Biochemistry (Powerpoint Presentation

Biochemistry
Introduction
JOEL R. SALAZAR, PhD.

 1.1 Distinctive Properties of Living
Systems
 1.2 Biomolecules: Molecules of Life
 1.3 A Molecular Hierarchy
 1.3 Properties of Biomolecules
 1.4 Organization and Structure of Cells
 Organisms are complicated and highly
organized
 Biological structures serve functional
purposes
 Living systems are actively engaged in energy
transformations
 Living systems have a remarkable capacity
for self-replication
Biochemistry: Life at the Molecular Level
Biochemistry is the
study of biological
processes
at a chemical level
Biochemistry = study of the chemistry of life
Biochemistry is an interdisciplinary science overlapping with chemistry, cell
biology, genetics, immunology, microbiology, pharmacology and physiology.
Main Issues of Biochemistry

1.) What are the chemical and three- dimensional structures of biological
molecules
2.) How do biological molecules interact with each other
3.) How does the cell synthesize and degrade biological molecules
4.0 How is energy conserved and used by the cell
5.) What are the mechanisms for organizing biological molecules and the
coordinating of their activities
6.0 How is genetic information stored, transmitted and expressed
- Lead us to fundamental understanding of life
- Understand important issues in medicine, health and nutrition
o Has led to greater molecular understanding of diseases
such as diabetes, sickle cell anemia and cystic fibrosis
o Next frontier: AIDS, cancer, Alzheimer’s Disease
Advance Biotechnology industries
o Biotechnology is the application of biological cells, cell

components, and biological properties to technically and
industrially useful operations
Living organisms operate within the same physical laws that apply to physics and
chemistry:
•Conservation of Mass, Energy

•Laws of Thermodynamics
•Laws of Chemical Kinetics
•Principles of Chemical Reactions
These physical laws describe several axioms that make up the Molecular Logic of
Life. These axioms define:
oEnergy converted to work

oCatalytic chemical transformations
oAssembly of molecules with great complexity from simple subunits.
oComplex molecules combine to form supra molecular components, organelles and
finally assemble into a cell.
oStore and pass on instructions for the assembly of all future generations from simple
non-living precursors
Three areas to study:
1. Structural and Functional Biochemistry: Chemical structures and 3D
arrangements of molecules
2. Informational Biochemistry: Language for storing biological data and for
transmitting that data in cells and organisms
3. Bioenergetics: The flow of energy in living organisms and how it is transfers
from one process to another
Elemental composition of the human body
Carbon -61.7 %; Nitrogen -11.0 %; Oxygen -9.3 %
Hydrogen -5.7 %; Calcium -5.0 %; Phosphorus -3.3 %
Potassium -1.3 %, Sulfur -1.0 % Chlorine -0.7 %
Sodium -0.7 %; magnesium -0.3 %
Trace: B, F, Si, V, Cr, Mn, Fe, Co, Cu, Zn. Se, Mo, Sn, I
Most organisms are about 70 % water

The earth is about 4.6 billion years old
Earliest known fossil is about 3.5 billion years old
(filamentous bacterium)
 What property unites H, O, C and N and
renders these atoms so appropriate to the
chemistry of life?
 Answer: Their ability to form covalent bonds

by electron-pair sharing.
Simple Molecules are the Units for Building
Complex Structures
 Metabolites and Macromolecules
 Organelles
 Membranes
 The Unit of Life is the Cell
 Macromolecules and Their Building Blocks
Have a “Sense” or Directionality
 Macromolecules are Informational
 Biomolecules Have Characteristic Three-
Dimensional Architecture
 Weak Forces Maintain Biological Structure
and Determine Biomolecular Interactions
- Self –assemble into cellular structures and complexes.
- Recognize and interact with one another in specific ways to
perform essential cellular functions (e.g. membranes are
complexes of lipids and proteins)
- Interactions are weak and reversible
- Molecules have three dimensional shapes.
Important numbers!
 van der Waals: 0.4-4.0 kJ/mole
 Hydrogen bonds: 12-30 kJ/mole
 Ionic bonds: 20 kJ/mole
 Hydrophobic interactions: <40 kJ/mole
 Biomolecular Recognition is Mediated by
Weak Chemical Forces
 Weak Forces Restrict Organisms to a Narrow

Range of Environmental Conditions
Prokaryotes and Eukaryotes
All modern organisms are based on the same morphological unit,

the cell
oProkaryotes –lack a nucleus (e.g., bacteria)
oEukaryotes –membrane enclosed nucleus encapsulating their
DNA
Viruses are not cells and are not living since they lack the
apparatus to reproduce outside of htier host cells
oProkaryotes range in size from 1 to 10 μM

oEukaryotes range in size fro m10 to 100 μM and thus have a
thousand to a million times as much volume as a prokaryotic cell.
Phylogenetic Tree of Showing Three domains of Organisms
Structural hierarchy in the molecular organization of cells
a. Class includes plants, animals, protozoans, yeasts and some algae
b. Large cells (10 -100μm in diameter) 10x bigger than prokaryotes
c. Surrounded by a membrane called plasma membrane
o Composed of lipids and protein
o Serves as chemical barrier to the outside environment
d. Contains internal membranes and compartments
o compartments –organelles
o Organelles contain organized complex of macromolecules that
perform certain biological function
o most enzymes are compartmentalized
e. No cell wall in animal cells

f. Plants, fungi, algae generally have a cell wall
Example: fatty acid synthesis enzymes (cytosol),
fatty acid breakdown enzymes (mitochondria)
 Cell =smallest living units of organisms
 Common in cells
i.) cell membrane = separates the inside from the environment
ii.) cytoplasm = jelly like fluid
iii.) DNA = cells genetic material
 Broad categories
i.) Eukaryotic cell (plants and animals) - nucleus
ii.) prokaryotes (bacteria) – no nucleus or membrane
- has a genetic material but not contain in the nucleus
 Organelles (parts of cell with specific function)
i.) Nucleus ( DNA)
o DNA dictates what the cell is going to do and how will it be done
o Chromatin (tangled spread out form of DNA found inside the nuclear
membrane
o When the cell is ready to divide, DNA condenses into structures known as
Chromosomes.
 Organelles
 The nucleus also contains a nucleolus
ii.)Nucleolus = where the ribosomes are made (r-RNA)
 When the ribosomes were made, they will leave the nucleus and will do important job/function
of synthesizing proteins.
 Ribosomes and other organelles will float around in the cytoplasm or may attach to
endoplasmic reticulum.
iii.) Endoplasmic Reticulum = enclosed membrane which allows the passage of transporting
materials (proteins and other materials emerge in the ER in small vesicle where Golgi Apparatus
receives the protein)
a.) Rough ER (with ribosome attach to it)
b.) Smooth ER (without ribosomes)
 1
 iv. Golgi Apparatus = the proteins from ER will flow to GA. The proteins
were customized (fit) by folding in the form that it can perform its
function. Aside from the protein other materials can attached into it like
lipids and carbohydrates.
 v. vacuoles = sac-like structures that stored different materials .

 in plant cell = central vacuoles stores water
 vi.) Lysosomes = garbage collectors

 In animal cell = they take in damaged or worn out cell parts. They are filled
with enzymes that break down this cellular debris
 vii.) Mitochondrion (power house in both animal and plant cell)

o During Cellular respiration = It produces ATP molecule that provides energy for all cells
activities . Cells that need more energy have more mitochondria
 Meanwhile the cells maintains it shape through cytoskeleton.
o thread-like microfilaments (made of protein)
o microtubules which are thin hollow tubes
 Plants (photoautotrophic) = meaning it captures sunlight for energy
o chloroplasts (where photosynthesis happens)
o Green (green pigment) = chlorophyll
o Cell wall (outside of the cell membranes) = shapes, support and protect the plant cell.
 In Human
 Respiratory tract is lined with cells that have cilia
o Cilia (microspcopic hair-like projections that can move and waves
o This feature help trap inhaled particles in the air and expelled them when you cough
 Bacteria
o Flagella like a little tail that can help the cell move or propel (drive forward ) itself
 Human Cell with flagellum (sperm cell)

Tissues
Epithelial Tissue
Connective Tissue
Nerve Tissue
Muscle Tissue

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Biochemistry

JOEL R. SALAZAR, PhD.

Main Issues of Biochemistry

Advance Biotechnology industries

o Biotechnology is the application of biological cells, cell

•Conservation of Mass, Energy

oEnergy converted to work

Most organisms are about 70 % water

 Answer: Their ability to form covalent bonds

 Weak Forces Restrict Organisms to a Narrow

All modern organisms are based on the same morphological unit,

oProkaryotes range in size from 1 to 10 μM

e. No cell wall in animal cells

 v. vacuoles = sac-like structures that stored different materials .

 vi.) Lysosomes = garbage collectors

 vii.) Mitochondrion (power house in both animal and plant cell)

 Human Cell with flagellum (sperm cell)

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