METABOLISME NITROGEN KRT

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What is Biochemistry ?

• Biokimia

 kimia terapan yang

mempelajari proses2 biologis pada

taraf cellular dan molecular

• Ilmu ini muncul pada awal abad 20

ketika para ilmuwan menggabungkan

kimia, fisiologi dan biologi untuk

meneliti sistem kimia kehidupan

melalui:

– Studi struktur dan sifat molekul complex

yang ditemukan dalam material biologis

– Studi cara molekul2 ini berinteraksi untuk

membentuk sel, jaringan dan organisme

secara keseluruhan

Principles of Biochemistry

• Sel (unit struktur dasar dari organisme hidup)

sangat terorganisir dan sumber energi secara

rutin dibutuhkan untuk mempertahankan

keberadaannya

• Proses kehidupan mengandung beribu-ribu

chemical pathways (=jalur kimia). Pengaturan

yang tepat & terintegrasi dari chemical pathways

ini dibutuhkan untuk mempertahankan kehidupan)

• Jalur yang penting, misal: Glycolysis ditemukan

dalam semua organisme

• Semua organisme menggunakan tipe molekul

yang sama:

carbohydrates, proteins, lipids &

nucleic acids.

• Instruksi untuk pertumbuhan, reproduksi dan

perkembangan untuk setiap organisme di

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Cells

• Basic building blocks of life

• Unit kehidupan terkecil dari

suatu organisme

• Tumbuh, reproduksi

menggunakan energi, adaptasi,

respon terhadap lingkungannya

• Banyak yang tak terlihat

dengan mata telanjang

• Organisme bersel Satu atau

berjuta-juta sel yang menyusun

suatu organisme

Nucleoid region contains the DNA

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Characteristic Bio-membranes and Organelles

Mitochondrion

Surrounded by a double membrane with a series of folds

called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a

captured bacterium.

Plasma Membrane

A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems.

Nucleus

Double 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.

.

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.

Ribosomes

Protein 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 apparatus

A 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.

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Vacuoles

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

Peroxisomes or Microbodies

Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.

Cell wall

Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm

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

Cytoskeleton

Arrays 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..

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Biochemical Evolution

?

CH

₄

, H

₂

O, NH

₃

, HCN

How did organic complex molecules evolved from

more simple molecules?

How did organic complex molecules evolved

from more simple molecules?

• Urea disintesis melalui pemanasan senyawa anorganik

ammonium cyanate (1828)

• Hal ini menunjukkan bahwa senyawa yang banyak

ditemukan dalam organisme hidup adapat disintesis dari

substansi anorganik

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The Urey-Miller experiment (1950)

Some amino acids could be produced:

Many Important Biomolecules

are Polymers

• Biopolymers

- macromolecules terbentuk melalui

penggabungan beberapa molekul organik yang lebih kecil

(

monomers

)

• Condensation reactions

penggabungan beberapa

monomer (H

₂

O dihilangkan dalam proses ini)

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Water

•Sekitar 60-90

percent dari organisme

berupa air

Air digunakan

dalam banyak

reaksi dalam

tubuh

Air disebut

pelarut universal

Bio-molecules

• Sel merupakan building blocks dari jaringan, demikian juga molecules merupakan building blocks dari sel

• Sel hewan dan tanaman mengandung sekitar 10, 000 macam molecules (bio-molecules)

• Air menyusun 50-95% dari berat cells • Ion seperti Na+, K+ dan Ca+ sekitar 1%

• Hampir semua jenis dari bio-molecules adalah organic (C, H, N, O, P, S)

• Umumnya berbagai molecules mengandung C.

• Kebanyakan bio-molecules merupakan turunan dari hydrocarbons. • Sifat kimia dari organic bio-molecules ditentukan oleh functional

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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

Linking Monomers

Cells link monomers by a process

called dehydration synthesis

(removing a molecule of water)

This process joins two sugar monomers

Remove H

Remove OH

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Breaking Down Polymers

• Cells memecah

macromolecules

melalui suatu

proses yang

disebut hydrolysis

(penambahan satu

molekul air)

Sugars

• Carbohydrates merupakan molekul organik yang ditemukan berlimpah di alam

• Awalnya disintesis dalam tanaman dari serangkaian reaksi complex yang melibatkan photosynthesis.

• Basic unit –nya adalah monosaccharides.

• Monosaccharides dapat membentuk molecules molekul yang lebih besar, misal: glycogen, plant starch or cellulose.

Fungsi:

• Penyimpanan energi dalam bentuk starch (photosynthesis in plants) or glycogen (in animals and humans).

• Penyediaan energy melalui metabolism pathways and cycles. • Supply carbon untuk sintesis senyawa lain

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Monosaccharides -Polysaccharides

Glycosidic bonds connecting glucose residues are in red

Fatty acids - Lipids

• Merupakan monocarboxylic acid yang mengandung sejumlah atom C • Dua type: saturated (C-C sb) and unsaturated (C-C db)

• Fatty acids merupakan komponen dari beberapa lipid molecules. • E,g. of lipids are triacylglycerol, steriods (cholestrol, sex

hormones), fat soluble vitamins. Fungsi:

• Energi cadangan dalam bentuk fat • Membrane structures

• Insulation (thermal blanket)

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Structure of a biological membrane

• A lipid bilayer with associated proteins

Nucleic Acids

•Store hereditary information

Mengandung informasi untuk membuat semua

protein tubuh

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Amino acids - Proteins:

• Amino acids:

• Building blocks dari protein.

• R Group (side chains) menentukan sifat-sifat kimia dari masing-masing amino

acids.

• Juga menentukan bagaimana protein folds dan fungsi biologisnya

• Berfungsi sebagai transport proteins, structural proteins, enzymes,

antibodies, cell receptors.

Proteins as Enzymes

• Banyak protein yang berperan sebagai biological

catalysts or enzymes

Ada ribuan enzim yang berbeda dalam tubuh

Enzymes mengendalikan

rate of chemical reactions

dengan cara melemahkan ikatan, sehingga

lowering

the amount of activation energy

yang diperlukan

untuk reaksi  Catalysator

-> No not interfere with the equilibrium of reaction

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Enzymes:

• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction

Egg white lysozyme

The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)

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Concepts of Life

Kehidupan dicirikan oleh:

•

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

,

yang harus

diketahui bagaimana:



Extract

• Transform

• Utilize

The Energetics of Life

• Photosynthetic organisms

menangkap energi cahaya

matahari dan

menggunakannya untuk

mensintesis senyawa

organik

• Senyawa organik

menyediakan energi untuk

semua organisme

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Using toxic O

₂

to generate energy

2 H

₂

O  O

₂

+ 4e

-

_{+ 4H}

+

_{(photosynthesis)}

Glucose + 6O

₂



6CO

₂

+ 6H

₂

O + Energy

Glycolysis: the preferred way for the

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Life needs (2)

SIMPLE MOLECULES

,

yang harus diketahui bagaimana:

•

Convert

• Polymerize

• Degrade

Life needs (3)

CHEMICAL

MECHANISMS

, to:

•

Memanfaatkan energy

• Mengendalikan serangkaian reaksi kimia

• Mensisntesis & mendegradasi macromolecules

• Mempertahankan suatu keadaan yang

terus-menerus dinamis

• Self-assemble complex structures

• Replicate secara akurat dan efisien

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Trick #1: Life uses chemical coupling to

drive otherwise unfavorable reactions

Trick #2: Life uses enzymes to speed up

otherwise slow reactions

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How does an enzyme do it,

thermodynamically?

How does an enzyme do it,

mechanistically?

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Chemical reaction types encountered in

biochemical processes

1. Nucleophilic Substitution

• Satu atom dari group disubstitusi untuk yang lain 2. Elimination Reactions

• Double bond terbentuk ketika atom dalam satu molecule dihilangkan 3. Addition Reactions:

• Dua molecules bergabung untuk membetuk satu produk tunggal A. Hydration Reactions

• Air ditambahkan pada alkene  alcohol (common addition pathway)

4. Isomerization Reactions.

• Melibatkan intramolecular shift dari atoms atau

groups

5. Oxidation-Reduction (redox) Reactions

• Terjadi bila ada transfer e- dari donor ke electron

acceptor

6. Hydrolysis reactions

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44

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

• Semua reaksi dikatalisis oleh enzymes

• Fungsi utama dari metabolisme adalah:

a. Perolehan dan pemanfaatan energy

b. Synthesis of molecules diperlukan untuk struktur dan fungsi sel (spt: protein, nucleic acid, lipid dan CHO)

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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

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