Year 13 Biology Textbook final.pdf

CURRICULUM DEVELOPMENT UNIT MINISTRY OF EDUCATION, HERITAGE & ARTS The Ministry of Education owns the copyright to this Year 13 Biology Textbook. Schools may reproduce this in part or in full for classroom purposes only. Acknowledgement of the Curriculum Development Unit (CDU) of the Curriculum...

CURRICULUM DEVELOPMENT UNIT MINISTRY OF EDUCATION, HERITAGE & ARTS The Ministry of Education owns the copyright to this Year 13 Biology Textbook. Schools may reproduce this in part or in full for classroom purposes only. Acknowledgement of the Curriculum Development Unit (CDU) of the Curriculum Advisory Services (CAS) of the Ministry of Education, Heritage & Arts copyright must be included on any reproductions. Any other use of this textbook must be referred to the Permanent Secretary for Education through the Director Curriculum Advisory Services. Issued free to schools by the Ministry of Education. First Edition 2018 © Ministry of Education, Fiji, 2018 Published by Curriculum Advisory Services Ministry of Education, Heritage & Arts Waisomo House, Private Mail Bag, Suva, FIJI Tel: (679) 331 4477 Website: www.education.gov.fj PREFACE Developed and written to provide students with appropriate information as stipulated in the Year 13 Biology syllabus, the Biology for All Year 13 text book is simplified for greater understanding and is enriching to read. However, this textbook is not limited to the confines of the syllabus, some areas will contain a little bit more information for the interest and knowledge of the students. It is anticipated that students of all capabilities will enjoy reading and learning from this book, and that the users will develop a curiosity to further supplement their knowledge beyond the areas of this syllabus content. The information in this book is organised in the three strands of Structure and Life Processes; Living Together and Biodiversity, Change and Sustainability. Self-test questions are included at the end of major topics to assess understanding and these contribute to the learning process. These self tests may be attempted by any pupil without assistance. These have been carefully graded to suit learners of all abilities. Teachers and students are also advised to resort to other resources to enhance teaching and learning. This textbook is a guide to accomplish the learning outcomes, and learning Biology in Year 13 will certainly be further enriching and enhanced with the use of other resources, online or otherwise. Using this Textbook  The learning outcome of every strand is on the cover page of that strand;  The main topics in the textbook are aligned to the syllabus topics;  The cloud contains fun facts for the content on that page;  The section is found at the end of main topics and contains questions;  A glossary at the end of the book contains words not explained in the content. 3|Page YEAR 13 - BIOLOGY FOR ALL ACKNOWLEDGEMENT The Curriculum Development Unit wishes to acknowledge the commitment and dedication of the following persons in the process of writing, vetting and making recommendations during the development of this text book. Their active participation insight, guidance and continued support from the beginning of this intensive process has resulted in the book you now hold. Mr. Mohammed Masud, Curriculum Advisory Services (CAS) Ms. Ruth Kuilamu, CAS Mr. Om Prasad, CAS Ms. Sneh Chand, CAS Ms. Swartika Devi, CAS Ms. Preet Prasad, CAS Ms. Shreiya Kumar, CAS Ms. Roselyn Dayal, Fiji National University Dr. Gilianne Brodie, University of the South Pacific Dr. Tamara Osbourne, University of the South Pacific Mr. Sepuloni Lolohea, University of the South Pacific Ms. Shalini Singh, Nabua Secondary School Ms. Parmeshwari Narayan, Rishikul Sanatan College Ms. Manorma Prasad, Pt. Shreedhar Maharaj College Ms. Ashwini R. Mudaliar, John Wesley College Mr. Malakai Taukalamaki, Sila Central High School Mr. William Eliesa, Tilak High School Ms. Nanise Peue, Lomaivuna Secondary School Ms. Ekta Lal, Yat Sen Secondary School Mr. Mika Mudreilagi, Queen Victoria School Mr. Wilden Ramanu, Ratu Kadavulevu School Mr. Lekima Nasau, Marist Brothers High School Mr. Ronesh Ram, Vunimono High School 4|Page YEAR 13 - BIOLOGY FOR ALL  Table of Contents STRAND 1: STRUCTURE AND LIFE PROCESSES........................................................................... 8 1.1 GENETICS..................................................................................................................................... 8 1.1.1 GENE CONCEPT................................................................................................................ 8 1.1.2 PROTEIN SYNTHESIS..................................................................................................... 16 SELF TEST: Gene Concept and Protein Synthesis............................................................. 27 1.1.3 VARIATION.......................................................................................................................... 28 SELF TEST: Genetic Variation.................................................................................................. 47 1.1.4 GENETIC ENGINEERING............................................................................................... 48 SELF TEST: Genetic Engineering.............................................................................................. 54 1.1.5 POPULATION GENETICS............................................................................................... 55 SELF TEST: Population Genetics.............................................................................................. 60 1.1.6 NATURAL SELECTION................................................................................................... 62 SELF TEST: Natural Selection.................................................................................................... 66 1.2 EVOLUTION................................................................................................................................ 67 1.2.1 ORGANIC EVOLUTION................................................................................................... 69 SELF TEST: Organic Evolution................................................................................................. 71 1.2.2 HUMAN EVOLUTION........................................................................................................ 72 SELF TEST: Human Evolution................................................................................................. 90 STRAND 2: LIVING TOGETHER........................................................................................................... 93 2.1 ORGANISMS AND THE ENVIRONMENT.......................................................................... 93 SELF TEST: Living together......................................................................................................... 117 STRAND 3: BIODIVERSITY, CHANGE AND SUSTAINABILITY............................................. 119 3.1 SUB-CELLULAR FORM OF LIFE........................................................................................ 119 3.1.1 VIRUSES............................................................................................................................ 119 SELF TEST: Virus....................................................................................................................... 122 3.2 DIVERSITY OF LIFE............................................................................................................... 123 3.2.1 CELLULAR ORGANISATION........................................................................................ 123 SELF TEST: Cellular Differentiation..................................................................................... 130 3.2.2 KINGDOM MONERA....................................................................................................... 134 SELF TEST Monera..................................................................................................................... 144 3.2.3 KINGDOM PROTISTA..................................................................................................... 145 SELF TEST: Algae......................................................................................................................... 158  SELF TEST: Protozoans.............................................................................................................. 163 3.2.4 KINGDOM FUNGI............................................................................................................ 164 SELF TEST: Fungi........................................................................................................................ 171 3.2.5 KINGDOM PLANTAE.................................................................................................. 172 SELF TEST: Mosses and Ferns............................................................................................... 179 SELF TEST: Seed Plants........................................................................................................... 188 3.2.6 KINGDOM ANIMALIA.................................................................................................... 189 SELF TEST: Cnidaria.................................................................................................................. 194 SELF TEST: Platyhelminthes.................................................................................................... 198 SELF TEST Annelida................................................................................................................... 206 SELF TEST Arthropods............................................................................................................. 212 SELF TEST Mollusca.................................................................................................................. 222 SELF TEST Echinodermata..................................................................................................... 228 SELF TEST Chordates................................................................................................................. 244 3.3 ENVIRONMENTAL ISSUES................................................................................................ 245 3.3.1 MANS’ MODIFICATION OF THE BIOSPHERE....................................................... 245 SELF TEST Environmental Issues.......................................................................................... 257 4.0 GLOSSARY................................................................................................................................. 258 5.0 BIBLIOGRAPHY........................................................................................................................ 263 6|Page YEAR 13 - BIOLOGY FOR ALL  STRAND 1 STRUCTURE AND LIFE PROCESSES STRAND 1: STRUCTURE AND LIFE PROCESSES 1.1 GENETICS Generally, genetics is the branch of biology that deals with the study of genes, heredity and genetic variation. It involves the understanding how characteristics or traits are transmitted from one generation to the next. 1.1.1 GENE CONCEPT Structure of a Gene DNA Molecule What do a human, a sunflower and a bee have in common? Along with every other living organism on earth, each of these have the molecular instructions for life called DNA. Encoded within the DNA are explicit instructions for every single characteristic of an organism. DNA (or Deoxyribo Nucleic Acid) is a double stranded molecule twisted to give a ladder-like appearance. It carries genetic information for growth, development, functioning and reproduction of all cellular forms of life, including viruses which are considered a subcellular form of life. DNA belongs to a class of molecules called the nucleic acids, also known as polynucleotides. https://www.merckmanuals.com These polynucleotides are formed by linking many nucleotides together. 8|Page Each nucleotide consists of three components:  a nitrogenous base: cytosine (C), guanine (G), adenine (A) or thymine (T) for DNA, uracil (U) for RNA  a five-carbon (pentose) sugar molecule (deoxyribose in the case of DNA and ribose in RNA)  a phosphate molecule A nucleotide chain consists of a 5' end (where the 5th carbon of the pentose sugar is exposed and 3' end (where the 3rd carbon of the pentose sugar is exposed). The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl group. The 5' end of the polynucleotide chain is usually the end with the free phosphate group. https://biochemaholic. wordpress.com (Note: The ' denotes prime) The backbone of the polynucleotide is a chain of sugar and phosphate molecules. Each of the sugar groups in this sugar- phosphate backbone is linked to one of the four nitrogenous bases. The bases link across the two strands in a specific manner using hydrogen bonds:  Cytosine (C) pairs with guanine (G) with three hydrogen bonds.  Adenine (A) pairs with thymine (T) with two H - bonds. Chargaff's Rules Chargaff’s rule states that: https://online.science.psu.edu/biol110_sandbox _8862/node/8928 Total no. of purine (AG) molecules = Total no. of pyrimidine molecules (TC) molecules  A = T and C = G; A+T+C+G= 100%  DNA from any cell of any organism should have a 1:1 ratio (base pair rule) of pyrimidine (single carbon – ringed nitrogenous bases i.e. thymine and cytosine) 9|Page YEAR 13 - BIOLOGY FOR ALL  and purine (double carbon – Example ringed nitrogenous bases i.e. adenine and guanine) bases. In a DNA sample, 14% of the bases are guanine. Calculate the percentage of the other three bases in this  The number of adenine sample. molecules is equal to thymine molecules and the If the sample has 14% G, then there will be 14% C number of guanine Total G+C = 14% + 14% = 28% molecules is equal to Total A+T will be 100-28= 72% cytosine molecules. Total % of A= 72/2=36%  Uracil is a pyrimidine. Total % of T= 36% (A= T: according to Chargaffs Rule). The double helix of the Hence in given double stranded DNA, if Guanine is 14% then; Answer: A=36%, T=36% and C=14% complete DNA molecule resembles a spiral staircase, with two sugar phosphate backbones and the paired bases in the center of the helix. This structure explains two of the most important properties of the DNA molecule:  First, it can be copied or 'replicated', as each strand can act as a template for the generation of the complementary strand.  Second, it can store information in the linear sequence of the nucleotides along each strand. Roles of DNA The four roles of DNA are replication, encoding information, recombination and mutation and gene expression. 1. Replication DNA exists in a double-helical arrangement, in which each base along one strand binds to a complementary base on the other strand. T’s can only bind to A’s and C’s only to G’s. When a cell divides, the chromosomes containing the DNA strands replicate, or make copies so that both daughter cells receive the full set of genetic material. Steps of Replication: The process occurs at several different points at the same time. At each point that replication occurs –called the origin (or fork) of replication, the process takes place in a bidirectional manner.  Initiation: the DNA strand unzips with the help of enzyme helicase  Elongation: each strand now acts as a template along which the complementary strand is generated 10 | P a g e YEAR 13 - BIOLOGY FOR ALL  Enzyme DNA polymerase adds correct nucleotides to the template strand synthesizing the new strand.  The two new strands are synthesized in the 5’ to 3’ direction. One strand will be synthesized continuously (the leading strand) while the other strand will be synthesized in short fragments called the Okazaki fragments. This fragmented strand is called the lagging strand.  These growing strands continue to be built until it has fully complemented the http://www.passbiology.co.nz original strand.  Termination: once the template strands are fully complemented and the original strands are bound to its own, the replication process will halt and two new completed DNA molecules are formed. The DNA molecule now contains one of each strand from the original and the newly synthesized one. The term for this mode of replication is known as semiconservative since half of the original DNA molecule is conserved in each new DNA molecule. This process will continue until the cell’s DNA complement or the entire genome is replicated. During replication, mistakes or errors such as accidental addition of inappropriate nucleotides have the potential to render a gene dysfunctional. A DNA proof reading process relies on the assistance of the enzyme RNA polymerase that scans the newly synthesized molecule for mistakes and corrects them. Once the process of DNA replication is complete, the cell is ready to undergo cell division. Enzymes Involved in Replication  DNA Helicase: unwinds and unzips the double helix by breaking the hydrogen bonds of the base pairs.  DNA Gyrase: relieves the tension from the unwinding of the double helix by cutting the strand, and re-joining once the tension has been released.  DNA Ligase: joins the Okazaki fragments during DNA replication. 11 | P a g e YEAR 13 - BIOLOGY FOR ALL   DNA polymerase: adds new free nucleotides to the 3’ end of the newly forming strand, elongating it in a 5’ to 3’ direction. 2. Encoding information The base sequences of A, T, C and G along a DNA strand are organized into units called genes. An adjacent triplet of bases, called a codon (on mRNA), specifies or codes for a particular amino acid. Therefore, the sequence of bases in genes determines the sequence of amino acids in proteins, which are the biochemical units of a cell’s structure and function. The cell first transcribes genes onto segments of mRNA using the base-pairing logic that holds the double helix together. However, RNA substitutes the base of U (Uracil) for that of T (Thymine). The cell later translates the RNA strands into proteins. 3. Recombination and Mutation DNA plays a significant role in the evolution of a species. Through the process of genetic recombination, segments of different chromosomes swap places with each other, creating new sequences of genetic material. If changes occur to the DNA sequences of sex cells, the changes can be inherited by the next generation. The new sequences might produce new proteins, some of which are beneficial to the organism. In this way, the characteristics of the organism might evolve over time. Natural selection of beneficial traits can produce changes that make an organism more fit for survival and reproduction. DNA can also repair itself through recombination. A mutation happens when an “illegal” base pairing occurs -- for example, when an A lines up opposite a G instead of opposite a T. An inheritable mutation must occur in the chromosomes of the sex cells. Mutations and recombination can be beneficial but can also be lethal or create genetic diseases and malformed offspring. Mutations can occur in the normal body cells, called somatic mutation; or in the sex cells, called germinal (or germline) mutations. Physical or chemical agents that change the genetic material (usually DNA) are called mutagens. Examples of mutagens are ultraviolet light, benzene, gamma rays, x-rays, alpha particles, ultraviolet radiation, colchicine, mustard gas, nitrous acid, cyclamate. 4. Gene Expression Each cell contains a full complement of genes, yet cells from different tissues and organs look and behave differently. The reason is that only some of the DNA of each cell is used to make proteins. DNA plays a role in controlling the types of proteins a 12 | P a g e YEAR 13 - BIOLOGY FOR ALL cell will make. It does this through interactions with proteins in the cells that cause only certain genes to express themselves. This is how a single fertilized egg cell differentiates into the many types of cells, tissues and organs found in complex organisms. The DNA can respond to the need for a particular protein by exposing the appropriate genes for transcription while keeping other genes inactive. This is the reason why women don’t produce milk all the time, only while they are lactating. Genes A gene is the basic physical and functional unit of heredity. It consists of a specific sequence of nucleotides at a given position on a given chromosome that code for a specific protein. Chromosomes DNA is tightly packed into structures called chromosomes, which consist of long chains of DNA and associated proteins. In eukaryotes, DNA molecules are tightly http://www.rugusavay.com wound around proteins called histone proteins - which provide structural support and play a role in controlling the activities of the genes In their replicated form, each chromosome consists of two chromatids. The chromosomes and the DNA they contain are copied as part of the cell cycle, and passed to daughter cells through the processes of mitosis and meiosis. 13 | P a g e YEAR 13 - BIOLOGY FOR ALL Karyotype Humans have 46 chromosomes, consisting of 22 pairs of autosomes and a pair of sex chromosomes (the 23rd pair): two X chromosomes for females (XX) and an X and a Y chromosome for http://www.passmyexams.co.uk males (XY). An illustration of a set of chromosomes in order of decreasing size is known as a karyotype. Cistron A length of DNA that specifies the synthesis of one polypeptide chain in protein synthesis. Gene Action Regulation The single chromosome of the common intestinal bacterium Escherichia coli (E. coli) is circular and contains about 4.7 million base pairs. It is nearly 1mm long and approximately two nanometers (nm) (10-9) wide. The chromosome replicates in a bidirectional method producing a figure resembling the Greek letter theta, θ. The promoter is the part of the DNA to which the RNA polymerase binds before unzipping the segment of the DNA to be transcribed. Structural gene is the segment of the DNA that codes for a specific polypeptide. These often occur together on a bacterial chromosome. The location of the polypeptides involves enzymes in a biochemical pathway. For example, allows for quick and efficient transcription of the mRNAs. Lactose, milk sugar, is split by the enzyme lactase. This enzyme is inducible, since it occurs in large quantities only when lactose, the substrate on which it operates, is present. The Operon Model (Jacob-Monod Model) The Operon model of prokaryotic gene regulation was proposed by Francois Jacob and Jacques Monod. Groups of genes coding for related proteins are arranged in units known as operons. An operon consists of an operator, promoter gene and structural genes. A regulator gene is attached to each operon. 14 | P a g e YEAR 13 - BIOLOGY FOR ALL  Operator: a small gene which determines the function of structural gene and will only function if it is not blocked by a repressor, which binds on this site to prevent transcription.  Promoter gene: acts as the site that RNA polymerase will bind, after which transcription proceeds.  Structural gene: gene that codes for a specific protein.  Regulator gene: is normally a large gene since it controls the function of the structural gene; it codes for the repressor protein that binds to the operator. This repressor-operator complex will prevent the RNA polymerase from binding to the promoter of the structural genes. If the repressor protein is removed, RNA polymerase binds to promoter and transcription occurs. Operons are either inducible (start) or repressible (stop) according to the control mechanism. Seventy-five different operons controlling 250 structural genes have been identified for E. coli. Repression is an example of negative control since the repressor proteins turn off transcription. The Lac Operon When lactose is present, it will bind to the repressor protein, changing its http://bodell.mtchs.org shape and hindering its ability to bind to the operator. RNA polymerase is free to bind to the promoter allowing transcription to proceed. Transcription results in the production of lactase that breaks down lactose. In the absence of lactose, the lac repressor protein binds to the operator preventing transcription. Once all lactose is broken down, the repressor protein is free to bind to the operator, thus stopping the production of lactase. 15 | P a g e YEAR 13 - BIOLOGY FOR ALL The Trp Operon Tryptophan is an amino acid that is synthesized by a biosynthetic enzyme. This enzyme is encoded by five genes located next to each other known as trp operon which is found in E. coli bacteria. https://www.boundless.com Features of the trp operon:  regulated by the trp repressor and repressed (turned off) when tryptophan is present in high amounts: the repressor protein binds to the operator sequence with the help of co- repressor which blocks (prevents) RNA polymerase from transcribing the trp- related genes (trp operon).  Trp operon is activated (turned on) when tryptophan is either absent or present in small amount: the repressor protein detaches itself from the operator sequence allowing RNA polymerase to transcribe trp related genes (trp operon). 1.1.2 PROTEIN SYNTHESIS What is RNA?  RNA (or Ribose Nucleic Acids) molecules are single stranded nucleic acids.  Its ability to fold into three dimensional structure forms hairpin loop enabling nitrogenous bases to bind to one another.  Like DNA, it has nitrogenous base (adenine, cytosine, guanine and uracil instead of thymine), a phosphate group and a five (5) carbon ribose sugar instead.  RNA performs a major role in the process of protein synthesis since it is involved in transcription, decoding and translation of the genetic code to produce proteins. Roles of RNA in Protein Synthesis Although DNA stores the information for protein synthesis and RNA carries out the instructions encoded in DNA, most biological activities are carried out by proteins. The accurate synthesis of proteins thus is critical to the proper functioning of cells 16 | P a g e YEAR 13 - BIOLOGY FOR ALL and organisms. The assembly of amino acids in their correct order, as encoded in DNA, is the key to production of functional proteins. Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel mRNA strand. Translation is the whole process by which the base sequence of an mRNA is used to order and join the amino acids in a polypeptide. The three kinds of RNA (messenger RNA, transfer RNA and ribosomal RNA) perform different but cooperative functions in protein synthesis. Messenger RNA (mRNA) performs a major role in the transcription process. Transcription is a process through which the genetic information is copied from DNA to RNA. As transcription proceeds, transcription factors (proteins) unwinds the DNA strand to allow RNA polymerase to transcribe DNA into mRNA molecule during which cytosine (C) pairs with guanine (G) and adenine (A) pairs with uracil (U). Once transcription is completed, mRNA is transported to the cytoplasm. Transfer RNA (tRNA) is the smallest RNA which transfers the amino acid during protein synthesis. The correct tRNA with its attached amino acid is selected at each step since each specific tRNA molecule contains a three-base sequence that can base-pair with its complementary code word in the mRNA. Ribosomal RNA (rRNA) Ribosomes are composed of large subunit and small subunit, each of which contains its own rRNA molecules. In the cytoplasm, rRNAs combine with proteins to form ribosomes which travel along the mRNA molecule during translation to facilitate the assembly of amino acids in polynucleotide https://www.microbe.net chain. 17 | P a g e YEAR 13 - BIOLOGY FOR ALL Protein synthesis The following factors must be present for transcription:  Gene (DNA) to act as a template  Supply of free RNA nucleotides  Enzymes  ATP The base sequence in a DNA molecule determines the type of amino acids and the order in which they are joined together to make a specific protein. The sequence of amino acids in a protein determines its structure and function. The DNA code is a triplet code. Each triplet, a group of three bases, codes for an amino acid:  The triplet of bases on the mRNA is known as a codon.  The triplet of bases on the tRNA is known as an anti-codon. The main stages of protein synthesis are transcription and translation. Transcription takes place in the nucleus whereby a particular segment of DNA is copied to result in an mRNA strand by RNA polymerase. The process occurs as follows:  At the point where the gene coding for the protein required, the DNA unwinds then unzips, and the hydrogen bonds between the strands break.  Free RNA nucleotides form complementary base pairs with the bases of one strand of DNA.  Weak hydrogen bonds form between base pairs (C≡G; A=T)  Sugar phosphate bonds form between RNA nucleotides.  The new mRNA strand that was synthesized moves out of the nucleus into the cytoplasm. Translation takes place on the ribosomes in the cytoplasm, or found on the rough Endoplasmic Reticulum (RER). Translation is the process by which mRNA is http://www.wordwizardsinc.com decoded and translated to produce a polypeptide sequence, otherwise known as a protein. 18 | P a g e YEAR 13 - BIOLOGY FOR ALL The process occurs as follows:  The ribosomes are the sites of protein synthesis.  Each ribosome has two sites that can accommodate two tRNA at any one time.  The two ribosome sites are the A-site or the amino-acyl complex site and the P-site or the polypeptide chain site.  The mRNA strand attaches to a ribosome.  Each mRNA codon codes for a specific amino acid.  The anti-codons and codons match up and form complementary base pairs.  tRNA molecules transport specific amino acids to the ribosome, specifically to the A-site first. A peptide bond forms between the new (incoming) amino acid and the amino acid on the P-site (where the chain is forming).  the tRNA on the A-site now moves to the P-site, the original tRNA on P-site now moves out because it has released its amino acid.  another tRNA-aminoacyl complex enters to the A site, and the process is repeated. Transfer RNA, or tRNA, translates the sequence of codons on the mRNA strand. The main function of tRNA is to transfer a free amino acid from the cytoplasm to a ribosome, where it is attached to the growing polypeptide chain. tRNAs continue to add amino acids to the growing end of the polypeptide chain until they reach a stop codon on the mRNA. The ribosome then releases the completed protein into the cell. Peptide bonds form between the adjacent amino acids to form the polypeptide (protein). It is important to note that  tRNA may be re-used to transport another specific amino acid.  Once the protein has been synthesized, mRNA may move to another ribosome to make a further protein or it can be broken down into free nucleotides to be reused.  After translation, the protein is then passed from the RER to the Golgi apparatus inside tiny fluid-filled sacs, called vesicles.  The golgi bodies are a system of membranes responsible for the modification, processing, and packaging of the proteins.  The protein may have a carbohydrate added, to form a glycoprotein.  The golgi packages the protein in a secretory vesicle, which fuses with the cell membrane and releases the protein from the cell. The Genetic Code The Genetic Code is a system of signals that select these amino acids in the sequence that is needed for the required polypeptide chain. 19 | P a g e YEAR 13 - BIOLOGY FOR ALL Basically, a codon consists of a set of three, sometimes referred to as the triplet code. There are 64 possible combinations of codons from which three codons are known as stop codons (UAA, UAG, UGA) which code for the termination of polypeptide chain synthesized on ribosomes. The other 61 codons encode for twenty amino acids. Some characteristics of the Genetic Code include:  As mentioned above, three STOP codons are UAA, UAG and UGA; the START codon is AUG and codes for the amino acid Methionine, and only one codon, UGG, codes for tryptophan.  The code is degenerate - each one amino acid is coded for by more than one codon. With the exception of tryptophan, which is coded for by the codon UGG, and Methionine (the start amino acid) being coded for by AUG, all other amino acids are coded for by more than one codon. For eg. Serine can be coded for by the codons UCU, UCC, UCA and UCG.  The code is not overlapping – when a base sequence such as GACUAC appears in the mRNA, it codes for two amino acids and is read as GAC (first amino acid) then UAC (second amino acid), rather than as an overlapping code and therefore would read as GAC ACU CUA UAC As a non-overlapping code, the effects of mutation is minimised. If a point mutation substituted the first C base by base G, the effect of this mutation is carried forth three times (highlighted below): GAC ACU CUA UAC  The code is universal – For almost all organisms, the codons have the same meaning in that they specify the same amino acids. 20 | P a g e YEAR 13 - BIOLOGY FOR ALL Using the Genetic Code https://www.slideshare.net Usually arranged in table form, the Genetic Code is structured so that the left-hand column gives the first base of the codon, the four middle columns give the second base, and the last column gives the third base. Where these three bases meet is the specific amino acid being coded for by the codon. The Central Dogma: DNA Encodes RNA, RNA Encodes Protein The central dogma of molecular biology describes the flow of genetic information in cells from DNA to messenger RNA (mRNA) to protein. It states that genes specify the sequence of mRNA molecules, which in turn specify the sequence of proteins. http://www.intechopen.com Since the information 21 | P a g e YEAR 13 - BIOLOGY FOR ALL stored in DNA is so central to cellular function, the cell keeps the DNA protected and copies it in the form of RNA. An enzyme adds one nucleotide to the mRNA strand for every nucleotide it reads in the DNA strand. The translation of this information to a protein is more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. Proteins  Proteins are long chains of amino acids and highly complex structure known to be the building blocks of life.  There are about twenty different amino acids which can be combined to make protein. The structure and function of protein relies on the sequence of amino acids.  Proteins consist of four different levels of structure. Primary Structure A protein's primary structure consists sequence (order) of amino acids in a polypeptide chain. The primary structure is held by the peptide bonds. For example, the pancreatic hormone insulin has two polypeptide chains, A and B. The A chain of insulin is 21 amino acids long and the B chain is 30 amino acids long, and each sequence is unique to https://biochemmybestfriend. com the insulin protein. Secondary Structure Secondary structures arise as hydrogen (H) bonds form between local groups of amino acids in a region of the polypeptide chain. In other words, the polypeptide starts to fold into its functional three-dimensional form. Thus, the two types of secondary structure that arise due to 22 | P a g e YEAR 13 - BIOLOGY FOR ALL   Alpha ( ) helix structure o Alpha helix is a helical arrangement of single polypeptide chain resembling a coiled spring, secured by hydrogen bonds in the polypeptide chain. o In this conformation, the carbonyl and N- H groups are orientated parallel to the axis. https://www.pinterest.com o All C=O and N-H groups are involved in hydrogen bonds giving it a cylinder like rigid structure. o The side chains project outward and contact solvent to produce structure similar to a bottle brush or round hair brush. An example of a protein with many a helical structure is the keratin that makes up human hair.  Beta (β) pleated sheets o In β pleated sheets, the polypeptide chain folds back on itself causing the sides of the peptide strands to be held by hydrogen https://www.pinterest.com bonds, giving it a rigid structure. To be more specific, the bonds are formed between the neighboring polypeptide chains. o Generally the primary structure folds back on itself in either a parallel or antiparallel arrangement, producing a parallel or antiparallel sheet. In this arrangement, side chains project alternately upward and downward from the sheet. Tertiary Structure The tertiary structure of a polypeptide chain is in three-dimensional (3D) shape since all the secondary structure elements folds among each other. Interactions between polar, nonpolar, acidic, and basic R group within the polypeptide chain creates complex three-dimensional tertiary structure of a protein. o Cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. All of these interactions, weak and strong, determine the final three-dimensional 23 | P a g e YEAR 13 - BIOLOGY FOR ALL  shape of the protein. When a protein loses its three-dimensional shape, it will no longer be functional. o The tertiary structure of proteins is determined by non-polar hydrophobic interactions, ionic bonding (salt bridges), hydrogen bonding, and disulfide linkages. https://biochem1362blog.files.wordpress.com Quaternary Structure The quaternary structure of a protein is made up of many polypeptide chains usually referred as subunits (these subunits can be same and is termed as homodimers or different as in heterodimer).  These subunits interact and arrange themselves to form a larger aggregate complex protein. The final shape of http://www.biochemden.com quaternary protein is determined by interactions such as hydrogen bonding, disulfide bridges and salt bridges.  For example, insulin is a ball-shaped, globular protein that contains both hydrogen bonds and disulfide bonds that hold its two polypeptide chains 24 | P a g e YEAR 13 - BIOLOGY FOR ALL  together. Silk is a fibrous protein that results from hydrogen bonding between different β-pleated chains. Classes of Proteins There are two main classes of protein: 1. Fibrous Protein  A Fibrous protein is a protein with an elongated shape. Fibrous proteins provide structural support for cells and tissues. There are special types of helices present in two fibrous proteins α-keratin and collagen. These proteins form long fibres http://www.differencebetween.net/ that serve a structural role in the human body.  Fibrous proteins are distinguished from globular proteins by their filamentous, elongated form. Also, fibrous proteins have low solubility in water compared with high solubility in water of globular proteins. Most of them play structural roles in animal cells and tissues, holding things together. Fibrous proteins have amino acid sequences that favour a particular kind of secondary structure which, in turn, confer particular mechanical properties on the proteins. 2. Globular Protein  Globular proteins are water soluble proteins with spherical shapes and irregular amino acid sequences. The polypeptide chains are folded in, to form their shapes, and this shape is specific for each globular protein type. The water solubility of globular proteins enables them to transport through blood and other body fluids to various locations where their action is required.  Globular proteins mainly involve in carrying http://www.differencebetween.net/science many chemical reactions, which enable organisms to convert outside energy sources to usable energy form. These proteins also act as catalysis for thousands of chemical reactions occurring in the body. Moreover, globulin proteins involve in glucose metabolism, oxygen 25 | P a g e YEAR 13 - BIOLOGY FOR ALL  storage in muscles, oxygen transport in blood, immune responses etc. Some examples for globular proteins are insulin, myoglobin, hemoglobin, and immunoglobulin. Summary of Protein Structure http://hdimagelib.com Roles of Protein Proteins are large complex molecules that play many critical and essential role in the body. They do most of the work in the cells, and are needed for structure, function and regulations of body tissues and organs. The different roles are summarised in the table below. Function Description Antibody Antibodies bind to specific foreign particles, such as viruses and bacteria, to help protect the body. Enzymes and Enzymes are proteins produced by living organisms which catalyzes the Catalysts chemical reaction by lowering the activation energy (energy required for a chemical reaction to occur). Enzymes often play key roles in bonding subunits to form the final, functioning protein. They also assist with the formation of new molecules by reading the genetic information stored in DNA. Messenger Messenger proteins, such as hormones, transmit signals to coordinate biological processes between different cells, tissues, and organs eg. insulin Structural These proteins provide structure and support for cells, eg. keratin and Component collagen Movement Some proteins facilitate movement of the body eg. actin and myosin in muscles Transport/storage These proteins bind and carry atoms and small molecules within cells and throughout the body eg. haemoglobin (Hb) – oxygen binds to Hb and is transported around body cells. 26 | P a g e YEAR 13 - BIOLOGY FOR ALL  SELF TEST: Gene Concept and Protein Synthesis 1. What units make up nucleic acids? What are the chemical compounds that make up those units? 2. What is the difference between DNA and RNA from the point of view of the nitrogenous bases that are present in their nucleotides? 3. According to the Watson-Crick model, how many polynucleotide chains does a DNA molecule have? 4. What is the complementary sequence of nitrogenous bases for an AGCCGTTAAC fragment of a DNA chain? 5. How do the two complementary nucleotide chains of DNA facilitate the replication process of the molecule? 6. Which chemical bonds in DNA molecules must be broken for replication to occur? 7. What is the production of RNA called and what enzyme catalyzes this process? 8. What are the similarities and the differences between the transcription process and the replication processes? 9. What is the difference between DNA and RNA with respect to their biological function? 10. What is the primary structure of a protein? What is the importance of the primary structure? 11. What is the tertiary structure of a protein? What are the main types of tertiary structures? 12. Use a Genetic Code chart to answer the following questions. i. What codon specifies the amino acid methionine? ii. What are the six codons that specify for the amino acid Arginine? iii. What amino acid does the codon UUA code for? iv. What amino acid does the codon GAC code for? 27 | P a g e YEAR 13 - BIOLOGY FOR ALL 1.1.3 VARIATION Variation is any difference between cells, individual organisms, or groups of organisms of any species caused either by genetic differences (genotypic variation) or by the effect of environmental factors on the expression of the genetic potentials (phenotypic variation). It is usually expressed via physical appearance, metabolism, fertility, mode of reproduction, behavior, learning, and mental ability and other obvious or measurable characters. There are two kinds of variation; continuous and discontinuous. Continuous variation: also known as quantitative variation which gives smooth grading between the two extremes with the majority of the organisms in the center. For instance, smooth graduation of height among individuals of human population. The shape of the graph is basically determined via the number of individuals measured that is the smaller the categories used; the closer the results will be to the curved line. This type of curve is called ‘bell shaped’ that shows normal distribution and the graph is the result of variables being normally distributed. Other examples of continuous variation are:  weight  heart rate  finger length  leaf length Discontinuous variation: also known as qualitative variation which divides the individuals of a population into two or more sharply distinct forms. For example, the four types of blood groups (A, B, AB and O). A discontinuous variation with 28 | P a g e YEAR 13 - BIOLOGY FOR ALL several different forms or types of individuals among members of a single species is known as polymorphic variation. For example, the occurrence of several forms of butterfly of the same species are colored which aids them to blend with the vegetation. Discontinuous variation is usually represented using a bar graph. Other examples of discontinuous variation are:  finger prints and tongue rolling  blood groups and eye color Note: The environment cannot change the discontinuous type of variation eg. No matter how much time is spent in the sun or what you eat will not change your blood group Variations are either genetically (genotypically) or environmentally caused. Genetic (Inherited) variation o Genetic variations are due to the differences in number or structure of chromosomes or by differences in the genes carried by the chromosomes. o Children usually look a little like both their mother and their father though not identical to either one of them. This is because they get half of their inherited features from each parent. For instance, each sperm cell and each egg cell contains half of the genetic information needed for an individual (each one is haploid - it has half the normal number of chromosomes). When these join at fertilization, a new cell is formed. This zygote has all the genetic information needed for an individual (it is diploid - it has the normal number of chromosomes). o Examples of genetic variation in humans include blood group, skin color, eye color, and body form and disease resistance. o Individuals with multiple sets of chromosomes are called polyploid; many common plants have two or more times the normal number of chromosomes and new species may arise by this type of variation. Environmental variation Characteristics of animal and plant species can be affected by factors such as climate, diet, accidents, culture and lifestyle. For example, if you eat too much 29 | P a g e YEAR 13 - BIOLOGY FOR ALL you will become heavier, and if you eat too little you will become lighter. A plant in the shade of a big tree will grow taller to reach more light. Other examples of features that show environmental variation include:  Flower color in hydrangeas - these plants produce blue flowers in acidic soil and pink in alkaline soil. Genetic and environmental interaction Some features vary because of a combination of genetic and environmental causes. For example, identical twins inherit exactly the same features from their parents. But if twin A eats more than twin B (and all other conditions stay the same), then twin A is likely to end up heavier. CAUSES OF GENETIC VARIATION a. MUTATION  A mutation is a change in the DNA sequence either due to the mistakes or due to the environmental factors such as UV light, ionizing radiation and chemical mutagens such as tar from cigarette smoke.  Genetic mutations can occur at one point and involves one base, or the change can involve a whole block or section of a chromosome.  Ionizing radiation includes gamma rays, X- rays and ultraviolet rays. The greater the dose of radiation a cell gets, the greater the chance of a mutation  Cells usually recognize potential mutation and repair it before it becomes a fixed mutation.  Mutations contribute to genetic variation within species.  Mutations can also be inherited for instance: the disorder sickle cell anemia (the red blood cells are abnormal, rigid and sickle in shape) is due to mutation in the gene that instructs the building of protein hemoglobin.  Mutation disrupts gene activity and causes disease like cancer. In multicellular organisms, mutations can be classed as either:  Somatic mutations - occur in a single body cell and cannot be inherited (can give rise to cancers)  Germinal (or germline) mutations - occur in gametes and can be passed on to offspring to either harmful, neutral or beneficial effect 30 | P a g e YEAR 13 - BIOLOGY FOR ALL  Effects of mutation  A mutation may be neutral and have no effect. For example, the protein that a mutated gene produces may work just as well as the protein from the non- mutated gene.  A mutation may sometimes be beneficial. For example, people who are carriers (heterozygous) for the sickle cell allele are more resistant to malaria (a tropical disease) than people who are homozygous for the gene.  Mutations can be harmful and reduce the survival chances of the organisms. For example, a white (albino) bird can be seen from further away by its predators. Lethal mutations cause death to the individuals. Types of mutations include: 1. Spontaneous - They are mainly caused during DNA replication or by the incorporation of incorrect nucleotides in the growing DNA chain. - They occur naturally by changes in DNA sequence during replication. 2. Induced - They are caused by the change in DNA brought about by environmental factors (mutagens such as UV light, X –rays, colchicine, mustard gas). 3. Point - Change in the nucleotide sequence involving only one gene. - Only involves a single nucleotide. 4. Block - Change involves a whole section of the chromosome. - The loss or gain of part of a chromosome. Examples of point and block mutation Addition (Insertion) - An insertion changes the number of DNA bases by the addition of one gene (point) or by adding a section of DNA (block). As a result, the protein made by the gene may not function properly, or functions differently from what was expected eg. Huntington’s Disease Deletion - A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s) eg is Cri du Chat syndrome Duplication - A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein eg. ‘Pallister Killian’ syndrome 31 | P a g e YEAR 13 - BIOLOGY FOR ALL Inversion – an inversion mutation is when two bases exchange places on a chromosome Frame-shift mutation - This type of mutation is caused by ‘indels’ (insertions or deletions) or the addition or loss of DNA bases thus changing a gene's reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A frame shift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, http://ghr.nlm.nih.gov/ deletions, and duplications can all be frame shift mutations. Repeat expansion Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3- base-pair sequences, and a tetra- nucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the http://ghr.nlm.nih.gov/ 32 | P a g e YEAR 13 - BIOLOGY FOR ALL number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly. Translocation – when a section of a chromosome breaks off and joins a non- homologous chromosome. http://kmbiology.weebly.com/ b. GENETIC RECOMBINATION AND SEGREGATION These are processes that occur during the formation of sex cells where homologous chromosomes in the nucleus forms doublets and mutually recombine. a. Recombination  DNA molecule is broken at the same place in both homologous chromosomes.  If a strand of one chromosome joins together with a strand from the second chromosome, the pair of recombined chromosomes will differ in the combination of their alleles from the two original chromosomes.  The recombined chromosomes contain part of the alleles from the father and part from the mother. http://www.mun.ca 33 | P a g e YEAR 13 - BIOLOGY FOR ALL  b. Segregation  Takes place during the separation of homologous chromosomes to the opposite ends of dividing cells.  One of the chromosomes of each pair moves quite randomly to the opposite end of the cell. Even if recombination did not occur before this, the segregation of the chromosomes of paternal and maternal origin would give the newly formed cells their own combination of paternal and maternal alleles, different from the combination of alleles of either of its parents.  Following separation of the pair of chromosomes in the first meiotic division, the two sister chromatids of each chromosome separate in the second meiotic division. Thus, four haploid sex cells, are formed from one diploid cell. c. CROSSING OVER Crossing over occurs in the first division of meiosis involving the exchange of genetic material between the non-sister chromatids of homologous chromosomes. Crossing over results in recombination of genes found on the same chromosome, https://www.slideshare.net/ called linked genes that would otherwise always be transmitted together. The frequency of crossing over between any two linked genes is proportional to the chromosomal distance between them, crossing over frequencies are used to construct genetic, or linkage, maps of genes on chromosomes. d. GENETIC LINKAGE AND MAPPING  Genes that are sufficiently close together on a chromosome will tend to “stick together” and the versions of alleles of those genes that are together on a 34 | P a g e YEAR 13 - BIOLOGY FOR ALL  chromosome will be inherited as a pair. This phenomenon is called genetic linkage.  When genes are linked, genetic crosses involving those genes will lead to ratios of gametes and offspring types  Genes on separate chromosomes or very far apart on the same chromosomes assort independently.  Genes on the same chromosome but far apart on the chromosome also assort independently due to crossing over (homologous recombination).  The frequency of recombination events between two genes is used to estimate its relative distances on the chromosome.  The information given by genetic crosses is used to calculate recombination frequency. How to Calculate Percentage Recombinants Step 1: Calculate recombination frequency 𝑹𝒆𝒄𝒐𝒎𝒃𝒊𝒏𝒂𝒏𝒕𝒔 % Recombination = 𝑻𝒐𝒕𝒂𝒍 𝑶𝒇𝒇𝒔𝒑𝒓𝒊𝒏𝒈𝒔 × 100% Step 2: Build linkage maps or map the distance Note: 1% recombination frequency = 1 map unit EXAMPLE 1 Calculate the % recombination and genetic distance in map units between the plant height gene and the flower color gene? Question Answer 831 tall plants with red 831 tall plants with red flowers Parental flowers 90 tall plants with 90 tall plants with purple Recombinant purple flowers flowers 84 short plants with red 84 short plants with red flowers Recombinant flowers 843 short plants with 843 short plants with purple Parental purple flowers flowers Total flowers = 831 + 90 + 84 + 843 = 1848 Total recombinants = 90 +84 = 174 𝑹𝒆𝒄𝒐𝒎𝒃𝒊𝒏𝒂𝒏𝒕𝒔 % Recombination = 𝑻𝒐𝒕𝒂𝒍 𝑶𝒇𝒇𝒔𝒑𝒓𝒊𝒏𝒈𝒔 × 100% 𝟏𝟕𝟒 = 𝟏𝟖𝟒𝟖 × 100% Recombination Frequency = 9.42% (9. 42 map units) 35 | P a g e YEAR 13 - BIOLOGY FOR ALL  EXAMPLE 2 Given the crossover frequency of each of the genes on the chart, construct a chromosome map. Gene Frequency of Crossover A-C 30% B-C 45% B-D 40% A-D 25% Step 1: Start with the genes that are the farthest apart first: B and C are 45 map units apart and would be placed far apart. B ----------------------------------------- 45% ------------------------------------------C Step 2: Solve it like a puzzle, using a pencil to determine the positions of the other genes. Step 3: Subtraction will be necessary to determine the final distances between each gene. 36 | P a g e YEAR 13 - BIOLOGY FOR ALL e. DISJUNCTION  Mitosis produces two genetically identical daughter cells where sister chromatids separate and move to opposite poles of a cell that is ‘pulled’ apart by the spindle fibres. This is disjunction.  In meiosis, disjunction is the point at which two homologous chromosomes separate during Anaphase I. The two members of the homologous pair of chromosomes go to the opposite poles of the cell. This ensures the chromosome number is now no longer diploid but haploid. Disjunction takes place again in Anaphase II of meiosis, when the sister chromatids separate and move to the opposite poles. http://www.vce.bioninja.com.au/ Non-disjunction  Non-disjunction is the failure of chromosomes to separate during cell division.  Occurs when the separation of chromatids in (mitosis) and homologous chromosomes in (meiosis) fails to occur. This has serious consequences in gamete formation of meiosis as the resulting cells may have gained an extra chromosome or lost one.  For instance, a sperm cell may have an X and a Y chromosome or none at all. The abnormal number of chromosomes will either lead to death of the cell but in some cases, the resulting abnormal gamete may still go on to fuse with another gamete during fertilisation. The resulting offspring will have an abnormal number of chromosomes in its genotype. Down syndrome is a condition where an extra chromosome exists. Non-disjunction may occur via: 1. Failure of homologues to separate in Anaphase I (resulting in four affected daughter cells) - Nondisjunction occurring during anaphase I of meiosis I indicates that at least one pair of homologous chromosomes did not separate. - The end result is two cells that have an extra copy of one chromosome and two cells that are missing that chromosome. - In humans, n + 1 designates a cell with 23 chromosomes plus an extra copy of one for a total of 24 chromosomes. n - 1 designates a cell missing a chromosome for a total of only 22 chromosomes in humans. 37 | P a g e YEAR 13 - BIOLOGY FOR ALL 2. Failure of sister chromatids to separate in Anaphase II (resulting in only two daughter cells being affected) http://www.vce.bioninja.com.au/  Nondisjunction occurring during anaphase II of meiosis II, indicates that at least one pair of sister chromatids did not separate. As a result two cells will have the normal haploid number of chromosomes.  Additionally, one cell will have an extra chromosome (n + 1) and one will be missing a chromosome (n - 1). Non-disjunction results in Aneuploidy; where individuals have 1 or 2 more or less chromosomes [2n + 1(2)]  Aneuploidy is a condition in which one or more chromosomes are present in extra copies or are deficient in number, but not a complete set.  The loss of a single chromosome from a diploid genome is called monosomy (2n-1) while the gain of one extra chromosome is called trisomy (2n+1).  The risk of non-disjunction occurring increases with the age of the parents.  Non-disjunction can occur during either meiosis I or II, with differing results.  If a gamete with two copies of the chromosome combines with a normal gamete during fertilization, the result is trisomy; if a gamete with no copies of the chromosomes combines with a normal gamete during fertilization, the result is monosomy.  Aneuploidy often results in serious conditions such as Turner’s syndrome, Klinefelter Syndrome and Down syndrome. 38 | P a g e YEAR 13 - BIOLOGY FOR ALL Meiotic division showing non-disjunction: http://www2.samford.edu Terminology for variation in chromosomal numbers Term Explanation Aneuploidy 2n ± x chromosomes Monosomy 2n-1 Disomy/Diploid 2n Trisomy 2n+1 Tetrasomy, pentasomy, etc. 2n +2, 2n+3 etc. Euploidy Multiples of n Diploidy 2n Polyploidy 3n, 4n, 5n, … Triploidy 3n Tetraploidy, pentaploidy, etc. 4n, 5n, etc. Nondisjunction disorders are when cell division development of the zygote has an imbalanced amount of genetic information. This imbalance affects the distribution of the chromosomes or genetic information that each cell has. Having abnormal 39 | P a g e YEAR 13 - BIOLOGY FOR ALL amounts of karyotype in the chromosome overloads the cell and this in turn kills the zygote or in some cases, a person with Nondisjunction disorder is born. Down Syndrome (Trisomy 21) Down syndrome is a developmental disorder caused by an extra copy of chromosome number 21. It is a somatic disorder and sometimes referred to as Trisomy 21. With an extra copy of this chromosome on the 21st pair, individuals have three copies of each of its genes instead of two, making it difficult for cells to properly control how much protein is made. People with this syndrome have:  Distinct facial features that is a flat face, a small broad nose, abnormally shaped ears, a large tongue, and upward-slanting eyes with small folds of skin in the corners.  An increased risk of developing a number of medically significant problems, including respiratory infections, gastrointestinal tract obstruction (blocked digestive tract), leukaemia, heart defects, hearing loss, hypothyroidism, and eye abnormalities.  have moderate to severe intellectual disability; children with Down syndrome usually develop more slowly than their peers and have trouble learning to walk, talk, and take care of themselves.  generally individuals with Down syndrome have a decreased life expectancy. https://palmreadingperspectives.wordpress.com/ 40 | P a g e YEAR 13 - BIOLOGY FOR ALL Klinefelter Syndrome  Characterised by 47, (chromosome number) XXY, or XXY karyotype and is a germinal disorder where human males have an extra X chromosome in the 23rd pair ( the sex pair) and is sometimes referred to as 47, XXY or XXY.  Males normally have a chromosomal makeup of XY, but an affected individual with Klinefelter Syndrome will have at least two X chromosomes and at least one Y chromosome.  During stage I or II of meiosis (sex cell division) a nondisjunction can occur which retains the extra X chromosome and cause the Klinefelter syndrome.  Mammals normally have more than one X chromosome, but the genes from only one is expressed. This is due to X- inactivation. This is a natural process which can be seen in female mammals, XX. In the XXY male, a few genes located in the pseudo autosomal regions of their X chromosomes, have corresponding genes on their Y chromosomes and are capable of being expressed. These triploid genes present in cells of male, may be what is causing the symptoms for Klinefelter Syndrome.  Some (about 10%) males have only the extra X chromosome present in some of their cells. This is described as mosaic Klinefelter Syndrome, and can be described with some variant of mosaic karyotype (e. g. 46, XY/47, XXY). This means that some of the cells from an affected individual will show a normal karyotype, while other cells can show the karyotype of Klinefelter Syndrome. These individuals usually show milder signs and symptoms of the condition, but this again depends on the number of cells expressing the affected trait.  The phenotype of the affected person is basically male, tall stature with elongated lower legs and forearms. The body shape, however, is more feminine (narrow shoulders, broad hips) with a lower muscle mass. One third of affected individuals show gynaecomastia (abnormal development of mammary glands in male resulting in breast enlargement). The risk for male breast cancer and osteoporosis is also increased.  One of the main symptoms of this condition is infertility that arises in the beginning of the third decade at its latest. 41 | P a g e YEAR 13 - BIOLOGY FOR ALL   The infertility is a result of atrophy of the seminiferous tubules. The individual expresses low libido and impotence.  Intelligence is usually normal. However, reading difficulties and problems with speech are more likely to be observed.  Symptoms are typically more severe if three or more X chromosomes are present.  Other features include reduced hair growth in pubic region, axillary region, chest and face; varicose veins and leg ulcers; diabetes mellitus in 8% of cases; thyroid gland problems are common; depression and lung disease. Turner’s syndrome This syndrome is characterized by a 45, X karyotype in females (in about 50% of cases), with the absence of one X chromosome (and therefore absence of a Barr body). The single X chromosome is of maternal origin in about 70% of cases; therefore there is loss of a sex chromosome due to paternal error. Its incidence is about 1:2000 (less common than Klinefelter’ s) and it is present in about 1.5% of all conceptions. As with Klinefelter, Turner’s Syndrome is a germinal disorder, and sometimes referred to as XO or 45,X or 45,XO. Features include:  short stature (without hormonal treatment, average height is 145cm)  ovarian dysgenesis (streak ovary); this is the most common cause of primary amenorrhea (absence of menstruation)  infertility  shield chest with widely-spaced nipples and webbing of the neck  low posterior hairline and average intelligence  renal and cardiovascular abnormalities (e.g. narrowing of the aorta). https://www.news-medical.net 42 | P a g e YEAR 13 - BIOLOGY FOR ALL f. POLYPLOIDY  Organisms which have more than 2 whole sets of chromosomes, are termed as polyploidy  When there are 3 sets, this is called triploid while 4 sets are called tetraploid.  Polyploidy is generally more common in plants because plants reproduce vegetatively. Further, polyploidy in plants can be advantageous as often it results in bigger and better (quality) crops.  Polyploidy also leads to speciation Polyploidy can result in both sterile and fertile offspring  In order to be fertile, the organism need to have an even number of chromosome (so they can line up in homologous pairs and separate during meiosis) Types of Polyploidy Autopolyploidy: organisms with multiple sets of chromosome from the same species.  E.g. a potato produces gametes with polyploidy and mates with another potato, giving rise to a new potato with autopolyploidy (3 sets of chromosome but all from potato family). Allopolyploid: organism with multiple sets of chromosomes from different species  E.g. a wheat plant fertilises a rye plant. http://www.cbs.dtu.dk/courses 43 | P a g e YEAR 13 - BIOLOGY FOR ALL   If the offspring has the uneven number of chromosome due to nondisjunction having occurred in one of the gametes then the offspring will be infertile.  If the offspring has an even number of chromosome due to nondisjunction occurring in both the gametes then the offspring will be fertile. Origin of Seedless fruits (Parthenocarpic)  Fruits that develop parthenocarpically are typically seedless.  The triploid seeds are obtained by crossing a fertile tetraploid (4n) plant with a diploid (2n) plant. For example: when you buy seedless watermelon seeds, you get two kinds of seeds, one for the fertile diploid plant and one for the sterile triploid. The triploid seeds are larger, and both types of seeds are planted in the same vicinity.  Male flowers of the diploid plant provide the pollen which pollinates (but does not fertilize) the sterile triploid plant. The act of pollination induces fruit development without fertilization, thus the triploid watermelon fruits develop parthenocarpically and are seedless. Polyploidy in Animals  Polyploidy is much rarer in animals. It is found in some insects, fishes, amphibians, and reptiles. In human, polyploidy foetuses are spontaneously aborted.  It occurs in highly differentiated human tissues in the liver, heart muscle and bone marrow. TYPES OF INHERITANCE 1. Multiple Alleles Involves more than just the typical two alleles that usually code for a certain characteristic in a species. With multiple alleles, that means there is more than two phenotypes available depending on the dominant or recessive alleles that are available in the trait and the dominance pattern the individual alleles follow when combined together. 2. Epistasis Gene Interaction  Epistasis is the modification of the expression of a gene by another.  Any single characteristics that results in a phenotypic ratio that totals 16 (such as 12:3:1, 9:3:4, 9:7, 15:1or 13:3) is typical of two gene interaction.  In epistasis, one gene masks or interferes with the expression of another. Supplementary Epistasis  This occurs when a recessive genotype masks the actions of another gene or when a dominant allele masks the effects of another gene. 44 | P a g e YEAR 13 - BIOLOGY FOR ALL   In other words, two independent pairs of genes which interacts to produce new trait. However, each dominant gene alone produces its own trait.  the normal dihybrid segregation ratio 9:3:3:1 is changed to 9:3:4. Example In mice, the wild-type coat color, agouti (A), is dominant to solid-colored fur (a). However, a separate gene (C) is necessary for pigment production. A mouse with a recessive c allele at this locus is unable to produce pigment and is albino regardless of the allele present at locus A. Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9 agouti: 3 solid color: 4 albino. In this case, the C gene is epistatic to the A gene. Genotypes 45 | P a g e YEAR 13 - BIOLOGY FOR ALL Complementary Genes- 9:7 (duplicate recessive)  Occurs when recessive alleles at either of the two loci masks the expression of dominant alleles at the two loci; hence the name duplicate recessive epistasis  In other words, two independent genes interact to produce a trait together however, each dominant gene alone does not show its effect.  Also known as complementary genes where the normal dihybrid segregation ratio 9:3:3:1 is changed into 9:7 Example The purple colour of flower in sweet pea is governed by two dominant genes: A and B. when these genes are in separate individuals (AAbb or aaBB) or recessive (aabb) they produce white flower. A cross between purple flower (AABB) and white flower (aabb) strains produced purple colour in F1. Inter-mating of F1 plants produced purple and white flower plants in 9:7 ratio in F2 generation. http://www.biologydiscussion.com/genetics/gene-interactions/top-6-types-of-epistasis-gene- interaction/37818 3. Polygenic Traits  A trait or phenotypic character that is controlled by a group of non-allelic genes.  For example, skin pigmentation is controlled by at least 3 genes: A, B and C. http://dragonflyissuesinevolution13.wikia.com/wiki/Recessive_Epistasis AABBCC results in darkest shade while aabbcc results in lightest shade. Each gene contributes equally: AaBbCc = AABbcc 46 | P a g e YEAR 13 - BIOLOGY FOR ALL   Should height be controlled by Genes P, Q and R and the dominant allele of all these genes are present, the person is very tall. Non –inheritable variation induced by environmental factors. Foetal Alcohol Syndrome (FAS):  Is a birth defect caused by drinking alcohol during pregnancy  Foetal death is the most extreme outcome from drinking alcohol during pregnancy.  People with FAS might have abnormal facial features, growth problems, and central nervous system (CNS) problems.  People with FAS can have problems with learning, memory, attention span, communication, vision, or hearing. SELF TEST: Genetic Variation 1. State three sources of genetic variation. 2. Why is Mendel’s Second Law not always valid for two or more phenotypical traits of an individual? 3. What are linked genes? 4. What is crossing over? How is meiosis related to this phenomenon? 5. In genetic recombination by crossing over, what is the difference between parental gametes and recombinant gametes? 6. What is percentage recombination? 7. How is crossing over important for the diversity of biological evolution? 8. Describe the karyotype of an individual in Down syndrome? 9. What is aneuploidy? What are the causes of aneuploidy? 10. What are genetic mutations? 11. Does every gene mutation cause an alteration in the protein the gene normally codes for? 12. How do genetic mutations influence biological diversity? 47 | P a g e YEAR 13 - BIOLOGY FOR ALL 1.1.4 GENETIC ENGINEERING Genetic engineering or recombinant DNA refers to the direct manipulation of DNA or genome to alter an organism’s characteristics (phenotype) in a particular way.  This means changing base pair, deleting a whole region of DNA or introducing an additional copy of a gene.  The DNA of an organism that is altered by incorporation of gene is known as recombinant DNA.  The replication of altered DNA is known as cloning. Recombinant DNA  Recombinant DNA is sometimes referred to as the chimera DNA since it involves combining two or more strands of DNA from two different organisms in order to create a new strand of DNA  Genetic engineering utilizes recombinant DNA, it is also known as recombinant DNA technology. Important Tools for Recombinant DNA Restriction endonuclease: These enzymes cut DNA molecules at specific sites in two ways:  Some restriction endonucleases cleave both strands of DNA simply at the same point within the recognition sequence. As a result of this type of cleavage, the DNA fragments with blunt ends are generated.  In the other style of cleavage by the restriction endonucleases, the two strands of DNA are cut at two different points. Such cuts are termed as staggered cuts and this results into the generation of protruding ends i.e., one strand of the double helix extends a few bases beyond the other strand. Such ends are, called cohesive or sticky ends. https://sites.google.com Terminologies used specifically in genetic engineering:  Exonucleases: is an enzyme that removes nucleotides from the ends of a nucleic acid molecule. 48 | P a g e YEAR 13 - BIOLOGY FOR ALL   DNA ligase: joins two fragments of DNA by synthesizing the phosphodiester bond.  DNA polymerase: synthesizes a new complementary DNA strand of an existing DNA or RNA template. Reverse transcriptase is also an important type of DNA polymerase enzyme which uses RNA as a template for synthesizing a new DNA strand called as complementary DNA (cDNA).  Vectors: DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell, where it can be replicated or expressed  Host organism: Bacteria E. coli is widely used as a host in recombinant DNA technology since cloning and isolation of DNA inserts is much easier to perform  Foreign DNA: The desired DNA segment which is to be cloned is called as DNA insert or foreign DNA.  Transgenic organism: it carries recombinant DNA. E.g. Bacteria Steps in Recombinant DNA Technology Basic steps in the recombinant DNA technology or genetic engineering: 1. Selection and isolation of DNA insert: First step in rDNA technology is the selection of a DNA segment of interest which is to be cloned. This desired DNA segment is isolated enzymatically. 2. Selection of suitable cloning vector: A suitable cloning vector is selected in the next step of rDNA technology. 3. Introduction of DNA cloning vector to form recombinant DNA molecule: The DNA which has been extracted and cleaved enzymatically by the selective restriction endonuclease enzymes are ligated (joined) by the enzyme ligase to vector DNA to form a rDNA molecule. 4. Recombinant DNA molecule is introduced into a suitable host: Suitable host cells are selected and the rec DNA molecule formed is introduced into these host cells. This process of entry of rec DNA into the host cell is called transformation. Usually selected hosts are bacterial cells like E. coli, however yeast, fungi may also be utilized. 5. Selection of transformed host cells: Transformed cells (or recombinant cells) are those host cells which have taken up the rDNA molecule. In this step the transformed cells are separated from the non-transformed cells by using various methods making use of marker genes. 6. Expression and multiplication of DNA insert in the host (Gene Cloning): Finally, it is to be ensured that the foreign DNA inserted into the vector DNA is expressing the desired character in the host cells. Also, the transformed host cells are multiplied to obtain sufficient number of copies. If needed, such genes may also be transferred and expressed into another organism. 49 | P a g e YEAR 13 - BIOLOGY FOR ALL Diagram showing basic steps in recombinant DNA technology http://www.biologydiscussion.com Advantages of GMO Genetically modified organisms (GMO) refers to the genetic material that has been artificially altered through genetic engineering to change its characteristics.  Few examples of genetically modified organisms with commercial value: - Golden rice: modified rice that produces beta- carotene - Goats: modified to produce important protein (FDA- approved human antithrombin which is used to treat a rare blood clotting disorder in humans). - Vaccine producing bananas: genetically engineered bananas that contain a vaccine. Bananas provide an easy means for delivering a vaccine especially to children. - Microorganisms, yeast, fungi, and bacteria modified to produce the enzyme chymosin, which splits milk to make cheese. - Blue roses: roses modified with pansy genes to express blue color in flowers. 50 | P a g e YEAR 13 - BIOLOGY FOR ALL Other advantages include: - Insect resistance. - Stronger crops. - High yield. - Extensive protection and more nutritious food. - Decreased use of pesticides. - Less deforestation. - Decrease in food prices and new products. Disadvantage of GMO  Allergic reactions.  Not 100% environmentally friendly.  Lower level of biodiversity.  Decreased antibiotic efficacy.  Food supply at risks.  New diseases.  Economic concerns and ethical issues. DNA Cloning  DNA cloning is the process of making multiple identical copies of a particular piece of DNA  Multiple copies of a DNA sequence in a plasmid: in certain occasions, lots of DNA copies are needed to conduct experiment or build new plasmids. In other cases, the piece of DNA encodes a useful protein, and the bacteria are used as “factories” to make the protein. For instance, the human insulin gene is expressed in E. coli bacteria to make insulin used by diabetics. Uses of DNA Cloning DNA molecules built through cloning techniques are used for many purposes in molecular biology:  Biopharmaceuticals  Gene therapy  Gene analysis Application of Recombinant DNA Technology  Production of transgenic plants and animals. 51 | P a g e YEAR 13 - BIOLOGY FOR ALL  Production of hormones, vaccines and biofuels.  Production of antibiotics and commercially important chemicals.  Prevention and diagnosis of diseases.  Application in enzyme engineering and forensic science. Economic Implication  Lower food prices due to the production of designer fruits – bigger, seedless, take shorter time to ripen.  Fruits have a longer shelf life so will not putrefy on keeping  Crop plants with genes to produce pest repellent will cut down on the use of harmful pesticides  Using this techniques, foods that are cold, drought, heat and frost resistant may be produced  In the health sector, defective genes may be corrected (gene therapy) to reduce the intake of regular doses of enzymes, hormones which are costly and inconvenient Dangers of Genetic Engineering Several dangers are associated with recombinant DNA technology  Spread of new diseases: new dangerous forms of micro-organisms can be developed through recombinant DNA technique either accidentally or deliberately.  Effect on Evolution: nature has provided several barriers for exchange of DNA between prokaryotes and eukaryotes. Recombinant DNA technology permits exchange of DNA between these two classes of organisms and thus interferes with the natural process of evolution.  Biological Warfare: there is a fear that genetic engineering techniques will be used for biological warfare. In such warfare, disease carrying microorganisms can be used against the enemy. BIOTECHNOLOGY  Biotechnology refers to the use of technologies to alter the characteristics of a particular organism.  Biotechnology in fact is the use of biological processes, organisms, or systems to manufacture products intended to improve the quality of human life. The earliest biotechnologists were farmers who developed improved species of plants and animals through cross breeding. 52 | P a g e YEAR 13 - BIOLOGY FOR ALL   In biotechnology, the organisms are not always modified to be different, but their natural processes are enhanced to get the optimum product.  Today, biotechnology provides breakthrough products and technologies to combat debilitating and rare diseases, reduce our environmental footprint, and feed the hungry. Benefits of Biotechnology  Fuel the world: Biotech uses biological processes such as fermentation and harnesses biocatalysts such as enzymes, yeast, and other microbes to become microscopic manufacturing plants  Feed the world: Biotech improves crop insect resistance, enhances crop herbicide tolerance and facilitates the use of more environmentally sustainable farming practices.  Heal the world: Biotech helps to heal the world by harnessing nature's resources and uses genetic makeup to heal and shed light on research. Biotechnology, like other advanced technologies, has the potential for misuse Ethical Aspects of Biotechnology Ethics refers to the act of defining what is morally right or wrong. Ethics is extremely essential in the applications of biotechnology since it deals with issues concerning the human nature, food and the environment.  Leads to green revolution.  Religious issues: playing GOD.  Economic corruption of safety issues.  Ethics of technology choices.  Ethics of disease prevention: methods used- is it worth it.  Ownership of biological innovations: can humans own a life?  Strong belief that GMO will cause the loss of biodiversity.  Violation of organism’s rights and values concerned.  Concerns with respect to threats on environment and human health.  Effects of synthesized substance on non-targeted organisms.  Possibility of horizontal gene transfer of transgenic DNA and the potential to create new virus or bacteria that cause disease. 53 | P a g e YEAR 13 - BIOLOGY FOR ALL SELF TEST: Genetic Engineering 1. At the present level of advancement of biotechnology, what are the main techniques of genetic engineering? 2. What are restriction enzymes? How do these enzymes participate in recombinant DNA technology? 3. What are DNA ligases? How do these enzymes participate in recombinant DNA technology? 4. What are plasmids and its importance in rDNA technology? 5. How is genetic engineering used to create bacteria capable of producing human insulin? 6. What is cloning? 7. Why are recombinant DNA technology and nucleus transplantation technology still dangerous? 8. Debate the moral problem (ethics) regarding the cloning of human individuals. 9. What are genetically modified (GM) organism and GM foods? 10. Discuss the benefits and the disadvantages of GM foods. 54 | P a g e YEAR 13 - BIOLOGY FOR ALL 1.1.5 POPULATION GENETICS This refers to the study of the distributions and changes of allele frequency and interaction of alleles in a population. A population is affected to the four main evolutionary forces namely: 1. Natural Selection 2. Genetic drift 3. Mutation 4. Gene flow (migration) The smaller a population, the more susceptible it is to mechanisms like natural selection. The study of population genetics helps understand the species adaptations and evolution. Population is defined as a group of individuals of a particular species occupying a definite space in which the organisms interact, interbreed and exchange genetic materials. Role of population in evolution  For the processes of evolution to occur in the system, there should be changes in the genetic equilibrium. Gene Pool Gene pool is the sum of total genes of all the individuals in a population. A gene pool of a population describes:  genes present in the population.  proportions of different kinds of genes.  pattern of distribution of genes in the individuals of population. Allele Frequency Represents the frequency of a gene (allele) variation in a population. Alleles are variant forms of a gene that are located at the same position, or genetic locus, on a chromosome. Changes in allele frequencies over time can indicate that genetic drift is occurring or that new mutations have been introduced into the population. Genotype frequency Refers to the total number of a kind of individuals form a population all of which exhibit similar character with respect to the locus under consideration. THE HARDY WEINBERG PRINCIPLE Also referred to as the Hardy-Weinberg equilibrium, it is the fundamental concept in population genetics (the study of genetics in a defined group). It is a mathematical equation describing the distribution and expression of alleles (forms of a gene) in a 55 | P a g e YEAR 13 - BIOLOGY FOR ALL population, and it expresses the conditions under which allele frequencies are expected to change. The Hardy Weinberg Principle was proposed independently by G. H. Hardy (a mathematician) and Wilhelm Weinberg (a physician), and is as stated below: The Hardy Weinberg Principle states that the relative frequencies of various kinds of genes and alleles in a population tend to remain constant from generation to generation in the absence of other evolutionary influences. The relationship between gene frequency and genotype frequency can be expressed as: Assumptions of the Hardy Weinberg Principle The Hardy-Weinberg Principle is only true if a population is