Download BIOL 313: Introduction to Biochemistry

BIOL 313: INTRODUCTION TO
BIOCHEMISTRY
Dr. Nadeem Asad
Lecture Objectives
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Applications and meaning of Biochemistry
Appreciate the basic molecular themes of life
The ultrastructure of the cell and it being the fundamental unit
of living organisms
Difference between prokaryotic and eukaryotic cells
Difference between plant and animal cells
Understanding of small molecules and macromolecules in the
human body
What is Biochemistry?
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Biochemistry and molecular biology are the scientific disciplines that aim to understand
life in molecular terms
Traditionally, Biochemistry is the study of the metabolism of food and small molecules
In the 21st century, the distinction between Biochemistry and Molecular Biology is blurred
and increasingly both are being merged and taught as one discipline
4 billion years ago, life forms started appearing on Earth; simple microorganisms came
into being that harnessed energy from sunlight or simple molecules to synthesize more
complex biomolecules essential to life
Biochemistry is therefore a study of how inanimate chemical structures and reactions
through interaction facilitate essential processes in living organisms which ensure their
survival and propagation
Three areas to study:
Structural and Functional Biochemistry: Chemical structures and 3D arrangements of
molecules
Informational Biochemistry: Language for storing biological data and for transmitting
that data in cells and organisms
Bioenergetics: The flow of energy in living organisms and how it is transferred from one
process to another
Applications of Biochemistry
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Medicine (clinical)-diagnose and monitor a wide range of infectious and
autoimmune diseases, cancer and neurodegenerative disorders
Designer drugs- producing new generation antibiotics, more efficacious
chemotherapy agents and vaccines
Agriculture-producing insecticides and herbicides
Transgenic crops
Genetically modified food and organisms
Industry-enzyme catalysis, synthesis, detoxification
Understanding metabolic disorders
Fundamental cellular living processes
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RESPIRATION-- the breakdown of nutrients to yield (or give off)
chemical energy there are 2 types 1) aerobic respiration- uses
oxygen 2) anaerobic respiration- doesn't use oxygen
REGULATION-- the process where a living thing controls and
coordinates its various activities. in animals-- 1) nervous system
uses nerve cells 2) endocrine system uses hormones in plants-some parts produce hormones like auxins and gibberellins
REPRODUCTION-- the process by which living things produce new
living things of the same kind there are 2 types 1) asexual
reproduction--involves one parent and the offspring are identical
to the parent 2) sexual reproduction--involves two parents and
the offspring is a combination of both parents
Fundamental cellular living processes II
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EXCRETION-- the process by which living things remove
waste products produced by cellular activities
GROWTH-- the process by which living things increase
in size or cell number
NUTRITION-- the process by which living things take in
material from their environment for growth and repair;
there are 2 types 1) autotrophic nutrition--where a
living thing can synthesize its own food 2) heterotrophic
nutrition--where a living thing must ingest (take in) its
food
Fundamental cellular living processes III
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TRANSPORT-- the process by which usable materials are taken into the living thing
(ABSORPTION) and distributed throughout the living organism (CIRCULATION)
SYNTHESIS-- the process by which smaller, simple substances are combined
chemically to form larger, more complex substances
When we refer to all of the life functions of an organism, we are referring to its
METABOLISM--the total of all the life functions required to sustain life (to stay alive)
R + R + R + E + G + N + T + S = METABOLISM
An organism's external (outside) environment is always changing. By keeping the
controlling and regulating it’s metabolic activities, an organism can maintain a stable
internal (inside) environment. This is called HOMEOSTASIS.
HOMEOSTASIS-- the process by which an organism's metabolic activities are in a
state of balance e.g. body temperature, blood sugar levels, hormone levels
The Living Cell
The cell
-is the structural and functional unit of all known
living organisms
-smallest unit of an organism often referred to as
the “building brick” of life
 All organisms consist of one or more cells
(viruses included)
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History of the cell
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1632-1723 Antonie van Leeuwenhoek- first to observe bacteria and
protozoa
1665 Robert Hook- first to coin the term “cell”
1839 Theodor Schwann and Mathias Jakob Schleiden- former is the
founder of modern histology as he defined the cell as the basic unit
of animal structure, the latter was a co-founder with Theodor of the
cell theory
1855 Rudolf Virchow- pioneer of pathological processes, explained
that diseases arose in individual cells not organs or tissues in general
1953 Watson and Crick put forward their first structure of DNA
being a double stranded helix, the cornerstone of genetics, cell
biology and molecular biology among other disciplines
General Classification of the Cell
1. Eukaryotic cell
- having a true nucleus
-compartmentalized membrane bound organelles
with specific metabolic activities
2. Prokaryotic cell
-no defined nucleus
-single celled
-no membrane bound organelles
Diagram of a Prokaryotic Cell
Diagram of a Eukaryotic Cell
Differences between prokaryotic and
eukaryotic cells
Plant and Animal Cells
Differences between plant and animal cells
Animal Cell
Plant Cell
Present (formed of
cellulose)
Round (irregular shape)
Rectangular (fixed
Shape
shape)
One or more small vacuoles (much smaller than plant One, large central
vacuole taking up
Vacuole cells).
90% of cell volume.
Cell wall
Centrioles
Absent
Present in all animal cells
Animal cells don't have chloroplasts.
Chloroplast
Cytoplasm Present
Endoplasmic Reticulum Present
(Smooth and Rough)
Ribosomes Present
Mitochondria Present
Plastids Absent
Golgi Apparatus Present
Only cell membrane
Plasma Membrane
Microtubules/ Microfilaments Present
May be found in some cells
Flagella
Lysosomes
Lysosomes occur in cytoplasm.
Nucleus Present
Cilia Present
Only present in lower
plant forms.
Plant cells have
chloroplasts because
they make their own
food.
Present
Present
Present
Present
Present
Present
Cell wall and a cell
membrane
Present
May be found in some
cells
Lysosomes usually not
evident.
Present
It is very rare.
Plasmodesmata are intercellular junctions between plant cells that enable the transportation
of materials between cells.
A tight junction is a watertight seal between two adjacent animal cells, which prevents
materials from leaking out of cells.
Desmosomes connect adjacent cells when cadherins in the plasma membrane connect to
intermediate filaments.
Similar to plasmodesmata, gap junctions are channels between adjacent cells that allow for
the transport of ions, nutrients, and other substances.
Source: Boundless. “Intercellular Junctions.” Boundless Biology. Boundless, 03 Jul. 2014.
Retrieved 02 Feb. 2015 from https://www.boundless.com/biology/textbooks/boundlessbiology-textbook/cell-structure-4/connections-between-cells-and-cellular-activities63/intercellular-junctions-325-11462/
Functions of Animal Cell Organelles I
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1. Cytoplasm/cytosol
- Viscous aqueous environment (NOT free flowing)
- Contains small molecules, nutrients, salts, soluble proteins
- 20-30% of cytosol is protein – Very concentrated
- Highly organized environment
- A major site of cellular metabolism (e.g. glycolysis)
- Contains cytoskeleton
2. Cytoskeleton
- 3-dimensional matrix made of protein fibers
- Functions to give cells shape, allows cells to move, guides internal organelle
movement.
3. Nucleus
- Site of most DNA and RNA synthesis
- Storage of genetic information
- Bound by a double membrane
- Largest organelle in eukaryotic cells
Functions of Animal Cell Organelles I
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1. Cytoplasm/cytosol
- Viscous aqueous environment (NOT free flowing)
- Contains small molecules, nutrients, salts, soluble proteins
- 20-30% of cytosol is protein – Very concentrated
- Highly organized environment
- A major site of cellular metabolism (e.g. glycolysis)
- Contains cytoskeleton
2. Cytoskeleton
- 3-dimensional matrix made of protein fibers
- Functions to give cells shape, allows cells to move, guides internal organelle
movement.
3. Nucleus
- Site of most DNA and RNA synthesis
- Storage of genetic information
- Bound by a double membrane
- Largest organelle in eukaryotic cells
FtsZ was the first protein
of the prokaryotic
cytoskeleton to be
identified. Like tubulin,
FtsZ forms filaments but
these filaments do not
group into tubules.
During cell division, FtsZ is
the first protein to move
to the division site, and is
essential for recruiting
other proteins that
synthesize the new cell
wall between the dividing
cells
MreB and ParM
Prokaryotic actin-like proteins, such as MreB, are involved in the maintenance of cell
shape.
Some plasmids encode a partitioning system that involves an actin-like protein ParM.
Filaments of ParM exhibit dynamic instability, and may partition plasmid DNA into the
dividing daughter cells by a mechanism analogous to that used by microtubules during
eukaryotic mitosis.
Crescentin
The bacterium Caulobacter crescentus contains a third protein, crescentin, that is related to
the intermediate filaments of eukaryotic cells. Crescentin is also involved in maintaining
cell shape, such as helical and vibrioid forms of bacteria, but the mechanism by which it
does this is currently unclear.
Functions of Animal Cell Organelles I
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1. Cytoplasm/cytosol
- Viscous aqueous environment (NOT free flowing)
- Contains small molecules, nutrients, salts, soluble proteins
- 20-30% of cytosol is protein – Very concentrated
- Highly organized environment
- A major site of cellular metabolism (e.g. glycolysis)
- Contains cytoskeleton
2. Cytoskeleton
- 3-dimensional matrix made of protein fibers
- Functions to give cells shape, allows cells to move, guides internal organelle
movement.
3. Nucleus
- Site of most DNA and RNA synthesis
- Storage of genetic information
- Bound by a double membrane
- Largest organelle in eukaryotic cells
Functions of Animal Cell Organelles II
4. Endoplasmic Reticulum (ER)
 - Network of interconnected, closed, membrane-bounded vesicles
 - Attached to cell and nuclear membrane
 - Used for manufacturing, modification and transport of cellular materials
 - Two types:
 * Smooth ER = site of lipid synthesis
 * Rough ER = site of protein synthesis via ribosomes
 - Ribosomes are made up of RNA and proteins not bound by a membrane
 5. Lysosomes
 - Internal sacs bound by a single membrane
 - Responsible for degrading cell components that have become obsolete for the cell
or organism.
- Internal pH ~5 (very acidic)
 - Compartmentalization ESSENTIAL! Sequesters this biological activity from the rest of
the cell.
 - Enzymes in lysosomes degrade polymers into their individual building blocks.
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Functions of Animal Cell Organelles III
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6. Golgi Apparatus
- Flattened vesicles of lipid/protein/sugar
- Usually found near smooth ER and nucleus
- Involved in protein and fat processing and trafficking to other organelles (e.g.
lysosomes, plasma membranes) – Distribution and shipping department for cell
materials.
7. Mitochondria
- Have double membrane (inner and outer)
- Place where most oxidative energy production occurs = “powerhouse” of the cell
- Form ATP – Convert oxygen and nutrients to energy
- Small, typically the size of a bacterium
- Contain a circular DNA molecule like that of bacteria (own genome)
- Because of the double membrane, size and presence of own genome,
mitochondria are believed to be descendents of a bacteria that was engulfed by a
larger cell billions of years ago = endosymbiotic hypothesis.
- A cell can have over 1000 mitochondria! Depends on need for energy---muscle
cells have a lot of mitochondria.
Underlying simplicity of the living cell
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LIVING SYSTEMS APPEAR COMPLEX BUT THERE IS
AN UNDERLYING SIMPLICITY AND ELEGANCE:
- Most biological compounds are made of only SIX
elements: C, H, O, N, P, S
- Only 31 chemical elements occur naturally in plants
and animals
- All organisms have similar biochemical pathways.
- All organisms use the - Limited number of molecular
building blocks make up larger macromolecules
4 major classes of biomolecules that make
up macromolecules
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1. Carbohydrates: e.g. glucose, fructose, sucrose - mainly used as sources of
cellular energy
Lipids: commonly known as fats
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Amino Acids:
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- 20 natural amino acids in total
- Used as building blocks for proteins
Nucleotides:
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- organic compounds that are not very water soluble
- used as sources of cellular energy
- components of cell membranes
- 5 in total
- Used as building blocks for DNA and RNA precursors
OTHER:
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- Vitamins: organic compounds necessary for proper growth and development
- Heme: Organometallic compound containing iron; important for transporting
oxygen in your blood stream.
Monomers to polymers
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Starch and Cellulose: polymers of glucose molecules that
differ only by how the glucose monomers are linked.
- Proteins/polypeptides: amino acid monomers linked
together
- DNA:deoxyribonucleic acid o Heteropolymer of
monomeric
nucleotides
o Storage of genetic information
- RNA: ribonucleic acid
o Heteropolymer of monomeric
nucleotides
o Involved in the TRANSFER
of the genetic information encoded by DNA
Monomers to polymers
Facts about biomacromolecules
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Biomacromolecules:
- 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 dimensions and shapes! Much
of biochemistry relies on this fact.
EVOLUTIONARY FOUNDATION
Reading List
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Lehninger “Principles of. Biochemistry”. Fourth
Edition. David L. Nelson and Michael M. Cox.
“Biochemistry and Molecular Biology”. Fifth
Edition. Despo Papachristodoulou, Alison Snape,
William H. Elliott, and Daphne C. Elliott
“Life: The Science of Biology. Ninth Edition by
David E Sadava et al.