The difference between chromatin, chromatid and chromosome

By chia | April 5, 2010

It’s easy to confuse these 3 terms! Let’s try to clear things up here.

DNA, the blueprint of life, is organized into structures called chromosomes. In prokaryotic cells, chromosomes are circular, whereas in eukaryotic cells, they are linear strands. Different organisms have different numbers of chromosomes: human cells usually have 46 chromosomes, dogs have 78 chromosomes, while kangaroos have only 12 chromosomes!

This karyotype of a human male cell shows the 46 chromosomes.

When you add all these chromosomes up, each cell actually contains about 2m of DNA! And all this DNA has to fit into a tiny nucleus of 5-10um in diameter. This is like trying to stuff a piece of string 2km long (it will take you about 20 minutes to walk from one end to the other) into a tiny bead smaller than 1cm!!! To do this seemingly impossible feat, cells devised an ingenious packaging system: it wraps DNA around proteins called histones. The resulting DNA-protein complex is called chromatin.

At the beginning of cell division (S-phase), the DNA is replicated, producing two identical copies of DNA, which are connected to each other at the centromere. This replicated X-like structure is now called a sister chromatid pair. A chromatid is therefore just one of the strands.

During mitosis, the sister chromatid pair condenses further, giving rise to the fat X chromosomes that you can see in the karyotype above. Therefore, chromosomes can be found in 3 forms: thread-like chromatin (during interphase), thread-like sister chromatids (during S-phase) and the condense, visible form (during mitosis).

When a cell divides, the sister chromatids separate, and each daughter cell receives one of the strands. The chromatid then decondenses back into a long single chromatin strand when the new cell goes into interphase.

For more information about DNA, check out this Scitable entry: DNA Is a Structure That Encodes Biological Information

Photosynthesis Lab: What to Expect

By chia | September 29, 2009

As mentioned earlier, the rate of photosynthesis should increase when you give the plant more light, more carbon dioxide and the optimum temperature. However, at high light and high carbon dioxide, photosynthesis will reach its maximum rate and won’t go any higher.

For more details, check this page on photosynthesis: http://click4biology.info/c4b/3/Chem3.8.htm
(I will eventually get around to writing more about photosynthesis on this website).

Other Important Points

Here are some extra notes about photosynthesis that could come in handy when discussing your results and writing your conclusion and evaluation sections.

  • Plants carry out respiration (the opposite of photosynthesis!) the entire time to make energy, and so they constantly USE oxygen and MAKE carbon dioxide (which lowers the pH). At low photosynthesis rates (e.g. in the dark), they are respiring but not photosynthesizing. You will only start to see bubbles or pH changes when the rate of photosynthesis is higher than the rate of respiration.
  • Having different number of leaves or mass of the plant cutting will affect your results. More leaves mean more photosynthesis! Also, they should all be healthy cuttings.
  • Remember to take your measurements only after a few minutes of exposing your plant to light so that it will be photosynthesizing at a constant rate. Similarly, be careful not to expose all your plant cuttings to light while running an experiment on one of them!
  • If you are using a pH probe, it needs to be properly calibrated before starting your experiments. If you are not able to do this, just remember that it might be a source of error…

Try to make a list of all the things you will need to run the experiment. Think about what you need to keep constant. You should also have a control experiment where photosynthesis won’t happen (no source of light or carbon dioxide, or a dead plant, for example).

Photosynthesis Lab: What to Measure?

By chia | September 29, 2009

What to Measure?

Now, how would you measure the rate of photosynthesis?

Again, let’s look at the equation for photosynthesis:

CO2 + H2O + light –> O2 + glucose

There are 2 things we can quickly measure in this experiment (the dependent variables): amount of oxygen produced, or, amount of carbon dioxide used.

If the rate of photosynthesis increases, the rate of oxygen production goes up, and the rate of CO2 consumption rises too! If the rate of photosynthesis goes down, then we can expect the opposite effect: oxygen production drops and carbon dioxide is not used as quickly.

But how can we measure oxygen or carbon dioxide levels?

It’s quite easy with Elodea!

Measuring Oxygen

In water, oxygen that is produced by the Elodea cutting is released as bubbles from its leaves. The rate of oxygen produced can be measured by either counting the number of bubbles released in a certain amount of time (bubbles/min), or by trapping the oxygen gas in an inverted syringe or tube and measuring the volume of oxygen produced in a certain amount of time (cm3/min).

It’s important that you give the plant a few minutes to photosynthesize before starting your measurements. This ensures that the plant is making oxygen at a constant rate. (You should also check this visually, before starting to count the bubbles). To have more accurate results, take the measurement at least 3 times. You could also vary the amount of time used to count the bubbles (10 seconds, 30 seconds, 1 minute). Then calculate the number of bubbles per minute or per second.

Measuring Carbon Dioxide

To measure carbon dioxide levels, we can measure the pH of the water. This is because when carbon dioxide dissolves in water, it forms carbonic acid and lowers the water pH. Therefore, in the opposite situation — i.e. when carbon dioxide is used — the pH goes up.

CO2 + H2O –> H2CO3 <–> H+ + HCO3-

pH probe by Sergei Golyshev (http://www.flickr.com/photos/29225114@N08/)

pH probe by Sergei Golyshev (http://www.flickr.com/photos/29225114@N08/)

As the changes in pH are probably quite small, it would be necessary to use a pH meter (or pH probe) with a digital readout. pH paper may not be sensitive enough to detect the changes. Measure the pH once before starting the experiment. Then, start taking pH measurements after the plant is consistently producing oxygen bubbles. Take a few measurements at 5 minute intervals (for example, you can run the experiment for 15 minutes and that would give you 3 readings).

Remember to rinse the pH probe with distilled water before transferring it to your test tube. You should also make sure that the test tube water is well-mixed before taking your measurement, by stirring with a glass rod, or inverting the tube a few times (make sure you use a rubber stopper so you don’t spill it all!).

Another important note: make sure you use really clean test tubes, plants and stoppers! Any contaminants could affect your pH reading. Rinse everything with tap water before you start your experiment!

Photosynthesis Lab: Set Up

By chia | September 29, 2009
Elodea by Kristian Peters (http://www.flickr.com/photos/fabelfroh/)

Photo of Elodea plant by Kristian Peters (http://www.flickr.com/photos/fabelfroh/)

A commonly-used plant for such experiments is the Elodea, an aquatic (underwater) plant also referred to as pondweed. You can buy this at aquarium stores.

The set up depends on which question you would like to study.

In general, the plant is placed in a test tube filled with diluted sodium bicarbonate solution (1%). Sodium bicarbonate (baking soda) gives the plant a source of carbon dioxide so that they photosynthesize more quickly.

You need to provide the plant with a fixed light source (a light bulb, for example). You could place a large beaker (around 2 liters) filled with water between the light source and the test tube so that the light heats up only the beaker water and not the plant!

For your experiment, you should change only ONE variable, never more than that (if you can help it!).

Light Intensity

Take the case of investigating the effects of light intensity on photosynthesis rates. To change this, you can either use different wattage light bulbs, add screens between the light bulb and the plant, or change the distance of the light bulb from the plant. If you want to be really accurate, get a light meter and measure the light intensities that the plant is receiving with the different settings.

from The Biology Web (http://faculty.clintoncc.suny.edu/faculty/michael.gregory/)

from The Biology Web (http://faculty.clintoncc.suny.edu/faculty/michael.gregory/)

Carbon Dioxide

To change carbon dioxide levels, just change the concentration of sodium bicarbonate in the solution (e.g. 0.5%, 1%, 1.5%, 2%).

Temperature

To change the temperature, you could warm the plant/test tube gently using a water bath method, i.e. place the test tube containing the plant in another large beaker which is filled with cool or warm water of known temperature. Place a thermometer in the test tube so that you know when the set temperature has been reached, and to make sure that it doesn’t change too much during the experiment.

Photosynthesis Lab

By chia | September 29, 2009

Here are some ideas for planning experiments for studying plant photosynthesis.

Remember that the simple equation for photosynthesis is:

CO2 + H2O + light –> O2 + glucose

Elodea by Kristian Peters (http://www.flickr.com/photos/fabelfroh/)

Photo of Elodea plant by Kristian Peters (http://www.flickr.com/photos/fabelfroh/)

There are many questions you can ask about photosynthesis, such as:

  • Does light intensity affect the rate of photosynthesis?
  • Does temperature affect the rate?
  • What about levels of carbon dioxide made available to the plant?

For your experiment, you can change what you provide the plant with (the independent variable) and see how this affects their ability to photosynthesize.

Read more about setting up your experiment, what variables you can measure, and what you should expect and look out for.

Hope the explanations here will help you write and plan your next lab report!

Feel free to send me more comments, suggestions and feedback!

Mitosis

By chia | September 29, 2009

Mitosis is a highly dynamic and controlled process in the cell cycle, during which DNA and components (organelles) of a cell are accurately divided into 2 identical daughter cells.

We can describe mitosis as consisting of 4 phases: prophase, metaphase, anaphase and telophase.

Quite a number of things happen during prophase.

  1. Chromatin (thread-like DNA) is supercoiled and condensed into chromosomes.
  2. The nuclear envelope breaks down, allowing the chromosomes to fill the entire cell space.
  3. The two centrosomes (or microtubule organizing centers, MTOCs) move apart to opposite ends of the cell.
  4. Microtubules from the centrosomes form mitotic spindles that can attach to the chromosomes to move them.
PROPHASE

PROPHASE

The chromosomes are then moved by the mitotic spindle until they are all lined up in the middle of the cell, forming what is known as a metaphase plate. This stage of mitosis is called metaphase.

METAPHASE

METAPHASE

Once all the chromosomes are “captured” by microtubules, the cell can proceed to anaphase. The mitotic spindles shorten, splitting the chromosome into two chromatids, and pulling each one to opposite ends of the cells.

If chromosomes are not segregated accurately, the resulting daughter cells will have errors and could become cancerous. To make sure that cells divide correctly, there are some internal checkpoints that stop the cell from continuing in the cell cycle if prior conditions are not met. For example, anaphase cannot take place until all chromosomes are attached to microtubules.

ANAPHASE

ANAPHASE

At the end of mitosis (telophase) we have two identical sets of DNA at the poles of the cell. This DNA starts to decondense back to the thread-like chromatin structure. A nuclear envelope reassembles around each set, forming 2 nuclei.

TELOPHASE

TELOPHASE

After mitosis has completed, the cell then divides into 2 daughter cells, a stage known as cytokinesis. Read more about this final stage of the cell cycle.

Animations make it really easy to understand the different phases of mitosis. Here’s a really good one!

* All images here were modified from Molecular Biology of the Cell, 4th edition, Garland Science

Cytokinesis

By chia | September 29, 2009

Cytokinesis is the final stage in the cell cycle. The cytoplasm of the dividing cell is separated in two. The way this happens is different for animal and plant cells.

In animal cells, the cell forms a contractile ring in the middle of the dividing cell. As the ring contracts, it creates a cleavage furrow, which eventually pinches the cell in two.

In plant cells, vesicles migrate to the middle of the cell and fuse to form a cell plate (which eventually becomes the plasma membrane). A cell wall then develops between the two cells.

Once cytokinesis is complete, cells once again return to interphase.

Interphase

By chia | September 28, 2009

Dividing cells spend most of their time (around 90%) in interphase. However, they are not just resting, but preparing for the next division.

The first part of interphase, the G1 phase (Gap 1), is the period during which cells are growing, synthesizing proteins and making more organelles. Cells need to double their organelles and size before dividing, otherwise they will get smaller after each division!

Cells then duplicate their DNA in S phase (Synthesis). This takes around 10-12 hours in human cells. Finally, it goes into a further growth phase, the G2 phase, before entering mitosis.

During interphase, the centrosome (or microtubule organizing center, MTOC) is also duplicated.

Here is an image of a cell in interphase. You can see its nucleus clearly, which contains chromatin (DNA in thread-like form, in blue).

A cell in interphase. DNA (blue) is contained within the nucleus, and microtubules (green) are not organized. From Molecular Biology of the Cell, 4th ed, by Alberts et al.

A cell in interphase. DNA (blue) is contained within the nuclues, and microtubules (green) are not organized. From Molecular Biology of the Cell, 4th ed, by Alberts et al.

Continue reading about mitosis to see the structural changes that occur in the cell as it divides.

Cell Division

By chia | September 28, 2009

Cell Theory states that cells come from pre-existing cells. What does this mean? Our body is made up of billions of cells, and all of them originate from only TWO basic cells – the sperm and egg. To get from 2 cells to a billion, these 2 cells divide many many MANY times. A lot of our cells (especially stem cells) continue to divide during our lives, for example, to replace dying cells or repair injured tissue.

Sometimes cells go a little hay-wire and start to divide uncontrollably. This can occur in any organ or tissue, and the result is a cancerous tumour. To learn more about cancer, click here.

To duplicate, cells go through a cell cycle which is divided into a number of stages: interphase, mitosis and cytokinesis.

For more information on each section, please click and read the individual topics :)

Lab Tests for Gases

By chia | September 28, 2009

Test for oxygen :

Gas collected is able to relight a glowing splint (light a wooden splint, blow it out and then insert it quickly into the gas chamber)

Test for carbon dioxide :

  1. Bubbling carbon dioxide through lime water (calcium hydroxide) makes it cloudy due to solid precipitates of calcium carbonate.
    Ca(OH)2 (aq) + CO2 (g) –> CaCO3 (s) + H2O (aq)
  2. Putting a lit splint into the gas collection chamber will put out the fire, as CO2 does not support combustion.
  3. Dissolved carbon dioxide lowers the pH of a solution. Carbon dioxide reacts with water to form carbonic acid.
    CO2 (g) + H2O (aq) <==> H2CO3 (aq)

Test for nitrogen :

Nitrogen is extremely neutral and there does not change the color of moist litmus or indicator paper, neither does it have color or smell. It is also non-combustible and will put out a lit splint.

Test for hydrogen:

Burns with a ‘pop’ sound – which is actually a small explosion as hydrogen is extremely flammable!

Test for chlorine gas :

  1. It is green-yellow in color, and smells pungent.
  2. It turns moist litmus/universal indicator paper red, then white.
  3. Since it is not combustible, it puts out a lit splint just like carbon dioxide.

To absorb carbon dioxide :

Place a strong alkaline/base in solid form (pellets, flakes) such as sodium hydroxide (NaOH), potassium hydroxide (KOH) or lithium hydroxide (LiOH) to absorb carbon dioxide.