INTRODUCTION TO BIOCHEMISTRYKhadijah Hanim Abdul Rahman9 September 2013Sem 1, 2013/2014khadijahhanim@unimap.edu.my

COURSE OUTCOME (C0 1)

• CO1: Ability to differentiate basic structure, properties, functions and classification of important biomolecules.

WHAT IS BIOCHEMISTRY?• A combination of the words biology and chemistry.

• Biology is the study of cells that form the fundamental units of all living organisms.

• Whereas, chemistry is the science that deals with the composition, structure, and properties of substances and the transformations that they undergo.

•Biochemistry involves various enzymatic activities of biomolecules.

•Biomolecules: any molecule produced by living organisms.

•Biomolecules: proteins, polysaccharides, lipids and nucleic acids polymeric molecules.

•Polymeric: molecule made up from millions of repeated linked units of numerous natural and synthetic compounds.

MEANING OF LIFE•What is the meaning of life?•Life is complex and dynamic – composed

of carbon-based (organic) molecules•Life is organised and self-sustaining –

composed of biomolecules (linked biomolecules formed polymers- macromolecules)

•Life is cellular •Life is information-based – genes•Life adapts and evolves – mutations

STRATEGIES IN ORIGIN OF LIFE STUDIES• TOP-DOWN APPROACH – phylogenetic

(evolutionary) history of modern organisms based on the similarities and differences among organisms that are clues to their evolutionary past

• BOTTOM-UP APPROACH – abiogenesis (mechanism of reconstructing and

transformation of early earth into the first primitive living organisms), and analyzing biomolecules as vestigial remanants of the prebiotic world

HISTORY OF LIFE

•Study of history - based on geological (fossil record), biological and chemical evidence

•Earth formed from a cloud of condensing cosmic dust and gas 4.5 billion years ago

•Earliest organisms stromatolites (compressed layers of bacterial remains) existed 3.6 billion years ago.

ABIOGENESIS

Essential issues•How were simple organic

molecules (sugars, amino acids, and nucleotides) formed?

•How did these primordial molecules link up to form proteins and nucleic acids?

•How did the first cells originate?

PHASES IN ABIOGENESISEARLY PHASE

Energy in the form of light, lightning and heat promoted the formation of organic molecules from inorganic

precursors

CHEMICAL EVOLUTIONPrimitive cell-like structures enclosed by lipid precursors

molecules possessed a richer diversity of organic molecules

POLYMERIZATIONCertain monomer molecules polymerized to form

polypeptides and nucleic acids

PRIMORDIAL CELLOnce the protocells became enclosed in a membrane-like

barrier, their evolution proceeded over time

ASSUMPTIONS EXPLAINING ABIOGENESIS•The first form of life was simple in both

structural and functional capabilities•The basic requirements of any form of life

is the presence of one or more molecules that are able to duplicate themselves using raw materials available in their environment

HYPOTHETICAL SCENARIO OF ORIGIN OF LIFE

• Short RNA segments may have originally encoded short peptides

• As protocells became more stable and complex form of genetic info, a reverse trascriptase started copying RNA sequences into DNA

• This resulted in the role of DNA as the major info macromolecule in all modern organisms

• Hence DNA is the genetic blueprint; PROTEINS, the devices that perform the tasks of all living processes; and RNA, the carrier of info used to manufacture protein.

THE RNA WORLD CONCEPT•RNA was the first information

molecule•It possess genetic info and also can

behave as an enzyme•Formation of peptide bonds during

protein synthesis is catalysed by an RNA component of ribosomes

•In certain conditions in living cells, DNA can be synthesized from an RNA molecule by an enzyme reverse transcriptase

THE LIVING WORLD• A protocell could have contained only

RNA to function as both genetic material and enzymes.

• First protocells were heterotrophs using ATP as energy and carrying out a form of fermentation.

Domains of Life on Earth: 3 domains1. ARCHAEA: Halophiles and

Thermophiles2. BACTERIA: Cyanobacteria and

Heterotrophic bacteria3. EUKARYA: Flagellates, Fungi, Plants

and Animals

EARLY CELLS

• Bacteria and Archaea are termed as PROKARYOTES –organisms whose DNA is not enclosed in a nucleus of the cell.

• EUKARYOTIC cells are aerobic and arose 2.1 billion years ago. They contain nuclei and organelles.

• PLANTS appeared on land (mud flats) during the ‘Paleozoic’ period, about 440 million years ago. They provided food for higher animals to evolve

EARLY BACTERIA•PRECAMBRIAN ERA

encompasses 87% of geological time scale and based on this, life began from 570 million to 4.6 billion years ago.

•Early bacteria resembled archaea that live in hot springs today.

•Archaeans resemble bacteria but developed separately from common ancestor nearly 4 billion years ago. They thrive under extreme conditions and are labeled as ‘extremophiles’.

PROKARYOTES

Prokaryotes are single-celled microorganisms

characterized by:• the lack of a membrane-bound

nucleus and • membrane bound organelles.

There are two domains of prokaryote: 1. Eubacteria / Bacteria 2. Archaebacteria/Archaea

DIFFERENCES BETWEEN BACTERIA AND ARCHAEA

Eubacteria Archaeabacteria

-cell walls composed of peptidoglycan- ester-linked straight-chain membrane lipids (fatty acids). - translation apparatus inhibited by antibiotics (e.g. streptomycin, tetracycline etc.).

cell walls composed of various different substances-have ether-linked branched-chain member lipids. - not affected by antibiotics

EUKARYOTIC CELLS•Eukaryotic cells are larger than

prokaryotes. •They have a variety of internal

membranes and structures, they are:1.Organelles 2.cytoskeleton composed of

microtubules, microfilaments and intermediate filaments

•Eukaryotic DNA is composed of several linear bundles called chromosomes.

Similarities between Eukaryotes and Prokaryotes• Both have DNA as their genetic material.1. Both are membrane bound.2. Both have ribosomes.3. Both have similar basic metabolism.4. Both amazingly diverse in forms.

FEATURES OF PROKARYOTIC CELL

• Has five essential structural components: 1.genome (DNA)2.ribosomes3.cell membrane4.cell wall5.surface layer

• Structurally, a prokaryotic cell has three architectural regions:

1.appendages (flagella and pili)2.cell envelope (capsule, cell wall , plasma

membrane)3.cytoplasm region (cell genome (DNA) and

ribosomes.

Other Important biochemical cell organelles (components)•Cytoskeleton•Cell wall•Nucleus•Cytoplasm•Ribosome•Mitochondrion•Chloroplast

Functions of important biochemical cell components• Cytoskeleton:

▫ Helps to maintain cell shape. ▫ The primary importance of the cytoskeleton is in cell

motility. ▫ Provides a supporting structure for the internal

movement of cell organelles, as well as cell locomotion and muscle fiber contraction could not take place without the cytoskeleton.

▫ It is composed of proteinaceous fibers

• Cell-wall: Every cell is enclosed in a membrane, a double layer of phospholipids (lipid bilayer) composed of peptidoglycan

• Nucleus: is enclosed in a double membrane and communicates with the surrounding cytosol (semi-liquid portion of cytoplasm) via numerous nuclear pores. Within the nucleus is the DNA providing the cell with its unique characteristics.

• Ribosome: is the site of protein synthesis

• Cytoplasm: This is a collective term for the cytosol plus the organelles suspended within the cytosol. The cytosol is full of proteins that control cell metabolism including signal transduction pathways, glycolysis, intracellular receptors, and transcription factors.

• Mitochondria (membrane-bound organelles (double membrane): are power centers of the cell. The different sections in a mitochodrion are: outer membrane; intermembrane space; inner membrane (where oxidation phosphorylation takes place) and matrix (where the Kreb Cycle takes place)

CHLOROPLAST IN PLANTS• Chloroplast:

▫ This organelle contains the plant cell's chlorophyll responsible for the plant's green color.

▫ Structurally it is very similar to the mitochondrion except it is larger than the mitochondrion, not folded into cristae, and not used for electron transport

• It contains: 1. A permeable outer membrane, 2. A less permeable inner membrane, 3. Inter membrane space4. A third membrane containing the light-absorbing

system, the electron transport chain, and ATP synthetase, that forms a series of flattened discs, called the thylakoids

Diagram of mitochondrion

COMPARING PROKARYOTES AND EUKARYOTES

SIZEProkaryotes are usually much smaller thaneukaryotic cells Eukaryotic cells are, on average, ten times the sizeof prokaryotic cells.CELL WALLProkaryotes have cell wall composed of

peptidoglycan (asingle large polymer of amino acid and sugar). Cell

wall ofeukaryotes is not made up of this polymer.SURFACE AREAProkaryotes have a large surface area /volume

ratio givingthem the advantage of having a higher metabolic

and growthrate with smaller generation time as compared to

theeukaryotes.

Differentiating Prokaryotes and Eukaryotes

SUPPORTIn Eukaryotes provided by cytoskeleton;

none in ProkaryotesPROTEIN SYNTHESISIn Eukaryotes (animals) Rough

Endoplasmic Reticulum (Rough ER) is involved

In Prokaryotes ribosomes are involved FAT SYNTHESIS In Eukaryotes – Smooth ER involvedNo fat synthesis in Prokaryotes

4. Differentiating Prokaryotes and Eukaryotes

ENERGY PRODUCTIONIn Eukaryotes – chloroplasts (plants);

mitochondrion (Kreb’s cycle)In Prokaryotes – chlorophyll (if present)

but has no covering or chloroplast; no mitochondrion and Kreb’s cycle replaced by fermentation

ENERGY DIGESTION Lysosomes involved in aging process of

cell in EukaryotesNo lysosomes in Prokaryotes

5. Differentiating Prokaryotes and Eukaryotes

MOVEMENT In Eukaryotes – cilia, flagella and

pseudopod movementIn Prokaryotes – flagella of different

structure involved in locomotionREPRODUCTION - DNA controlIn Eukaryotes – DNA in

chromosomes inside nucleusIn Prokaryotes – DNA in single

strand and floating freely without a nucleus

SUMMARYOrigin of life•A model for the origin of life

proposes that organisms arose from simple organic molecules that polymerized to form more complex molecules capable of replicating themselves.

•Compartmentation gave rise to cells that developed metabolic reactions for synthesizing biological molecules and generating energy.

Cells•All cells are prokaryotic or

eukaryotic.•Eukaryotic cells contain a variety

of membrane-bound organelles.•Phylogenetic evidence groups

organisms into 3 domains: archaea, bacteria, eukarya.

•Natural selection determines the evolution of species.