Unit 4: Building blocks of Life Part 2

Question 1

Describe the experiments that lead to the identification of nucleic acid as the genetic information carrier

Answer 1

19th century: Observations of Mendel and others indicate the genetic material is contained in cells.
1928: Frederick Griffith demonstrated the transmission of genetic instructions by a process we now call the ‘transformation principle’.
1944: Avery, MacLeod and McCarty suggest DNA is the ‘transforming factor’, and not proteins or other materials.
1952: Hershey and Chase proved that DNA was the genetic material in bacteriophage

Question 2

Describe the central dogma of molecular biology

Answer 2

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. it states that information can be transferred from DNA to RNA, from DNA to protein, or from DNA to protein, but not from protein to nucleic acid or protein.

Question 3

Define the structure of a nucleotide as the monomer from which nucleic acids are made

Answer 3

Nucleotides serve as the monomer units for forming the nucleic acid polymers of DNA and RNA. Nucleotides are composed of three subunit molecules: nitrogenous base, five-carbon sugar, at least one phosphate group. A five-carbon sugar molecule attached to a nitrogenous base is called a nucleoside.

Question 4

Describe the structure of DNA and RNA and define the differences between their structures

Answer 4

DNA: replicates and stores genetic information. Consists of two strands, arranged in a double helix, made up of nucleotide subunits. Longer polymers than RNA(E.g. a chromosome is a single DNA molecule, millions of bases). The sugar in DNA is deoxyribose. The bases in DNA are Adenine, Thymine, Guanine, and Cytosine.
RNA: Converts the genetic information contained within DNA to a format used to build proteins. Only has one strand, but like DNA, is made up of nucleotides. Variable in length, but typically quite short(E.g. mRNAs 100’s-1000’s bases). The sugar in RNA is ribose. The bases in RNA are Adenine, Uracil, Guanine and Cytosine.

Question 5

Explain how the functions of DNA emerge from the structure of its monomers and its antiparallel, double helical and three-dimensional strucutre

Answer 5

Structure: Polynucleotide chains have nitrogenous bases linked to a sugar-phosphate backbone. Nucleotides are linked by phosphodiester bonds(C-O-P-O) to form a DNA strand. Phosphodiester bonds of the DNA give the polarity of the DNA strand(5’ phosphate and 3’ hydroxyl end).
Double helix: hydrogen bonds between the bases of the opposite strands and base stacking of bases within a strand contribute to the stability of DNA double helix. Phosphodiester bond of the backbone is also relatively stable. dsDNA can withstand stress like heat and pH.

Question 6

Describe how a DNA molecule is replicated(semi-conservative DNA replication)

Answer 6

The basic principle of replication is base pairing to a template strand. Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication. In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules.
Semi conservative: Parental molecule–> separation of parental strands into templates–> Formation of new strands complementary to template strands. Semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand(‘conserved’ from the parent molecule) and one new strand. Competing models were the conservative model(the two parent strands rejoin after replication), and the dispersive model(each strand is a mix of old and new).

Question 7

Explain how genetic information is provided for protein synthesis and define the genetic code

Answer 7

The information content of genes is in the specific sequences of nucleotides. The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins. DNA must be replicated for cells to divide. Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation.
Genetic code: the means by which DNA and RNA molecules carry genetic information in living cells

Question 8

Describe transcription

Answer 8

RNA is the bridge between genes and the proteins for which they code. Transcription is the synthesis of RNA using information in DNA. Transcription produces mRNA for protein-coding genes. RNA polymerase is the primary enzyme of transcription.
DNA unwinds and RNA polymerase binds the appropriate ribonucleotides. RNA polymerase synthesises mRNA. When RNA polymerase reaches the end of the gene it releases the mRNA and DNA rewinds.
The stretch of DNA that transcribed is called a transcription unit. it includes a promoter, an RNA-coding region, and a terminator. RNA polymerase binds and initiates transcription at the promoter.
Initiation: Various transcription factors mediate the binding of RNA polymerase and the initiation of transcription. The completed assembly of transcription factors and RNA polymerase bound to a promoter is called a transcription initiation complex. A promoter element called a TATA box is crucial in forming the initiation complex in Eukaryotes.
Elongation: As RNA polymerase moves along the DNA, it untwists the double helix, 10-20 bases at a time. Transcription progresses at a rate of 40 nucleotides per second in eukaryotes. A gene can be transcribed simultaneoulsy by several RNA polymerases. Nucleotides are added to the 3’ end of the growing RNA molecule(5’ to 3’).
Termination: The mechanisms of termination are different in bacteria and eukaryotes. In bacteria, the polymerase stops transcription at the end of the terminator sequence and the mRNA can be translated without further modification. In eukaryotes, RNA polymerase transcribes the polyadenylation signal sequence; the RNA transcription is released 10-35 nucleotides past this polyadenylation sequence.

Question 9

Last: Explain the role of mRNA processing in eukaryotic gene expression

Answer 9

Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation.

Question 10

Understand the main stages of meiosis

Answer 10

Meiosis 1: Prophase 1: the chromosomes condense and homologous chromosomes pair up to form tetrads
Meiosis 1: Metaphase 1: the tetrads are all arranged at the metaphase plate.
Meiosis 1: Anaphase 1: the homologous chromosomes separate and are pulled toward opposite poles.
Meiosis 1: Telophase 1: movement of homologous chromosomes continues until there is a haploid set at each pole.
Cytokinesis by the same mechanisms as mitosis usually occurs simultaneously.
Meiosis 2: Prophase 2: a spindle apparatus forms, attaches to kinetochores of each sister chromatids, and moves them around.
Meiosis 2: Metaphase 2: The sister chromatids are arranged at the metaphase plate.
Meiosis 2: Anaphase 2: the centromeres of sister chromatids separate and the now separate sisters travel toward opposite poles.
Meiosis 2: Telophase 2: separated sister chromatids arrive at opposite poles.
Cytokinesis separate the cytoplasm.
At the end of meiosis, there are four haploid daughter cells.

Question 11

Explain the significance of meiosis in life cycles

Answer 11

A life cycle is the generation-to-generation sequence of stages in the reproductive history of an organism. It starts at the conception of an organism until it produces its own offspring.

Question 12

Explain how meiosis and fertilisation can lead to variation through the independent assortment of alleles

Answer 12

In humans, each somatic cell(all cells other than sperm or ovum) has 46 chromosomes, 23 homologous pairs. We inherit one chromosome of each homologous pair from each parent. The 46 chromosomes in a somatic cell can be viewed as two sets of 23, a maternal set and a paternal set. These homologous chromosome pairs carry genes that control the same inherited characters. As an organism develops from a zygote to a sexually mature adult, the zygote’s genes are passed on to all somatic cells by mitosis. Gametes, which develop in the gonads, are not produced by mitosis. If gametes were produced by mitosis, the fusion of gametes would produce offspring with four sets of chromosomes after one generation, eight after a second and so on. Instead, gametes undergo the process of meiosis in which the chromosome number is halved. Human sperm or ova have a haploid set of 23 different chromosomes, one from each homologous pair.

Question 13

Use genetic diagrams to solve problems including sex linkage and codominance

Answer 13

Codominance: two dominant alleles affect the phenotype in separate, distinguishable ways.
Sex-linked genes are located on the sex chromosome
X^B or X^b or Y””

Question 14

Describe the interactions between loci(epistasis)

Answer 14

In epistasis, a gene at one locus alters the phenotypic expression of a gene at a second locus. One gene determines the pigment colour(for example) and the other gene determines whether the pigment will be deposited in the hair(for example).

Question 15

Predict phenotypic ratios in problems involving epistasis

Answer 15

9(Dominant):3(Codominant):4(Recessive).

Question 16

Describe the differences between continuous and discontinuous variation

Answer 16

Continuous: For any species, a characteristic that changes gradually over a range of values shows continuous variation.
Discontinuous: A characteristic of any species with only a limited number of possible values shows discontinuous variation.

Question 17

Explain the basis of continuous and discontinuous variation by reference to the number of genes which influence the variation

Answer 17

Continuous: influenced by multiple genes. These genes have small effects of the phenotype. Traits that exhibit continuous variation, such as height or weight, often result from polygenic inheritance, where many genes have a combined effect.
Discontinuous: takes place only due to genetic factors. It means that the environment has no direct effect on discontinuous variation. At the genetic level, various genes have varying effects on the phenotype. Various alleles at a single gene locus have a huge effect on the phenotype.

Question 18

Describe how both genotype and environment contribute to phenotypic variation

Answer 18

Phenotypic variability results from interactions between genotype and environment and is a major driver of ecological and evolutionary interactions.

Question 19

Explain why variation is essential in selection

Answer 19

Genetic variation is essential for natural selection because natural selection can only increase of decrease frequency of alleles that already exist in the population. Survival of the fittest.

Question 20

Last: Use the Hardy-Weinberg principle to calculate allele frequencies in populations

Answer 20

The frequency of dominant and recessive alleles will remain constant from generation to generation provided certain conditions exist. No selection is taking place and all alleles are equal; no mutation occurring; mating is random; population is large; no migration.
If you have two alleles for a single trait, the frequency of each one must add up to 1: p(dominant)+q(recessive)=1
p^2(homozygous dominant)+2pq(heterozygous)+q^2(homozygous recessive)=1.0.

Question 21

Describe Darwin’s theory of evolution

Answer 21

In 1844, Darwin wrote an essay on natural selection as the mechanism of descent with modification, but did not introduce his theory publicly. Natural selection is a process in which individuals with favorable inherited traits are more likely to survive and reproduce. In June 1858, Darwin received a manuscript from Alfred Russel Wallace, who had developed a theory of natural selection similar to Darwin’s. Darwin quickly finished The Origin of Species and published it the next year.
The unity of life, diversity of life, and the match between organisms and their environment.

Question 22

Explain Darwin’s ideas in the context of Lamarck, Alfred Russel Wallace, Voyage of the Beagle, Lyell, geology and biogeoraphy

Answer 22

Lamarck: hypothesized that species evolve through use and disuse of body parts and the inheritance of acquired characteristics. The mechanisms he proposed are unsupported by evidence. Some doubt about the permanence of species preceded Darwin’s ideas.
Alfred Russel Wallace: naturalist who worked mainly in the Amazon basin. Independently came up with the same ideas as Darwin. Great support of Darwin and they published work together.
Voyage of the Beagle: during his travels on the Beagle, Darwin collected specimens of South American plants and animals. He observed that fossils resembled living species from the same region, and living species resembled other species from nearby regions. He experienced an earthquake in Chile and observed the uplift of rocks.
Lyell: Darwin was influenced by Lyell’s Principles of Geology and thought that the earth was more than 6,000 years old. His interest in geographic distribution of species was kindled by a stop at the Galapagos Islands west of South America. He hypothesized that species from South America had colonized the Galapagos and speciated on the islands.

Question 23

Give examples to explain the principles of natural selection

Answer 23

Individuals with certain heritable traits survive and reproduce at a higher rate than other individuals. Natural selection increases the match between organisms and their environment over time. If an environment changes over time, natural selection may result in adaptation to these new conditions and may give rise to new species.
Note that individuals do not evolve; populations evolve over time. Natural selection can only increase or decrease heritable traits that vary in a population. Adaptations vary with different environments.

Question 24

Explain, with examples, how evolution produces a tree-like relationship between organisms

Answer 24

As lineages evolve and split and modifications are inherited, their evolutionary paths diverge. This produces a branching pattern of evolutionary relationships. By studying inherited species’ characteristics and other historical evidence, we can reconstruct evolutionary relationships and represent them on a ‘family tree’ called a phylogeny.

Question 25

Show how examples from artificial selection can explain natural selection

Answer 25

Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called artificial selection.
Members of a population often vary in their inherited traits. All species can produce more offspring that the environment can support, and many of these offspring fail to survive and reproduce.
Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring that other individuals. This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations.

Question 26

Give examples of natural selection in the timescale of recorded history

Answer 26

Soapberry bugs use their ‘beak’ to feed on seeds within fruits. feeding is most effective when beak length is closely matched to seed depth within the fruit. In southern Florida soapberry bugs feed on the native balloon vine with larger fruit; they have longer beaks. In central Florida they feed on the introduced goldenrain tree with smaller fruit; they have shorter beaks. Correlation between fruit size and beak size has also been observed in Louisiana, Oklahoma and Australia. In all cases, beak size has evolved in populations that feed on introduced plants with fruits that are smaller or larger than the native fruits. These cases are examples of evolution by natural selection. In Florida this evolution in beak size occurred in less than 35 years.

Question 27

Explain how homology was fundamental to Darwin’s development of the theory of evolution

Answer 27

Homology is similarity resulting from common ancestry. Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor.

Question 28

Describe the role of fossils in the development of the theory

Answer 28

Fossils can document important transitions. For example, the transition from land to sea in the ancestors of cetaceans.

Question 29

Last: Introduce Biogeography as an evolutionary discipline

Answer 29

Biogeography: the scientific study of the geographic distribution of species, provides evidence of evolution. Earth’s continents were formerly united in a single large continent called Pangaea, but have since separated by continental drift. An understanding of continent movement and modern distribution of species allows us to predict when and where different groups evolved.

Question 30

Define the term recombinant DNA

Answer 30

Molecules of DNA from two different species that are inserted into a host organism to produce new genetic combinations that are of value to science, medicine, agriculture, and industry.

Question 31

Explain what genetic engineering involves

Answer 31

The alteration of genetic material (outside and/or inside) of an organism to obtain enhanced and desired characteristics in living organisms. Often involves the joining of DNA fragments from different species and subsequently inserting the hybrid ‘recombinant’ DNA into a host cell, often a bacterium, to make copies of it and/or express the genes within it.

Question 32

Describe how recombinant DNA technology works in practice

Answer 32

Agriculture: transgenic plants for drought/disease resistance
Forensic: DNA profiling
Medical: detecting genetic disorders, gene therapy, producing therapeutic agents
Human genome project: genetic mapping, DNA sequencing, genome analysis/comparison
Vaccine production
Research: understanding the function of genes

Question 33

Understand and explain the molecular basis and the use of the polymerase chain reaction

Answer 33

1. Amplify the gene of interest by PCR: Specific DNA fragment amplification by polymerase chain reaction in vitro. PCR is based on the DNA replication process catalysed by DNA polymerase. PCR uses the ability of DNA polymerase to synthesize a new strand of DNA complementary to the offered template strand. A primer is needed because DNA polymerase can add a nucleotide only onto a pre-existing 3’-OH group. DNA polymerase then elongates the primer’s 3’ end by adding more nucleotides to generate an extended region of double stranded DNA
   PCR reaction: Each cycle takes just seconds to a few minutes, so repeated cycles can produce large amounts of a specific DNA sequence in hours. Some details about the nucleotide sequence to be copied must be known in advance to design primers. Exponentially growing population of identical DNA molecules.
   Denaturation: separates the two nucleotide strands of the template DNA molecule.
   Annealing: the primers bind to the single-stranded template DNA
   Extension: nucleotides are added to the primers- in the 5’ to 3’ direction by DNA polymerase: forms a double stranded copy of the target DNA.
   Thermal regulation

Question 34

Define molecular cloning and describe it through an example

Answer 34

In biotechnology, “cloning” refers to processes used to create exact genetic copies of: DNA fragments, Cells, and Organisms. Copied material with the same genetic makeup as the original is called a ‘clone’.
1996: Dolly the sheep, the first mammal to be cloned from adult genetic material was born.
2018: Zhong and Hua, the first monkeys cloned from fetal fibroblasts

Question 35

Discuss the methods and the molecular basis of DNA sequencing

Answer 35

The process of determining the sequence of nucleotides in a piece of DNA. Like PCR, uses the concept of DNA replication. DNA polymerases drive the ‘DNA sequencing-by-synthesis’ technologies.

Question 36

Explain what gene therapy is

Answer 36

Gene therapy is the alteration of an afflicted individual’s genes in order to replace a defective allele with a normal allele. Gene therapy holds great potential for treating disorders traceable to a single defective gene: customized medicine. Vectors are used for delivery of genes into specific types of cells, for example bone marrow. To have long-lasting effect, it should be done in dividing cells that are renewing the cell population in certain tissues or generation the whole body(gametes).