Category Archives: DNA

Week 3: Structure and function of nucleic acids and proteins

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Learning Intention: To understand nucleic acids as information molecules that encode instructions for the synthesis of proteins in cells and the processes of transcription and translation in cells. Students will also understand protein functional diversity and the nature of the proteome as well as the functional importance of the four hierarchal levels of protein structure. They will perform experiments that demonstrate the effect of temperature and pH on enzymes.

  • Catalase is an enzyme found in liver extract that breaks down hydrogen peroxide (H2O2) into water and oxygen.
  • Hydrogen peroxide is a toxic product of digestion that needs to be eliminated from the body. Water and oxygen are the safe products of hydrogen peroxide breakdown.
  • Primary structure of protein – order of amino acids
  • Secondary structure – alpha helix, beta pleated sheets or random coils
  • Tertiary structure – folding of the polypeptide chain due to disulphide bridges and other attractions or repulsions between molecules.
  • Quarternary structure – two or more polypeptide chains folded together to form a complex protein.

Week 4: Molecular Biology in Medical Diagnosis

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This week we will study how molecular biology can be used for a range of applications in medicine, including diagnosis of deficiency conditions before and after birth, rational drug design and the production of hormones and plant vaccines. We will also consider some of the ethical concerns that may be associated with the application of molecular biology. First, we will review the process of DNA transcription and translation, as the first stage in the genetic process that results inherited diseases being expressed in an individual.

Welcome Back – Term 3!

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Year 12 students will be counting down the next 14 weeks until their VCE Biology exam on the morning of Friday 30th October. We will start this term with a review of the structure of DNA, using the GTAC resources, “Exploring the structure of DNA“.

On Wednesday 22nd July we will be heading to the University of Melbourne Genetics Department to complete three practical activities that will contribute to your school-based assessment:

  1. An investigation using a DNA tool and a manipulation technique
  2. An investigation of inheritance in Drosophila melanogaster including a review of meiosis in gamete formation
  3. Meiosis in Drosophila

On Friday 4th September you will have the opportunity to travel to Brauer College and participate in GTAC outreach program, “From Hominoids to Hominins”.

On Tuesday 13th October you will be able to attend a “Get into Genes” program as revision prior to your exam.

Cupcake mitosis

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Students in Year 11 Biology are learning the phases of mitosis, so we baked and decorated these cupcakes. Students now have a good understanding of what happens inside the nucleus during:

  • Interphase
  • Prophase
  • Metaphase
  • Anaphase
  • Telophase and
  • Cytokinesis.

Watch the Cells Alive Interactive and describe where in each cycle are the three checkpoints that allow DNA replication and mitosis to continue. Why is it incorrect to suggest that the cell is “resting” during interphase, between mitotic cycles?

Population genetics

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Population genetics is the study of distributions and changes in allele frequency in a population, as the population is subject to the four main evolutionary processes:

  • Natural selection
  • Genetic Drift
  • Mutation
  • Gene flow (by migration or distribution of pollen and seeds)

Variation between individuals and species and polymorphism: In any normal population there is some variation between individuals – a box of apples may have individual apples that are slightly different sizes and shapes with slightly different colour variations, even when they come from the same tree. So, not all variation is caused by genetic differences. It may be environmental differences that result in the variation – for example, the amount of light, temperature or soil nutrients in the case of plants or the nutrition and experiences provided to animals. Some characteristics , such as height or wing length might show continuous variation, while other characteristics can be clearly separated into different categories (discontinuous variation). An example of discontinuous variation in humans might be the ability to roll one’s tongue – you can either do this or you can’t – there is no blending, or in-between characteristic. Polymorphism occurs when two or more clearly defined phenotypes are present in the population. A classic example is the light and dark coloured morphs of the peppered moth. The ABO blood grouping is an example in human populations.

Inherited variationsFrom our Unit 3, Area of Study 2 work, we understand that the DNA molecule, present in every cell of living organisms, codes for proteins that determine the phenotype of an organism. DNA is passed from one generation to the next through reproduction, which can occur asexually or sexually (with the production of gametes (meiosis) and fusion of sperm and egg). So, families of individuals tend to look more alike than non-related individuals due to these inherited characteristics. This was seen in our work with pedigree trees, showing how genetic diseases can be passed on through several generations.

Mutations – sources of variation: The source of these variations is genetic mutations – check pages 371-372 and 477-478 in your textbook “Nature of Biology”. Genetic mutations may be spontaneous or may be induced by exposure to mutagenic agents (X-rays and Gamma rays and some chemicals, such as benzene and mustard gas).

Gene pool, gene flow, genetic drift (by chance): The gene pool is the set of all genetic information in a population, while gene flow describes how genes leave and arrive in a population by death and emigration or births and immigration. Genetic drift is the change of gene frequencies due to random sampling.

Polygenes, polygenetic traits: Polygenes are non-allelic genes that together influence a phenotypic trait – often the precise loci of these genes is unknown to biologists. Examples of polygenetic traits in humans are height, weight and skin colour.

Mitochodrial DNA: Mitochondrial DNA is a single, circular strand of DNA found in the mitochondria of eukaryotic cells. In most species, mitochondrial DNA is inherited solely form the mother. In humans, mitochondrial DNA was the first significant part of the human genome to be sequenced.

Founder and bottleneck effects:The founder effect is the lost of genetic variation that occurs when a new population is established by a small group of individuals from a larger population. The people of Easter Island and Pitcairn Island show limited genetic variability (small gene pools) due to this effect. A similar effect is the bottleneck effect, when large numbers of a population are removed, leaving a small gene pool.  As a species, cheetahs have famously low levels of genetic variation. In fact, cheetahs are so closely related to each other that transplanted skin grafts do not evoke an immune response. This can probably be attributed to a population bottleneck they experienced around 10,000 years ago, barely avoiding extinction at the end of the last ice age. However, the situation has worsened in modern times. Habitat encroachment and poaching have further reduce cheetah numbers, consequently snuffing out even more genetic variation and leaving cheetahs even more vulnerable to extinction.

 

 

Recombinant DNA technologies

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On Monday we had the opportunity to connect with the Gene Technology Access Centre via the video conferencing equipment, Polycom. Nicole and Frazer facilitated a great session about recombinant DNA technology, including a demonstration of gel electrophoresis to determine if genes had been successfully inserted into a plasmid.

Did you know that humans have the same gene sequences as other organisms?

  • 61% similarity to fruit flies
  • 99% similarity to mice
  • 99.9% similarity to chimpanzees

The human genome has 22 pairs of autosomes and 1 pair of sex chromosomes (XX in females and XY in males). Chromosomes exisit in the nucleus (as single strands) and there is also some (maternal – passed down from the mother) DNA in the mitochondria, which is circular. Prokatyotes (bacteria) also have circular DNA called ‘plasmids’.

Sea jellies have a gene that codes for a protein that is luminescent, called a “green fluorescent protein”. This gene is a useful marker, to determine if other genes have been successfully introduced to an organism.

Restriction enzymes (used for ‘cutting’ DNA) are used to open the plasmid, the new gene is inserted and then a DNA ligase is used to stick the ends together. We are using four different restriction enzymes (EcoRY13; BamH1; Nhe1 and Sma1). The DNA sequence at a restriction site is a palindrome – reads the same forwards and backwards. Some restriction enzymes cause ‘sticky’ ends (uneven or with a tail – exposed base pairs) while others cause ‘blunt’ ends (no overhanging base pairs). Once the new gene is inserted, complementary base pairs are joined by hydrogen bonds – or ‘pasted together’ with DNA ligase.

This is the process we will model using the paper cut-outs:

  1. E.coli is a bacteria that can be resistant to various antibiotics (eg. Amp R = ampicillin resistant).
  2. Cut the plasmid using a restriction enzyme.
  3. Insert the gene of interest into the plasmid, stick it together and produce the recombinant plasmid, which should contain the ampicillin resistance gene as well as the “GFP” (green fluorescent protein) gene.
  4. To test if the recombination has been successful, we need to use the restriction enzymes to produce various lengths of DNA. These are then pipetted into ‘wells’ in the gel. Because DNA is a negatively charged molecule, we load the wells at the negative end and attach the positive wire to the other end, so that the pieces of DNA a drawn through the gel matrix to the other side. The longest pieces move more slowly and travel the shortest distance, while the shortest molecules move most quickly through the gel and travel the greatest distance.