AP Biology Dr Haitham AbdAllah

0100 36 777 19

Biochemistry
Atoms,Molecules, and Compounds
• Atoms are fundamental units of the physical world , Individual atoms combine in
chemical reactions to form molecules

atom + atom → molecule

H + H → H2

• Thus, a molecule is just a combination of atoms. Molecules can react with other
atoms or other molecules to form larger molecules.

2 H2 + O2 → 2 H2O

Reactants → Products

• If a molecule contains different types of atoms (for ex : H 2 Oand CCl 4 ) It’ s called a
Compound……
• Every Compound is a molecule but not every molecule is a compound
• Reactants → Substances interacting (on left side of the arrow)
• Products → results of chemical interaction (on the right)

Organic Chemistry
• It’s chemistry of molecules and compounds that contain carbon
• Molecules and compounds that contain carbon are ORGANIC, while molecules
that don’t contain carbon are INORGANIC

Only 1 Exception : Carbon Dioxide (CO 2 ) Contains Carbon and is INORGANIC

• Biomolecules : Biologically Important organic molecules

• There are 4 Biologically Important Organic Macromolecules (Very Large
Molecules)
1. Proteins
2. Carbohydrates
3. Lipids
4. Nucleic acid

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Cellular and molecular biology
 AP Biology Dr Haitham AbdAllah
0100 36 777 19

1- Proteins
• Proteins are polymers of amino acids ( String ‫ ﺳﻠﺴﻠﺔ طﻮﯾﻠﺔ ﻣﻦ وﺣﺪات ﻣﺘﻜﺮرة‬of
repeated amino acids) ( the individual unit is called → Monomer ‫اﻟوﺣدة‬
‫اﻟواﺣدة ﺑس‬
• There are only 20 different amino acids but proteins are a lot
• all amino acids have same basic
backbone but differ in R group

Carboxylic group. COOH

• R could be anything from simple

hydrogen atom to a whole long chain of carbon atoms
with different groups bonded to it
Amino group • R is different from amino acid to another ( it gives amino acid its
identity)
• Ex 1 : In Glycine amino acid the R is hydrogen atom
• Ex 2 : In Cysteine .. R is Carbon with 2 H atoms and SH bonded to it

Glycine Cystiene

R
R

N.B : Enzymes are proteins

• Proteins are responsible for growth and repair

• Dietary sources of proteins include fish, poultry, meat, and certain
plants called legumes, like beans and peanuts
• 1 gram of protein burned in a calorimeter releases 4 calories of heat
• Proteins consist of the elements S, P, C, O, H, and N
• Amino acids bond together to form protein

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

• Formation of peptide bond involves removal of H2O molecule, so it’s

called dehydration synthesis ( condesnsation reaction)
• and breakage of it requires addition of water ( Hydrolysis)
• Protein is referred to as poly peptide ( poly=many) due to presence of
many peptide bonds between amino acids
• Proteins functions : They are enzymes, hormones , channels,
carriers,messengers and structural units ……
• function of protein depends on its shape

• The shape of a protein, in turn, is the result of 4 levels of structure:

primary, secondary, tertiary, and quaternary

• Primary structure results from sequence ( string ) of amino acids that

make up protein chain

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

• Secondary structure results from hydrogen bonding within protein (

The helical ‫ ﺣﻠﺰوﻧﻰ‬nature of many proteins is result of hydrogen
bonding ‫) ﺑﯿﻜﻮن ﻻﻓﻒ زى اﻟﺴﻠﻚ‬

- It refers to how the polypeptide coils or folds into two distinct

shapes: an alpha helix or a beta pleated sheet. Proteins that
exhibit either alpha helix or beta pleated sheet or both are called
fibrous proteins. Examples of fibrous proteins are wool, claws,
beaks, reptile scales, collagen, and ligaments.
- The protein that makes up human hair, keratin, is composed
mostly of alpha helixes, while silk and spider webs consist of
proteins made of beta pleated sheets

• Tertiary structure is the intricate ‫ ﻣﻌﻘﺪ‬3D shape or conformation of a

protein and most directly determines the way it functions and its
U

specificity

• ‫ ھﺎم‬Enzymes denature (lose their natural shape) in high

temperatures or adverse pH , When a protein/ enzyme denatures, it
cannot function because its tertiary structure has been altered ‫اﺗﻐﯿﺮ‬
beyond repair

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

The following intramolecular factors contribute to the tertiary structure:

■ Hydrogen bonding between R groups of amino acids

■ Ionic bonding between R groups
■ Hydrophobic interactions
■ Van der Waals interactions
■ Disulfide bonds between cysteine amino acids

• Quaternary structure refers to proteins that consist of more than one

polypeptide chain ex : Hemoglobin has quaternary structure because
it consists of four polypeptide chains

Responsible for
protein’s
function

Remember : Protein → polymer Amino acid → Monomer

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

2-Carbohydrates:
• Carbohydrates supply quick energy
• Saccharide is the monomer for carbohydrate .. saccharide refers to sweetness
• Dietary sources include rice, pasta, bread, potato, and cookies
• Carbohydrates are sugar molecules....all of them are made of Carbon, Hydrogen,
and Oxygen

a. Monosaccharides :

• are made of only 1 saccharide (1 monomer) ex : glucose, fructose, galactose ……

• The monomer itself is considered a carbohydrate
• Monosaccharides are made of carbon, oxygen and hydrogen in a FIXED RATIO ;
no. of carbon atoms = no. of oxygen atoms and no. of hydrogen atoms = Double
no. of oxygen or carbon…. The molecular formula for a Monosaccharide is

C n H 2n O n

• Ex: glucose, fructose and galactose → all are isomers of each other

o Isomers are compounds with → same molecular formula, but with

different structures ( different structural formula ) → so they have
different physical and chemical properties

Ex: glucose, Fructose and galactose → C 6 H 12 O 6

• They have same chemical formula and no. of atoms but differ in Orientation /
position / arrangement of atoms within the molecule

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

• Glucose and fructose differ in the way the double-bonded

oxygen is oriented within the molecule
• Glucose can also form a ring structure like this →

Also can form this shape :

N.B : Glucose is the primary form of cellular food

N.B : Glucose is the most readily used source of energy

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

• There are three types of isomers: structural isomers, cis-trans isomers, and
enantiomers. Structural isomers differ in the arrangement of their atoms. Cis-trans
isomers differ only in spatial arrangement around double bonds, which are not
flexible like single bonds are.
• Enantiomers are molecules that are mirror images of each other. The mirror
images are called the L- (left-handed) and D- (right-handed) versions. Knowledge
of enantiomers is important in the pharmaceutical industry because the two
mirror images may not be equally effective.
• For example, L-dopa is a drug used in the effective treatment of Parkinson’s
disease. However, D-dopa, its enantiomer, is biologically inactive and useless in
the treatment of the disease. For some reason that we do not understand, all the
amino acids in cells are left-handed.

b. Disaccharides :

• are made of 2 monomers ex : Maltose ( Malt sugar ‫ ) ﺳﻛر اﻟﺷﻌﯾر‬+ H2O = glucose +
glucose
• Sucrose (table sugar) + H 2 O = glucose + fructose
• Lactose (milk sugar) + H 2 O = glucose + galactose
• Like Proteins, disaccharides are synthesized by Dehydration synthesis

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

• Maltose , sucrose and lactose have the formula → C 12 H 22 O 11 not C 12 H 24 O 12

due to removal of H 2 O

c. Polysaccharides :

• ex: Starch, Glycogen , Cellulose , Chitin …. They are all polymers (large chains)
of glucose but differ in the way glucose molecules are linked together within the
molecule

• are made of more than 2 monosaccharides linked together,the result compound is

polysaccharide (poly=many)

Glycogen: the form in which animals including human store glucose (in liver and
muscles)

Starch: the form in which plants store glucose

Cellulose: it forms the plant’s cell wall ‫ → ھﺎم‬much stronger and have a rigid
structure ‫ ﺻﻠب‬due to the way glucose molecules are linked inside it….

Chitin : Makes up the exoskeleton in arthropods and cell walls in fungi

U U

3-Lipids ( Fats/Oils )
U

• Lipids are fats(oils), butter , waxes, lard ‫ ﺷﺣم‬and steroids

Functions:

o Energy storage compounds ( 1 gram of any fat will release 9 calories of heat per
gram when burned in a calorimeter ) ( releases the highest energy ‫) ھﺎم‬
o Structural : phospholipids are Major Components of cell membrane, also
cholesterol, serves as an important component of cell membrane of animal cells.
o In Endocrine glands : Some steroids are hormones ex: testosterone and
oestrogen
o Provide insulation ‫ ﻋزل زى ﻓﻰ اﻟدب اﻟﻘطﺑﻲ ﻣﺛﻼ‬and cushioning ‫ﯾﻌﻣل ﻛوﺳﺎدة‬

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

o Conservation ‫ اﻻﺣﺗﻔﺎظ‬of body heat

The 3 most common forms in which lipids are found in body are :

1) Triglycerides ( TGCs):

o consists of 3 fatty acids + 1 glycerol molecule

o fatty acid is a hydrocarbon chain with COOH (Carboxylic group) at one end
o The fatty acid chains can vary in length and are usually between 12 and 24
carbons long
o Hydrocarbon chains are very Hydrophobic ‫( ﻛﺎرھﺔ ﻟﻠﻣﺎء‬non-polar) ( they don’t
interact well with water ) so Lipids are non polar

o Fatty acids exist in two varieties: saturated and unsaturated

o A glycerol Molecule → CH 2 OH-CHOH-CH 2 OH is an alchol that has 3
carbon atoms

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Cellular and molecular biology
 AP Biology Dr Haitham AbdAllah
0100 36 777 19

 Most of the fats

we eat and stored in our bodies
are in form of TGCs

 In general, saturated fats come from animals, are solid at room temperature ex :
butter, and when ingested in large quantities, are linked to heart disease.
Saturated fatty acids contain only single bonds between carbon atoms
 Unsaturated fatty acids → are extracted from plants, are liquid at room
temperature, and are considered to be healthy dietary fats. Unsaturated fatty acids
have at least one double bond formed by → removal of hydrogen atoms in carbon
skeleton
• 2) Phospholipids
o Phospholipids look like TGCs but one of fatty acids is replaced by Phosphate
Group (–PO 3 )2

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

phosphate group is hydrophilic (Polar)(can interact with water)(it’s the polar head)So
phospholipids are hydrophilic at one end (the phosphate end) and hydrophobic at
the other (fatty acid end)

When phospholipids interact with each other they align ‫ ﯾﺗرﺻوا‬themselves so that
their polar phosphate head groups stay together and non polar fatty acid tails stay
together

• They form cell membrane ‫ ( ھﺎم‬lipid bi-layer )

U U

• 3) Cholesterol:
o It’s a unique ‫ ﻓرﯾد‬lipid>> it’s not made of long hydrocarbon chains, instead the
hydrocarbons form Steroid rings
o Found only in Animal cell, and in
cell membranes along with
phospholipids

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

o HDL → Good cholesterol

o LDL → Bad cholesterol, linked with cardiovascular diseases
o
o ‫ ھﺎم‬Estrogen, Testosterone, Progesterone (all steroid hormones in body
are derived ‫ ﻣﺷﺗﻘﺔ‬from Cholesterol )

4-Nucleic acids : (in nucleus of the cell )

• are polymers of repeated Nucleotides (monomer)
• acidic macromolecules found in nuclues of the cell ‫ ﻧواة اﻟﺧﻠﯾﺔ‬ex : DNA & RNA
• ‫ ھﺎم ﺟدااا‬1 Nucleotide consists :

( 1 deoxyribose sugar in DNA or ribose in RNA) + 1 phosphate gp. + 1

nitrogenous base ( the 4 bases are : Adenine, Thymine, Guanine, Cytosine)

• In RNA Uracil instead of thymine

• So we have only 4 possibilites of nucleotides but many many types of DNA or RNA
strands

• DNA is double-helix but RNA is single stranded

• DNA consists of 2 strands that pair up (according to base pairing rules) to form a
ladder- like structure
The sugar-phosphate portions form the side of ladder …..2. Bases form the
rungs ‫ درﺟﺎت اﻟﺳﻠم‬of the ladder acc. to base pairing rules :

Adenine with Thymine by 2 hydrogen bonds….. Guanine with Cytosine

by 3 hydrogen bonds (more strong)

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

The DNA ladder twists into a spiral to form double helix

N.B : in RNA : Adenine pairs with Uracil

DNA RNA

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

Double Stranded Single Stranded

Sugar Deoxyribose Sugar Ribose Sugar
Nitrogenous Bases Adenine thymine Guanine Adenine Uracil Guanine
Cytosine Cytosine

* RNA is single stranded, it can form base pairs with itself

N.B :

Adenine and guanine are called purines

Cytosine, thymine, and uracil are called pyrimidines

Polymer Monomer

Protein Amino acid

Carbohydrate (polysaccharide) Saccharide

Nucleic acid Nucleotide (nitrogenous base +

deoxyribose or ribose+ phosphate )
Lipids
TGs ( glycerol + 3 fatty acids )
Phospholipids ( glycerol + 2 fatty acids + phosphate )
Cholesterol ( hydrocarbons form a ring )

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

pH

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

N.B : As concentration of H + increases, pH decreases → more acidic

A substance with a pH of 5 is 10 times more acidic than a substance that has a

pH of 6, and 100 times more acidic than a substance with a pH of 7.

Characteristics of water :
1. Water is asymmetrical and very polar → It also has
intermolecular attractions. In addition to polar
attractions, water exhibits strong hydrogen bonding

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

2. Water has a high specific heat :

Specific heat is → amount of heat that must be absorbed in order for 1 gram of a
substance to change its temperature 1 ° Celsius

This means that large bodies of water, like oceans, absorb a lot of heat and resist
changes in temperature
As a result, they provide a stable environment for the organisms that live in them

Also, coastal areas exhibit relatively little temperature change because oceans
moderate their climates

3. has high heat of vaporization → a relatively great amount of heat is needed to

evaporate water. As a result, evaporation of sweat significantly cools body surface

4. has high adhesion properties ‫ → ﺗﻼﺻق‬Adhesion is clinging ‫ ﺗﺷﺑث‬of one substance

to another, and it plays an important role in plant survival. Forces of adhesion contribute
to capillary action → which helps water flow up from the roots of a plant to the leaves ( see
plants chapter )

5. Water is universal solvent ‫ ﻣذﯾب‬Because water is a highly polar molecule, it dissolves

all polar and ionic substances

6. has strong cohesion tension → This means that molecules of water tend to stick to
each other → Water moves up a tall tree from roots to leaves without expenditure of
energy by what is referred to as transpirational-pull cohesion tension→ It also results
in surface tension → that allows insects to walk on water without breaking the surface

7. Ice floats because it is less dense than water → In a deep body of water, floating
ice insulates the liquid water below it, allowing life to exist beneath the frozen surface
during cold seasons → The fact that ice covers the surface of water in a lake in the cold

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

months and melts in the spring results in a stratification of the lake during the winter and
considerable mixing in the spring → In the spring, surface ice melts, becomes denser
water, and sinks to the bottom of the lake, causing water to circulate throughout the lake.
Oxygen from the surface is returned to the depths, and nutrients released by activities of
bottom-dwelling bacteria are carried to the upper layers of lake → This cycling of
nutrients in lake is known as the spring overturn and is necessary to health of a lake

Life functions :

1. INGESTION → Intake of nutrients

2. DIGESTION → Enzymatic breakdown, hydrolysis, of food so it is small enough to

be assimilated by the body

3. RESPIRATION → Metabolic processes that produce energy (adenosine

triphosphate or ATP) for all life processes

4. TRANSPORT. →Distribution of molecules from one part of a cell to another or

from one cell to another

5. REGULATION. Ability to maintain internal stability, homeostasis

6. SYNTHESIS. Combining of small molecules or substances into larger, more

complex ones

7. EXCRETION →Removal of metabolic wastes

8. EGESTION → Removal of undigested waste ( feces )

9. REPRODUCTION → Ability to generate offspring

10. IRRITABILITY → Ability to respond to stimuli

11. LOCOMOTION →Moving from place to place (animal cells only)

12. METABOLISM → the sum of all the chemical reactions that take place in cells.
Some reactions break down molecules (catabolism); other reactions build up molecules
(anabolism)

The Protein-Folding Problem

Under normal cellular conditions, the primary structure of a protein determines how
it folds into its particular three-dimensional shape. Protein structure also depends on

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

physical and chemical conditions in the environment, such as pH, salt concentration,
and temperature. Adverse conditions alter the weak intramolecular forces, causing
the protein to lose its characteristic shape as well as its function, a phenomenon
known as denaturation or denaturing.

The concept that the shape or conformation of a protein determines how it functions
is a basic concept of modern biology. Scientists have yet to discover all the rules
about how proteins spontaneously fold into their proper conformation. However, one
important recent discovery is that molecules called chaperone proteins or
chaperonins assist in folding other proteins. A misfolded protein, one with an
incorrect shape, can present a serious problem for a cell. Learning more about protein
folding is important. Many serious diseases, such as Alzheimer’s, Parkinson’s, and
mad cow disease, result from the accumulation of misfolded proteins, called prions,
in brain cells.

Three complementary techniques are used to reveal the three-dimensional shape or

conformation of proteins. These are X-ray crystallography, nuclear magnetic
resonance (NMR) spectroscopy and a new field, bioinformatics. Bioinformatics uses
computers and mathematical modeling to integrate the huge volume of data
generated from the analysis of an amino acid sequence of a protein to predict the
three-dimensional structure of the resulting protein molecule.

Currently, the three-dimensional shape of more than 20,000 proteins has been
determined.

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Cellular and molecular biology
AP Biology Dr Haitham AbdAllah
0100 36 777 19

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Cellular and molecular biology