Reviewer: General Biology I – 2nd Quarter

Biological Macromolecules
• Large molecules, necessary for life, that are built from smaller organic molecules. There are four major classes of
biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids); each is an important cell component
and performs a wide array of functions. Biological macromolecules are organic, meaning they contain carbon. In
addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements.
• Most macromolecules are made from single subunits, or building blocks, called monomers.
• The monomers combine with each other using covalent bonds to form larger molecules known as polymers.
• In doing so, monomers release water molecules as byproducts. This type of reaction is known as dehydration
synthesis, which means “to put together while losing water.”
• Polymers are broken down into monomers in a process known as hydrolysis, which means “to split water,” a
reaction in which a water is added during the breakdown.

A. Carbohydrates (C,H,O) carbon, hydrogen, oxygen

 Carbohydrates can be represented by the stoichiometric formula (CH2O)n.

Classifications of Carbohydrates:
1. Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose.

a sugar molecule
Glucose - an important source of energy
during cellular respiration, energy is released from glucose, and that energy is used to help make adenosine
triphosphate (ATP)
Galactose - part of lactose, or milk sugar
Fructose - found in sucrose, in fruit) are other common monosaccharides

2. Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (also
known as a condensation reaction). A covalent bond formed between a carbohydrate molecule and
another molecule is known as a glycosidic bond.
Lactose – combination of the monomers glucose and galactose. It is found naturally in milk.
Maltose – malt sugar, formed by a dehydration reaction between two glucose molecules.
Sucrose – table sugar, composed of the monomers glucose and fructose.

3. Polysaccharides - A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly-=
“many”). Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Starch - is the stored form of sugars in plants and is made up of a mixture of amylose and amylopectin (both polymers of
glucose).
Glycogen - is the storage form of glucose in humans and other vertebrates and is made up of monomers
of glucose.
Cellulose - is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose;
this provides structural support to the cell. cellulose cannot be broken down by human digestive enzymes, because they lack
cellulase which can break down cellulose into glucose monomers that can be used as an energy source by the animal.

B. Lipids(C,H,O) carbon, hydrogen, oxygen

• Biomolecule is fundamental to the structure and function of biological membranes, such as cell membranes.
• Lipids include a diverse group of compounds that are largely nonpolar in nature. Non-polar molecules are
hydrophobic (“water fearing”), or insoluble in water.
• Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats.
• Lipids also provide insulation from the environment for plants and animals. Lipids include fats, oils, waxes,
phospholipids, and steroid hormones like testosterone.
• A fat molecule consists of two main components—glycerol and fatty acids.
 • Fatty acids may be saturated or unsaturated.
• In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty
acid is said to be saturated.
• When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated.

C. Proteins(C,H,O,N,S) carbon, hydrogen, oxygen, nitrogen, sulfur

• Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of
functions of all macromolecules.
• Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or
membranes; or they may be toxins or enzymes.
• Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually
complex or conjugated proteins.
• Amylase, lipase, pepsin, trypsin (Help in digestion of food by catabolizing nutrients into monomeric units)
• Casein is a protein which is commonly found in mammalian milk.
• Amino acids are the monomers that make up proteins.
• Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by
a dehydration reaction.

Factors Affecting Enzyme Activity

Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on, such that their active sites have
very precise shapes, that only one substrate can fit in each site and is chemically attracted to it.

a. Temperature
Chemical reactions increase as temperature increases because the reacting molecules move faster and collide more
often. Most enzymes in the human body have optimum temperature at 37°C
b. pH
Like the optimum temperature, optimum pH is different for different enzymes. It usually depends on what
environment the enzyme needs to work in. most enzymes found in the human body have optimum pH 6-8.
c. Substrate Concentration
If enzyme concentration remains constant, enzyme activity increases as substrate concentration increases, but only
as along as there are active sites available.

4. Nucleic Acids(C,H,O,N,P) carbon, hydrogen, oxygen, nitrogen, phosphorus

• Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a
cell and carry instructions for the functioning of the cell.
• The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
• DNA and RNA are made up of monomers known as nucleotides.
• Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a
phosphate group.
• Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and
thymine (T).
• Same nucleotides go with RNA except that Thymine is replaced by Uracil.
• In DNA molecule, hydrogen bonds hold together nitrogenous bases.

DNA
• It has a double-helix structure. The two strands of the helix run in opposite directions, meaning that the 5′ carbon
end of one strand will face the 3′ carbon end of its matching strand. Genetic material found in all living organisms,
ranging from single-celled bacteria to multicellular mammals.

RNA
• Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is
usually single-stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in
 the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the
phosphate group.

Energy Transformation
Photosynthesis
• Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process
that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds
(carbohydrates) that every organism uses to power its metabolism.
• Anabolic (small molecules combined)
• Endergonic (stores energy)
• Carbon dioxide (CO2) requiring process that uses light energy (photons) and water (H2O) to produce organic
macromolecules (glucose).
• Autotrophs – produce their own food (glucose)
• Mainly occurs in the leaves:
a. stoma - pores
b. mesophyll cells
Stomata
Pores in a plant’s cuticle through which water vapor and gases (CO2 & O2) are exchanged between the plant and the
atmosphere.

Chloroplast
Organelle where photosynthesis takes place.

Chlorophyll Molecules
• Located in the thylakoid membranes
• Thylakoids – disc shape structures inside the chloroplasts
• Grana – stacks of thylakoids
• Chlorophyll pigments harvest energy (photons) by absorbing certain wavelengths (blue-420 nm and red-660 nm are
most important)
• Plants are green because the green wavelength is reflected, not absorbed.

Two Parts of Photosynthesis

1.Light Reaction or Light Dependent Reaction -
• solar power to chemical energy from (photons) in the form of ATP and NADPH.
• occurs in the Thylakoid membranes
• The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a
photosystem, two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and
photosystem I (PSI).
(Reaction-center chlorophyll of photosystem II is known as P680 because this pigment is best at absorbing light with
a wavelength of 680 nm. Reaction-center chlorophyll of photosystem I is known as P700 because this pigment is
best at absorbing light with a wavelength of 700 nm)
• The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time through the electron
transport chain to PSI.
• When the electrons leave the PSII, it will be supplied again by another electrons coming from H2O molecules.
Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two
molecules is required to form one molecule of diatomic O2 gas. This process is called photolysis.
• The function of H+ made from the splitting of the water molecule is for ATP synthase to make ATP.
• As electrons move through the proteins that reside between PSII and PSI, they lose energy. That energy is used to
move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus
the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later
step.
• Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another
photon is absorbed.
• P700 is oxidized and sends two(2) high-energy electron to NADP+ to form NADPH.
• the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of
hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to
create ATP
• To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a specialized
protein channel called the ATP synthase.
 • The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP,
which forms a molecule of ATP. The flow of hydrogen ions through ATP synthase is called chemiosmosis because the
ions move from an area of high to an area of low concentration through a semi-permeable structure.
• Light Reactions By-product: Oxygen; Products: ATP and NADPH

2. Calvin Cycle or Light Independent Reaction

• also called Carbon Fixation or C3 Fixation

• uses energy (ATP and NADPH) from light reaction to make sugar (glucose).
• in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of
photosynthesis
• the most outdated name is dark reactions, because light is not directly required, it is light-independent
• the primary function of the Calvin cycle is to synthesize simple sugars from carbon dioxide

The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and
regeneration.

Stage 1: Fixation
• In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an
enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose
bisphosphate (RuBP).
• RuBP has five atoms of carbon, flanked by two phosphates.
• RuBisCO catalyzes a reaction between CO2 and RuBP.
• For each CO2 molecule that reacts with one RuBP, a 5-carbon compound to form an unstable 6-carbon compound,
which decomposes into two 3-carbon compound called 3-PGA. PGA has three carbons and one phosphate. This
process is called carbon fixation, because CO2 is “fixed” from an inorganic form into organic molecules.
Stage 2: Reduction
• ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called
glyceraldehyde 3-phosphate (G3P) or PGAL(phosphoglyceraldehyde).
• That is a reduction reaction because it involves the gain of electrons by 3-PGA.
• Recall that a reduction is the gain of an electron by an atom or molecule.
• Six molecules of both ATP and NADPH are used.
• For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both
energy and a hydrogen atom are lost, converting it into NADP+.
• Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized.
Stage 3: Regeneration
• Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to
contribute to the formation of other compounds needed by the plant.
• Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the Calvin cycle to
fix enough net carbon to export one G3P.
• One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which
enables the system to prepare for more CO2 to be fixed.
• Three more molecules of ATP are used in these regeneration reactions.
• It takes 6 turns of the Calvin cycle to produce 1 molecule of glucose.
Product: 1 glucose molecule requires 18 ATPs

Cellular Respiration
4 metabolic stages
Anaerobic respiration
1. Glycolysis
 respiration without O2
 occurs in cytosol
 first phase of most carbohydrate catabolism
 Glycolysis breaks down one(1) molecule of glucose and forms two(2) pyruvate with the production of two(2)
molecules of ATP. The pyruvate or pyruvic acid is the end product of glycolysis that can be used in either anaerobic
respiration if no oxygen is available or in aerobic respiration via the Krebs cycle which yields much more usable
energy for the cell. Each pyruvate has 3 carbons.
 What happens to 2 pyruvic acids? It depends on which organism it will be used. In yeast, the 2 pyruvic acid is broken
down into 2 molecules of ethyl alcohol(C2H5OH). From every molecule of pyruvic acid one(1)CO2 is given out. Since
there are 2 pyruvic acids being broken down so 2 CO2 molecules are released. This process is called fermentation.
Products of fermentation: ethanol(C2H5OH) and carbon dioxide (CO2)
 Application of fermentation: cereal, dairy and beverage products
 In muscle cells, 2 pyruvic acids are broken down into 2 molecules of lactic acid. Lactic acid is a 3-carbon compound.
Aerobic respiration
 respiration using O2
 occurs in mitochondria
2. Krebs cycle/ Citric Acid cycle
  Hans Krebs discovered citric acid cycle
 Overall, one turn of the citric acid cycle releases two(2) CO2 molecules and produces three(3) NADH, one(1) FADH2,
and one(1) ATP. The citric acid cycle goes around twice for each molecule of glucose that enters cellular respiration
because there are two pyruvates—and thus, two acetyl CoA —made per glucose.
3. Electron transport chain
4. Oxidative Phosphorylation