Intro to Biochemistry

By: Adrian E. Villavieja

Natural Sciences Department
Ateneo de Zamboanga University

 What is biochemistry?
➢ Biochemistry – study of chemical substances, structures, and processes related to or within living organisms
➢ Interactions of macromolecules that define components vital to life
➢ These molecules conform to physicochemical laws that describe the behavior of matter

 Where do we begin?
➢ Organic chemistry – study of carbon-hydrogen compounds and their derivatives
➢ Carbon, being a tetravalent element, is able to undergo catenation, resulting in long and complex molecular structures with
different characteristics
➢ Carbon also allows for cis-trans isomerism
➢ Hydrocarbons, compounds composed of only carbon and hydrogen, are the most basic organic molecule

 What makes certain hydrocarbons biomolecules? Element Electronegativity

➢ Presence of heteroatoms like oxygen, nitrogen, sulfur, and phosphorus, and Oxygen 3.5
certain metals like iron, calcium, lithium and magnesium Nitrogen 3.0
➢ Because elements like oxygen and nitrogen have high electronegativity, these Sulfur 2.6
compounds tend to have functional groups which are polar in nature Carbon 2.5
➢ Because of their polar nature, they interact favorably with water Phosphorus 2.2
Hydrogen 2.1

Important Functional Groups in Biochemistry

Name of
Class of Functional Group Class of Name of Functional Group
Functional
Compound Characteristic Compound Functional Group Characteristic
Group

Alkene Double bond Ketone Carbonyl group

Alcohol Hydroxyl group Carboxylic acid Carboxyl group

Ether Ether group Ester Ester group

Amine Amino group Amide Amide group

Phosphoric Phosphoric ester

Thiol Sulfhydryl group
acid esters group

Phosphoric Phosphoric
Aldehyde Carbonyl group
acid anhydride anhydride group
 What is water, and what are its properties?
➢ Water (H2O) is a molecule composed of two hydrogen atoms and one oxygen atom
➢ The hydrogen atoms are bound to the oxygen atom, forming an angle of 104.5°
➢ This bent angle results in a partially positive end and a partially negative end, making the
molecule polar
➢ This structure also makes water amphoteric
➢ Water has a large dielectric constant of 78.4
➢ Water has high heat capacity, making it an excellent modulator of temperature
o Humans can lose as much as 1.2kg of water daily through waste products like
exhaled air, sweat, and urine
➢ Due to its polar nature, water can dissolve ionic compounds (eg. NaCl) and polar compounds (eg. C2H5OH), giving it its
distinction of being the “universal solvent”
➢ This electrostatic attraction between unlike charges of covalent compounds is coupled with other types of non-covalent
interactions differ in strength

 What are some important non-covalent interactions?

➢ Electrostatic interaction – occurs between or among atoms with opposing charges. These include the ff:
o Ionic bonds – electrostatic attraction between opposing charges; biomolecules with opposite charges that are in
close proximity to each other form salt bridges
o Hydrogen bonds - due to the electrostatic interaction of the covalently bonded hydrogen, resulting in a partially
positive charge, with an unshared pair of electrons on an electronegative atom
o van der Waals force – distance-dependent attraction of particles based on electron charge density and
polarizability, resulting in three possible interactions: dipole-dipole, dipole-induced dipole, and induced dipole-
induced dipole

 Wait, why discuss hydrogen bonding separately?

➢ Water is capable of forming hydrogen bonds with polar compounds, ionic compounds, and other water molecules
➢ As certain ionic compounds are hydrated, water molecules are attracted to the charged ions, resulting in the reduced
attractive force between ions, fully dissolving them in water
➢ Since water is capable of forming hydrogen bonds with polar and ionic substances, the latter substances are said to be
hydrophilic (“water-loving”)
➢ Nonpolar compounds are not able to form hydrogen bonds with water, making them hydrophobic (“water-fearing”)
➢ When hydrophobic substances enter water, the preexisting hydrogen bonds between the water molecules are broken, and
new hydrogen bonds are formed around the hydrophobic substance, forming clathrate cages
➢ It is interactions like these that allow for complex structures to develop and for chemical processes to occur in an organized
system

 What makes hydrogen so important for biochemistry?

➢ Aside hydrogen bonding being vital for stabilizing the 3D structure of biomolecules, the biochemical behavior of many
compounds depend on their acid-base properties
➢ There are two definitions of acids and bases (alkalis)
o Brønsted–Lowry – acids are proton donors, while bases are proton acceptors
o Lewis definition – acids are electron acceptors, while bases are electron donors
➢ The amount of hydrogen ions released when an acid is dissolved in water determines its acid strength. The acid strength is
represented by the acid dissociation constant (pKa)
➢ The pH of a compound is defined as the hydrogen ion activity in a solution, and the pH scale is an inverse and logarithmic
measurement of how concentrated the hydrogen ions are in a solution
➢ In biochemistry, most vital reactions are sensitive to the pH of a solution, and any drastic changes to the pH may affect the
product or may prevent the reaction from occurring
➢ Buffer solutions, mixtures of weak acids and conjugate bases that resists change in pH, regulates the pH to a level favorable
to the desired reaction
 When do we actually start discussing biochemistry?
➢ Gases during the Earth’s early stage of development. such as H2, N2, CO, CO2, CH4, NH3 and H2S, reacted abiotically through
various mechanisms with and/or in water to form biologically important organic compounds
➢ These simple organic compounds eventually formed small
molecules called monomers
➢ The tetravalent structure of carbon allows for the
formation of different kinds of monomers, such as
monosaccharides, fatty acids, amino acids and
nucleotides
➢ These monomers bond to form polymers, or
macromolecules, with some being informational, like
nucleic acids and proteins
➢ Living cells are the result of complex and unique
assemblages of molecules

 What are cells?

➢ Cells are the basic biological unit of organisms, contributing to the organism’s total structure and function
➢ Cells provide an enclosed barrier where chemical processes can occur with limited outside interference
➢ DNA is contained within cells. The genome is the entire DNA of the cell, while genes are the individual units that are
responsible for controlling the production of a protein or RNA
➢ Important parts of an animal cell (organelles):

 What are the important parts of the animal cell?

➢ Nucleus – contains the genetic material that defines the function and processes of the cell; contains chromatin, a compact
and dense complex of genetic material and histones
➢ Nucleolus – allow for RNA synthesis from a DNA template and protein synthesis from RNA
➢ Cytoplasm – the area of the cell enclosed by the cell membrane, containing all organelles except for the nucleus
➢ Endoplasmic reticulum – allows for the transport and separation of molecules in the cytosol, the liquid within the
cytoplasm
➢ Smooth endoplasmic reticulum – does not contain ribosomes; responsible for lipid synthesis
➢ Rough endoplasmic reticulum – contains ribosomes; responsible for protein synthesis from RNA
➢ Ribosome – site of protein synthesis
➢ Mitochondria – location of chemical processes resulting in the production of energy, in the form of ATP, for the cell
➢ Lysosome – enclosed organelles containing hydrolytic enzymes responsible for breaking down target molecules
➢ Golgi apparatus – involved in the secretion of proteins from the cells and where sugars are linked to other components
➢ Cell membrane – separates the contents of the cell from the outside environment, and controls transport of substances in
and out of the cell