10.1 Meiosis

31/01/2013 § Leave a comment

Meet Gregor Mendel, the father of genetics.

He was perhaps the first scientist that experimented with the factors of organisms that could be passed on from generation to generation. Mendel worked with pea plants and when he crossed a variety with one trait and a variety of the opposite trait (i.e. wrinkled vs smooth), he found that all of the offspring would have the same trait as one of the parents. For example, all the peas in the F1 generation (the first generation) would be smooth. When Mendel let the first generation fertilize and pollenate itself, he found that the F2 generation showed both traits from the original parents, so both smooth and wrinkled peas were shown. The traits are controlled by the different forms of a gene called the alleles.

Some vocabulary:

  • homozygous, as implied in its name, are identical alleles in a gene; all gametes of a homozygote have the same allele
  • heterozygous, quite the opposite of homozygous, are two different alleles in a gene; where half of the gametes of a heterozygote have one allele and the other half has the other allele
  • dominant (alleles) are expressed when present in a heterozygote or a homozygote (so whether there is one dominant allele or two dominant alleles present)
  • recessive (alleles) are expressed only in homozygotes (where there are two of the alleles present)
  • genotype is all the alleles an organism possesses
  • phenotype the characteristics of an organism
  • segregation occurs in F1, when two alleles separate
  • Punnett grid is what is used to show all possible outcomes after a cross (named after the scientist, Punnett, who first used the grid)

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4.2/10.1 Meiosis

30/01/2013 § 2 Comments

This second blog of the unit will cover an overview of meiosis, its purposes, outcome, and different phases, as well as karyotypes and karyotyping.

There are three key things to know about meiosis:

  1. It involves two divisions, so one cell, or one nucleus, will end up becoming four cells (see image below!).
  2. The number of chromosomes is halved and so goes from a diploid state to a haploid state.
  3. The purpose of meiosis is to generate a massive amount of genetic variety in crossing-over and in the random orientation of bivalents.

Recall that a nucleus with two copies, or a pair of chromosomes is diploid while a nucleus with only one chromosome is haploid. In meiosis, the nucleus goes from diploid to haploid. Meiosis is also known as reduction division because it reduces the chromosomes from diploid to haploid. The chromosomes (each consisting of two identical chromatid) are replicated during interphase. The homologous chromosomes – homologous meaning chromosomes that are of the same type – partner up at the beginning of meiosis I. They then exchange genetic material by crossing over. By mitosis, the cell divides and results in two new haploid daughter cells. The cell divides again in meiosis II to produce a total of four haploid daughter cells.  « Read the rest of this entry »

4.1 Genes, Chromosomes, Mutations

27/01/2013 § Leave a comment

Welcome to the seventh unit of Year One! This blog will be a bit of an introduction to the next three units, in my opinion, which includes Meiosis (Unit 7), Genetics (Unit 8), and Reproduction (Unit 9!!).

Meiosis is centered on genetics, which is the study of variation and inheritance, and the basic unit of inheritance is the gene, which is a heritable factor that controls a specific characteristic. The normal nucleus in any organism contains thousands of genes – the exact number is and has mostly always been unknown. The collective whole of the genetic information in an organism is the genome.

Chromosomes have the same genes as one another and are arranged in the same sequence but not entirely in terms of the alleles in the genes. Alleles are different forms of a gene, seeing as genes are made of DNA (remember the four – or five – bases that make up DNA and RNA molecules? Yep, those).

Now, during mitosis or meiosis, which are both processes of division, the DNA in nuclei are replicated – we know this. The two strands on the chromosome (called chromatids) are connected by a centromere, which can be found either in the middle of the chromosome or towards the end.

Alright, sorry about that “boring” stuff (that’s a joke, genetics and reproduction are my favorite part of biology) but the slightly more interesting part comes in now: genetic mutation. When genes are passed from parent to offspring, it’s better if they don’t change and stay the same, maintaining the parents’ qualities and passing them on to the offspring (Natural selection! Evolution! Daaaarrwiiiinnn!). A male parent’s gamete and a female parent’s gamete (gametes are haploid, which means the nucleus has only one set of chromosomes, therefore one chromosome of each type – think of it like half of a full chromosome) to form a zygote, which is diploid, wherein the nucleus has two sets f the chromosome, so there are two chromosomes of each type.

But moving on – when the base sequence of a gene is changed, that is a gene mutation. The smallest change is when only one base changes (called a base substitution), but that change can make an entire difference. My 8th grade science teacher told us that it’s the difference between typing D-U-C-K on an English report and accidentally making a typo, i.e. replacing “D” with another letter very close to it on the keyboard. There are thousands of genetic diseases caused by genetic mutations, that have been discovered in humans, and the most commonly used example is sickle cell anemia.

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8.2c Photosynthesis; Limiting factors

15/01/2013 § 1 Comment

This next, and final blog, will focus on the limiting factors on the rate of photosynthesis, among other things. Say hello to the last biology blog post of the semester! (Only… three more semesters to go.)

Action spectra and absorption spectra

Well, basically an action spectra is a visual representation (a.k.a. a graph) that shows the rate of photosynthesis at each wavelength of light. In contrast, an absorption spectra shows the percentage of light absorbed at each wavelength by a pigment or a group of pigments. The difference is that photosynthesis only occurs where chlorophyll (or other photosynthetic pigments) can absorb light.

Quantum of light, or photons is the unit of light energy. The energy carried by photons is what excites electrons, which we now know is called photoactivation, and raises the electron to a higher level of energy. Once it is at this state, only then can it be absorbed (and pass through the transport chain). Different chlorophyll absorb in the red and blue parts of the spectrum but have slightly different properties. Other pigments, called accessory pigments absorb the rest of the wavelengths and transfer that energy to chlorophyll.

The concept of limiting factors

The three factors that affect the rate of photosynthesis are light intensity, carbon dioxide concentration, and temperature. We know this. We know how they affect the rate of photosynthesis. We know that they all have optimal levels of photosynthesis. But we didn’t know that if one of these factors were at a point lower than its optimal point of photosynthesis, it would then hinder the rate of photosynthesis and limit the organism. The factor that does this and is at the minimum point is therefore the limiting factor. Photosynthesis is determined by the rate of the current reaction taking the most time. That is the rate-limiting step, and all of the three limiting factors affect different rate-limiting steps.

  • light intensity: usually not the limiting factor because intensity is determined by the time of day (day/night), low intensities is when it could be the limiting factor, high intensities is when other factors are limiting
  • CO2 concentration: high concentrations are when other factors are limiting – because CO2 concentration in our atmosphere is low, CO2 is usually the limiting factor
  • temperature: low temperatures won’t let the enzymes work as fast as they can, intermediate temperatures are when other factors are limiting, high temperatures are pushing it – some enzymes denature

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all caught up now. (Chapter 10 Q & A)

14/01/2013 § Leave a comment

#5. 25 marks.

a) Explain the differences between monopolistic competition and oligopoly as market structures.

The main differences to point out between a monopolistic competitive market structure and an oligopoly are the number of firms, the concentration of market power for those firms, and the barriers of entry and exit. While monopolistic competitive markets are markets with many firms producing differentiated products, oligopolies are markets with a select few firms dominating that market for identical or differentiated goods. If we recall perhaps the scale of the concentration ratio (which measures the market power of the firm), perfect competition and monopoly are at the ends of the scale – they are the very end of the spectrum. Monopolistic competition is closer to perfect competition and oligopolies are closer to monopolies. In this sense, monopolistic competitions try to be more competitive with more firms striving to be more efficient and more like a perfect competitive market, but oligopolies are closer to being a monopoly and would rather try and be the number one firm in the market with all the power. In terms of power and since we’re on the topic of the concentration ratio, oligopolies have more market power than monopolistic competitive markets, in general. Finally, while monopolistic competitive markets have no barriers to enter or exit the market, oligopolies do, and their barriers are quite similar to a monopoly’s barriers (which adds in again to the statement that an oligopoly aims to be more of a monopoly), like high initial fixed costs and access to resources.


b) Discuss the differences between a collusive and a non-collusive oligopoly.

The biggest difference between a collusive and a non-collusive oligopoly is whether or not the firms in the market are helping each other or learning from other firms and then reacting from that. The number of firms and amount of market power each firm has in an oligopoly is just enough so that they competition is tight and all of the competitors watch each other’s moves. Oligopolies are interdependent and unlike other markets, like a perfect competitive market, the firms’ actions in an oligopoly can indeed affect the market.

That being said: a collusive oligopoly is one where firms work together with the biggest aim to maximize profits for the entire industry. There are formal collusions, where the agreements are explicit and firms come to a consensus of the plan of attack, per se. They may all choose to avoid advertising or refrain from producing to bring the prices up, resulting in an increase in total revenue. The other type of collusion is informal, or a tacit, wherein one dominant firm makes all the moves and establishes their price leadership. This firm usually has lots of market power (or else establishing the price wouldn’t really work out for them). Smaller firms follow lead and set considerably close prices but they don’t dare to cut down too much or threaten the price of the leader because that would be economic suicide. These smaller firms know that the dominant leader would be the only one who would survive moving prices down.

So those are collusive oligopolies. Non-collusive oligopolies are quite different in that the firms don’t work together. What did I say earlier? The biggest difference is whether or not the firms help each other (one way or another, explicitly or implicitly) or learn from studying their competitors behavior and then react from there. Price wars can occur with oligopolies and – as we know – this means that the demand curve is kinked, the upper half is more elastic, and the lower half is more inelastic. This means that firms can’t raise their price or else no one will follow and they would murder themselves. It also means that firms can’t lower their price or a price war would occur and everyone’s revenue would diminish. This is why oligopolies tend to focus on methods of non-price competition (ways to maximize profits via service, design, quality, brand power, etc.) and forces them to strive to maintain stable prices.

8.2b Photosynthesis Light-Independent Reactions

12/01/2013 § 1 Comment

Hi, still doing HL stuff. Today’s blog has to do with the reactions involved in the Calvin cycle!

Carbon fixation and carbohydrate synthesis

All organisms carry out their photosynthesis with carbon dioxide. For plants, and organisms that do photosynthesis, the conversion of carbon dioxide into another carbon compound occur in the stroma of the chloroplast, the fluid surrounding the thylakoids (think of a cytoplasm in a cell, that’s what I do). The product of this reaction is glycerate 3-phosphate, a 3-carbon compound. What happens is that carbon dioxide reacts with the five-carbon compound ribulose biphosphate (abbreviated to RuBP) to produce two molecules of glycerate 3-phosphate. As with all reactions, this carbon fixation reaction is done by an enzyme called ribose biphosphate carboxylase, which is clearly a mouthful, so we abbreviate it to rubisco. There is a large amount of rubisco in the stroma of the chloroplast in order to maximize this reaction.

Next, to produce carbohydrates, hydrogen is added to glycerate 3-phosphate via a reduction reaction (reduction is gain of electrons or hydrogen!). In this reaction, ATP and NADPH provide energy and hydrogen atoms (respectively) to the glycerate 3-carboxylase to create two molecules of triose phosphate, another 3-carbon compound.

Regeneration of RuBP

The products of the carbon fixation reactions and the reduction reactions in the first part of the Calvin cycle can be used to create carbohydrates such as starch and hexose phosphates. Eventually, the supply of RuBP (the original molecule) would be used up, therefore it would have to be regenerated through its own product. Five triose phosphates (the products of the first two reactions) react with three ATP molecules (which then changes back to ADP and an independent phosphate molecule) to produce three ribulose biphosphate molecules, which are five-carbon molecules. (What I’m trying to say is that the original fifteen carbon molecules with the five triose phosphate molecules – 5 x 3 carbons – at the beginning of regeneration are conserved at the end of generation, when there are three ribose biphosphate molecules as a product – 3 x 5 carbons.)

This means that three RuBP molecules are used at the beginning of the Calvin cycle to make six triose phosphates. But five of these triose phosphates are needed to regenerate the original three RuBP molecules, so that leaves one triose phosphate to convert into a sugar molecule. Furthermore, this means that the Calvin cycle needs to turn six times to produce one yield of sugar, like glucose.

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8.2a Photosynthesis Light Reactions

09/01/2013 § Leave a comment

Today I flipped to the pages of this reading assignment and was met with the uncannily familiar sight of the HL ribbon streaking down the lefthand side of page 109. Phase two has begun.

Light Absorption and Photosystems

The substances chlorophyll and accessory pigments are parts of groups of hundreds of molecules called photosystems, which are located in the thylakoids of chloroplasts. Photosystems are what harvest and absorb light for photosynthesis and there are two types of these “light harvesting arrays”: photosystems I and II. Both photosystems contain hundreds of stacks of chlorophyll (called grana), which absorbs energy from sunlight and raises its electron to a higher energy level. This makes the electron an excited electron, and makes that chlorophyll photoactivated. When electrons are excited anywhere in the photosystem, they are passed among the molecules until a special chlorophyll gets its hands on it at the reaction centre. This particular chlorophyll donates the electron to an electron acceptor, or a chain of electron carriers.

Photolysis and Byproducts of Photosynthesis

We know that oxygen is one of the byproducts of photosynthesis. It’s how we (humans) breathe. The production of oxygen occurs during photolysis, which is the splitting of water molecules in the light. In the thylakoid space, an enzyme at the reaction center splits water molecules and the electrons are given to chlorophyll. The oxygen and H+ ions (protons!) are the result of this process. The oxygen acts as waste and the protons add to the chemiosmotic (remember that from last unit?) concentration gradient in the membrane.

Photophosphorylation and ATP Production

Photophosphorylation is the non-cyclic process that produces ATP using the energy from excited electrons retrieved from Photosystem II, where light-dependent reactions begin. Thylakoids are in charge of this process with the following structures:

  • photosystem II
  • a chain of electron carriers (electron acceptors!)
  • ATP synthase
  • photosystem I

Electrons are carried throughout the chain of electron carriers and the energy released pumps protons across the thylakoid membrane. The diffusion of protons down their concentration gradient releases energy that ATP synthase uses to make ATP from ADP and inorganic phosphate – just like in respiration.

Completing Light-Dependent Reactions

Photosystem I is in charge of these last reactions in which NADPH is produced. The chlorophyll in photosystem I absorb light energy that raises electrons to a higher energy level, which is also photoactivation. A protein called ferredoxin are reduced with these electrons, and two molecules of reduced ferredoxin are used to reduce NADP+ (the oxidized form) to NADPH + H+. Photosystems I and II are linked and electrons are passed from photosystem II to photosystem I. The electrons are used to reduce NADP+ , and later, when NADP+ runs out (this will be explained later, I promise) electrons return to Photosystem II along the chain of electron carriers. The proton pumping the results allows for ATP production. This is called cyclic photophosphorylation.

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