Introduction to Biochemistry

Introduction to Biochemistry
Biochemistry : a multidisciplinary science that explores the chemistry of living organisms and molecular basis for changes occurring in living cells.
Principal areas of Biochemistry 1. Struture and Function of Biomolecules
Based on structure depend the function (structure function relationship)
Example:
Hemoglobin S differs from regular adult hemoglobin (hemoglobin A) by just one single amino acid. A valine replaces a glutamine in the 6th position of the beta chain of globin.

2. Metabolism
e.g. krebs cycle, photosynthesis, respiration

3. Storage and transmission of genes
Branches that deals with it: a. Bioinformatics -the application of computer science and information technology to the field of biology and medicine. Bioinformatics was applied in the creation and maintenance of a database to store biological information at the beginning of the "genomic revolution", such as nucleotide and amino acid sequences. b. Bioenergetics – concerns with the energy flow through living systems. i. Endergonic – “inside” input of energy ii. Exergonic – output of energy

Central Dogma of Molecular Biology

1. DNA replication – DNA to DNA 2. Transcription – DNA to RNA 3. Translation – RNA to protein 4. Reverse Transcription – RNA to DNA Biochemistry encompasses organic chemistry, genetics, physiology (study of function), microbiology, medical research, nutrition, biophysics, cell biology.
Cell
Fundamental and Structural unit of all organisms
Classification of cell: 1. Prokaryotic cell – (Greek: pro, before), which lack this organelle. 2. Eukaryotic cell – (Greek: eu, good or true _ karyon, kernel or nut), which have a membrane enclosed nucleus encapsulating their DNA (deoxyribonucleic acid) Difference between a prokaryotic cell and a eukaryotic cell: | PROKARYOTES | EUKARYOTES | Species | All species that belong to Kingdom Monera. | All other organisms that doesn’t belong to Kingdom Monera. | Nomenclature | ‘pro’ – before‘karyon’ - nucleus | ‘eu’ – true | Major Group | Eubacteria – true bacteriaArchaebacteria – ancient class | | Cellular organization | Unicellular | Multicellular (except unicellular Protist) | Nucleus | Absence of ‘true’ nucleusNucleoid | Presence of ‘true’ nucleus | Size | 0.2-5 μm in diameter | 10-50 μm in diameter |
Prokaryotes
* Prokaryotes are considered as ancestor of eukaryotic cell. * Only organisms in Kingdom Monera are prokaryotic cells. * Unicellular * Escherichia coli is the most studied prokaryote

Two major divisions: 1. Archaebacteria (ancient class) * Extremophiles
Examples:
a. Acidophiles – can withstand low pH b. Halophiles – can withstand gases c. Thermophiles – can withstand temperature d. Osmophiles – can withstand salt concentration 2. Eubacteria (true bacteria) Structure of a prokaryotic cell:

Membrane * There are two definite membranes in a bacterial cell: the cell wall and the plasma membrane (cytoplasmic membrane). * Some bacteria further encase themselves in a gelatinous polysaccharide capsule that protects them from the defenses of higher organisms.

Parts of the membrane of bacterial cell: 1. Cell wall – outer layer membrane; it is rigid and serves as mechanical support. It is made up of polysaccharides, lipids and protein molecules. 2. Porin – acts as channels that allow diffusion of solutes. 3. Plasma membrane – the inner membrane; it is a lipoprotein structure which serves as molecular barrier. Some enzymes involved in respiratory chain and photosystems maybe present.

* Sandwich between the cell wall and plasma membrane is the periplasmatic space.

Figure : Periplasmatic space in gram positive gram negative bacteria.

Cytoplasm Consist of: 1. Ribosomes – 20,000 to 30,000 ribosome particles are present in the cytoplasm. These are sites for protein synthesis. 2. Plasmids – a small extrachromosomal circular DNA, is also present. This may confer to antibiotic resistance. 3. Water, various RNAs, proteins (including enzymes) and small molecules also filled the cytoplasm.

Nucleoid region

* genetic material of the prokaryotic cell is contained here. It is a poorly demarcated region of the cell that lacks a boundary membrane to separate it from the cytoplasm. * A bacterial chromosome is a single circular molecule of naked DNA. At one point, it is anchored to plasma membrane. Organelles for Locomotion

1. Flagella

* made of protein and appear "whip-like". They are used by the prokaryotic cell for mobility. Flagella propel the microorganism away from harm and towards food in a movement known as taxis. * Each flagellum is made up of a single fibril that is attached to the cell through its “hook” and basal body.

Prokaryotic Flagella:

2. Fimbriae

* proteinaceous, sticky, bristle-like projections used by cells to attach to each other and to objects around them. * Fimbriae may be responsible for the clinging of cells that leads to biofilms and other thick aggregates of cells on the surface of liquids and for the microbial colonization of inanimate solids such as rocks and glass.

3. Pili * tubules that are used to transfer DNA from one cell to another cell * Some are also used to attach one cell to another cell. * The tubules are made of protein and are shorter in length than flagella and longer than fimbriae.

Eukaryotes

General organization of eukaryotic cell:

Main Components or Compartments | Subcomponents or Sub compartments | Main Function | Cell Membrane | Cell wallCell coatPlasma membrane | ProtectionCell InteractionPermeability, endocytosis and exocytosis | Nucleus | Chromatin & chromosomesNucleolusNucleoplasm | Genetic information system | Cytoplasm matrix, cytosol Cytoskeleton | Soluble enzymesMicrofilamentsMicrotubules Ribosomes | Glycolysis Cell shape and motilityProtein synthesis | Endomembrane System | Nuclear envelope Rough and smooth ERGolgi complex | Nuclear permeabilitySynthesis and transport of materialsSecretion | Membrane Organelles | MitochondriaChloroplastsLysosomes Peroxisomes | Cell respirationPhotosynthesisDigestionPeroxidation | Microtubular organelles | Centrioles and spindleBasal bodies, cilia and flagella | Cell divisionCell motility |

Cell Membrane

Plasma membrane
It is a thin film of lipid and protein molecules held together by noncovalent interactions
Fatty acid chains of lipid molecules form a bilayer that acts as a barrier to the diffusion of polar solutes. It prevents apoptosis (cell death).

Membrane Lipids
The major membrane lipids are the phospholipids, the glycolipids, and the sterols.

The relative ratios of different lipids vary in different membranes, but usually phospholipids are the major constituent (50–90% of total lipids), followed by glycolipids (5–20%) and cholesterol (0–10%).

Glycolipids * Often based on a glycerol framework and contain two acyl chains attached to a glycerol bound to a sugar chain; these are predominantly found in plants and in bacteria. * In animal cells, the backbone of glycolipids is sphingosine. When the amino group of the serine moiety of sphingosine is linked to a second acyl chain, a ceramide is produced.
Sterols
* cholesterol is the main sterol found in animal membranes, whereas various phytosterols predominate in plants. * Sterols are rare or absent in prokaryotes.
Membrane Proteins 1. Integral (intrinsic) protein – localized within the interior of the membrane. 2. Peripheral (extrinsic) proteins – lack transmembrane segments and are located on the membrane surface.

Membrane Carbohydrates * Only small proportion of membrane carbohydrate is present as glycolipid, but mostly in the form of glycoproteins. * Sugar chains of glycoproteins in plasma membrane are found only at the external surface of the cell membrane. They are important in cell-cell recognition; presumably involved in intercellular adhesion to form tissues and in antibody-antigen interaction.

Cell wall * The cell wall lies outside the plasma membrane. * Cellulose (glucose-monomer unit) is major component of the cell wall, which account for the structural strength of plants.

Nucleus * It is the principal feature that distinguishes eukaryotic from prokaryotic cells. * It serves both as repository of genetic information and as the cell’s control center * Processes involved: DNA replication, transcription and RNA processing
Internal structures of the nucleus: 1. Nuclear Envelope 2. Nuclear Pores 3. Nuclear Lamina 4. Nucleolus 5. Nucleoplasm

Cytoplasm 1. Cytosol - The fluid part of the cell 2. Organelles - membrane-bounded structures which has specific function to the cell
Endomembrane System

Endoplasmic reticulum * It is a network of membrane-enclosed tubules and sacs that extends from the nuclear membrane throughout the cytoplasm. * It is the largest organelle in the cell.
2 kinds: 1. Rough ER – with ribosome(for protein synthesis)
Proteins present in ER membrane: a. Transmembrane b. Water-soluble 2. Smooth ER * lipid synthesis/lacks ribosome/membrane assembly * It is involve in several cellular processes: drug detoxification, carbohydrate metabolism and synthesis of neutral fats, phospholipids and steriods * tubular in shape.

Parts of endoplasmic reticulum:

Golgi Apparatus (Complex) * It consists of a series of flattened, membranous sacs (cisternae) involved in modifying, sorting and packaging of macromolecules for secretion or for export to other organelles. * It is form by fusion of vesicles that bud off the ER. * Faces of Golgi stacks are biochemically distinct.
Divided to three distinct compartments: 1. Cisterna – found when ER vesicles accumulate and form 2. Cis face(forming face) – formed when cistern becomes embedded 3. Trans face ( maturing face) – when residues are released

Membrane organelles
Mitochondria
* It plays a critical role in the generation of useful energy derived from the breakdown of lipids and carbohydrates. * It contains their own DNA encoding for tRNA, rRNA and some mitochondrial proteins. * Most mitochondrial proteins are synthesized on free ribosomes.

It is surrounded by a double-membrane system: outer and inner mitochondrial membrane. a. Intermembrane space b. Cristae c. Matrix

Plastids * double-membrane bounded structures that are found only in plants, algae and some protists.
There are two types of plastids: 1. Leucoplasts – stores substances such as starch or proteins in storage organs (e.g. roots or tubers) 2. Chromoplasts – accumulate the pigments that are responsible for colors of leaves, flower petals, and fruits.

Chloroplast * Same as mitochondria, generate metabolic energy; photosynthetic generation of ATP. * They synthesize their own amino acids, fatty acids and lipid components of their own membranes. * Reduction of NO2- to NH3 also occurs in chloroplast

Parts: 1. Chloroplast envelope – double-membrane system 2. Thylakoid membrane – forms a network of flattened sacs called thylakoids, which are arranged in stacks to form grana.
3 distinct internal compartments: intermembrane space, stroma, thylakoid lumen(in thylakoid space).

Membrane Organelles
Lysosomes
* It is a membrane-enclosed organelle that functions to degrade materials taken into the cell and to digest worn out or unnecessary cell components. * It contains about 50 different hydrolytic enzymes that can breakdown macromolecules.
Peroxisome
It is a small, membrane-enclosed organelles that contain enzymes in variety of metabolic reactions: 1. Production and decomposition of H2O2. The enzyme catalase, which occurs in peroxisomes, catalyzes the conversion of H2O2 to H2O and O2. 2. Oxidative reactions of uric acid, amino acids and fatty acids. 3. Synthesis of cholesterol, dolichol and bile acids in specialized cells 4. In plants, glyoxylate cycle and photorespiration occurs.

Vacuole * functions as storage depots for nutrients, wastes, and specialized materials such as pigments.
Microtubular organelles

Centrosome * It is also called the microtubule organizing center. * Its function is to aid cellular division.

Cytoskeleton * It is a complex networks of protein filaments extending throughout the cytoplasm * It determines cell’s shape and internal organization; responsible for the movement of the cell.
Three principal types of cytoskeleton: 1. microfilaments 2. Intermediate filaments 3. Microtubules
Flagellum – 9 pairs of fused microtubules, surround 2 individual microtubules(9 + 2) - connected through the nucleus.

Comparison of Cell Organization in Prokaryotes and Eukaryotes

| PROKARYOTES | EUKARYOTES | Nuclear envelope | Present | Absent | DNA | Naked | Combined with proteins | Chromosomes | Single | Multiple | Nucleolus | Absent | Present | Division | Binary fission or budding; amitosis | Mitosis or meiosis | Ribosomes | 70S (50S + 30S) | 80S (60S + 40S) | Mitochondria | Absent; Respiratory and photosynthetic enzymes in the plasma membrane | Present | Chloroplast | Absent | Present in plant cells | Cell wall | Non-cellulosic | Cellulosic; only in plants | Exocytosis & endocytosis | Absent | Present | Locomotion | Single fibril, flagellum | Cilia and flagella |

Did Eukaryotes develop from prokaryotes?

Symbiosis plays a large role in current theories of the rise of eukaryotes; the symbiotic association between two organisms is seen as giving rise to a new organism that combines characteristics of both the original ones.

The type of symbiosis called mutualism is a relationship that benefits both species involved, as opposed to parasitic symbiosis, in which one species gains at the other’s expense.

e.g. Escherichia coli, that live in the intestinal tract. The bacteria receive nutrients and protection from their immediate environment. In return, they aid our digestive process.

In hereditary symbiosis, a larger host cell contains a genetically determined number of smaller organisms.

e.g. Protist, Cyanophora paradoxa,, a eukaryotic host that contains a genetically determined number of cyanobacteria (blue-green algae). This relationship is an example of endosymbiosis, because the cyanobacteria are contained within the host organism.

Much of the thinking depends on the idea of endosymbiosis, in which larger cells may have absorbed aerobic bacteria, eventually giving rise to mitochondria, or photosynthetic bacteria, eventually giving rise to chloroplasts.