglycerol(fat molecule): in making this (making a fat), three fatty acid molecules each join to
glycerol by an ester linkage (bond between a hydroxyl group and carboxyl group).

Structure of the chains…

Saturated fatty acid: if there are no double bonds between carbon atoms in the composing chains, then
as many hydrogen atoms as possible are bonded to the carbon skeleton. It is therefore saturated with
hydrogen. Lack of flexibility in the “tails” of the fat molecules allows the fat molecules to pack together
tightly.

“hydrogenated”: process where unsaturated fats have been synthetically converted to saturated fats to
adding hydrogen. Ex. Peanut butter and margarine to prevent lipids from separating out into liquid

Hydrogenating things like vegetable oil also contributes to trans fats with trans double bonds.

Unsaturated fatty acid: has one or more double bonds formed by the removal of hydrogen atoms from
the carbon skeleton; the fatty acid will have a kink in its hydrocarbon chain wherever a cid double bond
occurs.

Phospholipids: cells could not exist without another type of lipid, as this is essential to making up the
cell membrane. Similar to fat molecule but has only 2 fatty acids attached to glycerol rather than 3.
The 3rd group is therefore joined by a phosphate group with a negative electrical charge. Additional small
molecules which are usually charged or polar can be linked to the phosphate group to form a variety of
phospholipids.

Two ends show different behaviors toward water; hydrocarbon tails are hydrophobic and are excluded
from water, but heads are hydrophilic

Arranged in simple bilayer’s that shield their hydrophobic portions from water

Important because it creates cell membrane; protects

3 carbon backbone 2 fatty acids attached

Steroids: lipids characterized by a carbon skeleton consisting of four fused rings. Cholesterol is a
common component of animal cell membranes.

5.4 Proteins have many structures, resulting in a wide range of functions

50% dry mass of all cells

Enzymes: life would not be possible without them, in which most are proteins. Regulate metabolism by
acting as catalysts (agents that speed up chemical reactions with being consumed by it)

Enzymes can perform its function over and over again, therefore can be thought of as workhorses that
keep cells running.

Polypeptides: all polymers constructed from the same set of 20 amino acids. Polymers of amino acids
are called this, and a protein consists of one or more polypeptides

Amino acid monomers: amino acids posess both carboxyl and amino groups with carbon in the middle
(alpha carbon). About 20 amino acids cells use to build their thousands of proteins.

R=side chain which determines its functional role in a polypeptide

Amino Acid Polymers: two amino acids positioned so that the carboxyl group of one is adjacent to the
amino group of the other, they become adjoined by dehydration reaction. Resulting covalent bond =
peptide bond. Repeated over and over, this yields a polypeptide. One end has free carboxyl group(C-
terminus), and one end has an amino end (N-terminus).

Backbone= linked amino acids side chains=R (what is attached to each)

Linkage ultimately suggests; creation of polymers (linkage of smaller things;monomers)

Antibody: protein in the body

Protein Structure and Function: structure depends on ability to bind with others

Four Levels

Primary Structure: unique sequence of amino acids