University of Tripoli Faculty of Science / Zoology Department. Lecture notes

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1 University of Tripoli Faculty of Science / Zoology Department Lecture notes in General Zoology course Zo 105 Part one: cytology Textbook: Kenneth Saladin. Anatomy and Physiology: the unity of form and function. 1 st ed McGraw Hill. Lecture notes Cytology is a branch of biology, which deals with the study of cells in terms of structure, function and chemistry. Cell Discovery In 1591 the Dutch merchant Anton van Leewenhoek invented single lense microscope. He was the first man to witness live microscopic organisms, named them animalcules little animals. The invention of the microscope led to the discovery of cells. In 1665 the English scientist Robert Hooke introduced the term cell while examining very thin slices of cork using a compound microscope. He observed a multitude of pores that looked like the wall compartments of a honey comb, he called them cells. Three German scientists developed the concept of cell theory. The botanist Matthias Schleiden (in 1838) was the first to clearly state that all plants are made of cells. The zoologist Theodor Schwann (in 1839) was the first to clearly state that all animals are made of cells. The pathologist Rudolf Virchow (in 1855) was the first to identify that the nucleus controls the cell activities and cell come from pre existing cells. Modern Cell Theory 1) All living things are made of cells 2) The cell is the smallest fundamental unit of life 3) All cells arise from pre existing cells through cell division 4) Cells contain genetic material, which they pass to daughter cells during cell division 5) All cells have a similar chemical composition (proteins, nucleic acids, carbohydrates, lipids) 6) The metabolic processes associated with life occur within cells. 1

2 Cell Definition The cell is the fundamental structural and functional unit of all living organisms Classification of cells There are two major categories or types of cells: prokaryotic and eukaryotic. The main difference between these two cell types is that Prokaryotic cells do not have a nuclear membrane. The nuclear material consists of a single chromosome and lies in the cytoplasm. The nuclear region in the cytoplasm is called nucleoid. Membrane-bound organelles are absent. Prokaryotic cells are found in bacteria and cynobacteria (blue-green algae). Eukaryotic cells include: all other cells, such as protista, fungal, plant and animal cells. The nucleus in a eukaryotic cell is bound by a nuclear envelope and contains nucleoplasm. The cytoplasm, found between the plasma membrane and the nucleus, consists of fluid and the organelles. 2

3 Structural and functional differences between Prokaryotes and Eukaryotes: Prokaryotic Eukaryotic Features Plant Animal Size(diameter) µm 40 µm 15 µm Cell wall Yes (contains peptidoglycan) Yes (contains cellulose) No Genetic Material DNA is naked. A single circular molecule DNA linear, associated with histones (proteins), in a nucleus, surrounded by a nuclear envelope. Ribosomes 70S ribosomes (smaller) 80S ribosomes (larger) ER, Golgi apparatus Mitochondria No No(respiration occurs on an infolding of the cell membrane called the mesosome.) Yes Yes Chloroplasts No Yes No Cell sizes and shapes Cells can be remarkably different in size, shape and function. Cells come in many different sizes. Some cells are visible to the naked eye (such as eggs of birds), however, most cells are microscopic and cannot be seen by the naked eye. Microscopes were developed to visualize cells. The size of the cell is measured in micrometers (µm) in diameter. For example bacterial cells range 0.2 to 0.3 µm, liver cell 20 µm, plant cell 30 to 40 µm. 3

4 Cells also come in many different shapes (e.g. spindle, aster, and oval, spherical, cylindrical). Some cells change their shape (e.g. amoebae, macrophage) others have typical shape (e.g. spermatozoa, epithelial cells). The shapes of cells have evolved to help them carry out their specific function in the body. Cell Structure Despite the fact that there are many different cell types, sizes, and shapes, for descriptive purposes, the concept of a "generalized animal cell" is introduced. It includes features from all cell types. A cell consists of three parts: I) The cell membrane: a selective barrier which encloses a cell II) The cytoplasm: all the cellular contents between the plasma membrane and the nucleus. It includes: the cytosol (a jelly-like fluid ), all the organelles other than the nucleus, and the cytoskeleton III) The nucleus: contain genetic material (a fine network of treads called chromatin which is DNA (deoxyribonucleic acid) associated with particular proteins. At the time of cell division, chromatin becomes condensed to form rod-like bodies known as chromosomes) 4

5 Cell membrane = plasma membrane = plasmalemma Every cell is enclosed by a cell membrane. The cell membrane separates the material outside the cell (extracellular) from the material inside the cell (intracellular). It defines cell boundaries. It maintains the integrity of a cell. It regulates the exchange of materials between cytoplasm and extra cellular fluid due to its selective permeability. It is also important in intercellular communication and cell identity. STRUCTURE OF THE CELL MEMBRANE The cell membrane is a phospholipid bilayer made of membrane lipids (phospholipids, glycolipids, cholesterol) and membrane proteins (integral, peripheral). 5

6 The membrane lipids Phospholipids are the most abundant lipids in the membrane (75%), they form the lipid bilayer. Phospholipids are amphipathic molecules with polar heads (glycerol attached to phosphate) and nonpolar tails (two long fatty acid hydrocarbon chains). The phosphate heads are polar molecules and so are water-soluble (hydrophilic = water loving). They are oriented toward the extracellular space or cytoplasm (intracellular).the lipid tails are non-polar and therefore are not water-soluble (hydrophobic = water hating). They are oriented toward the interior of the membrane. Cholesterol (steroid lipid soluable) is also present in the membrane. Found in both leaflets of lipid bilayer in between the phospholipd tail molecules. It constitutes 20% of membrane lipids. It maintains the fluidity and increases the stability of the membrane. Glycolipids are phospholipids with short oligosaccharide chains. Always found on extra cellular side of cell membrane. Least common of the membrane lipids (2 to 5 %) Membrane proteins Much of the membrane is made up of a 'sea' of phospholipids with protein molecules 'floating' in between the phospholipids. Some of these proteins span the whole width of the cell membrane. They are called transmembrane or integral proteins. Peripheral proteins which do not protroude into the phospholipid layer, they always adhere to the intracellular face of the membrane. There are also short polysaccharide chains that are attached to the outer surface of the membrane. Most of these carbohydrates are attached to proteins and are called Glycoproteins. Proteins in the cell membrane provide structural support, form channels for passage of materials, act as receptor sites, function as carrier molecules, and provide cell identify markers (glycocalyx). 6

7 The plasma membrane structure is called the Fluid Mosaic Model, because the membrane is fluid (phospholipids and proteins are not fixed in one place = they float) and because of the mosaic (patterns) arrangement of the protein molecules created on the membrane s surface. Mehods of Membrane Transport Plasma membrane has selective permeability so some substances pass quickly, some with difficulty, and some not at all. It is important that the cell is supplied with all the substances it needs (e.g. oxygen) and that waste substances (e.g. carbon dioxide), or substances for export, leave the cell. There are various ways by which substances can be moved or transported through the cell membrane. There are three methods of membrane transport: Passive transport, Carrier mediated transport, and Bulk transport. Passive transport Movement of substances across a cell membrane without any direct energy expenditure by the cell. It includes diffusion and osmosis. Diffusion Diffusion is a movement of particles from an area of high concentration to an area of lower concentration of the particles or molecules, thus tending to equalize the concentration throughout. 7

8 This is the process that is used in oxygen entering a cell, and carbon dioxide leaving (respiratory gases) and any lipid soluble molecule (e.g. alcohol, steroids). Osmosis The movement of water molecules through a semi-permeable membrane in response to a concentration and or pressure gradient. Carrier mediated transport When substances are allowed to cross the cell membrane with the help of integral proteins (carrier or channel proteins). Two types: facilitated transport and active transport. Facilitated transport Facilitated transport: diffusion of molecules from high concentration to low concentration. Substances are moving down the concentration gradient so no energy is required. Example glucose molecules. 8

9 Active transport Movement of individual ions and molecules across cell membrane, against. (up) concentration gradient (from low to high) by ATP expenditure. Example Na K pump. Bulk transport Movement of particles or fluid through cell membrane by means of vesicles needs ATP. Two types: endocytosis and exocytosis. Endocytosis The ingestion of solid or fluid material by cells, materials entering the cell can do so when the plasma membrane invaginates to surround the material. The membrane seals off to form a vesicle, which can then move into the cell. Two types: phagocytosis and pinocytosis. Phagocytosis = cell eating The material is relatively large or solid, and is digested by enzymes after fusion of the vesicle with a lysosome. This occurs in white blood cells that ingest bacteria and other foreign bodies. 9

10 Pinocytosis = cell drinking The material is fluid, minute vesicles are formed. Exocytosis The material to be transported out of the cell is surrounded by membrane. The vesicle will fuse with the cell surface membrane and the contents leave. 10

11 Plasma membrane surface extensions On the apical surface of cell membrane 3 types of extensions could be found: 1) Cilia (cilium) short, numerous, hair-like projections that move in a wave like motion. In Human it is found in: I) upper part of respiratory tract (remove microbes and debris from lungs). II) Fallopian tubes (movement of ovum) 2) Flagella (flagellum) are long projections that move in a whip-like motion. In humans it is found only in sperm. Both cilia and flagella are cylindrical structures which arise from centrioles and anchored by basal body. They are made up of micrototubules. There are two microtubules at the center, surrounded by a pinwheel-like ring of nine microtubule pairs. An arrangement called structure. Flagella and cilia are the major means of locomotion in unicellular organisms, such as paramecium and euglena. 11

12 3) Microvilli (microvillus) are folds of plasma membrane to increase the surface area for greater absorption. Found at brush border of the epithelial cells of small intestine and kidney tubules. Intercellular junctions Intercellular junctions are important for cell communication and cell adhering. 5 types of intercellular junctions could be found on the lateral surface of plasma membrane: 1) Tight junction (zonula occludens) completely encircles an epithelial cell near its apex and joins it tightly to the neighbouring cells. This seals off the intercellular space forming a virtually impermeable barrier to fluid and substances between the cells. Found in stomach, intestine, bladder, and kidney. 2) Gap junction (communication junctions) is clusters of tightly packed channels that allow small molecules (metabolites, second messengers, and ions) to travel between adjoining cells. This molecular exchange is essential during embryonic development. Found in the intercalated discs of heart muscle. 3) Adherens junction (zonula adherens) are protein complexes that hold cells together, usually more basal than tight junctions. 4) Desmosome junction (macula adherens) is like a spot weld between two cells, a patch that holds cells together and enable a tissue to resist stress. Found in epidermis, cardiac muscle, and cervix of the uterus. 5) Hemidesmosome junction a structure representing half of a desmosome, that contribute to the attachment of epithelial cells to the underlying basement membrane (basal lamina). 12

13 II) Cytoplasm The cytoplasm is the gel-like fluid inside the cell. It is the medium for chemical reaction. It provides a platform upon which other organelles can operate within the cell. All of the functions for cell expansion, growth and replication are carried out in the cytoplasm of a cell. It includes the cytosol and all the organelles other than the nucleus and the cytoskeleton. Cytosol this is the gel like solution within the cell membrane. It contains enzymes for glycolysis (part of respiration) and other metabolic reactions together with sugars, salts, amino acids, nucleotides and everything else needed for the cell to function. Cytoplasmic organelles are "little organs" that are suspended in the cytoplasm of the cell. Each type of organelle has a definite structure and a specific metabolic task. Some are surrounded by one or two layers of unit membrane (membranous organelles which include: Nucleus, mitochondria, endoplasmic reticulm, Golgi apparatus, lysosomes, and perioxisomes). Organelles that are not surrounded by membranes (nonmembraneous organelles Include: ribosomes, centrioles, centrosome, 1) Mitochondrion (pl. Mitochondria). This may be cylindrical, rod-shaped or spherical shaped organelle (8µm long), where aerobic respiration takes place in all eukaryotic cells. Mitochondria are surrounded by a double membrane: the outer membrane is smooth and quite permeable, while the inner membrane is highly folded into cristae, which give it a large surface area. The space enclosed 13

14 by the inner membrane is called the mitochondrial matrix, and contains small circular DNA (mtdna). The inner membrane is the site of ATP synthesis. 2) Endoplasmic reticulum (ER), a system of flattened cavities (cisternae) lined by a thin membrane. It is the site of the synthesis of many substances in the cell and so provides a compartmentalised area in which this takes place. The cavities also function as a transporting system whereby substances can move through them from one part of the cell to another. There are 2 types of ER - rough (RER) and smooth (SER). Rough Endoplasmic Reticulum (RER) Contain numerous ribosomes on its outer surface, which give it its rough appearance. The ribosomes synthesize proteins, especially proteins secreted (exported) outside cell or packaged in other organelles such as lysosomes Smooth Endoplasmic Reticulum (SER) no ribosomes on its surface. Cisternae are more tubular and branch extensively. it is the site for phospholipids and steroid synthesis. It is also involved in detoxification (liver and kidney cells) and calcium storage and release (skeletal muscle). 14

15 3) Golgi Body (or Golgi Apparatus) another series of flattened stacked cisternae. The primary function of this organelle is to process (modify) and then package proteins and lipids after they are synthesized from ER but before they continue on to their destination. It Receives newly synthesized proteins (from RER) and lipids (SER) adds a functional group ( by enzymatically modifying the polypeptide chain, or adding carbohydrates). It package protein or lipids into a secretory vesicle. Some vesicles become lysosomes or peroxisomes. Some vesicles migrate to the plasma membrane and fuse with it (releasing their contents by exocytosis), contributing fresh protein and phospholipid to the membrane. 4) Lysosomes are tiny, spherical, sac-like structures scattered all over the cytoplasm. Their main function is intracellular digestion. They contain powerful hydrolytic enzymes (hydrolases) capable of digesting all organic material (proteins, nucleic acids, complex carbohydrates, phospholipids, and other substrates) They are also capable of digesting worn out cell organelles (autophagy), or even digesting the entire damaged cell containing them (autolysis). 15

16 5) Peroxisomes are small, membrane-bound sacs that resemble lysosomes but contain different enzymes. They contain powerful oxidative (oxidase) enzymes. Their chief function is to remove toxic substances (detoxification). Hence these organelles are abundant in liver and kidney cells. Peroxisomes oxidize various materials and then break down the hydrogen peroxide (H 2 O 2 ) that results into water and oxygen using an enzyme called catalase. H 2 O H 2 O + O 2 6) Ribosomes are the smallest and most numerous of the cell organelles, and are the sites of protein synthesis. They are composed of protein and ribosomal ribonucleic acid (rrna), and are manufactured in the nucleolus of the nucleus. Ribosomes are spherical, granular particles which occur free in the cytoplasm, where they make proteins for the cell's own use, or they are found attached to the rough endoplasmic reticulum, where they make proteins for export from the cell. Ribosomes are the machinery that provides a surface location for the assembly of amino acids into proteins. In living organisms, DNA produces RNA, which then makes protein for the body. Ribosomes are responsible for reading the information (genetic code) on the messenger RNA (mrna) and using that information to produce the right proteins. Ribosomes are often found in groups called polysomes. Polysomes are variable in length and are strings of ribosomes joined by messenger RNA. 7) Centrioles are a pair of short hallow cylindrical structures, usually found near the nucleus. They are composed of microtubules organized as pattern of microtubules triplets. Two centrioles lie perpendicular to each other within a small clear area of cytoplasm called the centrosome. Involved in cell division. Before each division the centriole replicates itself and the two centrioles move to opposite ends of the cell, where they initiate the formation of mitotic spindle fibers that organizes and separates the chromosomes. 16

17 8) Vacuoles These are membrane-bound sacs (vesicles) containing water or dilute solutions of salts and other solutes. Most cells can have small vacuoles that are formed as required. Some unicellular protoctists have feeding vacuoles for digesting food, or contractile vacuoles for expelling water. Cytoskeleton this is a network of protein fibers extending throughout all eukaryotic cells, used for support, transport and motility. The cytoskeleton is attached to the cell membrane and gives the cell its shape, as well as holding all the organelles in position. There are three types of protein fibers (microfilaments, intermediate filaments and microtubules). Microtubules: hollow rod-like structures with walls of tubulin protein. Provide the structural support of cells and can aid transport through the cell. Form components of cilia, flagella, centerioles, basal bodies, and mitotic spindle Microfilaments: rod-like structures made of contractile protein actin. Like microtubules, provide support and aid movement. Intermediate filaments: Network of fibrous protein (many different types depending on cell type ex. Keratin in hair, nail, epidermis). Provide physical support, resist stress, and hold cells together. 17

18 III) Nucleus This is a prominent, spherical or oval structure found at the centre of the cell. The nucleus is a highly specialized and serves as the information and administrative centre of the cell. The nucleus has two major functions: It stores the cell's genetic material, or DNA, and it controls and coordinates the cell's activities, which include intermediary metabolism, growth, protein synthesis, and reproduction (cell division). The nucleus is surrounded by a nuclear envelope, which is a double membrane with nuclear pores which allow the selective transfer of material between the nucleoplasm and the cytoplasm. The outer layer of nuclear envelope is continuous with the membrane of the rough endoplasmic reticulum. The interior is called the nucleoplasm, which is full of chromatin (DNA(deoxyribonucleic acid) associated with histone proteins) a DNA/protein complex containing the genes. During cell division the chromatin becomes condensed into discrete observable rod-like bodies known as chromosomes. The chromosomes contain genes, which are responsible for storing and transmitting hereditary characteristics from one generation to the next. Another structure within the nucleus is the nucleolus. The nucleolus is a dense, spherical granule responsible for the synthesis of ribosomal RNA (rrna). In the cytoplasm rrna will assemble into ribosomes (the organelles on which protein synthesis takes place). The genetic material is composed of the nucleic acid DNA = Deoxyribonucleic Acid 18

19 DNA is wrapped tightly around protein histones (nucleosomes) to form chromatin and coiled tightly to form chromosomes. Chromatin is a term designating the structure in which DNA exists within cells at interphase (non-dividing stage of cell), it is in uncoiled and dispersed. While a chromosome is a relative term, usually it is a term designating the structure in which DNA exists within cells at metaphase of cell division (mitosis or meiosis). Chromosomes are made up of duplicated DNA. At metaphase of cell division DNA condenses and super coils by a factor around x Chromatin structure The structure of chromatin is determined and stabilized through the interaction of the DNA with DNAbinding proteins: the histone proteins and non-histone proteins. The histone proteins are the major class of binding proteins involved in maintaining the compacted structure of chromatin. There are five different histone proteins, identified as H1, H2A, H2B, H3, and H4. The binding of DNA by the histones generates a structure called nucleosome. The nucleosome core contains an octamere protein structure consisting of 2 subunits each of H2A, H2B, H3, and H4. Histone H1 occupies the internucleosomal DNA and is identifies as the linker histone. These nucleosomal core structures would appear as beads-on-a-string if the DNA were pulled into linear structure and observed under an electron microscope. 19

20 The nucleosome cores themselves coil into a solenoid shape which itself coils to further compact the DNA (30nm fiber). These final coils are compacted further into the characteristic chromatin seen in a metaphase chromosome (200 nm fiber). There are two types of chromatin. 1) Euchromatin is the genetically active portion and is involved in transcription of mrna to produce proteins used in cell function and growth. It stains lightly. 2) Heterochromatin contains inactive DNA and is the portion of chromatin that is most condensed, since it not being used. It is found around centromer and telomere regions of chromosome, as well as the inactive X chromosome in females. It stains darkly. 20

21 Chromosome structure Each chromosome is made up of two longitudinal strands called chromatids. Each chromatid has a double helical DNA molecule. The two chromatids are held together by a structure called the centromere. Usually chromosomes have two arms: p arm (short arm) and q arm (long arm). Each chromatid has two telomere regions at its end. During cell division, the spindle fibers are attached to the centromeres. During anaphase, when chromosomes or chromatids separate, they form different shapes based on the position of the centromere. 4 types of chromosomes according to centromere position: 1) Metacentric the centromere ia at the centre and the chromosome is V shaped during anaphase. 2) Submetacentric the centromere ia a little away from centre and the chromosome gets an L shaped during anaphase. 3) Acrocentric- the centromere is nearer to one end and the chromosome is J shaped during anaphase. 4) Telocentric- the centromere is at the end and the chromosome is l shaped during anaphase. 21

22 Chromosomes are classified into two types: 1) Autosomal chromosomes- autosomes, chromosomes other than sex chromosomes. In humans Chromosomes exist in homologous pairs in diploid cells. 2) Sex chromosomes- X and Y. Females have two X chromosomes (XX) and males have one X chromosome (XY). Chromosome number Chromosome number is constant for each species. It is species specific. It is not correlated to the complexity of the organism. Somatic cells contain diploid chromosome number (2n). Gametes (sperm and ova) contain haploid chromosome number (n). 22

23 Karyotype Karyotype is the general appearance of individual s chromosomes taking from somatic cell. Aligned according to: size, number, and shape. It shows structural or numerical chromosome abnormalities. The karyotype of human male is 46 XY, for human female is 46 XX, for Down s syndrome female is 47 XX + 21, for Turner syndrome is 45 X0. Chromosome territory Recent research has identified that each interphase chromosome occupies a specific domain (chromosome territory) within the nucleus and is not scattered widely in a disordered manner. 23

24 Nucleic acids Two types of nucleic acids: 1) DNA = deoxyribonucleic acid 2) RNA = ribonucleic acid There are 3 types of RNA in the cell. They have different structures and functions. 1) Messenger RNA = mrna 2) Ribosomal RNA = rrna 3) Transfer RNA = trna Composition of nucleic acids All nucleic acids are made up of repeating molecules called nucleotides. A nucleotide is composed of 3 components: 1) Sugar 2) Nitrogen base 3) Phosphate group 24

25 Nitrogen bases Phosphodiester bond formation Nucleotides are linked in a chain of polynucleotides through phosphodiester bonds. Between 5 phosphate of one nucleotide and the 3 hydroxyl group of the previous nucleotide. The DNA chain is said to grow from 5 to 3, which means that the first DNA base has a free 5 end, with attached phosphates. The last nucleotide has a free 3 OH group on it. 25

26 All other bases have their 5 carbons attached to a phosphate, which is attached to the 3 OH group of the previous nucleotide. DNA structure In 1953, James Watson and Francis Crick discovered the DNA structure. They described it as double helix (DNA is double stranded helical structure). The strands have two important characteristics: complementary and antiparallel. Complementary means A will only base pair with T by 2 hydrogen bonds C will only base pair with G by 3 hydrogen bonds Antiparallel means they are oriented in different directions DNA replication DNA replication is the process where an entire double-stranded DNA is copied to produce a second, identical DNA double helix. It occurs in the nucleus. DNA is replicated by a process called semiconservative replication. This means one-half of each new molecule of DNA is old (template strand) one-half of new molecule of DNA is new (complementary strand). 26

27 Enzymes needed for DNA replication DNA helicase: separates DNA strands DNA polymerase: synthesize complementary strand. Primase: synthesize RNA primer DNA ligase: ligates Okazaki fragments DNA gyrase (DNA topoisomerase): loose supercoils Single-strand binding proteins bind to the separated DNA strands to keep them apart. DNA replication begins with a partial separation of the double helix at an area called replication fork. DNA helicase separates the two DNA strands by breaking the hydrogen bonds between them. 27

28 DNA synthesis can only proceed in one direction. This is because new nucleotides can only be added to a growing DNA polymer by addition onto the free hydroxyl group at the 3 end. The other end, the 5 end, has no free hydroxyl group. Hence, the direction of DNA synthesis is always from 5 to 3. Mechanics of DNA synthesis Eukaryotic gene structure Eukaryotic genes are monocistronic (produce only one mrna) and contain regions called exons which code for amino acids; and intron regions which don t code for amino acids. The introns must be removed from the mrna in order to be translated correctly. 28

29 Gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins. It is done in two steps: DNA transcription and mrna translation. DNA transcription Transcription is the process of making an RNA copy of a single gene. The enzyme used in transcription is RNA polymerase. 29

30 The template strand is the DNA strand being copied = antisense strand (3 5 ). The mrna strand is the same as the DNA strand 5 to 3 except U have replaced T. the mrna leaves nucleus and goes to ribosomes for translation to make protein. Genetic code The genetic code in mrna is translated into proteins by ribosomes. Each 3 nucleotides in mrna form a codon. Each codon specifies only ONE amino acid. There are 64 possible codons: 1 start codon (AUG) (which specifies methionine) 3 stop codons: UAA, UAG, UGA 61 code for amino acids Only 20 amino acids!!! 61 codons!!! Some amino acids can be specified by many codons. For example amino acid glycine has 4 different codons: GGU, GGC, GGA and GGG. Genetic code table Translation = protein synthesis Information in mrna is translated into primary sequence of a protein in 3 steps: 30

31 1) Initiation 2) Elongation 3) Termination Need 3 types of RNA: 1) mrna : carries genetic code 2) trna: carries amino acids to ribosome 3) rrna: forms ribosomes (site of protein synthesis) Functional sites of trna The trna has two important sites: one for amino acid attachment and the other for binding with mrna through complementary base pairing (anticodon). Functional sites of ribosome Ribosomes contain three discrete sites: Peptidyl site (P site), Aminoacyl site (A site), Exit site (E site). Initiation = Start: means the ribosome binds to mrna at start codon (AUG) Elongation: means Amino acids are added one by one. How? 31

32 1) trna complexes bind to mrna codon by forming complementary base pairs with the trna anticodon 2) The ribosome moves from codon to codon along the mrna. Termination: means stop synthesizing protein. It occurs when a stop codon is reached in the mrna. Three stop codons: UAG, UAA, and UGA, which is recognized by proteins called release factors not trnas. Cell division Cell division is a process by which cells reproduce. In prokaryotic organisms, cells divide by binary division. In eukaryotic organisms reproduce by either I) Asexual reproduction or II) Sexual reproduction 32

33 Sexual organisms have 2 types of cell division: Mitosis and Meiosis. Mitosis is the normal cell division, which goes on throughout life in all parts of the body. It is important for embryonic development, growth, replacement of dead cells, and for repair of damaged tissues. The chromosome number in mitosis is always diploid (2n). Diploid means two copies (pair) of each chromosome designated as 2n. For example, human body cells are diploid, they contain 46 chromosomes or 23 pairs of chromosomes. Meiosis is the special cell division that occurs in the gonads. It creates the sperm and ova (eggs), the gametes. It is important for sexual reproduction. The chromosome number in mitosis is always haploid (n). Haploid one copy of each chromosome designated as n. Human germ (sex) cells are haploid. Gametes (sperm& ovum) are haploid = 23 chromosomes. When body cells divide (enter mitosis), they need to copy (duplicate) their chromosomes, separate duplicated chromosomes to produce 2 new genetically identical body cells that have the same DNA and Same number of chromosomes as the original body cell. Cell cycle : Cell cycle is the sequence of events (phases: G1, S, G2, M) during the life of the cell. Cell cycle has two parts: 1- interphase growth and preparation. DNA uncondensed (chromatin). Longest part of the cell cycle, has 3 stages: G1, S, G2 2- mitosis (karyokinesis) separation of replicated chromosomes. DNA condensed (chromosomes). Mitosis is a nuclear division that preserves diploid number of chromosomes. It is the shortest part of the cell cycle, has 4 stages: prophase, metaphase, anaphase, telophase followed by cytokinesis. 33

34 Interphase Chromosomes are decondensed, chromosomes replicate, the centrosome (centrioles) divides. Prophase Chromosomes condense. Nuclear envelope dissociates. Centrioles move to opposite poles Mitotic spindle apparatus forms. Metaphase Pairs of sister chromatids align themselves at the metaphase plate. Centrioles at opposite ends of cell. Anaphase Centromeres divide: each 2-chromatid chromosome becomes two 1-chromatid chromosomes. Chromosomes pulled to opposite poles by the spindle fibers. 34

35 Telophase Chromosomes de-condense. Nuclear envelope reappears. Cytokinesis: the cytoplasm is divided into 2 cells. Cytokinesis Cytokinesis means cytoplasmic division. It is the actual division of the cell into two new cells. Meiosis is a reductional division. 46 chromosomes 23 chromosomes. 2n (diploid) n (haploid) Somatic cell - sex cell. Meiosis is always followed by fertilization. Fertilization means the fusion of male (sperm) and female (ovum) gametes. The resulting cell is called a zygote. Upon fertilization, a 1n sperm meets a 1n ovum and a zygote (2n) is formed. Meiosis is very important because it keeps the number of chromosomes constant generation after generation. Without meiosis, the number of chromosomes would continue to increase each generation. Each generation: 1 sperm (23 chromosomes) + 1 egg (23 chromosomes) = 1 zygote (46 chromosomes). The new zygote grows by mitosis. Each new cell has 46 chromosomes. Meiosis: is the process of nuclear division in gametogenesis in which one replication of chromosomes is followed by two successive divisions of the nucleus to produce four haploid nuclei. 35

36 Gametogenesis is the process of gamete formation. Two types: 1) Spermatogenesis: formation of male gametes (sperms). Occurs in testes. 2) Oogenesis: formation of female gametes (ova). Occurs in ovaries. 36

37 When gamete (sperm or egg) cells reproduce themselves the process is called MEIOSIS. During meiosis, a single (1) diploid cell divides and produces FOUR (4) haploid reproductive cells. In Meiosis there is one chromosome duplication followed by two cellular divisions (into four cells) so Meiosis is broken down into Meiosis I and Meiosis II. In meiosis I the homologous chromosomes separate. In meiosis II the sister chromatids separate. 37

38 Key differences between meiosis and mitosis Meiosis reduces the number of chromosomes by half. Daughter cells differ from parent, and each other. Meiosis involves two divisions, Mitosis only one. Meiosis I involves: Synapsis homologous chromosomes pair up. Chiasmata form (crossing over of non-sister chromatids). In Metaphase I, homologous pairs line up at metaphase plate. In Anaphase I, sister chromatids do NOT separate. Overall, separation of homologous pairs of chromosomes, rather than sister chromatids of individual chromosome. 38

39 Cellular respiration Cellular respiration is a process in which the energy in glucose is transferred to ATP. Cellular respiration allows organisms to use (release) energy stored in the chemical bonds of glucose (C 6 H 12 O 6 ). The energy in glucose is used to produce ATP. Cells use ATP to supply their energy needs. ATP = Adenosine Tri Phosphate How Cells Acquire ATP? By cellular respiration. Cellular respiration includes the various metabolic pathways that break down glucose to produce ATP. C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O + Energy (36 ATP) Two types of cellular respiration: 1) Aerobic = O 2 present 2) Anaerobic = O 2 absent (fermentation) Aerobic cellular respiration The complete breakdown of glucose to carbon dioxide and water involves four phases: a. Glycolysis b. Formation of Acetyl CoA c. Citric Acid Cycle = Krebs cycle d. Electron Transport Chain 39

40 Glygolysis The break down of glucose (6-carbon monosaccharides) into two molecules of pyruvic acid (3-carbon) Occurs in the cytoplasm (cytosol). There are ten steps in glycolysis and each one is catalyzed by a specific enzyme (which will be studied in Biochemisty course). Formation of acetyl CoA Pyruvic acid is decarboxylated CO 2 is removed and pyruvic acid, a C3 compound, becomes a C 2 compound. 40

41 NAD removes hydrogen atoms from the C 2 compound (an oxidation reaction) and converts it to an acetyl group (acetic acid). The acetyl group binds to coenzyme A. The result is acetyl-coenzyme A (acetyl-coa), which is ready to enter the citric acid cycle. Citric acid cycle Electron transport chain In the electron transport system, NADH and FADH 2 are oxidized and the energy is used to produce ATP. The system contains membrane-bound electron carriers that pass electrons from one to another. When a carrier reduces other, some of the energy that is released as a result of that reduction is used to pump hydrogen ions across the membrane into the intermembrane space. The remaining energy is used to reduce the next carrier. As a result of the electron transport system, hydrogen ions become 41

42 concentrated in the intermembrane space. These concentrated ions contain energy much like a dam. The enzyme ATP synthase is able to use the energy of this osmotic gradient to produce ATP as the hydrogen ions move under osmotic pressure through the enzyme back into the matrix of the mitochondrion. Oxygen is the final electron acceptor. The low-energy electrons that emerge from the electron transport system are taken up by O 2. The negatively charged oxygen molecules take up protons from the medium and form water (2H + + 2e - + 1/2 O 2 H 2 O). 42