YouTube Video Review #2-Protein Structure

Review of a video that explains protein structure; on all four levels.

The first protein structure discussed in the video was the primary structure. The primary structure consists of the aminoacid sequence that are joined by peptide bonds. The secondary structure; consists of a alpha helix, which is spiral shaped and held together by hydrogen bonds, between the NH–OC. In the video it was said that there are 3.5aa per turn, however, we learnt that there are 3.6aa amino acids per turn of the helix.  Also, the Beta pleated sheets are linear parallel primary structure, that are hydrogen bonded together, that stabilizes the structure. The tertiary structure was then discussed. It was said that the tertiary structure, consists of interactions between R groups. Interactions found in the tertiary structure; covalent disulphide bridges, hydrophobic side chains, Van Der Waals forces and ionic interactions or the salt bridge. In the video the concepts of domains, which are the basic units of the tertiary structure, that are functioning parts. Also the concept of a chaperon was mentioned, which as simply proteins that facilitate the correct folding of other proteins. These concepts, are not required for us to learn at this level. Finally the Quaternary structure was discussed, which are different poly peptide chains that interact to form the entire protein, e.g. hemoglobin. The Quaternary structure are composed of the same interactions as the tertiary structures.

In summary the video was well laid out and straight to the point. It was explained in a manner that was easy to follow and understand. The video also provided a short review about the structure of proteins.

Exam paper MCQ :)

Single answer MCQ

1. Where are the enzymes needed for glycolysis located in eukaryotic cells?

 

A.            intermembrane space

B.            plasma membrane

C.            cytosol

D.            mitochondrial matrix

E.            cytoplasm

 

Multiple answers MCQ

Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:

A. 1, 2 and 3 are correct

B. 1 and 3 are correct

C. 2 and 4 are correct

D. only 3 is correct

E. all are correct

 

Which of the following is/are non-essential amino acids?

1. Lysine

2. Proline

3. Valine

4. Glycine

 

C’mon don’t be shy; give it a try!

YouTube Video Review #1-Enzyme Inhibtion

While doing enzymes the first time around, everything about enzyme inhibition was quite strange to me, especially those graphs. The second time around Mr.Matthews video made it easy to understand what was going on in each type of inhibition, and I learnt a great amount. I found this video on YouTube that summarizes nicely everything we need to know about enzyme inhibition.

  • The definition of enzyme inhibition was given as; agents that bind covalently to enzymes and disrupt their functions are irreversible inhibitors.
  • There are three main types of inhibitors: Competitive, Non-competitive inhibition and Uncompetitive Inhibition.
  • Competitive inhibitors compete with the substrate for the active site by binding irreversibly with non-covalent bonds at the active site. The substrate is blocked from binding to the active site, forming an enzyme substrate complex. Km increases and V max remains the same. Inhibition is overcome by adding more substrate .
  • Non-competitive inhibition-states that inhibitors bond non covalently to a site other than the active site and changes the conformation of the enzyme. The substrate is not prevented  from binding to the enzyme. In this case the Vmax is lowered and Km remains the same.
  • Uncompetitive inhibition-The inhibitor  binds only to the enzyme substrate complex. Both Vmax and Km decreases.

Each type of inhibition was accompanied by the guy drawing, Line-weaver Burk plots, which he used to explain each type of inhibition and their effects of Vmax and Km. The video was quite good and straight to the point.  The guy had a good explanation that was easy to understand. Though, i felt his illustrations should have been a little bigger, it was still good overall.

The video helped me to reinforce what I learnt about enzyme inhibition and was a good review tool.

 

Carbohydrate Malabsorption.

While learning about carbohydrates, we stumbled upon lactose, a milk sugar. We also learnt that there is a condition associated with the inability of the body to digest this lactose molecule. The condition is known as lactose intolerance or carbohydrate malabsorption in a broader sense.

What is lactose?

Lactose is made from galactose and glucose units:

Lactose or milk sugar occurs in the milk of mammals – 4-6% in cow’s milk and 5-8% in human milk. It is also a by product in the the manufacture of cheese.

Thgalactose and glucosunits are joined by an acetal oxygen bridge in the beta orientation. To recognize galactose look for the upward projection of the -OH on carbon # 4.

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Structure of lactose.

What is lactose intolerance?

Lactose intolerance means the body cannot easily digest lactose, a type of natural sugar found in milk and dairy products.

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What causes lactose intolerance?

Lactose intolerance occurs when the small intestine does not make enough of an enzyme called lactase. Your body needs lactase to break down, or digest, lactose.

Lactose intolerance most commonly runs in families, and symptoms usually develop during the teen or adult years. Most people with this type of lactose intolerance can eat some milk or dairy products without problems.

Sometimes the small intestine stops making lactase after a short-term illness such as the stomach flu or as part of a lifelong disease such as cystic fibrosis. Or the small intestine sometimes stops making lactase after surgery to remove a part of the small intestine. In these cases, the problem can be either permanent or temporary.

In rare cases, newborns are lactose-intolerant. A person born with lactose intolerance cannot eat or drink anything with lactose.

Some premature babies have temporary lactose intolerance because they are not yet able to make lactase. After a baby begins to make lactase, the condition typically goes away.

What are the symptoms of lactose intolerance?

People with lactose intolerance may feel uncomfortable 30 minutes to 2 hours after consuming milk and milk products. Symptoms range from mild to severe, based on the amount of lactose consumed and the amount a person can tolerate.

Common symptoms include

  • abdominal pain
  • abdominal bloating
  • gas
  • diarrhea
  • nausea

How can lactose intolerance be diagnosed?

Lactose intolerance can be hard to diagnose based on symptoms alone. People may think they suffer from lactose intolerance because they have digestive symptoms; however, other conditions such as irritable bowel syndrome can cause similar symptoms. After taking a medical history and performing a physical examination, the doctor may first recommend eliminating all milk and milk products from the person’s diet for a short time to see if the symptoms resolve. Tests may be necessary to provide more information.

Two tests are commonly used to measure the digestion of lactose.

Hydrogen Breath Test. The person drinks a lactose-loaded beverage and then the breath is analyzed at regular intervals to measure the amount of hydrogen. Normally, very little hydrogen is detectable in the breath, but undigested lactose produces high levels of hydrogen. Smoking and some foods and medications may affect the accuracy of the results. People should check with their doctor about foods and medications that may interfere with test results.

Stool Acidity Test. The stool acidity test is used for infants and young children to measure the amount of acid in the stool. Undigested lactose creates lactic acid and other fatty acids that can be detected in a stool sample. Glucose may also be present in the stool as a result of undigested lactose.

Because lactose intolerance is uncommon in infants and children younger than 2, a health professional should take special care in determining the cause of a child’s digestive symptoms.

cow-cartoon

So..what should you do if you’re lactose intolerant?

There is no cure for lactose intolerance. But you can treat your symptoms by limiting or avoiding milk products. Some people use milk with reduced lactose, or they substitute soy milk and soy cheese for milk and milk products. Some people who are lactose-intolerant can eat yogurt without problems, especially yogurt with live cultures. You can also take dietary supplements called lactase products that help digest lactose. In time, most people who have lactose intolerance get to know their bodies well enough to avoid symptoms.

One of the biggest concerns for people who are lactose-intolerant is making sure they get enough of the nutrients found in milk products, especially calcium. Calcium is most important for children, teens, pregnant  women, and women after menopause. There are many nondairy foods that contain calcium, including:

  • Broccoli, okra, kale, collards, and turnip greens.
  • Canned sardines, tuna, and salmon.
  • Calcium-fortified juices and cereals.
  • Calcium-fortified soy products such as soy milk, tofu, and soybeans.
  • Almond

ALTERNATIVES TO LACTOSE-CONTAINING PRODUCTS

These products may be easier to digest for lactose intolerant people:

  • Buttermilk and cheeses (they contain less lactose than milk)
  • Fermented milk products e.g. yogurt etc.
  • Goat’s milk (drink it with meals; make sure it is taken together with essential amino acids and vitamins if it is for children)
  • Ice cream, milkshakes, and aged or hard cheeses
  • Lactose-free milk and milk products
  • Lactase-treated cow’s milk. For example, Lactaid. (for older children and adults)
  • Soy formulas (for infants younger than 2 years)
  • Soy or rice milk (for toddlers)

LactoseIntolerance                                 TolerateMe

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Chitin is Exctin’

While learning about carbohydrates we learnt about “chitin”, which I found to be a very interesting substance.

What is chitin?

Chitin is a long-chain polysaccharide that serves as an armor or cell wall for fungi andarthropods, including all crustaceans and insects. Less famously, it is used for the radula (teeth) of mollusks, and the beak of cephalopods such as squid and octopi. Chitin is a stronger version of keratin, fibrous structural proteins used by reptiles, birds, amphibians and mammals. In some animals such as crustaceans, the shell may be a combination of this substance and keratin. Its molecular formula is (C8H13O5N) n.

Chitin is a polysaccharide found in the outer skeleton of insects, crabs, shrimps, and lobsters and in the internal structures of other invertebrates. Chitin is composed of ß(1-4) linked units of the amino sugar N-acetyl-glucosamine, and is the main source of production of chitosan.

How is chitin formed?

Chemically, chitin is a polysaccharide. A polysaccharide is a polymer — a large molecule consisting of smaller (and in this case, sugar) molecules strung together. Chitin can be processed into many derivatives, the most readily available being chitosan, which is formed when chitin is heated with a chemical solution. Chitosan has some advantages over chitin because it is more water-soluble.

 Chemical Structure of chitin

 Chemical Structure if chitin.

Where is chitin found?

Chitin is found in the central position to the body plan of arthropods. Arthropod exoskeletons are made of this substance. Instead of growing gradually, like most other animals, arthropods grow in quick stages. When an arthropod grows too big for its exoskeleton, it sheds it in a process called molting. It has less than an hour to grow until its new underlying exoskeleton hardens and becomes incapable of growing any further. This molting process may be repeated dozens of times until the animal reaches its maximum size and eventually dies. As arthropods are among the world’s most successful animal groups, with millions of unique species, we can tell that chitin is a quite useful building material for animal bodies.

The exoskeletons of most arthropods are not actually pure chitin, but consist of this material embedded in a hard protein matrix. The difference between modified and unmodified chitin can be seen by observing caterpillars (unmodified) and beetles (modified). The beetle exoskeleton is more durable. In other arthropods, such as some mollusks and crustaceans, the substance is combined with calcium carbonate to create a much stronger  shell.

                                                                                                                              lobster_cartoon2

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What are the applications of chitin?

1. Medical uses-Chitin and Wounds

One of the more important things that chitin, and its products, could be used for is in treating burn patients. Chitin has a remarkable compatibility with living tissue, and has been looked at for its ability to increase the healing of wounds. Chitin itself is the subject of exciting medical experiments. When applied to human wounds and surgical cloths, it accelerates the skin healing process. An acidic mixture of chitin, when applied to burns, also accelerates the healing process. Left on for a few days, it can heal a third-degree bun completely. It has been shown to support the immune system during certain kinds of illness-blocking procedures.

Other medical uses for chitin include anti-bacterial sponges and hospital dressings, artificial blood vessels, contact lenses, tumor inhibition, dental plaque inhibition, and blood cholesterol control. Household products include sponges, diapers, feminine napkins, and tampons.

ChitinSutures

Chitin is used to make medical/surgical thread.

 2. Water Treatment

Water Purification — As a polymer, chitosan’s natural tendency is to form long chains of molecules with positive charges, which act like hooks. These natural hooks catch organic materials, such as oils, detergents, and other contaminants suspended in water. The material then coagulates to form flakes that are easily filtered out. Filtration companies are using chitin in clarifiers to help filter particulates and chemicals from water.

3. Dietary Supplements

 Chitosan has properties similar to plant fiber and can significantly bind fat, acting like a sponge in the digestive tract. It is not digestible itself and the bound fat leaves via the body without ever entering the bloodstream.

 4. Cosmetics

 Make-up powder; nail polish; moisturizers; face, hand, and body creams; and toothpaste are just a few consumer products that might contain chitin.

 5. Agriculture

Seeds treated with chitosan are larger and stronger and more resistant to fungal diseases. Treating seeds with chitin can increase crop yields by up to 50%.Chitin is added to commercial feed mixtures containing whey, a by-product of the cheese industry. Many animals find it hard to digest the high-lactose whey. But chitin supports the growth of beneficial microorganisms in the animals’ digestive tract — these bacteria produce enzymes that help the animals digest whey.

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Endosymbiotic theory.

This theory was unclear to me the when I did the course last year, but after going to the Cells Tutorial I came out with great understanding about what this theory entails. The concept was made quite simple for us to understand during the tutorial.

Who proposed the endosymbiotic theroy?

It was  proposed  by  Lynn  Margulis (University of Massachusetts), this model proposes that small, energy-transducing prokaryotes were either: ingested as prey or internal symbionts inside larger prokaryotes, where they survived and thrived. Eventually, host and symbiont became inextricably linked in a symbiotic relationship.

What is the endosymbiont theory?

The endosymbiotic theory simply postulates that several key organelles of eukaryotes originated as symbioses between separate single-celled organisms

Now what does that mean?

According to this theory, mitochondria and plastids (e.g. chloroplasts)–and possibly other organelles–represent formerly free-living bacteria that were taken inside another cell as an endosymbiont.

Evidence that support this theory:

  1. New mitochondria and plastids are formed only through a process similar to binary fission.
  2. In some algae, such as Euglena, the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell. In such a case, the plastids will not regenerate. This shows that the plastid regeneration relies on an extracellular source, such as from cell division or endosymbiosis.
  3. They are surrounded by two or more membranes, and the innermost of these shows differences in composition from the other membranes of the cell.
  4. Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (both in their size and circular form).
  5. DNA sequence analysis and phylogenetic estimates suggest that nuclear DNA contains genes that probably came from plastids.
  6. These organelles’ ribosomes are like those found in bacteria (70S).
  7. Proteins of organelle origin, like those of bacteria, use N-formylmethionine as the initiating amino acid.
  8. Much of the internal structure and biochemistry of plastids, for instance the presence of thylakoids and particular chlorophylls, is very similar to that ofcyanobacteriaPhylogenetic estimates constructed with bacteria, plastids, and eukaryotic genomes also suggest that plastids are most closely related to cyanobacteria.
  9. Mitochondria have several enzymes and transport systems similar to those of bacteria.
  10. Some proteins encoded in the nucleus are transported to the organelle, and both mitochondria and plastids have small genomes compared to bacteria. This is consistent with an increased dependence on the eukaryotic host after forming an endosymbiosis. Most genes on the organellar genomes have been lost or moved to the nucleus. Most genes needed for mitochondrial and plastid function are located in the nucleus. Many originate from the bacterial endosymbiont.
  11. Plastids are present in very different groups of protists, some of which are closely related to forms lacking plastids. This suggests that if chloroplasts originated de novo, they did so multiple times, in which case their close similarity to each other is difficult to explain.
  12. Many of these protists contain “primary” plastids that have not yet been acquired from other plastid-containing eukaryotes.
  13. Among eukaryotes that acquired their plastids directly from bacteria (known as Archaeplastida), the glaucophyte algae have chloroplasts that strongly resemble cyanobacteria. In particular, they have a peptidoglycan cell wall between the two membranes.

While reading, I also stumbled upon secondary endosymbiosis…

While,primary endosymbiosis involves the engulfment of a bacterium by another free living organism. Secondary endosymbiosis occurs when the product of primary endosymbiosis is itself engulfed and retained by another free living eukaryote. Secondary endosymbiosis has occurred several times and has given rise to extremely diverse groups of algae and other eukaryotes.

Image

The figure above, just gives us a brief look of an overview of endosymbiosis.

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