BIOLOGY

(KHAN ACADEMY)

Key terms
Term Meaning
Biological A large, organic molecule such as carbohydrates, lipids, proteins,
macromolecule and nucleic acids.
Monomer A molecule that is a building block for larger molecules (polymers).
 Term Meaning
For example, an amino acid acts as the building blocks for proteins.
A large molecule made of repeating subunits (monomers). For
example, a carbohydrate is a polymer that is made of repeating
Polymer monosaccharides.

Types of biological macromolecules

Biological
macromolecule Building blocks Functions Examples
Provide cells with
quick/short-term
Monosaccharides energy, source of Glucose, sucrose,
Carbohydrates (simple sugars) dietary fiber starch, cellulose, chitin
Provide cells with
long-term energy, Fats, phospholipids,
Fatty acids and make up biological waxes, oils, grease,
Lipids glycerol membranes steroids
Provide cell structure,
send chemical signals, Keratin (found in hair
speed up chemical and nails), hormones,
Proteins Amino acids reactions, etc enzymes, antibodies
Store and pass on
Nucleic acids Nucleotides genetic information DNA, RNA

Common mistakes and misconceptions

 Describing macromolecules as “large” is relative. We refer to them as “macro”
because they are large compared to other, smaller molecules. However, this does not mean that
they are large enough to view with the naked eye. Even a large protein, like hemoglobin, is still a
million times smaller than a grain of rice!
 Not all fats and carbohydrates are “bad.” Information about different kinds of diets
can be confusing and may lead someone to believe that all fats or all carbohydrates are
unhealthy. This simply isn’t the case. Fats and carbohydrates are actually essential for cellular
function!

Take Down Notes #1

I. Macromolecules:
1. Carbohydrates – also called saccharide
a. Glucose – monomer (monosaccharide)
b. Glycogen – polymer (polysaccharide)
Functions:
1. Energy
 2. Structural – plant cells
2. Protein – amino acids
a. Polypeptide – chain of amino acid
Functions:
1. Structural
2. Mechanical
3. Enzymes –catalyze reaction
4. Signaling – body, cells
3. Lipids – not all fats are lipids, not so water soluble i.e. trigyceride
Characteristics:
a. Hydrophilic – attracted to water
b. Hydrophobic – resistant to water
Functions:
1. Energy storage
2. Signaling – body, cells
3. Membranes – phospholipids
II. Nucleic Acid
1. Nucleic Acid – most important macromolecule 4 layf
- Acid part – more reactive

a. Deoxyribonucleic Acid
a. Nucleotides – building blocks of DNA; monomer
b. Deoxyadenosine Monophosphate
c.
b. Ribonucleic Acid
a. Adenosine Monophosphate

4 Unique Nucleotides of DNA – Nitrogenous Base

1. Adenine
2. Thymine
3. Cytosine
4. Guanine

Take Down Notes #2

Water (Hydrogen bonding in water)

1. H2O – bonded by covalent bonds
a. Oxygen – 2 lone electron pairs; extremely electronegative – hogs/keeps electrons
b. Hydrogen
c. Covalent bonds – pair of electrons
d. Polarity – positive end and negative end
2. Solvent – easy to dissolve
Example: Na⁺Cl⁻– attracted by ionic bond; hydrophilic
 Hexane – hydrophobia
3. Solute – material to dissolve
Key terms
Term Meaning
A neutral, or uncharged molecule that has an asymmetric internal
distribution of charge, leading to partially positive and partially
Polar molecule negative regions
Cohesion The attraction of molecules for other molecules of the same kind
Adhesion The attraction of molecules for other molecules of a different kind
Density The mass per unit volume of a substance
Specific heat The amount of heat needed to raise the temperature of one gram of a
capacity substance by one degree Celsius
Heat of The amount of energy needed to change one gram of a liquid substance
vaporization to a gas at constant temperature

Unique properties of water

1. Water is polar. Water molecules are polar, with partial positive charges on the
hydrogens, a partial negative charge on the oxygen, and a bent overall structure. This is because
oxygen is more electronegative, meaning that it is better than hydrogen at attracting electrons.
2. Water is an excellent solvent. Water has the unique ability to dissolve many polar and
ionic substances. This is important to all living things because, as water travels through the water
cycle, it takes many valuable nutrients along with it!
3. Water has high heat capacity. It takes a lot of energy to raise the temperature of a
certain amount of water by a degree, so water helps with regulating temperature in the
environment. For example, this property allows the temperature of water in a pond to stay
relatively constant from day to night, regardless of the changing atmospheric temperature.
4. Water has high heat of vaporization. Humans (and other animals that sweat) use
water’s high heat of vaporization to cool off. Water is converted from its liquid form to steam
when the heat of vaporization is reached. Since sweat is made mostly of water, the evaporating
water absorbs excess body heat, which is released into the atmosphere. This is known
as evaporative cooling.
5. Water has cohesive and adhesive properties. Water molecules have
strong cohesive forces due to their ability to form hydrogen bonds with one another. Cohesive
forces are responsible for surface tension, the tendency of a liquid’s surface to resist rupture
 when placed under tension or stress. Water also has adhesive properties that allow it to stick to
substances other than itself.
These cohesive and adhesive properties are essential for fluid transport in many forms of life. For
example, they allow nutrients to be transported to the top of a tree against the force of gravity.
6. Water is less dense as a solid than as a liquid. As water freezes, the molecules form a
crystalline structure that spaces the molecules further apart than in liquid water. This means that
ice is less dense than liquid water, which is why it floats.
This property is important, as it keeps ponds, lakes, and oceans from freezing solid and allows
life to continue to thrive under the icy surface.

Common mistakes and misconceptions

 Water dissolves everything because it is the “universal solvent." Water has the ability
to dissolve many substances but the term “universal solvent" is misleading. Water is able to
dissolve other polar molecules and ions, such as sugars and salts. However, nonpolar molecules
like oils lack partial positive or partial negative charges, so they are not attracted to water
molecules. This is why nonpolar substances like oil remain separate when added to water.

Introduction to macromolecules

Think back to what you ate for lunch. Did any of your lunch items have a “Nutrition Facts” label
on the back of them? If so, and if you had a look at the food's protein, carbohydrate, or fat
content, you may already be familiar with several types of large biological molecules we’ll
discuss here. If you’re wondering what something as weird-sounding as a “large biological
molecule” is doing in your food, the answer is that it’s providing you with the building blocks
you need to maintain your body – because your body is also made of large biological molecules!
Just as you can be thought of as an assortment of atoms(Opens in a new window) or a walking,
talking bag of water, you can also be viewed as a collection of four major types of large
biological molecules: carbohydrates (such as sugars), lipids (such as fats), proteins, and nucleic
acids (such as DNA and RNA). That’s not to say that these are the only molecules in your body,
but rather, that your most important large molecules can be divided into these groups. Together,
the four groups of large biological molecules make up the majority of the dry weight of a cell.
(Water, a small molecule, makes up the majority of the wet weight).
Large biological molecules perform a wide range of jobs in an organism. Some carbohydrates
store fuel for future energy needs, and some lipids are key structural components of cell
membranes. Nucleic acids store and transfer hereditary information, much of which provides
instructions for making proteins. Proteins themselves have perhaps the broadest range of
functions: some provide structural support, but many are like little machines that carry out
specific jobs in a cell, such as catalyzing metabolic reactions or receiving and transmitting
signals.
We’ll look in greater detail at carbohydrates, lipids, nucleic acids, and proteins a few articles
down the road. Here, we’ll look a bit more at the key chemical reactions that build up and break
down these molecules.
Monomers and polymers

Most large biological molecules are polymers, long chains made up of repeating molecular
subunits, or building blocks, called monomers. If you think of a monomer as being like a bead,
then you can think of a polymer as being like a necklace, a series of beads strung together.
Carbohydrates, nucleic acids, and proteins are often found as long polymers in nature. Because
of their polymeric nature and their large (sometimes huge!) size, they are classified
as macromolecules, big (macro-) molecules made through the joining of smaller subunits.
Lipids are not usually polymers and are smaller than the other three, so they are not considered
macromolecules by some sources^{1,2}1,2start superscript, 1, comma, 2, end superscript.
However, many other sources use the term “macromolecule” more loosely, as a general name for
the four types of large biological molecules^{3,4}3,4start superscript, 3, comma, 4, end
superscript. This is just a naming difference, so don’t get too hung up on it. Just remember that
lipids are one of the four main types of large biological molecules, but that they don’t generally
form polymers.

Dehydration synthesis

How do you build polymers from monomers? Large biological molecules often assemble
via dehydration synthesis reactions, in which one monomer forms a covalent bond to another
monomer (or growing chain of monomers), releasing a water molecule in the process. You can
remember what happens by the name of the reaction: dehydration, for the loss of the water
molecule, and synthesis, for the formation of a new bond.

In the dehydration synthesis reaction above, two molecules of the sugar glucose
(monomers) combine to form a single molecule of the sugar maltose. One of the glucose
molecules loses an H, the other loses an OH group, and a water molecule is released as a new
covalent bond forms between the two glucose molecules. As additional monomers join by the
same process, the chain can get longer and longer and form a polymer.
Even though polymers are made out of repeating monomer units, there is lots of room for variety
in their shape and composition. Carbohydrates, nucleic acids, and proteins can all contain
multiple different types of monomers, and their composition and sequence is important to their
function. For instance, there are four types of nucleotide monomers in your DNA, as well as
twenty types of amino acid monomers commonly found in the proteins of your body. Even a
single type of monomer may form different polymers with different properties. For example,
starch, glycogen, and cellulose are all carbohydrates made up of glucose monomers, but they
have different bonding and branching patterns.

Hydrolysis

How do polymers turn back into monomers (for instance, when the body needs to recycle one
molecule to build a different one)? Polymers are broken down into monomers
via hydrolysis reactions, in which a bond is broken, or lysed, by addition of a water molecule.
During a hydrolysis reaction, a molecule composed of multiple subunits is split in two: one of
the new molecules gains a hydrogen atom, while the other gains a hydroxyl (-OH) group, both of
which are donated by water. This is the reverse of a dehydration synthesis reaction, and it
releases a monomer that can be used in building a new polymer. For example, in the hydrolysis
reaction below, a water molecule splits maltose to release two glucose monomers. This reaction
is the reverse of the dehydration synthesis reaction shown above.

1. Carbohydrates
a. Dehydration Synthesis
b. Starch – polysaccharides in plants
c. Glycogen – polysaccharides in human
d. Hydrolysis
e. Cellulose - paper, cotton 98%, wood
f. Pyranose – 6th member ring (oxygen)
g. Furnose - 5th member ring (oxygen)
h. Sucrose – table sugar; disaccharide – glucose and fructose
Introduction

What’s in a spud? Besides water, which makes up most of the potato’s weight, there’s a little fat,
a little protein…and a whole lot of carbohydrate (about 37 grams in a medium potato).
Some of that carbohydrate is in the form of sugars. These provide the potato, and the person
eating the potato, with a ready fuel source. A bit more of the potato's carbohydrate is in the form
of fiber, including cellulose polymers that give structure to the potato’s cell walls. Most of the
carbohydrate, though, is in the form of starch, long chains of linked glucose molecules that are a
storage form of fuel. When you eat French fries, potato chips, or a baked potato with all the
fixings, enzymes in your digestive tract get to work on the long glucose chains, breaking them
down into smaller sugars that your cells can use.
 Carbohydrates are biological molecules made of carbon, hydrogen, and oxygen in a ratio of
roughly one carbon atom (\text CCstart text, C, end text) to one water molecule (\text H_2\text
OH2Ostart text, H, end text, start subscript, 2, end subscript, start text, O, end text). This
composition gives carbohydrates their name: they are made up of carbon (carbo-) plus water (-
hydrate). Carbohydrate chains come in different lengths, and biologically important
carbohydrates belong to three categories: monosaccharides, disaccharides, and polysaccharides.
In this article, we’ll learn more about each type of carbohydrates, as well as the essential
energetic and structural roles they play in humans and other organisms.

Monosaccharides

Monosaccharides (mono- = “one”; sacchar- = “sugar”) are simple sugars, the most common of

which is glucose. Monosaccharides have a formula of(\text {CH}_2\text O)_n(CH2O)nleft
parenthesis, start text, C, H, end text, start subscript, 2, end subscript, start text, O, end text, right
parenthesis, start subscript, n, end subscript, and they typically contain three to seven carbon
atoms.
[How is that formula different from carbohydrates in general?]
\text Cstart text, C, end text\text H_2\text Ostart text, H, end text, start subscript, 2, end
subscript, start text, O, end text
\text Cstart text, C, end text\text H_2\text Ostart text, H, end text, start subscript, 2, end
subscript, start text, O, end text
\text Hstart text, H, end text\text Ostart text, O, end text\text Cstart text, C, end text
Most of the oxygen atoms in monosaccharides are found in hydroxyl (\text {OH}OHstart text, O,
H, end text) groups, but one of them is part of a carbonyl (\text C=\text OC=Ostart text, C, end
text, equals, start text, O, end text) group. The position of the carbonyl (\text C=\text OC=Ostart
text, C, end text, equals, start text, O, end text) group can be used to categorize the sugars:
 If the sugar has an aldehyde group, meaning that the carbonyl C is the last one in the
chain, it is known as an aldose.
 If the carbonyl C is internal to the chain, so that there are other carbons on both sides of
it, it forms a ketone group and the sugar is called aketose.
Sugars are also named according to their number of carbons: some of the most common types are
trioses (three carbons), pentoses (five carbons), and hexoses (six carbons).
Glucose and its isomers

One important monosaccharide is glucose, a six-carbon sugar with the formula\text C_6\text
H_{12}\text O_6C6H12O6start text, C, end text, start subscript, 6, end subscript, start text, H,
end text, start subscript, 12, end subscript, start text, O, end text, start subscript, 6, end subscript.
Other common monosaccharides include galactose (which forms part of lactose, the sugar found
in milk) and fructose (found in fruit).
Glucose, galactose, and fructose have the same chemical formula (\text C_6\text H_{12}\text
O_6C6H12O6start text, C, end text, start subscript, 6, end subscript, start text, H, end text, start
subscript, 12, end subscript, start text, O, end text, start subscript, 6, end subscript), but they
differ in the organization of their atoms, making them isomers of one another. Fructose is
a structural isomer of glucose and galactose, meaning that its atoms are actually bonded
together in a different order.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides join together via a dehydration
reaction, also known as a condensation reaction or dehydration synthesis. In this process, the
hydroxyl group of one monosaccharide combines with the hydrogen of another, releasing a
molecule of water and forming a covalent bond known as a glycosidic linkage.
For instance, the diagram below shows glucose and fructose monomers combining via a
dehydration reaction to form sucrose, a disaccharide we know as table sugar. (The reaction also
releases a water molecule, not pictured.)

In some cases, it’s important to know which carbons on the two sugar rings are connected by a
glycosidic bond. Each carbon atom in a monosaccharide is given a number, starting with the
terminal carbon closest to the carbonyl group (when the sugar is in its linear form). This
numbering is shown for glucose and fructose, above. In a sucrose molecule, the 111 carbon of
glucose is connected to the 222 carbon of fructose, so this bond is called a 111-222 glycosidic
linkage.
Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide
consisting of glucose and galactose and is found naturally in milk. Many people can't digest
lactose as adults, resulting in lactose intolerance (which you or your friends may be all too
familiar with). Maltose, or malt sugar, is a disaccharide made up of two glucose molecules. The
most common disaccharide is sucrose (table sugar), which is made of glucose and fructose.

Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as
apolysaccharide (poly- = “many”). The chain may be branched or unbranched and may contain
different types of monosaccharides. The molecular weight of a polysaccharide can be quite high,
 reaching 100,100,100, comma000000000 daltons or more if enough monomers are joined.
Starch, glycogen, cellulose, and chitin are some major examples of polysaccharides important in
living organisms.
Storage polysaccharides
Starch is the stored form of sugars in plants and is made up of a mixture of two polysaccharides,
amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose using
light energy gathered in photosynthesis, and the excess glucose, beyond the plant’s immediate
energy needs, is stored as starch in different plant parts, including roots and seeds. The starch in
the seeds provides food for the embryo as it germinates and can also serve as a food source for
humans and animals, who will break it down into glucose monomers using digestive enzymes.
In starch, the glucose monomers are in the α form (with the hydroxyl group of
carbon 111 sticking down below the ring), and they are connected primarily by111-
444 glycosidic linkages (i.e., linkages in which carbon atoms 111 and 444 of the two monomers
form a glycosidic bond).
 Amylose consists entirely of unbranched chains of glucose monomers connected by 111-
444 linkages.
 Amylopectin is a branched polysaccharide. Although most of its monomers are
connected by 111-444 linkages, additional 111-666 linkages occur periodically and result in
branch points.
Because of the way the subunits are joined, the glucose chains in amylose and amylopectin
typically have a helical structure, as shown in the diagram below.

That’s great for plants, but what about us? Glycogen is the storage form of glucose in humans
and other vertebrates. Like starch, glycogen is a polymer of glucose monomers, and it is even
more highly branched than amylopectin.
Glycogen is usually stored in liver and muscle cells. Whenever blood glucose levels decrease,
glycogen is broken down via hydrolysis to release glucose monomers that cells can absorb and
uses.
Structural polysaccharides
Although energy storage is one important role for polysaccharides, they are also crucial for
another purpose: providing structure. Cellulose, for example, is a major component of plant cell
walls, which are rigid structures that enclose the cells (and help make lettuce and other veggies
crunchy). Wood and paper are mostly made of cellulose, and cellulose itself is made up of
unbranched chains of glucose monomers linked by 111-444 glycosidic bonds.

Unlike amylose, cellulose is made of glucose monomers in their β form, and this gives it very
different properties. As shown in the figure above, every other glucose monomer in the chain is
flipped over in relation to its neighbors, and this results in long, straight, non-helical chains of
cellulose. These chains cluster together to form parallel bundles that are held together by
hydrogen bonds between hydroxyl groups^{4,5}4,5start superscript, 4, comma, 5, end
superscript. This gives cellulose its rigidity and high tensile strength, which are important to
plant cells.
The β glycosidic linkages in cellulose can't be broken by human digestive enzymes, so humans
are not able to digest cellulose. (That’s not to say that cellulose isn’t found in our diets, it just
passes through us as undigested, insoluble fiber.) However, some herbivores, such as cows,
koalas, buffalos, and horses, have specialized microbes that help them process cellulose. These
microbes live in the digestive tract and break cellulose down into glucose monomers that can be
used by the animal. Wood-chewing termites also break down cellulose with the help of
microorganisms that live in their guts.
Cellulose is specific to plants, but polysaccharides also play an important structural role in non-
plant species. For instance, arthropods (such as insects and crustaceans) have a hard external
skeleton, called the exoskeleton, which protects their softer internal body parts. This exoskeleton
is made of the macromolecule chitin, which resembles cellulose but is made out of modified
glucose units that bear a nitrogen-containing functional group. Chitin is also a major component
of the cell walls of fungi, which are neither animals nor plants but form a kingdom of their own.
Take Down Notes #3
I. Triglyceride - fats/oils aka triacylglycerol/
a. Glycerol – sugar alcohol; back bone
b. Acyl – carboxyl; 3 axyl groups attached to fatty acids
c. Fatty Acids –
1. Saturated Fat – saturated by hydrogen as possible; butter; bad fats
2. Unsaturated Fats – mono unsaturated fat; one double bond; good fats; olive oils
3. Poly Unsaturated Fats – many double bond
a. Cis configuration – same side

b. Trans configuration – opposite side

4. trans fat – not typically found in nature; unhealthy

5. Lipids – not so soluble in water
a. Amphipathic – both hydrophilic/hydrophobic; phospholipids
b. Phospholipids – hydrocarbon (hydrophobic) phosphate (hydrophilic); good for cellular
membranes
c. Ester Group – carbon double bonded with oxygen and single bonded with oxygen attached
hydrocarbon chain; bees wax; repel water
d. Steroid – six carbon rings (3) one carbon ring
e. Sterol – steroid attached to OH (alcohol); cholesterol
a. Testosterone
b. Cortisol
Lipids

Introduction

We sometimes talk about fat as if it were a malevolent substance bent on our dietary destruction.
In reality, fats are elegant little molecules, each one made of three long hydrocarbon tails
attached to a little coathanger-like molecule called glycerol. Like the other large biological
molecules, they play essential roles in the biology of humans and other organisms. (Also, many
recent dietary studies see sugar as causing a lot more health problems than fat!)
Fats are just one type of lipid, a category of molecules united by their inability to mix well with
water. Lipids tend to be hydrophobic, nonpolar, and made up mostly of hydrocarbon chains,
though there are some variations on this, which we'll explore below. The different varieties of
lipids have different structures, and correspondingly diverse roles in organisms. For instance,
lipids store energy, provide insulation, make up cell membranes, form water-repellent layers on
leaves, and provide building blocks for hormones like testosterone.
Here, we’ll look in greater detail at some of the most important types of lipids, including fats and
oils, waxes, phospholipids, and steroids.
 Fats and oils

A fat molecule consists of two kinds of parts: a glycerol backbone and three fatty acid tails.
Glycerol is a small organic molecule with three hydroxyl (OH) groups, while a fatty acid consists
of a long hydrocarbon chain attached to a carboxyl group. A typical fatty acid contains 12–18
carbons, though some may have as few as 4 or as many as 36.
To make a fat molecule, the hydroxyl groups on the glycerol backbone react with the carboxyl
groups of fatty acids in a dehydration synthesis reaction. This yields a fat molecule with three
fatty acid tails bound to the glycerol backbone via ester linkages (linkages containing an oxygen
atom next to a carbonyl, or C=O, group). Triglycerides may contain three identical fatty acid
tails, or three different fatty acid tails (with different lengths or patterns of double bonds).

Fat molecules are also called triacylglycerols, or, in

bloodwork done by your doctor, triglycerides. In the human body, triglycerides are primarily
stored in specialized fat cells, called adipocytes, which make up a tissue known as adipose
tissue^11start superscript, 1, end superscript. While many fatty acids are found in fat molecules,
some are also free in the body, and they are considered a type of lipid in their own right.

Saturated and unsaturated fatty acids

As shown in the example above, the three fatty acid tails of a triglyceride need not be identical to
each other. Fatty acid chains may differ in length, as well as in their degree of unsaturation.
 If there are only single bonds between neighboring carbons in the hydrocarbon chain, a
fatty acid is said to be saturated. (The thing that fatty acids are saturated with is hydrogen; in a
saturated fat, as many hydrogen atoms as possible are attached to the carbon skeleton.)
 When the hydrocarbon chain has a double bond, the fatty acid is said to be unsaturated,
as it now has fewer hydrogens. If there is just one double bond in a fatty acid,
it’s monounsaturated, while if there are multiple double bonds, it’s polyunsaturated.
The double bonds in unsaturated fatty acids, like other types of double bonds, can exist in either
a cis or a trans configuration. In the cis configuration, the two hydrogens associated with the
bond are on the same side, while in a transconfiguration, they are on opposite sides (see below).
A cis double bond generates a kink or bend in the fatty acid, a feature that has important
consequences for the behavior of fats.

Saturated fatty acids tails are straight, so fat molecules with fully saturated tails can pack tightly
against one another. This tight packing results in fats that are solid at room temperature (have a
relatively high melting point). For instance, most of the fat in butter is saturated fat^22squared.
In contrast, cis-unsaturated fatty acid tails are bent due to the cis double bond. This makes it hard
for fat molecules with one or more cis-unsaturated fatty acid tails to pack tightly. So, fats with
unsaturated tails tend to be liquid at room temperature (have a relatively low melting point) –
they are what we commonly call oils. For instance, olive oil is mostly made up of unsaturated
fats^22squared.

Trans fats

At this point, you may be noticing that I’ve left something out: I didn’t say anything about
unsaturated fats with trans double bonds in their fatty acid tails, or trans fats. Trans fats are rare
in nature, but are readily produced in an industrial procedure called partial hydrogenation.
In this process, hydrogen gas is passed through oils (made mostly of cis-unsaturated fats),
converting some – but not all – of the double bonds to single bonds. The goal of partial
hydrogenation is to give the oils some of the desirable properties of saturated fats, such as
solidity at room temperature, but an unintended consequence is that some of the cis double bonds
change configuration and become trans double bonds^33cubed. Trans-unsaturated fatty acids
can pack more tightly and are more likely to be solid at room temperature. Some types of
shortening, for example, contain a high fraction of trans fats^33cubed.
Partial hydrogenation and trans fats might seem like a good way to get a butter-like substance at
oil-like prices. Unfortunately, trans fats have turned out to have very negative effects on human
health. Because of a strong link between trans fats and coronary heart disease, the U.S. Food and
Drug Administration (FDA) recently issued a ban on trans fats in foods, with a three-year
deadline for companies to remove trans fats from their products^44start superscript, 4, end
superscript.
Omega fatty acids

Another class of fatty acids that deserves mention includes the omega-3 andomega-6 fatty acids.
There are different types of omega-3 and omega-6 fatty acids, but all of them are made from two
basic precursor forms: alpha-linolenic acid (ALA) for omega-3s and linoleic acid (LA) for
omega-6s.
The human body needs these molecules (and their derivatives), but can't synthesize either ALA
or LA itself^55start superscript, 5, end superscript. Accordingly, ALA and LA are classified
asessential fatty acids and must be obtained from a person’s diet. Some fish, such as salmon,
and some seeds, such as chia and flax, are good sources of omega-3 fatty acids.
Omega-3 and omega-6 fatty acids have at least two cis-unsaturated bonds, which gives them a
curved shape. ALA, shown below, is quite bent but isn’t the most extreme example – DHA, an
omega-3 fatty acid made from ALA by the formation of additional double bonds, has six cis-
unsaturated bonds and is curled up almost in a circle! 
[What makes a fatty acid omega-3 or omega-6?]

Fat molecules are also called triacylglycerols, or, in bloodwork done by your

doctor, triglycerides. In the human body, triglycerides are primarily stored in specialized fat
cells, called adipocytes, which make up a tissue known as adipose tissue^11start superscript, 1,
end superscript. While many fatty acids are found in fat molecules, some are also free in the
body, and they are considered a type of lipid in their own right.

Saturated and unsaturated fatty acids

As shown in the example above, the three fatty acid tails of a triglyceride need not be identical to
each other. Fatty acid chains may differ in length, as well as in their degree of unsaturation.
 If there are only single bonds between neighboring carbons in the hydrocarbon chain, a
fatty acid is said to be saturated. (The thing that fatty acids are saturated with is hydrogen; in a
saturated fat, as many hydrogen atoms as possible are attached to the carbon skeleton.)
 When the hydrocarbon chain has a double bond, the fatty acid is said to be unsaturated,
as it now has fewer hydrogens. If there is just one double bond in a fatty acid,
it’s monounsaturated, while if there are multiple double bonds, it’s polyunsaturated.
The double bonds in unsaturated fatty acids, like other types of double bonds, can exist in either
a cis or a trans configuration. In the cis configuration, the two hydrogens associated with the
bond are on the same side, while in a transconfiguration, they are on opposite sides (see below).
A cis double bond generates a kink or bend in the fatty acid, a feature that has important
consequences for the behavior of fats.

Saturated fatty acids tails are straight, so fat molecules with fully saturated tails can pack tightly
against one another. This tight packing results in fats that are solid at room temperature (have a
relatively high melting point). For instance, most of the fat in butter is saturated fat^22squared.
In contrast, cis-unsaturated fatty acid tails are bent due to the cis double bond. This makes it hard
for fat molecules with one or more cis-unsaturated fatty acid tails to pack tightly. So, fats with
unsaturated tails tend to be liquid at room temperature (have a relatively low melting point) –
they are what we commonly call oils. For instance, olive oil is mostly made up of unsaturated
fats^22squared.

Trans fats

At this point, you may be noticing that I’ve left something out: I didn’t say anything about
unsaturated fats with trans double bonds in their fatty acid tails, or trans fats. Trans fats are rare
in nature, but are readily produced in an industrial procedure called partial hydrogenation.
In this process, hydrogen gas is passed through oils (made mostly of cis-unsaturated fats),
converting some – but not all – of the double bonds to single bonds. The goal of partial
hydrogenation is to give the oils some of the desirable properties of saturated fats, such as
solidity at room temperature, but an unintended consequence is that some of the cis double bonds
change configuration and become trans double bonds^33cubed. Trans-unsaturated fatty acids
can pack more tightly and are more likely to be solid at room temperature. Some types of
shortening, for example, contain a high fraction of trans fats^33cubed.
Partial hydrogenation and trans fats might seem like a good way to get a butter-like substance at
oil-like prices. Unfortunately, trans fats have turned out to have very negative effects on human
health. Because of a strong link between trans fats and coronary heart disease, the U.S. Food and
Drug Administration (FDA) recently issued a ban on trans fats in foods, with a three-year
deadline for companies to remove trans fats from their products^44start superscript, 4, end
superscript.

Omega fatty acids

Another class of fatty acids that deserves mention includes the omega-3 andomega-6 fatty acids.
There are different types of omega-3 and omega-6 fatty acids, but all of them are made from two
basic precursor forms: alpha-linolenic acid (ALA) for omega-3s and linoleic acid (LA) for
omega-6s.
The human body needs these molecules (and their derivatives), but can't synthesize either ALA
or LA itself^55start superscript, 5, end superscript. Accordingly, ALA and LA are classified
asessential fatty acids and must be obtained from a person’s diet. Some fish, such as salmon,
and some seeds, such as chia and flax, are good sources of omega-3 fatty acids.
Omega-3 and omega-6 fatty acids have at least two cis-unsaturated bonds, which gives them a
curved shape. ALA, shown below, is quite bent but isn’t the most extreme example – DHA, an
omega-3 fatty acid made from ALA by the formation of additional double bonds, has six cis-
unsaturated bonds and is curled up almost in a circle! 
[What makes a fatty acid omega-3 or omega-6?]

Omega-3 and omega-6 fatty acids play a number of different roles in the body. They are
precursors (starting material) for the synthesis of a number of important signaling molecules,
including ones that regulate inflammation and mood. Omega-3 fatty acids in particular may
reduce the risk of sudden death from heart attacks, decrease triglycerides in the blood, lower
blood pressure, and prevent the formation of blood clots.

Role of fats

Fats have received a lot of bad publicity, and it’s true that eating large amounts of fried foods
and other “fatty” foods can lead to weight gain and cause health problems. However, fats are
essential to the body and have a number of important functions.
For instance, many vitamins are fat-soluble, meaning that they must be associated with fat
molecules in order to be effectively absorbed by the body. Fats also provide an efficient way to
store energy over long time periods, since they contain over twice as much energy per gram as
carbohydrates, and they additionally provide insulation for the body.
Like all the other large biological molecules, fats in the right amounts are necessary to keep your
body (and the bodies of other organisms) functioning correctly.

Waxes

Waxes are another biologically important category of lipids. Wax covers the feathers of some
aquatic birds and the leaf surfaces of some plants, where its hydrophobic (water-repelling)
properties prevent water from sticking to, or soaking into, the surface. This is why water beads
up on the leaves of many plants, and why birds don’t get soaked through when it rains.
tructurally speaking, waxes typically contain long fatty acid chains connected to alcohols by
ester linkages, although waxes produced by plants often have plain hydrocarbons mixed in as
well^66start superscript, 6, end superscript.

Phospholipids

What keeps the watery goo (cytosol) inside of your cells from spilling out? Cells are surrounded
by a structure called the plasma membrane, which serves as a barrier between the inside of the
cell and its surroundings.
Specialized lipids called phospholipids are major components of the plasma membrane. Like
fats, they are typically composed of fatty acid chains attached to a backbone of glycerol. Instead
having three fatty acid tails, however, phospholipids generally have just two, and the third
carbon of the glycerol backbone is occupied by a modified phosphate group. Different
phospholipids have different modifiers on the phosphate group, with choline (a nitrogen-
containing compound) and serine (an amino acid) being common examples. Different modifiers
give phospholipids different properties and roles in a cell.
A phospholipid is an amphipathic molecule, meaning it has a hydrophobic part and a
hydrophilic part. The fatty acid chains are hydrophobic and do not interact with water, whereas
the phosphate-containing group is hydrophilic (because of its charge) and interacts readily with
water. In a membrane, phospholipids are arranged into a structure called a bilayer, with their
phosphate heads facing the water and their tails pointing towards the inside (above). This
organization prevents the hydrophobic tails from coming into contact with the water, making it a
low-energy, stable arrangement.
If a drop of phospholipids is placed in water, it may spontaneously form a sphere-shaped
structure known as a micelle, in which the hydrophilic phosphate heads face the outside and the
fatty acids face the interior of this structure. Formation of micelle is an energetically favored
because it sequesters the hydrophobic fatty acid tails, allowing the hydrophilic phosphate head
group to instead interact with the surrounding water^{7,8}7,8start superscript, 7, comma, 8, end
superscript. 
[More details]
^{7,8}start superscript, 7, comma, 8, end superscript

Steroids

Steroids are another class of lipid molecules, identifiable by their structure of four fused rings.
Although they do not resemble the other lipids structurally, steroids are included in lipid
category because they are also hydrophobic and insoluble in water. All steroids have four linked
carbon rings and several of them, like cholesterol, also have a short tail. Many steroids also have
an –OH functional group attached at a particular site, as shown for cholesterol below; such
steroids are also classified as alcohols, and are thus called sterols.
Cholesterol, the most common steroid, is mainly synthesized in the liver and is the precursor to
many steroid hormones. These include the sex hormones testosterone and estradiol, which are
secreted by the gonads (testes and ovaries). Cholesterol also serves as the starting material for
other important molecules in the body, including vitamin D and bile acids, which aid in the
digestion and absorption of fats from dietary sources. It’s also a key component of cell
membranes, altering their fluidity and dynamics.
Of course, cholesterol is also found in the bloodstream, and blood levels of cholesterol are what
we often hear about at the doctor’s office or in news reports. Cholesterol in the blood can have
both protective effects (in its high-density, or HDL, form) and negative effects (in its low-
density, or LDL, form) on cardiovascular health.
DNA
Take Down Notes #4
DNA
1. DNA – 1800 studies; found in nucleus of a eukaryote;
a. Gregor Mendel – Father of Genetics
b. Back bone – combination of sugar and phosphate (deoxyribose)
c. Rungs – basis
a. Adenine pairs Thymine
b. Guanine pairs Cytosine
d. Human genome – 6 billion base pairs; 46 chromosomes
2. DNA Replication
a. Replication
b. Expression
a. DNA – structure
b. Chromosomes – patch together with other structure; broader structure
c. Gene – a section of DNA use to express a certain trait or code a type of protein
c. RNA – messenger on a certain DNA
a. mRNA – transcription (protein)
i. Adenine pair Uracil
ii. Thymine pair Adenine
iii. Guanine pair Cytosine
b. tRNA – translation
i. 3 basis – amino acid code (codon)
ii. 64 possible codon
3. Molecular Structure of DNA
a. Group of nucleotides
a. Phosphate – makes the DNA acid
b. Ribose – 5 carbon ring; no oxygen
 c. Nitrogenous Bases
i. 2 rings – purines (adenine and guanine)
ii. 1 ring – pyrimidine (thymine and cytosine)
d. Bond by hydrogen

Take Down Notes #4 (Cells)

I. Introduction of Cells
1. Robert Hooke – primitive microscope; name ‘cells’
2. Antonie Van Leeuwonhoek – sperm, protist, animalcules
3. Modern Cell Theory
a. Schleiden
b. Schwann
a. All life is composed of one or more cells
b. Cell is basic unit of life
4. Remak – all cells comes from other cells
a. Virchow – plagiarize Remak work

II. Cell Size

1. Egg Cells – one of the largest cells

III. Prokaryotic and Eukaryotic Cells – Bacteria – Archaea – Eukaryote

1. Eukaryote
a. Nuclear Membrane
b. Mitochondria – plant and animal cells
c. Nucleolus – rRNA produced
d. DNA – multiple single strand
e. Larger
f. Multicellular Organisms
g. Protist – unicellular but a eukaryote
h. number of membrane-bound organelles
2. Prokaryote
a. No Nuclear Membrane
b. No Mitochondtria
c. DNA – circular
d. Simpler/Smaller
e. Bacteria
f. Archaea
IV. Prokaryotic Cells
1. Prokaryotes—pro means before and kary means nucleus
2. Eukaryotes—eu means true i.e Animals, plants, fungi, and protists
3. Components of Prokaryotic Cells
a. Plasma membrane- outer covering that separates the cell’s interior from its surrounding
environment.
b. Cytoplasm- consists of the jelly-like cytosol inside the cell, plus the cellular structures suspended
in it. In eukaryotes, cytoplasm specifically means the region outside the nucleus but inside the
plasma membrane.
c. DNA- genetic material of the cell.
d. Ribosomes- molecular machines that synthesize proteins.
4. Nucleoid - majority of prokaryotic DNA is found, circular chromosome
5. Peptidoglycan - rigid cell wall, polymer composed of linked carbohydrates and small proteins
6. Cell wall - extra layer of protection, helps the cell maintain its shape, and prevents dehydration
7. Capsule - outermost layer of carbohydrates, sticky and helps the cell attach to surfaces in its
environment.
8. Flagella - whip-like structures that act as rotary motors to help bacteria move. Move, stick to surfaces,
or even exchange genetic material with other bacteria. 
9. Fimbriae- numerous, hair-like structures that are used for attachment to host cells and other
surfaces. 
10. Pili - rod-like structures, ¹allow a bacterium to transfer DNA molecules to other bacteria, ² bacterial
locomotion—helping the bacterium move.
V. Eukaryotic Cells
1. Lysosomes- recycling centers for the cell, must maintain an acidic pH in order to dispose of cellular
waste. 
2. Peroxisomes - carry out chemical reactions called oxidation reactions and produce hydrogen
peroxide, both of which would damage the cell if they weren’t safely stored away in their own “room.”
3. Animal Cell vs. Plant Cell

VI. The Plasma Membrane and Cytoplasm

1. Plasma membrane
a. Prokaryotic and eukaryotic
b. Double layer of lipids - phospholipids
c. Separates the cell interior from the outside environment.
d. Phospholipid bilayer - hydrophobic tails pointing inward and their hydrophilic heads facing
outward
e. Microvilli- the membranes of some nutrient-absorbing cells are folded into fingerlike projections
i.e small intestine
2. Cytoplasm
a. Eukaryotic cells- cytoplasm is everything between the plasma membrane and the nuclear
envelope
b. Prokaryotes cells- cytoplasm simply means everything found inside the plasma membrane.
c. Cytosol- water-based solution that contains ions, small molecules, and macromolecules
d. Cytoskeleton- network of fibers that supports the cell and gives it shape, part of the cytoplasm,
helps to organize cellular components.
VII. Nucleus and Ribosomes
1. Nucleus
a. Eukaryotic- DNA never leaves the nucleus; transcribed (copied) into RNA molecules, travel out of
the nucleus. In the cytosol, some RNAs associate with structures called ribosomes, where they
direct synthesis of proteins.
b. houses the cell’s genetic material, or DNA
c. site of synthesis for ribosomes
d. nucleoplasm- chromatin is stored; gel-like
e. nuclear envelope- enclosing the nucleoplasm; outer membrane and an inner membrane; thin
space between the two layers of the nuclear envelope, and this space is directly connected to
the interior of another membranous organelle, the endoplasmic reticulum.
f. Nuclear pores- small channels that span the nuclear envelope; substances enter and exit the
nucleus
g. nuclear pore complex- lined by a set of proteins; control what molecules can go in or out
h. chromosomes- very long string or loop of DNA; 46 in humans; visible as distinct structures when
the cell is getting ready to divide
i. chromatin- complex formed by DNA and its supporting structural proteins
2.  Ribosomes
a. Molecular machines responsible for protein synthesis; made out of RNA and proteins
b. Rough endoplasmic reticulum- endoplasmic reticulum with bound ribosomes

VIII. Endoplasmic Reticulum and Golgi Bodies

1. Transcription Nucleus (DNA →mRNA) → (Ribosomes) Protein (Translation)
2. Nuclear Pore- tunnel to let the chromatin out; proteins.
3. Cytosol – all the fluids between the organelles
4. Cytoplasm- everything inside the cells, cytosol and the organelles