Introduction to the Course Biochemistry I (2578) Semester: Fall 2013

Lecture I (Jan 05, 2014)

Rules and Regulations

Study Material 15 Lectures Attendance Continuous Assessment Assignment I Home Assignment: 20 marks 3 Class Assignments: 60 marks 5 Minutes Test 5th Assignment: 20 marks Total marks = 100 Assignment II Based on three Class Tests: x 100 x 3 Total marks = 100
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Course Contents
Biomolecules Water and its Effects on Dissolved Biomolecules Amino Acids and Peptides Proteins Three Dimensional Structure of Proteins Enzymes Lipids Carbohydrates Nucleic Acids

Biochemistry
Inorganic reaction Organic reaction You expect a product. You get that product If you do not get that you repeat till you get that Biochemical Reaction Similar to Organic You may get the desired product You may not get the desired product You have to look for reasons why you dont get the product
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Biochemistry
Anabolism Catabolism Metabolism Glycolysis Krebs cycle Urea from CO2, Ammonia and Aspartic acid
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Drug discovery
Plant Plant extract Active fraction Active component More effective from gram to milligram Same effect Similar effect No effect

In vitro In vivo

Biomolecules
Cell structure

Prokaryotes and Eukaryotes

Animal and Plant Cells Chemical Composition

Three Dimensional Structure

Chemical Reactivity Macromolecules & their Monomeric Subunits

Prebiotic Evolution

Prokaryotic Cell

Cell Components
A flagellum (flagella) is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and functions in locomotion.
Mesosomes are clusters of folds in the plasma membrane, protruding toward the interior of the cell. These structures are important in the performance of the aerobic parts of aerobic cellular respiration. A key part of this process requires a lot of membrane surface, and mesosomes greatly increase the membrane surface of the cell. The capsule is not found in all prokaryotic cells. The capsule is composed of rather amorphous polysaccharide material. This material is hygroscopic, meaning that it has a great capacity to retain water. Water is a vital component of any living cell, and this layer around the cell can be very advantageous for the cell.

Cell components
Pili - Hair-like structures on the surface of the cell that attach to other bacterial cells. Shorter pili called fimbriae help bacteria attach to surfaces. A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell. Most commonly found as small circular, double-stranded DNA molecules in bacteria, plasmids are sometimes present in eukaryotic organisms. In nature, plasmids carry genes that may benefit survival of the organism (e.g. antibiotic resistance)
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Plant cell

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Raphides
Raphides are needle-shaped crystals of calcium carbonate or calcium oxalate found in specialized plant cells called idioblasts. It is believed that the raphides are a defense mechanism against plant predators, as they are likely to tear the soft tissues of the throat or esophagus of a plant predator chewing on the plant's leaves. Idioblasts: A cell that differs greatly from the surrounding cells or tissu e. Predator: An organism that lives by preying on other organisms.

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Druse
Druse is a kind of crystal present in plants. It is usually made of calcium oxalate (CaOx). CaOx crystals are distributed among many photosynthetic organisms, Oxalate-producing plants accumulate oxalate in the range of 3%-80% (w/w) of their dry weight.
Plant CaOx crystals accumulate via a biomineralization process to form a variety (shapes and sizes) of aggregate histological structures. Some of the purposes of CaOx crystal formation in plants are high-capacity calcium (Ca) regulation and protection against herbivores
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Animal Cell

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Comparison of Pro & Eukaryotic cells

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Nucleus

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Nucleus
Nucleus is the master organelle of all living cells . It is called as the brain of the cell. All the major functions of the cell are performed under the instruction of nucleus. In animal cells it is present in the middle of the cell In plant cells it is pushed towards the periphery. Nucleus contains chromatin material. The chromatin material consist of DNA which is the hereditary material of the cell.

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Nucleus
The major functions are: It is involved in cell division. It stores all the information that is to be transferred to the next generation. DNA replication and transcription processes take place inside the nucleus. Transcription is the formation of mRNA.

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Nucleus
The messenger RNA then plays its role in the translation, the process of protein synthesis. Thus the information generated by nucleus governs the formation of enzymes and other proteins that carry out all the processes of body

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Mitochodrion

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Mitochondria
The most important function of the mitochondria is to produce energy. The food that we eat is broken into simpler molecules which combine with oxygen and produce ATP molecules. This entire process is known as oxidative phosphorylation. Mitochondria helps in the building of certain parts of the blood, and hormones like testosterone and estrogen.

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Mitochondria
Mitochondria in the liver cells have enzymes that detoxify ammonia. Although most of the genetic material of a cell is contained within the nucleus, the mitochondria have their own DNA. They have their own machinery for protein synthesis and reproduce by the process of fission like bacteria do.

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Amino acids and Peptides

Classification of amino acids Amino acids as acids and bases Characteristic chemical reactions of amino acids and peptides Chemical synthesis of polypeptides

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Chloroplast

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Chloroplast
Chloroplast refers to any of the structures (organelles) within a plant cell containing the green pigment chlorophyll. Chloroplasts occur in most cells of the green plant undergoing photosynthesis. Plant chloroplasts are typically lens-shaped and bounded by a double membrane. They contain membranous structures called thylakoids, which are piled up into stacks, surrounded by a gel-like matrix (stroma). The light reaction of photosynthesis occurs on the thylakoid membranes while the dark reaction takes place in the stroma.

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Ribosomes
Ribosomes are the protein synthesizers of the cell. They are like construction guys who connect one amino acid at a time and build long chains. Ribosomes are found in many places around the cell. You might find them floating in the cytoplasm (cytosol). Those floating ribosomes make proteins that will be used inside of the cell. Other ribosomes are found on the endoplasmic reticulum. Endoplasmic reticulum with attached ribosomes is called rough. It looks bumpy under a microscope. Those attached ribosomes make proteins that will be used inside the cell and proteins made for export out of the cell.

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Ribosomes
mRNA is made in the nucleus and sent into the cell. The mRNA then combines with the ribosome subunits. Another nucleic acid lives in the cell - tRNA, which stands for transfer RNA. tRNA is bonded to the amino acids floating around the cell. With the mRNA offering instructions, the ribosome connects to a tRNA and pulls off one amino acid. Slowly the ribosome makes a long amino acid chain that will be part of a larger protein.

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Ribosomes
A ribosome is composed of two pieces or subunits. 60-S (large) and 40-S (small). When the cell needs to make protein, mRNA is created in the nucleus. The mRNA is then sent into the cell and the ribosomes. When it is time to make the protein, the two subunits come together and combine with the mRNA. The subunits lock onto the mRNA and start the protein synthesis. Prokaryotic cells have ribosomes made of 50-S and 30-S subunits. It's a small difference, but one of many you will find in the two different types of cells. Scientists have used this difference in ribosome size to develop drugs that can kill prokaryotic microorganisms that cause disease.

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Svedberg Unit
A svedberg unit (symbol S, sometimes Sv) is a non-SI unit for sedimentation rate. The sedimentation rate for a particle of a given size and shape measures how fast the particle 'settles', or sediments. It is often used to reflect the rate at which a molecule travels to the bottom of a test tube under the centrifugal force of a centrifuge.
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Ultracentrifuge
The ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as 2 000 000 G (approx 19 600 km/s).

There are two kinds of ultracentrifuges, the preparative and the analytical ultracentrifuge. Both classes of instruments find important uses in molecular biology, biochemistry, and polymer science.
G-force (with g from gravitational) is a measurement of acceleration felt as weight
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Ribosomes

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Protein Synthesis

The process of making proteins is quite simple. mRNA is made in the nucleus and sent into the cell. The mRNA then combines with the ribosome subunits. Another nucleic acid lives in the cell tRNA. tRNA is bonded to the amino acids floating around the cell. With the mRNA offering instructions, the ribosome connects to a tRNA and pulls off one amino acid. Slowly the ribosome makes a long amino acid chain that will be part of a larger protein.
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Cytoplasm
The cytoplasm plays an important role in a cell, serving as a "molecular soup" in which the organelles are suspended and held together by a fatty membrane. It is found within the plasma membrane of a cell and surrounds the nuclear envelope and the cytoplasmic organelles. The cytoplasm plays a mechanical role, i.e. (example) to maintain the shape, the consistency of the cell and to provide suspension to the organelles.
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Cytoplasm
Cytoplasm is a homogeneous, generally clear jelly-like material that fills cells. The cytoplasm consists of cytosol and the cellular organelles, except the nucleus. The cytosol is made up of water, salts and organic molecules and many enzymes that catalyze reactions.

It is also a storage place for chemical substances indispensable to life. Vital metabolic reactions take place here, for example anaerobic glycolysis and protein synthesis.
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Water
Weak interactions in aqueous systems Ionization of water Weak acids and weak bases

Buffering against pH change in biological systems

Water as a Reactant

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