Biochemistry ORGANELLES (little organs)

• All living things make use of the same types of biomolecules, and all use - are specialized structures that perform various jobs inside cells.
energy. As a result, all living things can be studied using the methods of
ENZYMES
chemistry and physics.
• The fundamental similarity of cells of all types makes it interesting to - a class of protein that displays catalytic activity.
speculate on the origins of life both cells and the biomolecules of which
- the catalytic effectiveness of a given enzyme depends on its amino acid
they are made must have arisen ultimately from very simple molecules,
sequence
such as H2O, CH4, CO2, NH3, N2, and H2.
• Field of Biochemistry draws many disciplines allows us to answer GENETIC CODE
questions related to molecular nature of life.
- the relationship between the nucleotide sequence in nucleic acids and the
Terminology amino acid sequence in proteins
DNA (Deoxyribonucleic acid) • theories of the origin of life consider how such a coding system might have
arisen
– is the hereditary material in humans and almost all other organisms.
Levels of Structural Organization in the Human Body
- the chain of basic materials in the chromosome of the human cell.
1. Atoms 5. Cell
RNA (Ribonucleic acid)
2. Molecules 6. Tissue
- is a nucleic acid present in all living cell that has structural similarities to DNA.
3. Macromolecules 7. Organ
- an important biological macromolecule that is present in all biological cells.
4. Organelles
CATALYCTIC ACTIVITY
CHEMICAL FOUNDATIONS IN BIOCHEMISTRY
- is the increase in the rate of a specified chemical reaction caused by an enzyme
or other catalyst under specified assay conditions. ORGANIC CHEMISTRY
ATP (Adenosine Triphosphate) - the study of the compounds of carbon
- substance present in all living cells that provides energy for many metabolic - the cellular apparatus of living organisms is made up of carbon compounds
processes and is involved in making RNA.
- biomolecules are part of the subject matter of organic chemistry
ADP (Adenosine Diphosphate)
- the reactions of biomolecules can be described by the methods of organic
-also known as adenosine pyrophosphate (APP) chemistry
- is an important organic compound in metabolism and is essential to the flow of
energy in living cells.
- The experiment of Friedrich Wöhler in 1828 Biomolecules

– molecules present in a living organisms

- Experiments have demonstrated that important biomolecules, such as proteins

and nucleic acids, could have arisen under abiotic (nonliving) conditions from
Functional Group reactions of these simple compounds • in the earth’s oceans

- an atom or group of atoms that show • on the surface of clay particles

characteristic physical and chemical
- Living cells include very large molecules, such as proteins, nucleic acids,
properties.
polysaccharides, and lipids

- these biomolecules are polymers (Greek: poly + meros, many + parts)

- they are derived from monomers (Greek: mono + meros, single + part)

--amino acids → proteins

--nucleotides → nucleic acids

The Beginnings of Biology: Origins of Life
--monosaccharides → polysaccharides/ carbohydrates
The “big bang” theory
--glycerol and 3 fatty acids → lipids
- all matter was originally confined in a very small space
• Proteins and Nucleic Acids play a role in life processes.
- as the result of an explosion, it started to expand with great force; temperature
The RNA World
approx. 15 x 109 K
- The appearance of a form of RNA capable of coding for its own replication was
- the average temperature of the universe has been decreasing ever since
the pivotal point in the origin of life
- in the earliest stages of the universe, the only elements present were H, He, and
- This original RNA both encoded for and catalyzed its own replication
Li
- In time, this system evolved to encode for the synthesis of protein catalysts
- other elements formed by
- Even later, DNA became the primary genetic material, and RNA took on only an
•thermonuclear reactions in stars
intermediary role in the synthesis of proteins
• explosions of stars
- It has been discovered recently that certain types of RNA have catalytic activity
• the action of cosmic rays outside the and are capable of catalyzing their own further processing RNA is now considered
stars by many scientists to have been the original coding material

Relative Abundance of Important Elements - it still serves this function in some viruses
Molecules to Cells:

- A key point in the development of living cells is the formation of membranes

that separate cells from their environment

- Some theories of the origin of life focus on proteins

- according to one model, proteinoids aggregated to form microspheres

DOUBLE-ORIGIN THEORY

- the development of a coding system and the development of catalysis came

about separately

- a combination of the two later in time produced life as we know it.

PROKARYOTES AND EUKARYOTES

Prokaryotes

- before the nucleus Biochemical Energetics

- single-celled organism • All cells require energy to functions

- includes bacteria and cyanobacteria • Light from the sun is the ultimate source of energy for all life on earth

Eukaryotes • photosynthetic organisms use light energy to drive the energy-requiring

synthesis of carbohydrates
- true nucleus
• non-photosynthetic organisms consume these carbohydrates and use them as
- contains a well-defined nucleus surrounded a nuclear membrane energy sources
- can be single-celled, such as yeasts and Paramecium or multicellular, such as • The energetics of a chemical reaction
animals and plants.
• if the change in free energy is negative (free energy decreases), the reaction is
spontaneous as written

• if the change in positive (free energy increases), the reaction will not occur as
written unless energy is supplied from an external source

THERMODYNAMICS - branch of science that answers questions about processes

that are energetically favorable

SPONTANEOUS – fast
WATER AS THE SOLVENT VAN DER WAALS FORCES

SOLVENT – ability of the matter to dissolve - bonds that do not involve electrostatic interactions

SOLUTE – needs to be dissolve DIPOLE-DIPOLE INTERACTIONS

POLAR BOND - unequal sharing of electrons (more negative charge) (e.g., water) - Forces that occur between molecules with dipoles, one positive and one
negative
NON-POLAR BOND – equal sharing of electrons
- with Ion-Dipole interaction, both of them can help ionic and polar compunds
ELECTRONEGATIVITY
dissolve in water
- a measure of the force of an atom’s
DIPOLE INDUCED-DIPOLE INTERACTIONS
attraction for electrons it shares in a
chemical bond with another atom - weak and generally do not lead to solubility in water

- Oxygen and Nitrogen, more

electronegative than carbon and
hydrogen
INDUCED DIPOLE-INDUCED DIPOLE/ LONDON DISPERSION FORCES
- Fluorine is most electronegative (4)
- extremely weak attractive forces between atoms or molecules caused by the
constant motion of eelectrons between temporary induced dipoles
CO2 (Carbon Dioxide) – have polar bonds but
given their geometry, are nonpolar molecules;
that is they have zero dipole moments.

SOLVENT PROPERTIES OF WATER (H2O)

IONIC BONDS HYROPHILIC (water-loving)

- held together by positive and negative ions - tend to dissolve in water
SALT BRIDGE HYDROPHOBIC (water-fearing)
- Attraction that occurs when oppositely charged molecules are in close proximity - tend to dissolve in water
ION-DIPOLE INTERACTIONS AMPHIPATHIC
- When ions in solution intreract with molecules with dipoles, e.g., KCl dissolved - has a characteristic of bothe properties
in H2O
- molecules that contain one or more hydrophobic and one or more hydrophilic
regions, e.g., sodium palmitate
- both polar and nonpolar character

- Interaction between nonpolar molecules is very weak (van der Waals

interactions)

MICELLE

- a spherical arrangement of organic molecules in water

solution clustered

- hydrophobic parts are buried inside the sphere, while the

hydrophilic parts are on the surface of the sphere

- formation depends on the attraction between temporary

induced dipoles
ACID, BASES, AND pH
HYDROGEN BOND
ACID
- the attractive interaction between dipoles when:
- a molecule that behaves as a proton donor
- positive end of one dipole is a hydrogen atom bonded to an atom of high
electronegativity, most commonly O or N, and STRONG BASE

- the negative end of the other dipole is an atom with a lone pair of electrons, - a molecule that behaves as a proton acceptor
most commonly O or N ACID STRENGTH
- Hydrogen bond is non-covalent - amount of hydrogen ion released when a given amount of acid is dissolved in
- bonding of H to a more electronegative atom water

- Even though hydrogen bonds are weaker than covalent bonds, they have a
significant effect on the physical properties of hydrogen-bonded compounds DISSOCIATION OF WATER
- Hydrogen bonding is important in stabilization of 3-D structures of biological IONIZATION OF H20 and pH
molecules such as: DNA, RNA, proteins.

- WATER MOLECULE CAN BE INVOLVED IN 4 HYDROGEN BONDS (2 as a donor,

and 2 as acceptor): due to the tetrahedral arrangement of water molecule
K = dissociation constant
POTENTIAL OF HYDROGEN (pH) BUFFERS

- measures how acidic/basic water is - a solution whose pH resists change

upon addition of small to moderate
- reflects the chemical condition of the body
amounts of a strong acid or base
- it controls the availability of nutrient, biological function and behavior of
- consists of a weak acid and its
chemical
conjugate base
- was introduced in 1909 by Sörensen, who defined pH as the negative logarithm
BUFFERING CAPACITY
of the hydrogen ion concentration.
- is related to the concentrations of the weak acid and its conjugate base
- Low pH values correspond to high concentrations of H+ and high pH values
correspond to low concentrations of H+. - the greater the concentration of the weak acid and its conjugate base, the
greater the buffer capacity
Log scale means 10x change per unit
NATURALLY OCCURING BUFFERS

- H2PO4-/HPO4 ²- is the principal buffer in cells

HENDERSON-HASSELBALCH
- H2CO3/HCO3- is an important (but not the only) buffer in blood
- an equation to connect Ka to pH of solution containing both acid and base
ACID-BASE BALANCE IN THE BODY

TITRATION
- an experiment in which measured amounts of acid (or base) are added to
measured amounts of base (or acid)
EQUIVALENCCE POINT
- the point in an acid- base titration at which enough acid has been added to
exactly neutralize the base (or vice versa)
• a monoprotic acid releases one H+ per mole
• a diprotic acid releases two H+ per mole
• a triprotic acid releases three H+ per mole
- the pH of the body must be maintained within narrow range. Most body
systems function optimally at a pH of near 7.4
- at the pH changes (either higher or lower), enzymes may cease to function,
nerve, and muscle weakens, and finally all metabolic activity becomes deranged.
ALKALOSIS OR ALKALEMIA
- arterial blood pH rises above 7.45
ACIDOSIS OR ACIDEMIA
- arterial pH drops below 7.35
SELECTING A BUFFER
• suitable pKa and it’s non-biological nature
• no interference with the reaction or detection of the assay
• suitable ionic strength and solubility
THE pH of a solution SIGNIFICANT FIGURES IN pH

- is used to indicate the acidity of a solution - When expressing log values, the value of the coefficient of the hydronium ion is
equal to the pH value.
- has values that usually range from 0 to 14

- is acidic when the values are less than 7

- is neutral with a pH of 7

- is basic when the values are more than 7

Testing the pH of Solutions

The pH of solutions can be determined using a

- pH meter

- pH paper

- indicators that have specific color at different pH values

CALCULATING pH
Calculating H3O+ from pH
pH = negative logarithm of hydronium ion concentration
Example: Calculate the H3O+ for a pH value of 7.0
Example:
Given: pH= 7
Find the pH of a solution with a [H3O+] of 1.0 x 10^ -7
Step 1: Get the pH value and change the sign to negative.
Step 1: Write the given and what you are going to find.
pH= -7
Given: [H3O+] = 1.0 x 10^ -7
Step 2: In your calculator, press shift. Then, press log and -7. It would be like this:
Find: pH=?
10 -7
Step 2: Write the formula and substitute its corresponding value
Step 3: Once you press the equal sign, you’ll end up with an answer of:
pH= - log [H3O+]
1 x 10 ^ -07
pH= - log [ 1.0 x 10^ -7]
With this, adjust the significant figure of the coefficient. The written answer
Step 3: Type in the step 2 and you’ll end up with an answer of:
should be 1 x 10 ^-7
pH= 7
BUFFERS FORMULAS:

- resist changes in pH from the addition of acid or base

- in the body absorb H3O+ OR OH- from foods and cellular processes to maintain
pH

- are important in the proper functioning of cells and blood

- in blood maintain a pH close to 7.4; a change in the pH of the blood affects the
uptake of oxygen and cellular processes

When an acid or base is added

- to water, the pH changes drastically

-to a buffer solution, the pH does not change very much; pH is maintained

COMPONENTS OF A BUFFER SOLUTION

NUCLEIC ACID AND PROTEIN SYNTHESIS
- are acid – base conjugate pairs
COMPONENTS OF NUCLEIC ACIDS
- can be weak acid and a salt of its conjugate base
NUNCLEICC ACIDS are
- typically have equal concentrations of the weak acid and its salt
- molecules that stores information for cellular growth and reproduction.
- can also be a weak base and a salt of its conjugate acid
- Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA)
An acetic acid/acetate buffer contains the weak acid acetic acid (HC2H3O2) and
the salt of its conjugate base sodium acetate (NaC2H3O2) - Large molecules consisting of long chains of monomers called nucleotides.
- The function of the weak acid in a buffer is to neutralize added base. The nucleic acids DNA and RNA consist of monomers called nucleotides that
consists of a
BUFFER ACTION occurs because
- Pentose sugar
- the weak acid in a buffer neutralizes base
- Nitrogen-containing base
- the conjugate base in the buffer neutralizes acid
- Phosphate
- the pH of the solution is maintained

The [H3O+] in the Ka expression is used to determine the pH of a buffer

Weak acid + H2O H3O + conjugate base

NITROGEN BASES -Has carbon atoms numbered with primes to distinguished them from the atoms
in nitrogen bases.
The nitrogen bases in DNA and RNA are:

PYRAMIDINES: Cytosine, Thymine, and Uracil

NUCLEOSIDES

- has nitrogen base linked by a glycosidic

PURINES: Adenine and Guanine
bond to C1’ of a sugar

- sugar + base

- is named by changing the nitrogen base

ending to -osine for purines (Adenosine,
Guanosine); and -idine for pyramidines
(Cytidine, Uridine, Thymidine)

NUCLEOTIDES
DNA contains the nitrogen bases: RNA contains the nitrogen bases: - is a nucleoside that forms a phosphate ester
- Cytosine (C) - Cytosine (C) with the C5’ -OH group of a sugar

- Guanine (G) - Guanine (G) - sugar bonds to phosphoric acid.

- Adenine (A) - Adenine (A) - is named using the name of the nucleoside
followed by 5’-monophosphate
- Thymine (T) - Uracil (U)
A nucleotide forms with -OH on C5’ of a sugar bonds to phosphoric acid
PENTOSE SUGAR

The pentose (five carbon) sugar

- in RNA is ribose

-in DNA is deoxyribose with no Oxygen atom on carbon 2’

AMP, ADP, and ATP

- adding phosphate groups to

AMP forms the diphosphate
(ADP) and triphosphate (ATP)