lect 1 introductory lecture biochemistry

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Introduction to the Course

BiochemistryI (2578)

Semester: Fall 2013

Lecture I (Jan 05, 2014)

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Rules and Regulations

Study Material

15 Lectures

Attendance

Continuous Assessment

Assignment I

Home Assignment: 20 marks

3 Class Assignments: 60 marks

5 Minutes Test 5thAssignment: 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

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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 theproduct

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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 6


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Biomolecules

Cell structure

Prokaryotes and Eukaryotes

Animal and Plant Cells

Chemical Composition

Three Dimensional Structure

Chemical Reactivity

Macromolecules & their Monomeric Subunits Prebiotic Evolution

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Prokaryotic Cell

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http://upload.wikimedia.org/wikipedia/commons/9/99/Prokaryote_cell_diagram.svg


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Cell Components

A flagellum (flagella) is a tail-like projection that protrudes from thecell body of certain prokaryotic and eukaryotic cells, and functionsin locomotion.

Mesosomes are clusters of folds in the plasma membrane, protruding

toward the interior of the cell. These structures are important in theperformance of the aerobic parts of aerobic cellular respiration. A key partof this process requires a lot of membrane surface, and mesosomesgreatly 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 vitalcomponent of any living cell, and this layer around the cell can be veryadvantageous for the cell.

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Cell components

Pili- Hair-like structures on the surface of the cell thatattach to other bacterial cells. Shorter pili calledfimbriae help bacteria attach to surfaces.

A plasmidis a small DNA molecule that is physicallyseparate from, and can replicate independentlyof, chromosomal DNA within a cell. Most commonlyfound as small circular, double-stranded DNAmolecules in bacteria, plasmids are sometimes presentin eukaryotic organisms.

In nature, plasmids carry genes that may benefitsurvival of the organism (e.g. antibiotic resistance)

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Plant cell

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Raphides

Raphidesare needle-shaped crystals of calcium carbonateor calcium oxalate found in specialized plant cells calledidioblasts.

It is believed that the raphides are a defense mechanismagainst plant predators, as they are likely to tear the softtissues of the throat or esophagus of a plant predatorchewing on the plant's leaves.

Idioblasts:A cell that differs greatly from the surrounding cells or tissue.

Predator: An organism that lives by preying on other

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Druse

Druse is a kind of crystal present in plants. It is usuallymade of calcium oxalate (CaOx). CaOx crystals aredistributed among many photosynthetic organisms,

Oxalate-producing plants accumulate oxalate in therange of 3%-80% (w/w) of their dry weight.

Plant CaOx crystals accumulate via a biomineralizationprocess to form a variety (shapes and sizes) of

aggregate histological structures. Some of the purposesof CaOx crystal formation in plants are high-capacitycalcium (Ca) regulation and protection againstherbivores

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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 thehereditary 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 thatdetoxify ammonia.

Although most of the genetic material of a cell iscontained within the nucleus, the mitochondria havetheir own DNA. They have their own machinery forprotein synthesis and reproduce by the process of fissionlike 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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http://en.wikipedia.org/wiki/File:Chloroplast_diagram.svg


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Chloroplast

Chloroplastrefers to any of the structures (organelles) withina plant cell containing the green pigment chlorophyll.

Chloroplasts occur in most cells of the green plant undergoingphotosynthesis.

Plant chloroplasts are typically lens-shaped and bounded by adouble membrane.

They contain membranous structures called thylakoids, whichare piled up into stacks, surrounded by a gel-like matrix(stroma).

The light reaction of photosynthesis occurs on the thylakoidmembranes

while the dark reaction takes place in the stroma.

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http://en.wikipedia.org/wiki/File:Chloroplast_diagram.svg


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Ribosomes

Ribosomes are the protein synthesizers of the cell. They arelike construction guys who connect one amino acid at atime and build long chains.

Ribosomes are found in many places around the cell. Youmight find them floating in the cytoplasm (cytosol). Thosefloating ribosomes make proteins that will be used inside ofthe cell.

Other ribosomes are found on the endoplasmic reticulum.Endoplasmic reticulum with attached ribosomes is calledrough. It looks bumpy under a microscope. Those attachedribosomes make proteins that will be used inside the celland proteins made for export out of the cell.

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Ribosomes

mRNA is made in the nucleus and sent into the cell. ThemRNA then combines with the ribosome subunits.

Another nucleic acid lives in the cell - tRNA, which standsfor transfer RNA.

tRNA is bonded to the amino acids floating around thecell.

With the mRNA offering instructions, the ribosomeconnects to a tRNA and pulls off one amino acid.

Slowly the ribosome makes a long amino acid chain thatwill 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, mRNAis created in thenucleus.

The mRNA is then sent into the cell and the ribosomes. Whenit is time to make the protein, the two subunits come togetherand combine with the mRNA. The subunits lock onto themRNA 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 findin the two different types of cells.

Scientists have used this difference in ribosome size todevelop drugs that can kill prokaryotic microorganisms that

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Svedberg Unit

A svedbergunit (symbol S, sometimes Sv) is anon-SI unit for sedimentation rate.

The sedimentation rate for a particle of a givensize and shape measures how fast the particle'settles', or sediments.

It is often used to reflect the rate at which amolecule travels to the bottom of a test tubeunder the centrifugal force of a centrifuge.

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Ultracentrifuge

The ultracentrifuge is a centrifuge optimized forspinning a rotor at very high speeds, capable ofgenerating acceleration as high as

2 000 000 G (approx 19 600 km/s).

There are two kinds of ultracentrifuges, the preparativeand the analytical ultracentrifuge. Both classes ofinstruments find important uses in molecularbiology, biochemistry, and polymer science.

G-force(with gfrom gravitational) is a measurementof 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 madein the nucleus and sent into the cell. The mRNA thencombines with the ribosome subunits. Another nucleic acid

lives in the celltRNA. tRNA is bonded to the amino acidsfloating around the cell. With the mRNA offering instructions,the ribosome connects to a tRNA and pulls off one aminoacid. Slowly the ribosome makes a long amino acid chain thatwill be part of a larger protein.

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Cytoplasm

The cytoplasm plays an important role in a cell, serving asa "molecular soup" in which the organelles aresuspended and held together by a fatty membrane.

It is found within the plasma membrane of a cell andsurrounds the nuclear envelope and the cytoplasmicorganelles.

The cytoplasm plays a mechanical role, i.e. (example) tomaintain 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-likematerial that fills cells.

The cytoplasm consists of cytosol and the cellular

organelles, except the nucleus.

The cytosol is made up of water, salts and organicmolecules and many enzymes that catalyze reactions.

It is also a storage place for chemical substancesindispensable to life. Vital metabolic reactions take placehere, for example anaerobic glycolysis and proteinsynthesis.

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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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lect 1 introductory lecture biochemistry

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