Kuliah Pengantar Biokimia

Pengantar Biokimia

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Bagian Biokimia Fakultas Kedokteran Universitas Hasanuddin Makassar

Dr. Marhaen Hardjo, M.Biomed, PhD

What is Biochemistry ? • Biochemistry is the application of chemistry to

the study of biological processes at the cellular and molecular level.

• It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to

investigate the chemistry of living systems by:

A. Studying the structure and behavior of the complex molecules found in biological material and

B. the ways these molecules interact to form cells, tissues and whole organism

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Principles of Biochemistry • Cells (basic structural units of living organisms) are highly

organized and constant source of energy is required to maintain the ordered state.

• Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life

• Certain important pathways e.g. Glycolysis is found in almost all organisms.

• All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids.

• Instructions for growth, reproduction and developments for each organism is encoded in their DNA

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Ilmu Biokimia :mempelajari macam-macam molekul yang ada di dalam sel mahluk hidup dan organisme

dan reaksi-reaksi kimia yang terjadi diantara molekul-molekul tersebut. Ilmu Biokimia dapat perkawinan

antara ilmu kimia dan ilmu biologi.

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Ilmu yang memperhatikan (concerned) dengan ilmu kimia dasar dari kehidupan (the chemical basis of life)

Two notable breakthroughs in the history of biochemistry

(1) Discovery of the role of enzymes as catalysts

(2) Identification of nucleic acids as information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein

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Manusia organ ( otak, mata, organ-organ pencernaan,paru, jantung, ginjal, organ-organ reproduksi, dan lainnya)Organ jaringan,Jaringan sel

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Organism, Organ, CellOrganism

Organ

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The ER modifies proteins, makes macromolecules, and transfers substances throughout the cell.

Ribosome translates mRNA into a polypeptide chain (e.g., a protein).

Mitochondrion manufactures adenosine triphosphate (ATP), which is used as a source of energy.

The Cell

• circa 100 trillion (1014) cells in a human organism• 200 different forms of cells

Nucleus only in eukaryotic cells. Contains most of the cell's genetic material.

Cells• Basic building blocks of life

• Smallest living unit of an organism

• Grow, reproduce, use energy, adapt, respond to their environment

• Many cannot be seen with the naked eye

• A cell may be an entire organism or it may be one of billions of cells that make up the organism

• Basis Types of Cells

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Nucleoid region contains the DNA•Cell membrane & cell wall• Contain ribosomes (no membrane) to make proteins intheir cytoplasm

Contain 3 basic cell structures:• Nucleus• Cell Membrane• Cytoplasm with organelles

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Two Main Types of Eukaryotic Cells

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Characteristic Bio-membranes and Organelles

MitochondrionSurrounded by a double membrane with a series of foldscalled cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.

Plasma MembraneA lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. NucleusDouble membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome

Chloroplasts (plastids)Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium.

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Rough endoplasmic reticulum (RER)A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes.RibosomesProtein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatusA series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes

A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell. 13

VacuolesMembrane surrounded "bags" that contain water and storage materials in plants.

Peroxisomes or MicrobodiesProduce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.

Cell wallPlants have a rigid cell wall in addition to their cell membranes

Cytoplasmenclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.

CytoskeletonArrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.

http://www.biology.arizona.edu copyright © 1997 - 2004.. 14

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Fig 1.15 (a) Eukaryotic cell (animal)

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Structure of a biological membrane

• A lipid bilayer with associated proteins

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Di dalam sel ada organel (mitokhondria dll), supra molekul (ribosom, enzim), makromulekul (polisakarida, polipeptida), building block (asam amino, glukosa, asam lemak, deoksinukleotida, ribonukleotida dll) metabolit (asam piruvat, asam sitrat, asetoasetil-KoA, asam urat dll).

20Biochemistry

Biolog. Nanostructures

Biochemical Evolution

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CH4, H2O, NH3, HCN

How did organic complex molecules evolved from more simple molecules?

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How did organic complex molecules evolved from more simple molecules?

• Urea was synthesized by heating the inorganic compound ammonium cyanate (1828)

• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

The Urey-Miller experiment (1950)

Some amino acids could be produced:

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Many Important Biomolecules are Polymers

• Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)

• Condensation reactions join monomers (H2O is removed in the process)

• Residue - each monomer in a chain

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Molecular Organisation of a cell

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Water•About 60-90 percent of an organism is water

Water is used in most reactions in the bodyWater is called the universal solvent

Bio-molecules• Just like cells are building blocks of tissues likewise molecules are

building blocks of cells.

• Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)

• Water constitutes 50-95% of cells content by weight.

• Ions like Na+, K+ and Ca+ may account for another 1%

• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

• Infinite variety of molecules contain C.

• Most bio-molecules considered to be derived from hydrocarbons.

• The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.

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Biomolecules – Structure

• Building block• Simple sugar• Amino acid• Nucleotide• Fatty acid

• Macromolecule• Polysaccharide• Protein (peptide)• RNA or DNA• Lipid

Anabolic

Catabolic

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Linking MonomersCells link monomers by a

process called dehydration synthesis (removing a

molecule of water)

This process joins two sugar monomers to make a double

sugar

Remove H

Remove OH

H2O Forms

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Breaking Down Polymers• Cells break down

macromolecules by a process called hydrolysis (adding a molecule of water)

Water added to split a double sugar

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Macromolecules

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Macromolecules

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Concepts of Life

Life is characterized by

• Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, manta

rays, gila monsters, & you

• Chemical unity: living systems (on earth) obey the rules of physical and organic chemistry – there are no new principles

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Life needs 3 things:

(1) ENERGY, which it must know how to:

• Extract• Transform• Utilize

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The Energetics of Life

•Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds

•Organic compounds provide energy for all organisms

Using toxic O2 to generate energy

2 H2O O2 + 4e- + 4H+ (photosynthesis)

Glucose + 6O2 6CO2 + 6H2O + Energy

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Glycolysis: the preferred way for the formation of ATP

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Life needs (2) SIMPLE MOLECULES, which it must know how to:

• Convert• Polymerize• Degrade

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Life needs (3) CHEMICAL MECHANISMS, to:

• Harness energy• Drive sequential chemical reactions• Synthesize & degrade macromolecules• Maintain a dynamic steady state• Self-assemble complex structures• Replicate accurately & efficiently• Maintain biochemical “order” vs outside

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Trick #1: Life uses chemical coupling to drive otherwise unfavorable reactions

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Trick #2: Life uses enzymes to speed up otherwise slow reactions

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How does an enzyme do it, thermodynamically?

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How does an enzyme do it, mechanistically?

Chemical reaction types encountered in biochemical processes

1. Nucleophilic Substitution • One atom of group substituted for another

2. Elimination Reactions• Double bond is formed when atoms in a molecule is

removed

3. Addition Reactions:• Two molecules combine to form a single product. • A. Hydration Reactions• Water added to alkene > alcohol (common addition

pathway)

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4. Isomerization Reactions. • Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions• Occur when there is a transfer of e- from a donor

to an electron acceptor

6. Hydrolysis reactions• Cleavage of double bond by water.

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Summary of Key Concepts

Biochemical Reactions • Metabolism: total sum of the chemical reaction happening

in a living organism (highly coordinated and purposeful activity)

a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production

of energy for cellular function

• All reactions are catalyzed by enzymes

• The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products

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Even though thousands of pathways sound very large and complex in a tiny cell:

• The types of pathways are small

• Mechanisms of biochemical pathways are simple

• Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number

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Energy for Cells

• Living cells are inherently unstable.

• Constant flow of energy prevents them from becoming disorganized.

• Cells obtains energy mainly by the oxidation of bio-molecules (e- transferred from 1 molecule to another and in doing so they lose energy)

• This energy captured by cells & used to maintain highly organized cellular structure and functions

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