1. What is Chemistry? Why is it important in Biology?

- Chemistry is the rational and empirical study of the structure of matter in natural

processes and in planed experiments1.

- Chemistry is defined as the study of the composition, structure, and properties of

matter and of the reactions by which one form of matter may be produced from our

converted into other form2 .

Chemistry is important to Biology because it studies the chemical composition,

structure, and reactions occuring in life forms (such as animals and plants)as well as

microscopic organisms (such as bacteria, protozoa, virus,etc.) . The collaboration of

these two fields of science leads to the emergence of a field known as Biochemistry, the

science which studies the chemistry of living organisms, including human beings, the

chemistry of biological substances and processes.

To give a colored picture why chemistry is important to Biology, the researcher gives

the cell as a good illustration. Cell is the structural and functional basis of all living

organisms. The cell has the abundant organic compounds called proteins3 . These

proteins are the main constituents of protoplasm. Proteins are made up of carbon,

hydrogen, and nitrogen atoms, sulfur, phosporous and irons. The role of proteins is to

build and repair body cells and make-up protein and protein synthesis (such as mRNA,

tRNA, and rRNA; and serves as transport molecules, reserve food, and provide protection

like antibodies.1

1 Keenan, Charles W. and Wood, Jesse H. (1966). College Chemistry. Quezon City: Ken Incorporated, pp.22 Committee in College Chemistry of PUP (Revised Ed.2007). General Chemistry- Lecture Guide 1, pp.23 Capco, Carmelita M. and Yang, Gilbert C. (1990). Biology. Quezon City: Phoenix Press Incorporated, pp. 32-33;93

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2. Differentiate the meaning of atoms, elements, and molecules. Providing the

examples to substantiate your answers.

- Atom is the smallest particle of an element that has the chemical characteristics of

that element4. The atom is composed of inner structures called electrons, protons, and

neutrons.

- An element is a substance which cannot e decomposed or separated into simpler

substances by chemical means, or a pure substance that contain only one kind of

atom5. Examples are hydrogen (H), nitrogen (N), iron (K), oxygen (O), antimony (Sb)

, and copper (Cu).

- A molecule is defined as an electrically neutral group of at least two atoms in a

definite arrangement held together by very strong (covalent) chemical bonds6. A

molecule may consist of atoms of a single chemical element, as with oxygen (O2), or

of different elements, as with water (H2O).

3. What is the difference between Inorganic and Organic Chemistry?

- Inorganic Chemistry is the study of chemical elements of their compounds with the

exception of carbon compounds while Organic Chemistry is the study of substances

produces by living organisms7.

4 Committee in College Chemistry of PUP (Revised Ed.2007). General Chemistry- Lecture Guide 1, pp.585 Committee in College Chemistry of PUP (Revised Ed.2007). General Chemistry- Lecture Guide 1, pp.436 http://en.wikipedia.org/wiki/Molecules7 Committee in College Chemistry of PUP (Revised Ed.2007). General Chemistry- Lecture Guide 1, pp.2

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4. What are the three (3) types of Carbohydrates? Provide a graphical presentation of

each.

- The Three Types of Carbohydrates are the following8:

4a. MONOSACCHARIDES- simple sugars; important source of energy for the cells;

subunit of which most polysaccharides are made.

4a.1. Glucose (Blood Sugar) - the

most abundant sugar in the body. It is

the body’s main fuel and is broken

down during aerobic respiration to

release by digesting other

carbohydrates such as starch or

sucrose. The level of glucose in the blood is controlled by hormones. Glucose can be

stored by converting it into glycogen and released again by breaking down the

glycogen.

4a.2. Fructose (Fruit Sugar/ Laevulose)- a very sweet sugar found in all sweet

fruits, leaves, roots of plants and honey and used as preservative for food stuffs, and

as an intravenous nutrient.2

4a.3. Galactose – a sugar derived from the milk (lactose).

4b. DISSACCHARIDES – double sugar; the monosaccharide bonded together; principle

sugar transported throughout the bodies of land plants.

28 Mangahas , Rosal.Hand-Outs in Biological Science (NASC 1083).2009, pp.17

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4b.1. Lactose (Milk Sugar) – glucose +

galactose. Lactose is a sugar that provides energy

for growing infants. It is found in human milk, and

also in cow’s milk and dairy products. Lactose is broken down during digestion by an

enzyme called lactase. Some adults can’t make the enzyme lactase and so cannot digest

the lactose found in the milk.

4b.2. Maltose (Malt Sugar) - glucose +

glucose; formed during the formation of starch

and also occurring in germinating cereal grains.

4b.3. Sucrose (Cane Sugar/ Table Sugar) –

glucose + fructose; found in plant sap, mainly

sugar cane and sugar beet, and used widely as a

sweetener, preservative and in the manufacture of

plastics and cellulose. Also called “sugar

saccharose”.

c. POLYSACCHARIDES – complex sugar; multiple monosaccharide (usually glucose) bonded

together9.

4c. 1. Starch – energy storage in plants,

and main carbohydrates in food. They are

found in cereals such as wheat and rice, and in

other crops, including potatoes. Its molecules

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form long branching chains. During digestion, starch is broken down to form maltose,

which is made of two glucose units. Maltose is broken down into glucose itself.

4c. 2. Glycogen – the principal

carbohydrates storage material in the body. It is a

polysaccharide, consisting of many saccharide

(sugar) molecules linked to form a new chain,and

is found mainly and liver and muscles.

4c. 3. Cellulose – structural materials in

plants; not digested by humans but aids movement

of food through intestines. Leaves and the pulpy

and fibrous parts are good sources of cellulose

which serves as a roughage.

4c. 4. Chitin – a semi-transparent

horny substance, primarily a

monosaccharide, forming a principal

component of arthropod exoskeleton and

the cell of certain lungs.

9 Mangahas , Rosal.Hand-Outs in Biological Science (NASC 1083).2009, pp.18

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5. What are the four types of protein (according to structure)? Briefly describe each of them and name at least two examples of each.

- The Four Types of Protein (According to structure) are the following:

1. Primary Structure – is defined by the amino acids residue sequence of the polypeptide

chain. This sequence determines the shapes, or conformations, into which protein can be

arranged10.

11In general, polypeptides are unbranched polymers, so their primary structure can often be

specified by the sequence of amino acids along their backbone. However, proteins can become

cross-linked, most commonly by disulfide bonds, and the primary structure also requires

specifying the cross-linking atoms, e.g., specifying the cysteines involved in the protein's

disulfide bonds. Other crosslinks include desmosine...

The chiral centers of a polypeptide chain can undergo racemization. In particular, the L-amino

acids normally found in proteins can spontaneously isomerize at the Cα atom to form D-amino

acids, which cannot be cleaved by most proteases.

Finally, the protein can undergo a variety of posttranslational modifications, which are briefly

summarized here.

The N-terminal amino group of a polypeptide can be modified covalently, e.g.

acetylation − C( = O) − CH3

10 Shier,David; Butler, Jackie; and Lewis, Ricki. Hole’s Human Anatomy and Physiology. 2004 McGrawHill Companies Inc., pp.809 11 http://en.wikipedia.org/wiki/Primary_structure

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N-terminal acetylation

The positive charge on the N-terminal amino group may be eliminated by changing it to

an acetyl group (N-terminal blocking).

formylation − C( = O)H

The N-terminal methionine usually found after translation has an N-terminus blocked

with a formyl group. This formyl group (and sometimes the methionine residue itself, if

followed by Gly or Ser) is removed by the enzyme deformylase.

pyroglutamate-

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Formation of pyroglutamate from an N-terminal glutamine

An N-terminal glutamine can attack itself, forming a cyclic pyroglutamate group.

myristoylation

Similar to acetylation. Instead of a simple methyl group, the myristoyl group has a tail of

14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular

membranes.

The C-terminal carboxylate group of a polypeptide can also be modified, e.g.,

C-terminal amidation

amidation (see Figure)

The C-terminus can also be blocked (thus, neutralizing its negative charge) by amidation.

glycosyl phosphatidylinositol (GPI) attachment

Glycosyl phosphatidylinositol is a large, hydrophobic phospholipid prosthetic group that

achors proteins to cellular membranes. It is attached to the polypeptide C-terminus

through an amide linkage that then connects to ethanolamine, thence to sundry sugars and

finally to the phosphatidylinositol lipid moiety.

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2. Secondary Structure12 – is a regular, repeating three-dimensional conformation held together

by hydrogen bonding between components of the amide bonds of the primary chain. Hydrogen

bonding

can be between bond in the same chain. Hydrogen bonding can be between bonds in the same

chain

(for instance, the α-helix) or between bonds in the adjacent chains (for instance, the β-pleated

sheet).

The secondary structure imparts strength to proteins.

13The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe

the protein secondary structure with single letter codes. The secondary structure is assigned

based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before

any protein structure had ever been experimentally determined). There are eight types of

secondary structure that DSSP defines:

G = 3-turn helix (310 helix). Min length 3 residues.

H = 4-turn helix (α helix). Min length 4 residues.

I = 5-turn helix (π helix). Min length 5 residues.

T = hydrogen bonded turn (3, 4 or 5 turn)

12 Shier,David; Butler, Jackie; and Lewis, Ricki. Hole’s Human Anatomy and Physiology. 2004 McGrawHill Companies Inc., pp.809

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E = extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2

residues.

B = residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)

S = bend (the only non-hydrogen-bond based assignment)

Amino acid residues which are not in any of the above conformations are assigned as the eighth

type 'Coil': often codified as ' ' (space), C (coil) or '-' (dash). The helices (G,H and I) and sheet

conformations are all required to have a reasonable length. This means that 2 adjacent residues in

the primary structure must form the same hydrogen bonding pattern. If the helix or sheet

hydrogen bonding pattern is too short they are designated as T or B, respectively.

but they are less frequently used. Other protein secondary structure assignment categories exist

(sharp turns, Omega loops etc.), but they are less frequently used.

13 http://en.wikipedia.org/wiki/Secondary_structure#DSSP_H-bond_definition

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The left panel shows the hydrogen bonding in an actual α-helix backbone. Note that the nth

residue O (Lys 143) bonds to the (n 4)th following residue's N (Arg 147). The actual values of

some displayed H-bond distances give you some idea about the variations to expect within a

helix. The center panel includes the side chains which were omitted in the left panel for clarity.

You see the side chains pointing towards the N-terminal of the chain (lower residue numbers)

and thus it is usually possible to determine the direction of the helix quite well during initial

model building. A 0.2 nm electron density is shown in the right panel.

3. Tertiary Structure14 – is the overall three-dimensional structural conformation of the protein

molecule. Various kinds of bonding interactions between the components of the amino acid side

chains stabilize the tertiary structrure.

15Tertiary structure refers to a higher level of

folding in which the helices and sheets of the

secondary structure fold upon themselves. This

higher level folding arises for several reasons.

First, different regions of the amino acid chain are

hydrophilic or hydrophobic and arrange themselves accordingly in water. Second different

regions of the chain bond with each other via hydrogen bonding or disulfide linkages. 

This kind of structure is most important in globular proteins such as this insulin molecule, shown

in cartoon form by RasMol to indicate the folding of helices.

14 Shier,David; Butler, Jackie; and Lewis, Ricki. Hole’s Human Anatomy and Physiology. 2004 McGrawHill Companies Inc., pp.80915 http://staff.jccc.net/pdecell/biochemistry/protstruc.html

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4. Quaternary Structure16 – present in some proteins, describes the three-dimensional

arrangement of subunits linked together by non-covalent bonds. The subunits have their own

primary, secondary, and tertiary structures. Quarternary structure is often a prerequisite for

protein involved in the control of metabolic process.

17Quaternary structure arises when polypeptide chains are bound together usually by hydrogen

bonds. For example hemoglobin the oxygen carrying protein in blood has four subunits hydrogen

bonded together. Most proteins with a molecular weight of 50,000 or more are made of such

units. 

Sometimes quaternary structure maybe very complex. For example, beef glutamate

dehydrogenase is an enzyme with a molecular weight of 2,200,000. Each enzyme molecule

consists of eight large subunits. In turn, each of these consists of numerous smaller units. 

The interesting thing about proteins made of polypeptide subunits is that given the right solution,

they self assemble into a complete and functional protein.

The cell takes full advantage of this property to rapidly generate the cytoskeleton much of which

consists of very long chains or helices, or tubes of protein sub-units as in the example below. 

 This is just a small section of a long double helix made

out

of thousands of small protein sub units, and illustrates

the size of structures the cell can build using protein

subunits.

16 Shier,David; Butler, Jackie; and Lewis, Ricki. Hole’s Human Anatomy and Physiology. 2004 McGrawHill Companies Inc., pp.80917 http://staff.jccc.net/pdecell/biochemistry/protstruc.html

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