DNA and Heredity Biology MYP4&5 PDF

MYP4&5 BIOLOGY 2023-2025 Title DNA and Heredity Timeframe 5 UNIT 4 Global Conte...

MYP4&5 BIOLOGY 2023-2025 Title DNA and Heredity Timeframe 5 UNIT 4 Global Context: Identities and relationships Relationships Key Concept: Evidence. Models. Patterns Related Concept: The identity and relationship with other people are determined by genetic factors: scientific Statement of Inquiry: evidence has led to models that help to understand observed patterns of inheritance Factual What evidence proves the relationship between species’ genome and identity? Conceptual How are patterns of inheritance justified by the model of DNA? Inquiry Questions Debatable Should humans base their moral reasoning and ethical judgement on phenotypical differences? DISCLAIMER The following booklet is a collage of the theoretical content of the following sources: ▪ Biology for the IB MYP 4&5: By Concept. Davis & Deo. Hodder Education. 2015. ISBN: 9781471841705 ▪ Cambridge IGCSE Biology Study and Revision Guide 2nd Edition. Hayward. Hodder Education. 2016. ISBN: 9781471865138 ▪ Oxford IB Study Guides: Biology for the IB Diploma. Allot. Oxford University Press. 2014. ISBN: 9780198393511 ▪ IB Biology Course Book: Oxford IB Diploma Programme. Allot and Mindorff. Oxford University Press. 2014. ISBN: 9780198392118. ▪ Oxford IB Course Preparation: Biology for IB Diploma Programme Course Preparation. Bkerat. Oxford University Press. 2018. IBN:978019842350-8. (1) Genome – Chromosomes and genes A. DNA DNA (deoxyribonucleic acid) is a molecule common to all life on Earth. It contains the code that determines the shape and structure of living things. The discovery of the structure of DNA was one of the biggest breakthroughs in science. Scientists could then understand how organisms reproduce and pass on their characteristics to offspring - are the young born of living organisms, produced either by a single organism or, in the case of sexual reproduction, two organisms. DNA is a macromolecule, made up of two strands in a double helix structure. Each strand is a chain of units called nucleotides. It can be thousands of nucleotides long. Nucleotides are themselves made from three parts: a phosphate; a sugar; and a base. There are four bases: adenine, A; cytosine, C; thymine, T; and guanine, G. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 1 Figure 1 - Zoom-in dispiction of part of a DNA sequence: DNA → nitrogen base pairing. Source: https://microbenotes.com/dna-structure-properties-types-and- functions/ The phosphate and sugar from one nucleotide join with the other nucleotides to form two long chains. These chains are joined in a double helix structure by the bases. Base pairing is a remarkably simple phenomenon: adenosine (A) always pairs with thymine (T); and guanine (G) always pairs with cytosine (C). This biologic phenomenon is called complementary base pairing. While the sugar and phosphates form the ‘backbone’ of DNA, the bases determine the genetic code - the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells – which determines the characteristics of the organism. B. Chromosomes Each cell in an organism contains the molecule DNA. The DNA in cells is not stored as one long molecule, but it is divided into several individual lengths called chromosomes. Chromosomes are the small bodies in the nucleus of a cell that carry the chemical “instructions” for reproduction of the cell. They consist of strands of DNA wrapped in a double helix around a core of proteins. Figure 2 - Schematic zoom-in representation of a nucleus of a cell until one of it's genes. Source: https://www.civilsdai ly.com/biotechnology -basics-of-cell- nucleus- chromosomes-dna- genes-etc/ Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 2  ▪ A diploid cell is a cell that has a nucleus containing two sets of each chromosome - nearly all body, or somatic cell. While a haploid cell is a cell that contains only a single set of unpaired chromosomes – sex cells, sperm, and egg (gametes). Figure 3 - Schematic representation of a haploid and a diploid cell with one set of chromosomes. Adapted from: https://www.dreamstime.com/difference- homologous-chromosomes-pair-homologous-chromosomes-sister-chromatids-difference-homologous-image158332961 ▪ The number of chromosomes is a characteristic feature of members of a species. The karyotype is the number. o Humans’ karyotype consists of 46 chromosomes, or 23 pairs of chromosomes. The twenty- third pair of chromosomes in humans determines whether an individual is male or female. Figure 4 - Human karyotype. All 46 chromosomes are in their diploid form. This means that each pair of 2 is 2 from mom and 2 from dad. Source: https://www.differencebetween.com /difference-between-autosomes- and-vs-chromosomes/ Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 3  o There are two types of sex chromosomes, a larger X and a smaller Y. If two X chromosomes are present, a baby develops as a female. If one is X and the other Is Y, then the baby will develop as a male. C. Genes and alleles Each chromosome contains lengths of genetic code that determine different characteristics – these lengths of code are called genes. A gene is the unit of inheritance, passed down from one generation to the next. In other words, a gene is a heritable factor that consists of a length of DNA and influences a specific characteristic. Every gene occupies a specific position on a chromosome. And even though the total number of genes is not yet known precisely for humans or other species, there are estimates which show some trends: ▪ Bacteria have fewer genes than eukaryotes. ▪ Some other animals have fewer genes than humans, but some have more. ▪ Plants may seem less complex than humans, but some have more genes. A gene consists of a sequence of 3 bases on a piece of DNA (i.e., a codon – see (3) B). And each gene will code for a specific protein molecule. There are different versions of some gene that have almost the same base sequence but differ in just one or a very small number of bases. These variant forms are called alleles. Figure 5 – Gene and alleles for eye colour. Source: https://ib.bioninja.com.au/standard-level/topic-3-genetics/31-genes/alleles.html Alleles are different forms of the same gene because they influence the same characteristic, occupy the same position on a type of chromosome and have base sequences that differ from each other by one or only a few bases. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 4  For example, the human gene for the protein of haemoglobin is adenine (A) in the most common allele of the gene. However, there is a less common allele which has a thymine (T). This allele causes the genetic disease called sickle cell anaemia (type of blood disorder). All chromosomes of one particular type are called homologous chromosomes, which means that Figure 6 - Two pairs of homologous chromosomes. Source: although they have the same genes in the same https://www.assignmentpoint.com/science/biology/homologous- chromosome.html sequence/place, they may not have the same alleles of those genes. D. Genome The genome is the whole of the genetic information of an organism. The size of a genome is therefore the total amount of DNA in one set of chromosomes in that species. It can be measured in millions of base pairs (bp) of DNA. Genome sizes vary considerably. Five examples are shown below. Escherichia coli is a gut bacterium and T2 phage is a virus that attacks E.coli. The fruit fly, Drosophila melanogaster, has been widely used in genetics research. Paris japonica is a woodland plant with a remarkably large genome. Table 1 - Genome size for different types of Kingdoms Organism Genome size (millions of base pairs) T2 phage 0.18 E. coli 5 D. melanogaster 140 Homo sapiens 3,000 P. japonica 150,000 Until here, you can now do the following formative questions at the end of the packet: 1; 2; 3. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 5 (2) Cell division In eukaryotes nearly all the DNA of a cell is stored in the nucleus. A human nucleus contains about 2 meters of DNA and yet the nucleus is only about 5 µm in diameter. However, DNA fits the nucleus because it is attached to proteins that coil the genetic information into structures called chromosomes. This process of shortening by coiling is called Figure 7 - Representation of DNA condensation. The DNA needs to uncoil to allow access to its' genes. But if the genes no longer need to be read, then the DNA will condense back DNA condensation. (supercoil) to its 'tight' form. Source: https://www.quora.com/Is-there-a-real-pictu The uncoiling of DNA is necessary for three important cellular phenomena: 1. DNA replication. The uncoiling of chromosomes allows the ‘unzipping’ of the double helix structure. In turn this allows for the genetic information to be read and replicated. it is not a type of cell division; however, it is an essential step before cell division! 2. Mitosis. Both uncoiling and condensation are vital steps in the several stages of cell duplication. 3. Meiosis. Both the uncoiling and condensation are vital steps in the several stages of production of sexual cells, also called gametes. Figure 8 - Schematic representation of mitosis and meiosis side-by-side. While mitosis simply replicates one parental cell (2n) to two daughter cells (2x 2n). Meiosis produces four gametes (4x n) from one parental cell (2n). Source: http://themagicschoolbus.blogs Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 6  A. DNA replication When Francis Crick and James Watson discovered the structure of DNA, its model immediately suggested a method of copying called semi-conservative replication. The two strands of the DNA molecule are separated by breaking the hydrogen bonds between their bases. New polymers of nucleotides are assembled on each of the two single strands. A strand of DNA on which a new strand is assembled is called a ‘template strand’. Because of complementary base pairing, each of the new strands has the same base sequence as the old strand that was separated from the template strand. The two DNA molecules produced in this way are identical to each other and to the original parent DNA molecule. This is semi-conservative replication because each of the DNA molecules produced has one new strand and one strand conserved from the parent molecule. The stages of DNA replication are depicted in Figure 9. Thus, the purpose of DNA replication is to produce two identical copies of a DNA molecule. This is essential for cell division during growth or repair of damaged tissues. DNA replication ensures that each new cell receives its own copy of the DNA: 1. Helicase → Unwinds the double helix and separates the two strands. 2. DNA polymerase → Attaches to the old strand, using it as a template to define the new strand (complementary base pairing). 3. Once DNA polymerase detaches, so does the new DNA strand. Helicase is released and the old double- helix is closed. Figure 9 - DNA replication (simplistic view). Source: http://miasbioswag.blogspot.com/2014/03/b5-describe-dna-replication.html Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 7  B. Mitosis – Diploid cells Mitosis is the process of cell duplication, or reproduction, during which one cell gives rise to two genetically identical daughter cells. DNA replication is not mitosis, mitosis only separates the newly replicated chromosomes! Before cells divide, each chromosome must copy itself to produce two identical strands. This DNA replication occurs in a stage of the cell called interphase. The process produces double-stranded chromosomes. Each strand is called a chromatid. Chromatids are held together by a protein structure called a centromere. And the two chromatids held together are called sister chromatids. Figure 10 - Representation of sister-chromatids (two chromatids in the same homologous chromosome) and non-sister chromatids (two chromatids from different homologous chromosomes). Source: https://www.dreamstime.com/difference-homologous-chromosomes-pair-homologous-chromosomes-sister-chromatids-differen During mitosis, each double-stranded chromosome reverts to being single-stranded, with one copy of each chromosome ending up in each of the two new cells. Mitosis can be divided into four separate stages: Figure 11 - Steps of mitosis: prophase; metaphase; anaphase; and telophase 1. Prophase. Chromosomes undergo condensation to me easily moved around. The chromosomes become visible as distinct threads. The nuclear membrane breaks down so that the chromosomes can Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 8  move freely within the cell. A series of protein fibers (called the spindle) are formed that attach to the centromere to each chromosome. 2. Metaphase. The chromosomes line up in the center of the cell (the ‘equator’). They are moved into place using the spindle fibers. 3. Anaphase. The spindle fibers contract and separate the chromatids, which are pulled to opposite ends of the cell. 4. Telophase. The nuclear membrane reforms and the chromosomes unwind so they can carry out their function once more. Following mitosis, the nuclear division, the cytoplasm divides in two, separating the two cells. This is called cytokinesis. Figure 12 - Last phase of mitosis (telophase) and cytokinesis. Source: https://ib.bioninja.com.au/standard-level/topic-1-cell- biology/16-cell-division/cytokinesis.html During mitosis, one cell has become two, with each daughter cell a genetically identical copy of the original parent cell. This means that mitosis creates diploid cells. C. Cell cycle The cell cycle is an ordered set of events which culminates in the division of a cell into two daughter cells. The cell cycle is divided into the following phases: First growth phase (G1) – The cell grows in size to prepare for DNA replication. Again, the cell needs to ensure that the doubling of all its chromosomal content can fit inside itself. Cell is diploid, 2n. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 9  Synthesis phase (S) – The cell undergoes DNA replication (see (2) A), doubling its chromosomal content. Cell becomes tetraploid, 4n. o For example, human beings have 23 pairs of chromosomes/46 chromosomes, so by the end of S phase, the cell will have 46 pair of chromosomes/92 chromosomes. Second growth phase (G2) – The cell grows in content. The cell needs to ensure that all its organelles are at least doubled before cytokinesis, so that the daughter Figure 41 – The Cell Cycle. Source: https://science11botany.blogspot.com/2018/08/cell- cells are fully functional. Cell is still a biology.html tetraploid, 4n. Mitosis – Nuclear division (see (2) B), the nucleus 4n is divided into 2x 2n. Cytokinesis – Cytoplasmic division, whereby cellular contents are segregated, and the cell physically splits into two individual diploid cells (2x 2n). D. Meiosis – Haploid cells Meiosis is the process that halves chromosome number to create sex cells - sperm and egg cell - also called gametes. Sex cells are formed in the gonads (ovaries and testes). While all the egg cells formed will always carry a X chromosome. Half of the produced sperm cells will carry a X chromosome, and the other half a Y chromosome. In meiosis, a diploid nucleus divides twice to produce four haploid cells. The DNA of the chromosome is replicated before the first division, so each chromosome consists of two sister chromatids, but the DNA is not replicated between the first and second divisions. It is the separation of pairs of homologous chromosomes in the first division of meiosis that halves the chromosome number. In summary: 2n → DNA replication: 4n → Cell cycle: 2x 2n → Meiosis, 4x n. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 10  You do not need to know the steps of meiosis in detail. But you need to know that it involves the following steps: prophase I; metaphase I; anaphase I; telophase I; prophase II; metaphase II; anaphase II; and telophase II. At the end of the process, the haploid cells produced are not identical – meiosis results in genetic variation. This means that whichever sperm cell and/or egg cell are produced, both the maternal and paternal chromosomes always contain new combinations of genetic material. Figure 13 - Side by side comparison of meiosis vs. mitosis: complete steps. Source: https://www.diffen.com/difference/Meiosis_vs_Mitosis Until here, you can now do the following formative questions at the end of the packet: 4; 5; 7 & 8 (3) The Manufacture of Proteins A. RNA DNA molecules remain in the nucleus, which means that all their information is ‘stranded’ in the core of cells. If genes - which consist of a sequence of 3 bases on a piece of DNA (i.e., codon) – are responsible for coding for specific protein molecules, then all the information needed to manufacture proteins at the ribosome level (outside the nucleus - cytosol) is also stranded. However, this is overcome by DNA coding for RNA, which in turn codes for proteins – biology’s ‘central dogma’. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 11 RNA is a much smaller molecule than a DNA molecule and is made up of only one strand. Three major types of RNA play a role during the journey from DNA to protein. Although the functions of each type of RNA are different, one type of RNA is called messenger RNA, or simply mRNA, and it is responsible for coping and transferring the information from the DNA (nucleus). The copying of the base sequence of a gene – part of the DNA – by making a mRNA molecule is called transcription. mRNA then travels from the nucleus to the ribosome in the cytoplasm where it is decoded in and read by the ribosomes to make the protein. Translation is the synthesis of proteins on ribosomes by reading of the mRNA. In summary, DNA codes for proteins in the following way: 1. Helicase → DNA in the nucleus unwinds and ‘unzips’ – the bases are exposed. 2. RNA polymerase → Transcription allows for a copy of the genetic code to be taken – the copy itself is mRNA. 3. The mRNA travels out of the nucleus into the cytosol, reaching the ribosome. 4. Ribosome → Translation occurs at the ribosome – mRNA is read, determining the order of amino acids (building blocks Figure 14 - DNA to mRNA: overall view. Source: Biology for the IB MYP of proteins) (see figure 15). 4&5: By Concept. Davis & Deo. Hodder Education. 2015. ISBN: 9781471841705 Figure 15 - Translation at the ribosome: mRNA chain sits on the small subunit of the ribosome; the large subunit unites and attaches the correct amino acid. mRNA chain is read in 3-base units (i.e., a codon). Source: https://www.khanacademy.org /scienc Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 12 It is important to note that there are two differences between DNA and RNA nucleotides: 1. The type of sugar: ribose in RNA; and deoxyribose in DNA. 2. In both DNA and RNA there are four possible bases. Three of these are the same: adenine (A); cytosine (C); and guanine (G). The fourth base is thymine (T) in DNA but uracil (U) in RNA. B. Synthesis of amino acids. The amino acid sequence of proteins is determined by mRNA according to the genetic code. The genetic code that is translated on the ribosome is a triplet code, this means that three bases code for one single amino acid. A group of three basis called a codon. If there are 4 bases (A, T, G and C) that can assume 3 positions for each codon, then there are a total of 64 codons (43). This gives more than enough codons to code for the 20 amino acids in proteins. Figure 16 - Translation chart, from codon to amino acid. Source: https://sosal.kr/615 Amino acids are then linked together by condensation reactions to make proteins or peptides - a short chain of amino acids. The amino acids in a peptide are connected to one another in a sequence by bonds called peptide bonds. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 13  ▪ Chains of fewer than 40 amino acids are called peptides. ▪ A dipeptide is a molecule consisting of two amino acids linked together. ▪ A polypeptide consists of many amino acids linked by peptide bonds that form an unbranched (linear chain). ▪ A protein consists either of a single polypeptide or more than one polypeptide linked together. Until here, you can now do the following formative questions at the end of the packet: 9 & 10. (4) Mutations Mutations are random changes to the base sequence of a gene. The change may or may not result a change to the physical characteristics (or phenotype) of an organism. Mutations that occur in a sex cell (gamete: sperm; or egg) can be passed to the next generation, whereas mutations that occur in the body (somatic) cells may be harmless or may lead to irreversible damage. Although mutations are important as they are a source of the genetic variation (different alleles) that is necessary for evolution to occur, very few mutations prove to be beneficial and some cause genetic diseases or cancer. Figure 17 - Representation of types of point mutation compared to the normal sequence. Source: https://kids.frontiersin.org/article/10.3389/frym.2019.00046 Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 14 Mutagens – agents of substances that can bring about a permanent alteration to the physical composition of a DNA – can also cause mutations. The mutagen rate is increased by two types of mutagens: 1. High energy radiation. This includes X-rays, short or medium wave UV gamma rays and radioactive isotopes. effects of radiation can be studied using two incidents: Chernobyl’s nuclear accident; and nuclear bombing in Hiroshima. 2. Mutagenic chemicals. This includes nitrosamines in tobacco, mustard gas that was used as a chemical weapon and the solvent benzene. A point mutation is a change in one base in the genetic code. It can be the result of: ▪ Substitution. The change of one base to a different base, often caused by incorrect DNA replication. ▪ Insertion. The addition of a base into the DNA. ▪ Deletion. The removal of a base from the DNA. It is important to note that mutations can occur during any stage of cell division and DNA replication. Until here, you can now do the following formative questions at the end of the packet: 11 – 21. (5) Patterns of Inheritance Inheritance is the transmission of genetic information from one generation to the next, leading to the continuity of the species and the variation within it. While an organism born from sexual reproduction always inherits half of its genetic information from the female- parent and the other half from the male-parent. Organisms born from sexual reproduction always inherit an exact copy of its’ parent genetic information, making it a clone. Figure 18 - The cell cycle of human beings. From diploid organisms (parents) to the production of gametes (haploid cell). Gametes then fuse together and a new life - a baby - is formed (diploid organism). Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 15 Independently of the type of reproduction, an organism always shows a genotype and a phenotype. The genotype is all the genetic information that makes-up an organism in terms of the alleles that are present. And the phenotype is the observable characteristics of an organism; only the alleles that are read from its DNA. It is important to note that, the content of this chapter focuses only on sexual reproduction since little (mutations) to no variations are seen in organisms born from asexual reproduction. A. Mendel – Pea plants’ 3:1 Ratio Gregor Mendel is often regarded as the father of genetics. He crossed varieties of pea plants that had different characteristics, and, from his results, he deduced the principles on which inheritance is based. Mendel crossed two varieties of pea together and found out that all the offspring – F1 generation – had the same characteristics as one of the parents. He allowed the F1 generation to self-fertilize – each plant produced offspring by fertilizing its female gametes with its own male gametes. The offspring – the F2 generation – contained both the original parental types in a 3:1 ratio. Using modern terms, Mendel’s explanation is that each pea plant has two alleles of the gene that affects the character: ▪ The parents are homozygous because they have two identical alleles present for the same gene. Homozygous dominant alleles are Figure 19 - Mendel’s pea cross, 3:1 ratio. Source: Oxford IB Study Guides: Biology for the IB Diploma. Allot. Oxford represented always as 2 capitalized letters, University Press. 2014. ISBN: 9780198393511 ex: AA. Homozygous recessive alleles are represented always as 2 lower-case letters, ex: aa. ▪ The F1 plants are heterozygous because they have two different alleles present for the same gene. Represented always as 1 capitalized letter and 1 lower-case letter, ex: Aa. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 16  ▪ The F1 plants all have the character of one of the parents because that parent has at least one dominant allele – an allele that is always expressed if present. ▪ The fact that F1 plants are heterozygotes masks the effect of the other parent’s recessive allele – an allele that is expressed only when there is no dominant allele of the gene present. ▪ One quarter of F2 plants have two recessive alleles and so show the character caused by this allele. B. Monohybrid Inheritance A Punnett square is a graphical representation of the possible genotypes of an offspring arising from a particular genetic cross. Monohybrid inheritance involves the study of how a single gene* is passed on from parents to offspring. Here are all the possible combinations that arise from this inheritance: A A A A a a A a A AA AA a Aa Aa A Aa Aa A AA Aa a Aa Aa a Aa Aa a aa aa a Aa aa Phenotype: Phenotype: Phenotype: Phenotype: 50% AA & 50% 100% Aa 50% aa & 50% 50% Aa & 25% AA & 25% Aa Aa aa If two identical homozygous individuals are bred together, the product of the cross will be pure-breeding:AA x AA = 100% AA; and aa x aa = 100% aa *A single gene is always expressed as 2! Do not forget that you always get 1 maternal chromosome and 1 paternal chromosome, making you a diploid organism, 2n. If you mean 1 gene, then n = 1. When building your own Punnett Square, it is important that you (based on genetic cross of figure 20): 1. Make sure you state what symbols present what, for example: T = tall, t = dwarf. 2. Make sure you label each line in the cross (phenotype, genotype, etc.). 3. Circle the gametes to show that meiosis has happened. 4. Read the question really careful – are you asked to state the outcome in terms of genotype or the phenotype? For example, an offspring Tt: genotype = heterozygous, carrier of dwarf; and phenotype = tall. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 17 Figure 20 - Example of how to build and present a Punnett Square. Source: Biology for the IB Diploma. Allot. Oxford University Press. 2014. ISBN: 9780198393511 Until here, you can now do the following formative questions at the end of the packet: 22 – 26. C. Pedigree diagrams The term pedigree often refers to the pure-breeding nature of animals but is also used to describe human inheritance. Pedigree diagrams are like family trees and can be used to demonstrate how genetic diseases can be inherited. They can include symbols to indicate whether individuals are male or female and what their genotype is for a particular genetic characteristic. A disease can be autosomal recessive, when it is manifested by the presence of two recessive alleles; or autosomal dominant, when it is manifested by the presence of two dominant alleles. A carrier is an individual that does not have the disease but has the allele of it is present in its gene (heterozygous). One disease is called cystic fibrosis. Cystic fibrosis is an autosomal recessive disease (cc) and sufferers tend to have a much shorter lifespan than normal and suffer from respiratory, digestive, and reproductive problems. Let us look into the possible scenarios for the inheritance of this disease (see figure 21): ▪ A man who is not a carrier (CC) who has children with a woman who is not a carrier (CC) will produce 100% children who are not carriers (all CC). ▪ If one parent is a carrier for cystic fibrosis (Cc) and the other parent is not a carrier (CC), 50% of their children are likely to be carriers (Cc) and 50% will not be carriers (CC). Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 18  ▪ However, if both parents are carrier, then the likely ratio of offspring of non-carriers/carriers/cystic fibrosis sufferers (CC:Cc:cc) is 1:2:1. So, there is a 1 in 4 chances of a child born to these parents having cystic fibrosis. Figure 21 - Pedigree diagram for the autosomal recessive disorder cystic fibrosis. Source: Biology for the IB Diploma. Allot. Oxford University Press. 2014. ISBN: 9780198393511 Until here, you can now do the following formative questions at the end of the packet: 27. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 19  Formative Questions, Unit 4 – DNA and Heredity 1. Classify the following words from a greater to a smaller magnification: chromosome; DNA; nucleus; nucleotide; gene; codon. 2. Identify if the statements below are correct. If a statement is not correct, change the underlying word to make the statement true. a. The offspring of two parents obtains a single copy of every gene from each parent. b. A gamete must contain one complete set of genes. c. Genes are located at specific positions on spindles. d. A pair of corresponding chromosomes is homozygous. e. One member of each homologous chromosome pair comes from each gene. f. A cell that contains both sets of homologous chromosomes is haploid. g. The gametes of sexually reproducing organisms are haploid. h. If an organism’s haploid number is 6, its diploid number is 3. Figure 1 3. Label the structures that make-up part of a DNA sequence on figure 1. 4. When cells reach a certain need to be replenished or simply need to have copies made, they divide. The process of cell division can be visualized as a whole or in more detail. a. Label the cell cycle (A-J) on figure 2 b. State where in the cell cycle does DNA replication take place Figure 2 Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 20  Figure 3 c. Explain how DNA replication leads to a semi-conservative outcome. d. Label and outline the steps of mitosis and cytokinesis (A-E & 1-10) on figure 3 5. Recognize if the statements are a case of interphase OR mitosis by checking the correct column Statement Interphase Mitosis a. Cell growth occurs b. Nuclear division occurs c. Chromosomes are distributed equally to daughter cells d. Protein production is high e. Chromosomes are duplicated f. DNA synthesis occurs g. Cytoplasm divides immediately after this period h. Mitochondria and other organelles are made Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 21 6. Identify if the following statements are either a case of SEXUAL or ASEXUAL reproduction: a. Produces genetically identical organisms b. Occurs in most animals and plants and in many single-celled organisms c. Increases genetic diversity, which aids species survival in changing environments. d. Occurs in many single-celled organisms and in some multicellular organism. e. Produces organisms with genetic information from both parents f. Allows rapid reproduction of organisms in favorable environments. 7. Mitosis and meiosis are two types of cell division, both preceded by DNA replication to ensure that all genetic information is kept within the daughter cells. a. Compare and contrast mitosis and meiosis b. Define gamete 8. Recognize the missing word or words to make each statement correct and complete a. A diploid cell that enters mitosis with 16 chromosomes will divide to produce ____ daughter cells. Each of these daughter cells will have ____ chromosomes. b. If a diploid number of chromosomes for an organism is 16, each daughter cell after mitosis will contain _____ chromosomes. c. A diploid cell that enters meiosis with 16 chromosomes will pass through ____ cell divisions, producing ____ daughter cells, each with ____ chromosomes. d. Gametes have a ______ number of chromosomes. e. If an organism’s haploid number is 5, its diploid number is _____. f. While a haploid number of chromosomes may be even or odd, a diploid is always ____. 9. RNA is a much smaller molecule than a DNA molecule and is just made up of only one strand. Different types of RNA have different functions, all ultimately leading to the synthesis of proteins. a. Outline the two differences between DNA and RNA nucleotides b. Describe mRNA and its functions in the nucleus c. Summarize in four steps how DNA is coded into proteins d. Construct the mRNA sequence for the following original DNA strand Original sequences TACACCTTGGCGACGACT Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 22  mRNA sequence 10. The amino acid sequence of proteins is determined by mRNA according to the genetic code. a. If you have a RNA transcript that is 105 nucleotides long. Calculate how many amino acids will be in the resultant protein? b. Define a codon. c. State one amino acid that has only one codon. d. Look back at your answer 9. d., construct the amino acid sequence with the help of the table. 11. Mutations are random changes to the base sequence of a gene. a. Describe the three types of point mutations b. Analyze the following mutations based on the original sequence: Original sequence: TACACCTTGGCGACGACT Mutated TACGACCTTGGCGACGAT TACACCTTAGCGACGACT TACACCTTGGGACGACT sequence Circle the mutation on the mutated sequence Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 23  What kind of mutation is this? What is the amino acid sequence? c. Compare and contrast the amino acid sequence that you constructed in 10. d. with the three new sequences obtained due to mutation. d. Suggest which mutation would be more severe (less beneficial to the organism). 12. Chromosomes are located in the _____ of d. TATGCA the cell a. Cell wall b. Cytoplasm 15. Where does replication occur in eukaryotic c. Mitochondria cells? d. Nucleus a. Wherever there is DNA b. Only in the nucleus 13. Which of the following represent the four c. Only in the ribosome nucleotide components of DNA? d. Only in the mitochondria a. A-T-C-U b. A-T-C-G c. T-U-C-G 16. Replication is when... d. A-T-U-C a. Proteins are made b. RNA is made from the DNA template c. Another copy of DNA is made 14. The following strand of DNA: TATGCA. d. DNA is made from the RNA template According to the rule of base-pairing which one would be the complementary to this 17. A DNA molecule is shaped like a strand? a. Long, thin rod a. ATAGGT b. Twisted ladder b. ATACCA c. Straight ladder c. ATACGT d. Triple helix. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 24 18. What forms a genetic code? a. The number of daughter cells in an organism b. The order of nitrogen bases along a gene c. The order of proteins along a gene d. The number of phosphates in a DNA strand 19. A DNA nucleotide is made up of 3 parts, which of the following is NOT a part a. Nitrogen base b. Phosphate group c. Deoxyribose sugar d. Ribosome 20. Translation occurs in the _____ by the action of _____. a. Nucleus, ribosomes b. Nucleus, DNA polymerase c. Endoplasmatic reticulum, ribosomes d. Endoplasmatic reticulum, DNA polymerase 21. Transcription occurs in the ____ and results in the formation of ____. a. Nucleus, DNA b. Nucleus, mRNA c. Cytoplasm, DNA d. Cytoplasm, mRNA Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 25  22. For all of the following questions, use these facts: the trait is fur color (letter F/f). Black fur is dominant over grey fur. i. Write the letter of the dominant allele. _________ ii. Write the letter of the recessive allele. _________ iii. Write out the homozygous dominant genotype (2 alleles). _________ iv. Write out the heterozygous genotype (2 alleles). _________ v. Write out the homozygous recessive genotype. _________ vi. Write the genotype for gray fur. _________ vii. Write the genotype for Black fur. _________ or _________ viii. Write the phenotype for #3. _________________________ ix. Write the phenotype for #4. _________________________ x. Write the phenotype for #5. _________________________ 23. Still using fur color, do the following monohybrid cross problems. (Remember: Black fur is dominant over gray) a. If the mother is homozygous recessive and the father is homozygous dominant. i. Write the genotype probabilities. ii. Write the phenotype probabilities. b. If the mother is heterozygous, and the father is heterozygous. i. Write the genotype probabilities. ii. Write the phenotype probabilities. c. If the mother is heterozygous, and the father is homozygous dominant. i. Write the genotype probabilities. ii. Write the phenotype probabilities. d. If the mother is homozygous recessive, and the father is heterozygous. i. Write the genotype probabilities. ii. Write the phenotype probabilities. 24. In pea plants, yellow seed color is dominant to green seed color. If a heterozygous pea plant is crossed with a plant that is homozygous recessive for seed color, what is the probability that the offspring will have green seeds? Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 26  25. In humans, six fingers is the dominant trait and five fingers is the recessive trait. Both parents are heterozygous for six-fingers. Indicate the genotypes and phenotypes of the parents and their possible offspring. What is the probability of producing a five fingered child? 26. In a certain species of plant, one purebred variety has hairy leaves and another purebred variety has smooth leaves. A cross of the two varieties (P) produces offspring that all have smooth leaves (F1). Predict the phenotypic and genotypic of the offspring (F2) that result from inbreeding of F1. 27. Autosomal recessive trait is one of several ways that a trait, disorder, or disease can be passed down through families. An autosomal recessive disorder means two copies of an abnormal gene must be present in order for the disease or trait to develop Trait: Falconi anemia Forms of the trait: The dominant form is normal bone marrow function - in other words, no anemia. The recessive form is Falconi anemia. Individuals affected show slow growth, heart defects, possible bone marrow failure and a high rate of leukemia. A typical pedigree for a family that carries Falconi anemia. Note that carriers are not indicated with half-coloured shapes in this chart. a. How do you represent the three possible genotypes of the trait? b. What is George's (I-1) genotype? c. What is Alan’s (III-2) genotype?. d. If Christophe (IV-1) was born with Falconi anemia, what does this mean about his heaçthy mother, Tina’s (III-3) genotype? Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 27  a. MARKSCHEME of Formative Questions 1. Classify the following words from a greater to a smaller magnification: chromosome; DNA; nucleus; nucleotide; gene; codon Nucleus > Chromosome > DNA > gene > codon > nucleotide 2. Identify if the statements below are correct. If a statement is not correct, change the underlying word to make the statement true. a. The offspring of two parents obtains a single copy of every gene from each parent. True b. A gamete must contain one complete set of genes. True c. Genes are located at specific positions on spindles. False - chromosomes d. A pair of corresponding chromosomes is homozygous. False - homologous e. One member of each homologous chromosome pair comes from each gene. False - parent f. A cell that contains both sets of homologous chromosomes is haploid. False - diploid g. The gametes of sexually reproducing organisms are haploid. True h. If an organism’s haploid number is 6, its diploid number is 3. False – 12 3. Label the structures that make-up part of a DNA sequence on figure 1. Y – thymine; X – sugar; W – phosphate; and Z – guanine 4. When cells reach a certain need to be replenished or simply need to have copies made, they divide. The process of cell division can be visualized as a whole or in more detail. a. Label the cell cycle (A-J) on figure 2 A – Interphase; B – G1 , Growth; C – S, Synthesis; D – G2 , Preparation; E – Prophase; F – Metaphase; G – Anaphase; H – Telophase; I – Mitosis; J – Cytokinesis b. State where in the cell cycle does DNA replication take place. DNA replication takes place in the nucleus during interphase, more specifically durinf S phase. c. Explain how DNA replication leads to a semi-conservative outcome The four nucleotides that form the basis of DNA pair up in a phenomenum called complementary base pairing. This allows for A and T always to be paired, and G always paired with C. When DNA is being replicated, the strand being read will always be completed due to complementary base pairing, leading to two new strands that are semi- conservative: one new and one old. d. Label and outline the four steps of mitosis and cytokinesis on figure 3 A – Prophase; B – Metaphase; C – Anaphase; D – Telophase; E – Interphase; 1 – centriole; 2 – spindle fibers; 3 – chromatids; 4 – daughter cells; 5 – chromatin; 6 – cell membrane; 7 – nucleolus; 8 - centrioles; 9 – chromosome. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 28 5. Recognize if the statements are a case of interphase OR mitosis by checking the correct column Statement Interphase Mitosis a. Cell growth occurs X b. Nuclear division occurs X c. Chromosomes are distributed equally to daughter cells X d. Protein production is high X e. Chromosomes are duplicated X f. DNA synthesis occurs X g. Cytoplasm divides immediately after this period X h. Mitochondria and other organelles are made X 6. Identify if the following statements are either a case of SEXUAL or ASEXUAL reproduction: a. Produces genetically identical organisms. Asexual b. Occurs in most animals and plants and in many single-celled organisms. Sexual c. Increases genetic diversity, which aids species survival in changing environments. Sexual d. Occurs in many single-celled organisms and in some multicellular organism. Asexual e. Produces organisms with genetic information from both parents. Sexual f. Allows rapid reproduction of organisms in favorable environments. Asexual 7. Mitosis and meiosis are two types of cell division, both preceded by DNA replication to ensure that all genetic information is kept within the daughter cells. a. Compare and contrast mitosis and meiosis. Mitosis is the process of cell duplication, during which one cell gives rise to two genetically identical daughter cells. While meiosis is the process that halves chromosomes number to create sex cells – sperm and egg cell – also called the gametes. Mitosis is preceded by interphase, having DNA replication in S- phase more specifically, and then cytokinesis. While meiosis follows a second mitosis and a second cytokinesis without being preceded by a second interphase. b. Define gamete A gamete is a haploid cell, a sperm and/or egg cell. In other words, a gamete is a cell that only has a single set of unpaired chromosomes. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 29 8. Recognize the missing word or words to make each statement correct and complete c. A diploid cell that enters mitosis with 16 chromosomes will divide to produce 2 daughter cells. Each of these daughter cells will have 16 chromosomes. d. If a diploid number of chromosomes for an organism is 16, each daughter cell after mitosis will contain 16 chromosomes. e. A diploid cell that enters meiosis with 16 chromosomes will pass through 2 cell divisions, producing 4 daughter cells, each with 8 chromosomes. f. Gametes have a haploid number of chromosomes. g. If an organism’s haploid number is 5, its diploid number is 10. h. While a haploid number of chromosomes may be even or odd, a diploid is always even. 9. RNA is a much smaller molecule than a DNA molecule and is just made up of only one strand. Different types of RNA have different functions, all ultimately leading to the synthesis of proteins. a. Outline the two differences between DNA and RNA. RNA is a much smaller molecule than DNA molecule and is made up of only one strand. While RNA is defined by a ribose sugar and as an Uracil nucleotide paired with Adenine. DNA is defined by a deoxyribose sugar and as a Thymine paired up with Adenine. b. Describe mRNA and its functions in the nucleus. mRNA is a type of RNA that is responsible for “passing down the message” from the nucleus, where the DNA is at, to the ribosomes, where the information is read. Thus, mRNA is the actual transcript of the DNA. c. Summarize in four steps how DNA is coded into proteins 1. DNA in the nucleus unwinds and unzips – the bases are exposed 2. Transcription allows for a copy of the genetic code to be taken – the copy itself is the mRNA 3. The mRNA travels out of the nucleus into the cytosol, reaching the ribosome. 4. Translation occurs at the ribosome – mRNA is read, determining the order of amino acids d. Construct the mRNA sequence for the following original DNA strand Original sequences TAC-ACC-TTG-GCG-ACG-ACT mRNA sequence AUG-UGG-AAC-CGG-UGC-UGA 10. The amino acid sequence of proteins is determined by mRNA according to the genetic code. a. If you have a RNA transcript that is 105 nucleotides long. Calculate how many amino acids will be in the resultant protein? 105/3 = 35 amino acids b. Define a codon. A codon is a group of three nucleotide basis Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 30  c. State one amino acid that has only one codon. Methionine, Tryptophan d. Look back at your answer 9. d., construct the amino acid sequence with the help of the table 1 Methionine + Tryptophan + Asparagine + Arginine + Cysteine + STOP 11. Mutations are random changes to the base sequence of a gene. a. Describe the three types of point mutations A point mutation can be of three types: substitution; insertion; and deletion. Substitution is the change of one base to a different base, often caused by incorrect DNA replication. Insertion is the addition of a base into the DNA. Deletion is the removal of a base from the DNA. b. Analyze the following mutations based on the original sequence: Original sequence: TACACCTTGGCGACGACT Mutated TACGACCTTGGCGACGAT TACACCTTAGCGACGACT TACACCTTGGGACGACT sequence Circle the mutation on the mutated sequence What kind of mutation is this? Insertion and a deletion Substitution Deletion What is the amino acid AUGCUGGAACCGCUGCUA AUGUGGAAUCGCUGCUGA AUGUGGAACCCUGCUG sequence? A MET+LEU+GLUT.AC+PRO+LEU+LE MET+TRYPT+ASP+ARG+CYS U +STOP MET+TRYPT+ASP+PRO+A LA c. Compare and contrast the amino acid sequence that you constructed in 10. d. with the three new sequences obtained due to mutation. Original amino acid sequence MET+THR+LEU+ALA+THR+THR Insertion + deletion MET+LEU+GLUT.AC+PRO+LEU+LEU Substitution MET+TRYPT+ASP+ARG+CYS+STOP Deletion MET+TRYPT+ASP+PRO+ALA d. Suggest which mutation would be more severe (less beneficial to the organism). Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 31 12. Chromosomes are located in the _____ of the cell a. Long, thin rod a. Cell wall b. Twisted ladder b. Cytoplasm c. Straight ladder c. Mitochondria d. Triple hélix d. Nucleus 18. What forms a genetic code? 13. Which of the following represent the four a. The number of daughter cells in an nucleotide components of DNA? organism a. A-T-C-U b. The order of nitrogen bases along a gene b. A-T-C-G c. The order of proteins along a gene c. T-U-C-G d. The number of phosphates in a DNA strand d. A-T-U-C 19. A DNA nucleotide is made up of 3 parts, which of 14. The following strand of DNA: TATGCA. According the following is NOT a part to the rule of base-pairing which one would be the a. Nitrogen base complementary to this strand? b. Phosphate group a. ATAGGT c. Deoxyribose sugar b. ATACCA d. Ribosome c. ATACGT d. TATGCA 20. Translation occurs in the _____ by the action of _____. 15. Where does replication occur in eukaryotic cells? a. Nucleus, ribosomes a. Wherever there is DNA b. Nucleus, DNA polymerase b. Only in the nucleus c. Endoplasmatic reticulum, ribosomes c. Only in the ribosome d. Endoplasmatic reticulum, DNA d. Only in the mitochondria polymerase 16. Replication is when... 21. Transcription occurs in the ____ and results in the a. Proteins are made formation of ____. b. RNA is made from the DNA template a. Nucleus, DNA c. Another copy of DNA is made b. Nucleus, mRNA d. DNA is made from the RNA template c. Cytoplasm, DNA d. Cytoplasm, mRNA 17. A DNA molecule is shaped like a 22. For all of the following questions, use these facts: the trait is fur color (letter F/f). Black fur is dominant over grey fur. i. Write the letter of the dominant allele. F Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 32  ii. Write the letter of the recessive allele. f iii. Write out the homozygous dominant genotype (2 alleles). FF iv. Write out the heterozygous genotype (2 alleles). Ff v. Write out the homozygous recessive genotype. ff vi. Write the genotype for gray fur. ff vii. Write the genotype for Black fur. Ff or FF viii. Write the phenotype for #3. Black fur ix. Write the phenotype for #4. Black fur x. Write the phenotype for #5. Grey fur 23. a. A A %Gen = 4/4 = 100% Aa, heterozygous ↔ carriers of blue eyes! a Aa Aa a Aa Aa %Phen = 4/4 = 100% Brown eyes b. A a %Gen: ▪ ½ = 50% Aa, heterozygous ▪ 1/4 = 25% aa, homozygous recessive ▪ ¼ = 25% AA, homozygous dominant A AA Aa a Aa aa %Phen: ▪ ½ = 50% Brown eyes (carriers of blue) ▪ ¼ = 25% Blue eyes ▪ ¼ = 25% Brown eyes c. A A %Gen ▪ ½ = 50% AA, homozygous dominant ▪ ½ = 50% Aa, heterozygous/carriers of blue A AA AA a Aa Aa %Phen = 4/4 = 100% Brown eyes d. a a %Gen: ▪ ½ = 50% Aa, heterozygous ▪ ½ = 50% aa, homozygous recessive Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 33  A Aa Aa a aa aa %Phen: ▪ ½ = 50% Brown eyes (carriers of blue) ▪ ½ = 50% Blue eyes 24. Seed colour: G = Yellow, dominant & g = green, recessive g g %Gen: ▪ ½ = 50% Gg, heterozygous ▪ ½ = 50% gg, homozygous recessive G Gg Gg g Gg Gg %Phen: ▪ ½ = 50% Yellow seeds (carriers of green) ▪ ½ = 50% Green seeds. Answer: The probability of the offspring having green seeds if 50% 25. Number of fingers: F = Six, dominant & f = five, recessive F f %Gen: ▪ ½ = 50% Ff, heterozygous ▪ 1/4 = 25% ff, homozygous recessive ▪ ¼ = 25% FF, homozygous dominant F FF Ff f Ff ff %Phen: ▪ ½ = 50% Six fingers (carriers of ‘five fingers’) ▪ ¼ = 25% Five fingers ▪ ¼ = 25% Six fingers Answer: The probability of producing an offspring with five fingers is 25% 26. Interpretation: 1. Assume trait: leaves, as L = dominant and l = recessive 2. Purebred means that there is no variation, so either LL or ll (at this point we do not know which trait is dominant or recessive). 3. If two purebreds (P) are cross and all (F1) offspring are of one phenotype, then that phenotype is dominant. Thus, smooth leaves = L and hairy leaves = l The genetic cross is: Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 34  Leaf type: L = Smooth, dominant & l = hairy, recessive l l ▪ %Gen = 4/4 = 100% Aa, heterozygous ↔ carriers of blue eyes! L Ll Ll L Ll Ll ▪ %Phen = 4/4 = 100% Brown eyes All F1’s have smooth leaves (L) but all are carriers of hairy (l) 4. F2 generation is the offspring of the cross between two F1’s: Leaf type: L = Smooth, dominant & l = hairy, recessive L l %Gen: ▪ ½ = 50% Ff, heterozygous ▪ 1/4 = 25% ff, homozygous recessive ▪ ¼ = 25% FF, homozygous dominant L LL Ll 27. Solved pedigree: a. HH = healthy Hh = healthy but carrier of falconi anemia hh = falconi anemia b. HH c. Hh d. For Tina to be healthy but to have a child with falconi anemia from a carrier parent means that Tina herself is a carrier too, so Hh. Booklet created by Mrs. Margarida Coimbra Edited for academic year 2023-2024 at Oeiras International School (OIS) | Page: 35