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Week 1 - Intro to Biochemistry

Biochemistry, also known as biological chemistry, is the study of the molecular basis of life, focusing on the chemistry of living organisms and their biochemical reactions. The document outlines the historical roots of biochemistry, key figures, and the classification of biochemical substances into bioinorganic and bioorganic categories, highlighting the importance of biomolecules such as amino acids, sugars, fatty acids, and nucleotides. Additionally, it discusses biochemical reactions and methods for determining biomolecular structures.

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3 views

Week 1 - Intro to Biochemistry

Biochemistry, also known as biological chemistry, is the study of the molecular basis of life, focusing on the chemistry of living organisms and their biochemical reactions. The document outlines the historical roots of biochemistry, key figures, and the classification of biochemical substances into bioinorganic and bioorganic categories, highlighting the importance of biomolecules such as amino acids, sugars, fatty acids, and nucleotides. Additionally, it discusses biochemical reactions and methods for determining biomolecular structures.

Uploaded by

jetolosa6988ant
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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What is

Biochemistry? § Is sometimes called as “Biological


Chemistry”
§ May be defined as the investigation of
molecular basis of life
§ Is the study of the Chemistry in living
organisms. It deals with biomolecules
and biochemical reactions viewed in
context of biological structures.
Roots of Biochemistry
• Carl Scheele – Swedish founder of biochemistry. Studied the chemical
composition of matter in mid 1700.
• Friedrich Wohler (1828) – prove the fallacy that biochemicals can only be
produced by living organisms by producing urea by heating ammonium cyanate.
• Schleiden & Schwann – formulated the cell theory in 1840.
• Walther Flemming – discovered chromosomes in 1875.
• Carl Neuberg – German scientist who coined the word “biochemistry”
• Eduard & Hans Buchner – found that extracts from yeasts could bring about
fermentation of sugar into alcohol in 1897.
Roots of Biochemistry
• Embden & Meyerhof – describe the glycolytic pathway in 1925.
• Hans Krebs – Proposed the Krebs cycle of the TCA in 1937.
• Avery, MacLeod & McCarty (1944) – identified DNA as information molecules
• James Watson & Francis Crick (1953) – propose the double helical structure of
DNA.
• Francis Crick (1958) – proposed the central dogma of biology
• Paul Boyer & J. Walker – discovered the “rotary engine” that generated ATP in
1997.
• Jens Christian Skou – Danish biochemist who studied the “pump” that drives
sodium and potassium across membranes
Roots of Biochemistry
• Stanley Prusiner – discovered the organism that caused “mad cow disease”
• Ruska, et.al. – discovered the electron microscope and provided a whole new
level of insight into cellular structure.
Biochemical substance

Ø a chemical substance found within a living organism


Ø divided into 2 groups: Bioinorganic substances and
Bioorganic substances
Biochemical substance
Bioinorganic substances

Ø Substances that do not contain carbon


Øincludes water and inorganic salts
Ø The bioinorganic substance water constitutes over two-thirds of
the mass of the human body
ØAnother 4%–5% of body mass comes from inorganic salts
Biochemical substance
Bioorganic substances (biomolecules)

Ø Substances that contain carbon


Øinclude carbohydrates, lipids, proteins, and nucleic acids
Ø bioorganic molecules make up only about one-fourth of body
mass
Biomolecules
Ø Present in plant and animal cells
Ø Composition of the cell:
• 50-95% - H2O
• 1% - Ions
• others: organic molecules
Organic molecules ?
- Carbon based molecule that are covalently bonded to itself or other
elements like H, O, N, S, P.
- One important organic molecule is the Hydrocarbon.
Biomolecules: Hydrocarbon
Hydrocarbons
§ Biomolecules are derived from HC
§ Is non-polar, therefore, they are ________ in H2O
§ Hydrophobic
- Biomolecules with HC group – has hydrophobic character (Cell
membranes)
Biomolecules
Ø two broad types: small biomolecules and macromolecules
Ø Importance of Macromolecules:
a) Essential structures for the basis of life
b) Control and regulate this processes
c) Responsible for energy exchanges, irritability, metabolism, mobility
and reproduction
4 major classes of small
biomolecules
Ø 4 families of small molecules are found inside the cell
1. Amino acids
2. Sugars
3. Fatty acids
4. Nucleotides
What are their functions ?
a. They are used to synthesize larger molecules like polymers (proteins, nucleic
acids)
b. Some have special biological functions (ATP – a nucleotide)
c. Involve in complex reaction pathways
Amino acids (AA)
Ø There are 20 common α-amino acids (usually in protein)

Ø The chemical properties of the AA are determined largely by the R group


Amino acids
Ø are being used as to synthesize long chain polymer called __________.

Ø Short polypeptide – AA is less than 50 (and are called peptide)


ØLonger polypeptides – are called Proteins

ØEx of polypeptides:
1. Transport proteins
2. Structural proteins
3. Enzymes
Amino acids: Peptide bonds
Ø is the bond connecting the amino acids in the polypetide
Ø also called as “Amide Bond”

Ø note: the R groups of the polypeptide determines its final 3-D shape and
therefore its biological functions.
Sugars
Ø are called as carbohydrates
Ø the most abundant organic molecules in nature
ØFunctions as:
1. Energy source
2. Structural components
3. Intercellular communication
Basic Unit of Sugar is ______________. It is also known as simple sugar.
Monosaccharides can be described in terms of functional group:
a. Polyhydroxyl Aldehyde
b. Polyhydroxyl Ketone
Sugars
Ø Sugar containing an Aldehyde is called ____________
Ø Sugar containing a ketone group is called ____________

Examples of Sugars:
1. Glucose
2. Fructose
3. Ribose
4. Deoxyribose
Sugars: Polysaccharides
Ø a polymer containing large amount of monosaccharides

Examples:
1. Glycogen – energy storage molecule
2. Starch – energy storage molecule
3. Cellulose – structural material
Fatty Acids (FA)
1. FA
- Monocarboxylic acid
- usually contains an even number of carbon atoms
- FAs are components of Lipids
2 Types of FA
I. Saturated FA – are single bonded
II. Unsaturated FA – contain one or more double bonds

Ex. of Saturated FA
1. Palmitic acid – hexadecenoic acid
Fatty Acids (FA)
Ex. of Unsaturated FA
2. Oleic Acid (18:1)

2. Triacylglycerols (Fats and Oils)


- are ester containing glycerol and 3 FAs

Glycerol- a three carbon-alcohol with


3 hydroxyl group
Fatty Acids (FA)
Triacylglycerol (TAG)-

A lipid molecule that resembles triacylglycerol


is Phosphoglycerides
3. Phospholipids
- major component of
cell membrane
Other examples of Lipids
1. Steroids
Ex. Cholesterol
- a sex hormone
- an important part of animal cell membranes

2. Fat-soluble Vitamins
- Vitamin E and Vitamin A

3. Carotenoids
- a plant pigment molecule that plays a role in photosynthesis
Nucleotides
Ø the primary component of Nucleic Acids
Ø 3 Components of Nucleotides
1. 5-C sugar
2. Phosphate group
3. Nitrogenous Base

Ø 2 classes of the Bases:


1. Purine – A and G
2. Pyrimidine – T, C and U
Nucleotides: Nitrogenous Bases
Nucleic Acids
2 Types of Nucleic Acids
1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA)

Function of DNA?
- Contains/Stores – Genetic Information

Function of RNA?
- Involves in expressing the information primarily in protein synthesis
Other role of Nucleotides
Ø involves in biosynthetic and energy generating reactions

Ø Ex: Formation of Phosphate bonds to form ATP


Biochemical Reactions
Ø The sum of all the enzyme-catalyzed reactions in a living organism is
called “Metabolism”

Ø 4 Functions of Metabolism
1. Acquisition and utilization of energy
2. Synthesis of molecules needed to cell structure and function
3. Growth and development
4. Removal of waste products
Biochemical processes
Ø there are 5 frequent chemical reactions:

1. Nucleophilic substitution
2. Elimination
3. Addition
4. Isomerization
5. Redox
Nucleophilic Substitution

Ø Electrophile
- Electron-loving specie; usually a cation, radical or lewis acid
ØNucleophile
- Nucleus-loving specie; usually an anion or atom with a lone-pair
ØLeaving group
- leaves with the bonding pair of electrons, and is replaced by the
nucleophile; can be negatively charged or neutral
Nucleophilic Substitution
Ø Reaction of glucose with ATP

+ H+
Nucleophilic Substitution: Hydrolysis reaction

Ø is the cleavage of covalent bonds by WATER


Ø a kind of SN reaction and can be catalyzed by an acid, base and enzymes

Ø Importance: digestion of food involves Hydrolysis


Hydrolysis
Ø Hydrolysis of ATP – involves breaking of phosphate bonds

Energy +
Elimination
Ø A double (=) bond forms when atoms are removed from the molecule.

ØDehydration of 2-phosphoglycerate
Addition Reactions
Ø Two molecules combine to form a single product

ØFrom double bond to single bond


Isomerization Reactions
Ø It involves intra-molecular shift of atoms
ØExample of biochemical isomerization
1. Aldose-ketose pair
REDOX
Ø involves transfer of electron from a donor (RA) to an
electron acceptor (OA).

ØOxidation – Gain of Oxygen, Loss of Hydrogen


ØReduction – Loss of Oxygen, Gain of Hydrogen
Ex.
Methods of Determining Biomolecular
Structures
Ø Elemental Analysis
Ø UV, visible, infrared, and NMR spectroscopy
Ø Mass Spectroscopy (MS)
Ø X-ray Crystallography
Ø Specific sequencing methods (e.g., for proteins and nucleic acids)
Ø Use of battery of enzymes of known specificity to degrade biomolecule of
study
Ø Use of acid or alkaline hydrolysis to the degrade the biomolecule of study

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