MODULE 5

Sun

the ultimate source of almost all the
energy that powers life.

Energy

defined as the capacity to do
work.

Kinetic and Potential Energy

Kinds of Energy

Kinetic Energy

Is the energy
associated with motion; when energy
is utilized, and work is performed

Potential Energy

Is stored in the
location of matter; stored in molecular
structure of substances

Chemical
Mechanical
Electrical
Light
Heat

Forms of Energy

Thermodynamics

study of energy and its transformation.

1. Conservation of Energy
2. Entropy

2 Laws of Energy, respectively

Conservation of Energy

The 1st law of thermodynamics; It states that energy cannot be created
or destroyed; it can only be transformed or converted from one form to another.

Entropy

The 2nd law of thermodynamics; It states that when energy is converted
from one form to another, some of the usable energy is converted to heat that
disperses into the surroundings and will no longer be available to do work.

Metabolism

All chemical reactions that enable an organism to carry on its activities; is the totality of an organism’s chemical reactions; Arises from interactions between
molecules.

Biochemical Pathways

organizational units of metabolism

Anabolism

a constructive process;
involves the building up of complex
molecules using simpler substances;
this takes up energy and stores it in the
bonds holding the components of a
complex molecule. It is also referred as
biosynthetic pathway

Catabolism

a degradative process;
involves the breakdown of complex
molecules into their component
materials; energy is released as bonds
are broken and provides the energy
needed by the cell.

Bioenergetics

In any chemical reaction e.g. metabolic
process, chemical bonds are either formed
or broken.

enthalpy

Measured as the total bond energy is equivalent to the
total potential energy of the system

free energy

The available energy to do work in a system

H = G + TS

Enthalpy, free energy, and entropy are
involved in a reaction that occurs in a
system as follows:

Exergonic

Proceeds with a net release
of free energy; this releases energy and
is said to be a spontaneous reaction. ΔG free
energy has a negative value.

Endergonic

Absorbs energy from the
environment; a non-spontaneous
reaction. ΔG has a positive
value.

adenine, ribose sugar,
and 3 phosphate groups

Adenosine triphosphate (ATP) consists of
three main parts:

adenosine diphosphate (ADP)

When the cell uses ATP as energy source, one of the phosphate group is broken to produce? It is also an inorganic phosphate group and energy is
released to drive an endergonic reaction.

Enzymes

are biological catalysts to increase the speed
of a chemical reaction without being used
up or integrated into the reaction.

Activation Energy

The initial amount of energy needed to start a chemical reaction which bring reactants close together and weakens existing bonds.

Add Energy (Heat)

(INCREASING REACTION RATES) molecules
move faster so they collide more
frequently and with greater force.

Add a catalyst

(INCREASING REACTION RATES) reduction of
activation energy needed to cause a
reaction.

enzyme-substrate complex or
ES complex

Enzymes perform their catalyzing activity by
forming an unstable intermediate
complex with the substrate

Temperature, pH, Inhibitors and Activators

Enzyme Factors

inorganic or organic cofactors

Enzyme Cofactors

Temperature

with this the rate of an enzyme-catalyzed reaction increases

pH

ionic interactions also hold
enzymes together.

1. Ions
2. Trace Elements

Inorganic Cofactors

Carrier molecules

Organic Cofactors

Allosteric site

receptor site of enzymes

Allosteric regulators

These chemicals that bind on the allosteric
site are called

Polypeptide subunits

Most allosterically regulated enzymes are
made from

Activator

stabilizes the active
form of the enzyme.

Inhibitor

stabilizes the inactive
form of the Enzyme

Competitive inhibitors

inhibitors that bind to the active site
of an enzyme, competing with the
substrate

Noncompetitive inhibitors

inhibitors bind to another
part of an enzyme, changing the function

Cooperativity

A form of allosteric regulation that can
amplify enzyme activity

DNA

contains all of a cell's genetic
information. This information has to be
converted into structural and functional
components that makes the cell or the
organism alive.

Chromatins

Every cell has DNA packed within its
nucleus as

Nucleosomes

DNA is coiled tightly on proteins called histones to form this; they are the fundamental units of chromatin

Chromosomes

These chromatins are
assembled as tightly coiled structures
called

A:T & C:G

Four nitrogenous bases that exhibit specific
base pairing

transcription

The genetic information in DNA provides
the template to synthesize a strand of
RNA, more like copying the information in
DNA into RNA; DNA directed
synthesis of RNA

Translation

The conversion of this
information into a sequence of amino acids
forming the polypeptide chain or protein is
called; Occurs on ribosomes in the cell cytoplasm; is the RNA-directed synthesis of a polypeptide

messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)

Protein synthesis
proceeds using three types of RNA

messenger RNA (mRNA)

contains the genetic information
copied from DNA

transfer RNA (tRNA)

delivers amino acids to the ribosomes

Ribosomal RNA (rRNA)

assembles and builds the polypeptide chain

Nucleotides

Contains carbon, hydrogen, oxygen,
nitrogen, and phosphorus

a. 5-carbon sugar
b. Phosphate group
c. Nitrogenous base

The components of a nucleotide include:

pyrimidine (thymine, cytosine, and uracil)
purines (adenine and guanine)

Nitrogenous bases:

Central Dogma

Cells are governed by a cellular chain of
command

Transcription and Translation

Protein Synthesis involves two main
processes:

Initiation, Elongation, Termination

Stages of Transcription are

Initiation of Transcription

Promoters signal the initiation of
RNA synthesis

Elongation of Transcription

RNA polymerase synthesizes a
single strand of RNA against the
DNA template strand

Termination of Transcription

Specific sequences in the DNA
signal termination of transcription

Codon

The genetic instructions carried by
messenger RNA is read as a code; consists of three
nucleotides.

64

How many possible combinations
of nucleotides are there?

1. mRNA
2. Ribosomes - Ribosomal RNA
3. Transfer RNA
4. Genetic coding – codons

Translation involves:

Initiation, Elongation, Termination

The translation stage occurs in the
cytoplasm of the cell. It consists of three
phases: namely,

Transfer RNA (tRNA)

A 3 dimensional molecule that is roughly “L” shaped

1. one acts as anticodon
2. the other binds to a free
amino acid, specified by the codon

The transfer RNA (tRNA) has two
attachment sites:

polypeptide chain

Where the rRNA joins the amino acids through a peptide bond

Ribosomes

facilitate the specific
coupling of tRNA anticodons with mRNA
codons during protein synthesis

Ribosomal RNA (rRNA)

2 ribosomal subunits that are constructed of proteins and RNA molecules

The P site
The A site
The E site

The ribosome has three binding sites for tRNA

UAA, UAG, UGA

STOP Codons

AUG

START Codon

Initiation of Translation

brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome

Elongation of Translation

amino acids are added one by one to the preceding amino acid

Termination of Translation

When the ribosome reaches a STOP codon, there is no corresponding transfer RNA. Instead, a small protein called a “release factor” attaches to the stop codon.

translated many times

The messenger RNA can be _________ _____ _____, to produce many protein copies.

Polyribosome

A number of ribosomes can translate a
single mRNA molecule simultaneously
forming a

enable

Polyribosomes ______ a cell to make many
copies of a polypeptide very quickly

fold spontaneously

Polypeptides ____ __________ into
their active configuration, and they
spontaneously join with other polypeptides
to form the final proteins.

Cellular Respiration

A process by which cells in plants and
animals break down sugar and turn it
into energy

Glucose

the fuel that cells most often
use.

1. Movement
2. Maintaining Constant Body Temperature
3. Anabolic Processes
4. Active Transport
5. Secretion
6. Bioluminescence

Importance of Cellular Respiration

Adenosine Triphosphate (ATP)

also known as the Energy Currency; is a high
energy molecule that functions as an
immediate power source for cells.

1. Solar Energy
2. Oxidative Processes

ATP is Synthesized from ADP from:

1. energy currency of the
cell
2. It may transfer the released phosphate
group to other organic molecules

Functions of ATP

Aerobic and Anaerobic

Two Types of Respiration

Aerobic Respiration

a process that uses oxygen; Involves the complete breakdown of
organic molecules for a larger yield of ATP

Water, Carbon Dioxide, and Energy

End Products of Aerobic Respiration

C6H12O6 + 6CO2 -> 6CO2 + 6H2O + ATP

Chemical Equation for Aerobic Respiration

1. Glycolysis
2. Formation of Acetyl CoA
3. Krebs Cycle (Citric Acid Cycle)
4. Electron Transport and Chemiosmosis

Major Stages of Aerobic Respiration

Glycolysis

Glucose is converted into pyruvate and occurs in the cytosol of the cell; this is when a hexose sugar (6C) is broken down into two molecules of pyruvate (3C)

1. Phosphorylation
2. Lysis
3. Oxidation
4. ATP Formation

Glycolysis Steps

Phosphorylation

A hexose sugar (typically glucose) is
phosphorylated by two molecules of ATP
(to form a hexose bisphosphate)

Lysis

The hexose biphosphate (6C sugar) is
split into two triose phosphates (3C sugars)

Oxidation

Hydrogen atoms are removed from each
of the 3C sugars (via oxidation) to reduce
NAD+ to NADH (+ H+)

ATP Formation

Some of the energy released from the
sugar intermediates is used to directly
synthesize ATP

Reactions at the end of Glycolysis

Glucose (6C) has been broken down into two molecules of pyruvate (3C); Two hydrogen carriers have been reduced via oxidation (2 × NADH + H+)

2 ATP
2 NADH
2 pyruvate

Output of Glycolysis

Linked Reaction

In aerobic cell respiration pyruvate is
decarboxylated and oxidized, and
converted into acetyl compound and
attached to coenzyme A to form acetyl
coenzyme A; occurs in the mitochondrial matrix