CIE IGCSE Biology - Chromosomes, Genes, and Proteins

Chromosomes, Genes, and Proteins

Overview

This chapter covers the fundamental concepts of chromosomes, genes, and proteins, and how they relate to inheritance and cell function.

Key Concepts

1. Chromosomes and DNA

• Chromosomes are made of DNA, which contains genetic information in the form of genes.
• DNA (Deoxyribonucleic acid) is a double helix joined by complementary base pairing (Adenine to Thymine, and Cytosine to Guanine).
• DNA carries genes, which are segments of DNA that code for proteins.
• Males have X and Y chromosomes, while females have two X chromosomes.

2. Genes and Proteins

• A gene is a length of DNA that codes for a protein.
• The sequence of bases in a gene determines the sequence of amino acids needed to make a specific protein.
• Different sequences of amino acids give different shapes to protein molecules.

3. Gene Expression and Cell Function

• DNA controls cell function by controlling the production of proteins, including enzymes, membrane carriers, and receptors for neurotransmitters.
• Most body cells contain the same genes, but only express the genes needed for their specific function.

4. Inheritance

• Inheritance is the transmission of traits from one generation to another.
• Chromosomes are involved in inheritance and are located in the nucleus of each body cell.
• Alleles are different forms of the same gene.

5. Protein Synthesis

• Protein synthesis is a two-step process: making of mRNA in the nucleus which carries genetic information from DNA, followed by making of protein in the cytoplasm which determines traits.

DNA Organization

• DNA carries genetic information important for cellular functions like cell division and differentiation.

Relationship between Chromosomes, Genes, and Proteins

• A DNA molecule consists of two parallel strands joined by nitrogenous bases: adenine (A), cytosine (C), guanine (G), and thymine (T).
• The DNA double helix is a coiled structure.

Definitions

• Gene: A unit of heredity carrying instructions for traits.
• Chromosome: A structure containing genes, found in the cell's nucleus.
• Inheritance: The passing of traits from parents to offspring through genes on chromosomes.

Detailed Explanation

1. Chromosomes and Genes

• Chromosomes are thread-like structures of DNA, carrying genetic information in the form of genes.
• A gene is a short length of DNA found on a chromosome that codes for a specific protein.
• DNA building blocks are called nucleotides, consisting of a sugar, a phosphate group, and a nitrogenous base.

2. Gene Function

• A DNA molecule carries many genes along its length.
• Each gene is a segment in the DNA that controls the production of a particular protein, enzyme, membrane carrier, or neurotransmitter.

3. Gene Control of Cell Function

• The nucleus in every cell contains all the genes to construct the human body.
• Genes can be switched on or off to form different types of cells through a process called differentiation.
• Differentiation is crucial in the development of multicellular organisms, where cells undergo changes to become specific cell types, like muscle cells, nerve cells, or skin cells.

4. Gene to Phenotype

• Genes are segments of DNA.
• Each gene contains information about a certain trait.
• Genes are transcribed and translated by the cell to make proteins.
• Proteins create a visible phenotype.
• Example: A gene might code for eye color, creating green pigment.

Genetic Locus and Alleles

• A locus (plural: loci) refers to the specific physical location of a gene or DNA sequence on a chromosome. It's like an address for a particular gene within the genome.
• Most organisms have at least two alleles, either dominant or recessive.
• In a pair of homologous chromosomes, one is inherited from the male parent (paternal homologue), and the other from the female parent (maternal homologue).
• Use alphabet to represent alleles: Upper case - Dominant, Lower case - Recessive.
• Examples:
  • BB - Homozygous Dominant
  • Bb - Heterozygous
  • bb - Homozygous Recessive
• A genetic locus is the location of a particular gene on a chromosome.

Allele Combinations

• When an individual has two identical dominant alleles for a particular gene, resulting in the expression of the dominant trait.
• When an individual has two identical recessive alleles for a particular gene, resulting in the expression of the recessive trait.
• When an individual has two different alleles for a particular gene (e.g., "Aa"), with one dominant and one recessive allele. In this case, the dominant allele often masks the expression of the recessive allele.

Genes and Characteristics

• Genes control our characteristics as they code for proteins.
• Genes act as a unit of inheritance.
• Genes control the morphology and phenotype of individuals.
• Genes control the structure and metabolism of the body.

Alleles

• Alleles are different versions of a particular gene.
• Example: The ABO gene for blood group type has three alleles, I^A, I^B and I^O
• Alleles give all organisms their characteristics.

Genes vs. Alleles

• A gene is an inheritance unit, while the allele is an alternative form of it.
• The gene is responsible for a particular trait, while the alleles are responsible for variations in that particular trait.

Examples

• Gene: eye color, hair color, height, etc.
• Alleles: alternative forms of a gene (e.g., blue eye, black eye, red eye for eye color).
• Eye color is developed from the activity of the OCA2 gene, while various shades of it are developed by different alleles of it.

OCA2 Gene

• The gene that primarily influences eye color in humans is called OCA2 (oculocutaneous albinism II) located on chromosome 15.
• This gene plays a role in producing melanin, the pigment responsible for eye, skin, and hair coloration.
• Multiple genes can contribute to eye color, but OCA2 is one of the major ones influencing this trait.

OCA2 Alleles

• Example: OCA2 gene with different alleles encoding for different eye colors.
  • CGTAAAAGGATCT - Brown shade eye
  • CTTAAAAGGATCT - Green shade eye
  • CCTAAAAGGATCT - Black eye
  • CATAAAAGGATCT - Dark hazel eye

Dominant vs. Recessive Traits

• Dominant Trait: An inherited characteristic that appears in an offspring if it is contributed from a parent through a dominant allele (e.g., freckles, dark hair, dimples).
• Recessive Trait: A trait that is expressed when an organism has two recessive alleles, or forms of a gene.
• A dominant allele only needs to be inherited from one parent in order for the characteristic to show up in the phenotype.
• A recessive allele needs to be inherited from both parents in order for the characteristic to show up in the phenotype.

Beyond Dominance and Recessiveness

• There are more than one dominant allele.
• In the heterozygous condition, both alleles are expressed equally (codominance).
• Example: Camilla flowers.
• Codominance occurs when both alleles in heterozygous organisms contribute to the phenotype.

Incomplete Dominance

• In incomplete dominance, neither allele is completely dominant nor completely recessive.
• Codominant alleles will both be completely expressed.
• The flower will show both red and white.

Genotype vs. Phenotype

• Different combinations of alleles are called genotype.
• The expressed characteristic or outward appearance is called phenotype.
• Example:
  • D = dominant allele; d = recessive allele.
  • Genotype: DD, Phenotype: double eyelid
  • Genotype: Dd, Phenotype: double eyelid
  • Genotype: dd, Phenotype: single eyelid
• Genotype: The genetic information of all organisms on earth.
• Phenotype: The observable physical traits of the organism.
• Genotype of an organism is defined as an actual or complete genetic makeup of an organism. It also refers to the pair of alleles inherited in an individual for a particular gene.

Observable Traits

• Phenotype refers to an individual's observable traits, such as height, eye color and blood type. A person's phenotype is determined by both their genomic makeup (genotype) and environmental factors.

Homozygous vs. Heterozygous

• Homozygous: A cell is said to be homozygous for a particular gene when identical alleles of the gene are present on both homologous chromosomes. The cell or organism in question is called a homozygote.
• Heterozygous: A diploid organism is heterozygous at a gene locus when its cells contain two different alleles (one wild-type allele and one mutant allele) of a gene. The cell or organism is called a heterozygote.

Examples

• Homozygous: Parent 1: Black hair (B), Parent 2: Black hair (B), Offspring: Black hair (BB)
• Heterozygous: Parent 1: Black hair (B), Parent 2: Blonde hair (b), Offspring: Black hair (Bb)

Genotypic and Phenotypic Ratios

• Heterozygous Tall (Tt) x Heterozygous Tall (Tt)
• F2 Generation:
  • TT - homozygous tall
  • Tt - heterozygous tall
  • tt - homozygous dwarf
  • phenotypic ratio = 3:1
  • genotypic ratio = 1:2:1
  • tallness = dominant character

Haploid and Diploid Cells

• Haploid (n): one set of chromosomes (n=23 in humans)
• Diploid (2n): two sets of chromosomes (n=46 in humans)
• Non-Homologous Chromosome
• Pairs of Homologous Chromosome
  Sperm: Haploid, Somatic Cells: Diploid

Chromosome Numbers

• Humans have 46 chromosomes (two sets of 23) in each cell.
• You began your life as a single cell – a zygote – formed by the fusion of an egg cell and a sperm cell.
• The nuclei of each of these gametes contained a single complete set of 23 chromosomes.
• When they fused together, they produced a zygote with 46 chromosomes.
• Haploid = Half the normal number of chromosomes. Remember that the human diploid chromosome number is 46.

Mitosis

• Mitosis is a process where a cell divides resulting in two identical cells.
• Each cell contains the same number of chromosomes and genetic content.
• Mitosis is a type of nuclear division. It produces daughter nuclei which contain the same number of chromosomes as the parent nucleus.
• Mitosis results in two identical daughter cells.
• This type of cell division is used for growth, repair of damaged tissues, replacement of cells and asexual reproduction and is known as mitosis.
• Continuous mitosis results in the increase in the number of cells enabling the organism to grow from a single cell to a complex living organism.
• Different cells in the body like the cells on the skin and red blood cells are continuously replaced by mitosis. About 5 Imes 10^9 cells are formed per day in humans via mitosis.
• Mitosis is also involved in the repair and regeneration of body structures like in the starfish.

Mitosis and Stem Cells

• Many tissues in the human body contain a small number of unspecialized cells called stem cells. Stem cells divide by mitosis and produce new daughter cells that can become specialized within the tissue and be used for different functions.
• The ultimate stem cell is the zygote.
• A zygote divides several times by mitosis to become a ball of unspecialised cells (around 200-300 cells).
• These are embryonic stem cells. They start differentiating as the fetus develops with recognisable features.

Meiosis

• Meiosis is a type of nuclear division that gives rise to cells that are genetically different.
• It is used to produce the gametes (sex cells).
• The number of chromosomes must be halved when the gametes (sex cells) are formed, otherwise there would be double the number of chromosomes after they join at fertilization in the zygote (fertilized egg).
• Meiosis is said to be a reduction division because it produces four daughter cells each with half the number of chromosomes, the haploid number (n).
• Meiosis produces haploid gametes for fertilization.
• Meiosis produces gametes that are genetically different.

Purpose of Meiosis

• Meiosis keeps the number of chromosomes in sexually reproducing organisms constant.
• Meiosis creates genetic variety among species by causing the exchange of genes that occurs when cells cross over. These differences are the building blocks of the evolutionary process.

Mitosis vs. Meiosis

• Mitosis:
  • Start: Diploid (46)
  • End: Diploid (46)
  • Two cells produced (daughter cells)
  • Daughter cells are diploid
  • Daughter cells are genetically identical to each other and to the parent cell
  • One cell division occurs
• Meiosis:
  • Start: Diploid (46)
  • End: Haploid (23)
  • Four cells produced (daughter cells)
  • Daughter cells are haploid
  • Daughter cells are genetically different from each other and the parent cell
  • Two cell divisions occur

You should also know the reasons for a specific type of cell division taking place and the types of cells where each happen.

Inheritance of Traits

• Examples: hair type (straight, wavy or curly), earlobe (attached or detached), skin color (fair, dark, etc.), eyelid (single or double), chin (with or without cleft)

Sex Determination

• Sex is determined by an entire chromosome pair.
• Females have the sex chromosomes XX.
• Males have the sex chromosomes XY.
• As only a father can pass on a Y chromosome, he is responsible for determining the sex of the child.
• He produces (ejaculates) around 250 million sperm cells during sexual intercourse. Of those, half (125 million sperm) will be carrying his X chromosome. If one of these sperm fertilises the egg, the fetus will be female. The other 125 million of his sperm will be carrying his Y chromosome, which will result in a male fetus if one of these fertilises the egg.

Genetic Diagrams (Punnett Squares)

• A genetic diagram, also known as a Punnett square, is a graphical representation used to predict the outcomes of a particular genetic cross between two individuals.
• A Punnett square diagram shows the possible combinations of alleles that could be produced in the offspring.
• Monohybrid inheritance refers to the inheritance of a single gene with two alleles from each parent. It focuses on the study of the transmission of a single trait, such as flower color or seed shape in pea plants studied by Gregor Mendel.
• In monohybrid inheritance, individuals inherit one allele from each parent, resulting in three possible genotype combinations: homozygous dominant, heterozygous, and homozygous recessive.

Examples of Crosses

• Example 1: 100% chance that all the offspring will be tall. (TT x TT)
• Example 2: There is more variation in this cross, with a 3:1 ratio of tall : short, meaning each offspring has a 75% chance of being tall and a 25% chance of being short. (Tt x Tt)
• Example 3: In this cross, there is a 1:1 ratio of tall to short, meaning a 50% chance of the offspring being tall and a 50% chance of the offspring being short. (Tt x tt)

You should always write the dominant allele first, followed by the recessive allele. If you are asked to use your own letters to represent the alleles in a Punnett square, try to choose a letter that is obviously different as a capital than the lower case so the examiner is not left in any doubt as to which is dominant and which is recessive. For example, C and c are not very different from each other, whereas A and a are!

Pedigree Charts

• Family pedigree diagrams are usually used to trace the pattern of inheritance of a specific characteristic (usually a disease) through generations of a family.
• This can be used to work out the probability that someone in the family will inherit the genetic disorder.
• Males are indicated by the square shape and females are represented by circles.
• Affected individuals are red and unaffected are blue.
• Horizontal lines between males and females show that they have produced children (which are shown underneath each couple).

Test Cross

• Breeders can use a test cross to find out the genotype of an organism showing the dominant phenotype. This involves crossing the unknown individual with an individual showing the recessive phenotype - if the individual is showing the recessive phenotype, then its genotype must be homozygous recessive.
• By looking at the ratio of phenotypes in the offspring, we can tell whether the unknown individual is homozygous dominant or heterozygous.

Steps for a Test Cross

1. Select Parent: Choose an individual with the dominant phenotype (unknown genotype) and a homozygous recessive individual (known genotype).
2. Perform Cross: Cross the individual with the dominant phenotype with the homozygous recessive individual.
3. Observe Offspring: Examine the phenotypes of the offspring resulting from the cross.
4. Analyze Results: If all offspring display the dominant phenotype, the individual is likely homozygous dominant. If approximately half display the recessive phenotype, the individual is likely heterozygous.
5. Repeat (if necessary): Repeat the test cross with additional offspring to confirm the genotype of the individual.

Example

• A plant breeder has a tall plant of unknown genotype. How can they find out whether it is homozygous dominant or heterozygous?
• Cross the unknown tall plant with a short plant (homozygous recessive).
• If the tall plant is homozygous dominant, all offspring produced will be tall.
• If the tall plant is heterozygous, half of the offspring will be tall and the other half will be short.

Sex-Linked Characteristics

• Alleles on the same chromosome are said to be linked.
• When alleles that control a particular characteristic are found on the sex chromosomes, we describe the inheritance that results as ‘sex linked’.
• In almost all cases, there are only alleles on the X chromosome as the Y chromosome is much smaller.

Hemizygosity in Males

• Males are indeed more likely to show sex-linked recessive conditions due to their hemizygous nature for the X chromosome.
• Males have only one X chromosome and one Y chromosome (XY), whereas females have two X chromosomes (XX).
• This means that males lack a second copy of the X chromosome to compensate for any defective genes on their single X chromosome.

Expression of Recessive Alleles in Females

• In females, a recessive allele on one X chromosome is often masked by the presence of a dominant allele on the other X chromosome. This phenomenon, known as X chromosome inactivation or Lyonization, results in only one X chromosome being active in each cell of a female's body.

No Masking in Males

• Since males have only one X chromosome, there is no second X chromosome to mask the effects of recessive alleles.
• As a result, if a male inherits a recessive allele for a sex-linked trait from his mother, he will express the phenotype associated with that allele because there is no dominant allele on the Y chromosome to counteract it.

Sex-Linked Conditions

• Because males only have one X chromosome, they are much more likely to show sex-linked recessive conditions (such as red-green colour blindness and haemophilia).
• Females, having two copies of the X chromosome, are likely to inherit one dominant allele that masks the effect of the recessive allele.
• A female with one recessive allele masked in this way is known as a carrier; she doesn’t have the disease, but she has a 50% chance of passing it on to her offspring.
• If that offspring is a male, he will have the disease.

Example: Color-Blindness

• The results of a cross between a normal male and a female who is a carrier for colour-blindness is as follows:
• In the cross above, there is a 25% chance of producing a male who is colourblind, a 25% chance of producing a female carrier, a 25% chance of producing a normal female and a 25% chance of producing a normal male.

Pedigree for Color-Blindness

• Disease never transfers from father to son
• Disease tends to transfer from mother to son and father to daughter

Phenotypes

• Normal vision: 50%
• Carrier of red-green color blindness: 25%
• Red-green color blindness: 25%

Modes of Inheritance

4 Types of Mode for a disease

Genes and Protein Synthesis

• Chromosomes are made of DNA.
• DNA is made up of two long strands of molecules called nucleotides.
• There are four different nucleotides – A, C, T or G.

DNA Base Sequence Determines Amino Acid Sequence

• The DNA code (a series of bases) is converted into proteins (a series of amino acids).
• The process of protein synthesis has two stages:
  • Transcription (rewriting the base code of DNA into bases of RNA).
  • Translation (using RNA base sequence to build amino acids into sequence in a protein).

Sequences of Bases and Amino Acids

• Therefore, the sequence of bases in a gene determines the sequence of amino acids that make a specific protein.
• Different sequences of amino acids give different shapes and functions to protein molecules.

The Central Dogma

• Sequence of bases in DNA controls sequence of amino acids in a protein.
• Shape of the protein controls function of the protein (e.g. enzyme).
• Function of the protein controls metabolic reactions in a cell.
• Metabolic reactions control features of the organism.

Protein Synthesis Location

• DNA is found in the nucleus. Protein synthesis happens on the ribosomes, in the cytoplasm.
• To carry information from the DNA to the ribosome, a messenger molecule called messenger RNA (mRNA) is used.

Protein Synthesis Process

• Proteins are made by ribosomes with the sequence of amino acids controlled by the sequence of bases contained within DNA.
• DNA cannot travel out of the nucleus to the ribosomes (it is far too big to pass through a nuclear pore) so the base code of each gene is transcribed onto an RNA molecule called messenger RNA (mRNA).
• mRNA then moves out of the nucleus and attaches to a ribosome.
• The ribosome ‘reads’ the code on the mRNA in groups of three.
• Each triplet of bases codes for a specific amino acid.
• In this way the ribosome translates the sequence of bases into a sequence of amino acids that make up a protein.
• Once the amino acid chain has been assembled, it is released from the ribosome so it can fold and form the final structure of the protein.

Triplet Code

• The triplet code of DNA (carried by mRNA) is read by the ribosome and amino acids are attached together in a specific sequence to form the protein.

Control of Cell Function

• In this way, DNA controls cell function by controlling the production of proteins.
• The proteins may be enzymes, antibodies, or receptors for neurotransmitters.
• Although all body cells in an organism contain the same genes, many genes in a particular cell are not expressed because the cell only makes the specific proteins it needs.
• Expression of a gene means whether that gene is transcribed and translated in a particular cell or not.

Gene Expression

• Most genes are not expressed in a particular cell.
• They are 'switched off' because that would be a waste of energy and other resources in the cell.
• Only the genes whose proteins are vital to that cell's function are expressed ('switched on').