Biology: what is non-competitive inhibition?

Tutoring biology, non-competitive inhibition may be mentioned. The tutor explains it.

In yesterday’s post I explain competitive inhibition.

Non-competitive inhibition is similiar to competitive inhibition in that it hinders enzyme function. The difference is that, with non-competitive inhibition, the inhibitor doesn’t bind to the enzyme’s active site; with competitive inhibition, it does.

A non-competitive inhibitor may be a bulky atom such as a heavy metal, or a bulky molecule. This bulky species will attach itself to the enzyme somewhere other than the active site. However, the enzyme’s function is still impeded by one of two possible ways:

  1. The bulk of the inhibitor, though not occupying the active site, may still make it hard to reach, just as a long vehicle in a parking stall can prevent the use of the stall past it.
  2. The inhibitor may change the chemistry of the enzyme, making it less attractive to its intended substrate.

HTH:)

Source:

Biology 12, module 1. Open School BC, 2007.

Mader, S. Inquiry into Life, 11th ed. Toronto: McGraw-Hill, 2006.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: what is competitive inhibition?

Tutoring biology, you might be asked about competitive inhibition. The tutor explains it.

In my November 25, 2013 post, I explain what an enzyme is. Simply put, an enzyme is a biological catalyst that the body uses to speed up a chemical process. An enzyme is not consumed by the reaction, but works alongside it, so can be reused.

Competitive inhibition reduces the effectiveness of an enzyme, possibly with fatality. Along with some preliminary ideas, here’s how it happens:

  1. The molecule an enzyme works on is called the substrate. The enzyme speeds the transformation of the substrate into what the body needs.
  2. The substrate, normally, binds to the enzyme at what’s called the enzyme’s active site in order for the enzyme to work on it.
  3. Therefore, let’s imagine that enzyme E works on substrate S to make necessary molecule M.
  4. Once S transforms to M, enzyme E is released; E is not attracted to M.
  5. Competitive inhibition starts with the arrival of a different substrate, ¬S, that is
    • attractive to enzyme E at the active site
    • not transformable to the necessary molecule M
    • will not become M, so will not release E (or not very quickly, anyway)
  6. The result is that E becomes busy with ¬S, so its active site is inaccessible to S.
  7. Without access to the active site of E, S can’t transform into M.
  8. The body needs M; without it, health consequences, possibly even death, will manifest.

Such is the mechanism of competitive inhibition. Some poisons are competitive inhibitors.

Source:

Biology 12 Module 1. Open School BC, 2007.

Mader, Sylvia. Inquiry into Life, 11th ed. Toronto: McGraw Hill, 2006.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: glycolysis: the first step in producing energy from glucose

The tutor gives a few facts about glycolysis.

Glycolysis happens in the cytoplasm of the cell. It takes a glucose molecule (C6H12O6) and reacts it to two pyruvic acid (C3H4O3) molecules. The process involves inputs and outputs of water and other species, which is why the equation doesn’t balance:

C6H12O6 → 2C3H4O3 + 2ATP

The mechanism is actually quite complex; its important concept for high school biology is the equation above.

Interestingly, glycolysis requires an investment of two ATP (energy units), but yields four; hence, the net gain is two ATP.

Putting the process in perspective, the full reaction of glucose to produce CO2 and H2O yields 36 to 38 ATP.

Glycolysis is the beginning of fermentation.

Source:

www.brynmawr.edu

Mader, Sylvia S. Inquiry into Life, 9th ed. Toronto: McGraw-Hill, 2000.

newworldencyclopedia.org

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: winter survival

The tutor shares a fact that surprises him.

Winter here is fairly mild; I think the mean daily temp in Jan might be around 5 deg Celsius, with the mean nightly low being around -1 deg Celsius. That being said, this place is a rarity in Canada; even places further south than here, but east of the Rockies, are typically much colder. For places both east of the Rockies, and north of here as well, winter might as well be spent in a deep-freeze. How do the animals living there cope with it?

Recent reading informs me that some amphibians – e.g., frogs – actually freeze solid during winter as a survival mechanism. The wood frog and chorus frog are two examples given.

I’ve spent time around Prince George and know that, in May, the temp can reach 15 deg Celsius during the day but still plunge to -5 deg Celsius at night. In spite of the hard nightly freeze, flies abound in forest clearings. They must, I’ve always suspected, freeze at night, yet thaw the next day and live on. This Biology text confirms my suspicion. However, I wouldn’t have known for sure that frogs could do so as well.

To me, the point is surprising, yet makes a lot of sense. After all: how could those frogs avoid freezing solid through weeks in Jan or Feb, during which the temperature may not climb above -5 deg C, and certainly plunges below -20 deg C most nights?

Source:

Ritter, Bob et al. Nelson Biology. Scarborough: Nelson Canada, 1996.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: oxygen and carbon dioxide transfer through the blood

Tutoring biology 12, you cover the circulatory system.  The tutor mentions a specific issue about it.

The number one reason for the circulatory system is transport of oxygen to the cells and carbon dioxide away from them.  This is done via the blood, which is water-based.  The immediate problem might be that gases don’t necessarily dissolve very well in water.

Red blood cells contain hemoglobin (which is why they are red).  Hemoglobin attracts and holds oxygen very effectively, enabling the red blood cells to carry the oxygen through the circulatory system to the capillaries.  There, the oxygen is dropped off to the cells.

Carbon dioxide can be carried by red blood cells (as carbaminohemoglobin), but not very effectively.  In the blood, most carbon dioxide combines with water to form carbonic acid (H2CO3), next breaking into hydrogen ion H+ and bicarbonate ion HCO3. Ions travel easily in water. At the lungs, the hydrogen ion and bicarbonate ion recombine into carbonic acid, which then separates into carbon dioxide and water. The carbon dioxide is exhaled.

HTH:)

Source:

Mader, Sylvia S. Inquiry into Life, 11th edition. New York: McGraw-Hill, 2006.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: monomers and polymers

Tutoring Biology 12, you cover this concept.  The tutor approaches it from a simple, practical point of view.

You normally hear about monomers and polymers in organic chemistry.  Think of the name polyester:  it’s a polymer of esters.  The esters, then, are the monomers.

A commonly used analogy is a necklace of beads.  The entire necklace, altogether, is the polymer.  The beads are the monomers.  They don’t have to be the same as each other, but are similar.

So, a polymer is a molecule consisting of many monomers bonded together. The monomers found in a polymer are of the same chemical family, if they’re not the same.

Let’s accept the idea that the biological molecules fall into four basic categories: carbohydrates, lipids (aka fats and oils), proteins, and nucleic acids.  Three of these can easily be imagined as polymers, with their monomers shown below:

Polymer Monomer
carbohydrate (incl. starch, sugar, or glycogen) simple sugar, aka, monosaccharide; eg, glucose
nucleic acid (DNA, RNA) nucleotide
protein amino acid

So, you might say that “protein is to amino acid as carbohydrate is to monosaccharide.” Or, “DNA is to nucleotide as necklace is to bead.” However you imagine it, familiarity with the concept – as well as the specific cases – is important for biology and organic chemistry students.

While lipids are made from smaller units, the units are not all from the same chemical family. Hence, lipids don’t easily fit the “polymer” idea the way that carbohydrates, proteins, or nucleic acids do. However, I’ll talk more about lipids in a future post.

Good luck to all my students in this weekend’s biology conference:)

Source:

Mader, Sylvia S. Inquiry into Life, 11th Ed. New York: McGraw-Hill, 2006.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: diffusion

When you tutor biology, molecular movement and transport are topics you need to explain.  Front and centre is diffusion.

Diffusion is the tendency of particles to move from an area of high concentration to lower concentration.  It happens spontaneously, meaning it does not require an output of energy.

Moving from high concentration to lower concentration can be referred to as following the concentration gradient.  Therefore, diffusion follows the concentration gradient. The gradient can be thought of as a “slope” that the molecules “roll down” to get to lower concentration.

In everyday life, diffusion is everywhere.  Consider, for instance, a pleasant walk on a calm, dark night.  You smell steaks barbecuing.  You look around, but can’t seem them. Yet, the airborne aromatic molecules have reached you from the barbecue.  That movement of the molecules from the cooking steaks to your nose is an example of diffusion.  Note that it happens by itself; it’s spontaneous.

The human body relies on diffusion for some means of transport.  For instance, at the cell membrane, oxygen passes in and carbon dioxide leaves by diffusion.  It’s perfect: since the cell is constantly using oxygen, its concentration is always low inside.  The concentration of oxygen in the surrounding blood is much higher.  Therefore, oxygen constantly diffuses into the cell.  Carbon dioxide, on the other hand, is constantly being produced in the cell, but is much lower in the blood.  Therefore, it diffuses out of the cell into the blood, whence it is carried away.

The cell can depend on diffusion for gas exchange for two reasons:

1)  The cell membrane is permeable to oxygen and carbon dioxide.

2)  Diffusion happens fast enough, at the cellular level, to be effective.

Permeable means that it can be passed through.  The cell membrane is permeable to oxygen and carbon dioxide, allowing them to diffuse in and out.  The cell membrane is not permeable to many molecules and/or ions, however.  For briefing on that issue, check my post here about the cell membrane.

The reason that diffusion happens fast enough, at the cellular level, for effective gas exchange is that the cell is very small. Therefore, it has high efficiency. See my post here about cell efficiency.

Diffusion is only one method of transport in the body. It is spontaneous, but depends on permeability and efficiency. It is sufficient, for example, for gas exchange between the cells and the blood. However, there are many other contexts in which diffusion is not sufficient. Therefore, I’ll be discussing other transportation methods in future posts:)

Source: Mader, Sylvia S. Inquiry into Life, 11th edition. New York: McGraw-Hill, 2006.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Biology: Three kinds of respiration

Tutoring Biology 12, you cover the cardiovascular system.  The biology tutor discusses the gas exchange aspect.

People commonly associate respiration with breathing.  However, from a biology point of view, the meanings are different.  Breathing is the physical process of bringing fresh air into the lungs and then pushing out “used” air.  Respiration means gas exchange.

There are three kinds of respiration:  external, internal, and cellular.

External respiration is the one everyone thinks of:  in the lungs, the blood drops off its carbon dioxide and picks up oxygen.

Internal respiration happens in the tissues.  Blood drops off its oxygen to the tissue fluid (whence it reaches the cells), while collecting the carbon dioxide that the cells are constantly producing.

Cellular respiration happens inside the cell, in the mitochondria.  It is the chemical process of burning glucose with oxygen to produce energy, carbon dioxide, and water. (The carbon dioxide produced by cellular respiration is, of course, what you breathe out when you’re running:))

Each of these aspects of respiration needs more discussion, but this is a good starting point.  Drop in again for more about them:)

Source:  Mader, Sylvia S.  Inquiry into Life, 11th edition.  New York:  McGraw-Hill, 2006

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Urine Regulation: Aldosterone

Tutoring Biology 12, you realize that with most organ systems, the hormonal control is the most difficult to retain.  The Biology tutor continues about urine regulation with this discussion of aldosterone.

Of course, urine is produced by the kidneys.  If you missed it, you can read how a kidney works in my post here.

In my previous post I talked about ADH and how the body uses it to regulate urine volume. There is another hormone – called aldosterone – that the body uses to control how much water is reclaimed from the filtrate. (Recall that the filtrate is the mix of water, ions, and small molecules first removed from the blood by the kidneys.)

Aldosterone is released by the adrenal cortex. However, the adrenal cortex needs to be informed to do so by the presence of renin in the blood. Renin is secreted by the cells of the juxtaglomerular apparatus, which are adjacent to the glomerulus and sense the blood pressure within. Specifically, when the cells of the juxtaglomerular apparatus sense that the blood pressure is too low, they respond by secreting renin into the bloodstream.

The renin circulates through the body to the adrenal cortex. Detecting the renin, the adrenal cortex responds by secreting aldosterone.

Aldosterone targets the cells of the distal convoluted tubule, telling them to let go of more K+ (K+ means potassium ions), but reclaim more Na+ (sodium ions) in compensation. The effect is that more water is reabsorbed from the filtrate, increasing blood volume and decreasing urine volume.

Unlike ADH, aldosterone does not result in blood dilution, since more ions are reclaimed alongside the extra water that is reabsorbed. Someone might ask, “If aldosterone increases the reclamation of sodium ions, how does that mean increased water reabsorption?” The answer is that sodium ions have a powerful pull on water – more powerful than potassium ions. So if you reabsorb sodium ions instead of potassium ions, more water will be drawn back into the blood as well.

Ultimately, the kidneys release renin – which leads to the release of aldosterone – in order to defend their own function.  If blood pressure is too low, the kidneys cannot filter the blood properly.  By increasing water reabsorption and therefore blood volume, aldosterone helps maintain the necessary blood pressure for proper filtration.

Source: Biology 12, Module 4: Human Biology 2. Open School BC, 2007.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.

Urine regulation: ADH

Tutoring biology 12, you cover kidney function.  The biology tutor introduces ADH, which is a hormone used to regulate urine volume.

For explanation of how a kidney works, see my post here.

Today, we focus on the fine tuning of urine volume. The hypothalamus monitors the concentration of the blood. It may decide, for instance, that the blood risks dehydration. How can the hypothalamus respond to help prevent dehydration?

The hypothalamus has the option of ordering the posterior pituitary to release ADH (anti diuretic hormone). ADH acts on the cells of the distal convoluted tubule and the collecting duct, causing them to be more permeable to water. The result is that more water will be reabsorbed back into the blood. Subsequently, blood volume will stay higher, while urine volume will decrease.

Let’s imagine the other situation: the person has just drunk lots of water to flush themselves out. In such a case, the hypothalamus will detect the surplus of water in the blood, so won’t order the secretion of ADH. The cells of the distal convoluted tubule and collecting duct will allow less water to be recollected, so more will be left in the urine. Urine volume will increase, while blood volume will decrease.

At night, the hypothalamus may order the secretion of ADH to keep urine acculumation low during sleep. The benefit: the person will not have to get up as often to urinate – or maybe not at all until morning.

Another hormone – aldosterone – can also be used to influence urine volume. It will be discussed in a future post:)

Source: Biology 12, Module 4, Open School BC, 2007.

Jack of Oracle Tutoring by Jack and Diane, Campbell River, BC.