3.2 & 7.5 Proteins

15/10/2012 § Leave a comment

I’d just like everyone to know that I found another publishing mistake in the textbook – and this one’s a formatting error! Okay, that is all.

Proteins and their functions

There are two categories by which proteins differ – fibrous or globular. Fibrous proteins are elongated, narrow, tough, and more importantly, insoluble in water. Globular proteins are compact, rounded and more importantly soluble in water. As mentioned a while ago in a previous blog, proteins have numerous functions and some more include: food storage (like casein in milk), pigmentation (like opsin in the retina of our eyes), toxins (like snake venom!), hormones (e.g. insulin), and enzymatic activity.

Fibrous examples of proteins include collagen and myosin.

  • collagen‘s main functions are structural, which explains why plenty of collagen can be found in bone, tendons, and skin. Collagen fibers in the spaces between the tissue cells help strengthen the structure.
  • myosin‘s main function is movement, along with another protein called actin, and causes muscle fibers to contract in order for animals to move.

Globular examples of proteins include hemoglobin (notice the -globin in the name “hemoglobin”) and immunoglobulin (ditto).

  • hemoglobin is used for transport, and can bind to oxygen in the lungs and transport that oxygen to where it’s needed (like respiring tissues)
  • immunoglobulin is used for defense; they are antibodies, which are proteins that identify and neutralize foreign objects like bacteria and viruses.

Amino acids and the deal on polarity

Amino acids can be separated into two groups depending on the characteristics of their R-group. Polar amino acids have hydrophilic R-groups and non-polar amino acids have hydrophobic R-groups. The polarity of the amino acids determines its function and position on a protein.

  • polar amino acids: surface amino acids make the protein soluble in water; can create channels where other hydrophilic (water-lovin’) substances can pass through (this is called a protein channel, guys, sound familiar?); the polar amino acids of integral and transmembrane proteins to protrude from the membranes
  • non-polar amino acids: stabilizes structure from centre of the protein; (in lipase) determines specificity of an enzyme in an active site; helps keep integral and transmembrane proteins inside membranes

Bonding

Polypeptides have chains of repeating sequences of bonded carbon and nitrogen atoms. The nitrogen atom always has a carbon atom attached to it while every second carbon atom has oxygen attached to it. These bonds determine the shape of the polypeptide and can create a α-helix and β-pleated sheet structures. Hydrogen bonds and non-polar covalent bonds aren’t the only bonds going on between amino acids, though. There are obviously more, including hydrophobic interactions, disulfide bridges, ionic bonds, etc.

Proteins and their structure

Proteins are complex in that they have four levels of their structure.

  1. Primary structure: the number and sequence of amino acids in a polypeptide; seeing as there are infinite numbers of possible amino acid sequences, this basic structure varies greatly
  2. Secondary structure: regular repeating structures (α-helices and β-pleated sheets) stabilized by hydrogen bonds between groups of in the main chain of the polypeptide; some parts of the polypeptide form secondary structures while others do not
  3. Tertiary structure: the three-dimensional conformation of a polypeptide; when the polypeptide folds up after translation; stabilized by intramolecular bonds (listed above)
  4. Quaternary structure: the linking of two or more polypeptides to form a single protein; some proteins have a non-polypeptide structure called a prosthetic group – these are conjugated proteins; two or more polypeptides link to each other (e.g. insulin has two polypeptides, hemoglobin has four, etc.)

 

Essay Questions

  1. Outline the thermal, cohesive, and solvent properties of water. (5 marks)
  2. Describe the significance of water to living organisms. (6 marks)
  3. Describe the use of carbohydrates and lipids for energy storage in animals. (5 marks)
  4. List three functions of lipids. (3 marks)
  5. Describe the significance of polar and non-polar amino acids. (5 marks)
  6. Outline the role of condensation and hydrolysis in the relationship between amino acids and dipeptides. (4 marks)
  7. Describe the structure of proteins. (9 marks)
  8. List four functions of proteins, giving an example of each. (4 marks)
  9. Distinguish between fibrous and globular proteins with reference to one example of each protein type. (6 marks)
  10. option i – Lactase is widely used in food processing. Explain three reasons for converting lactose to glucose and galactose during food processing (3 marks)
    option ii – Simple laboratory experiments show that when the enzyme lactase is mixed with lactose, the initial rate of reaction is highest at 48°C. In food processing, lactase is used at a much lower temperature, often at 5°C. Suggest reasons for using lactase at relatively low temperatures. (2 marks)
  11. Outline how enzymes catalyze reactions. (7 marks)
  12. Explain the effect of pH on enzyme activity. (3 marks)
  13. Compare the induced fit model of enzyme activity with the lock and key model. (4 marks)
  14. Draw graphs to show the effect of enzymes on the activation energy of chemical reactions. (5 marks)
  15. Explain, using one named example, the effect of a competitive inhibitor on enzyme activity. (6 marks)

 

DATA BASED QUESTIONS

Page 57 chapter 4 questions

1. Distinguish between the following pairs of words.

  • a) protein and polypeptide – a polypeptide is made up of linked amino acids, a protein is made up of linked polypeptides
  • b) fat and oil – both triglycerides but are fats if solid at room temp., and oils if liquid at room temp.
  • c) starch and glycogen- starch found in plants, glycogen in humans/animals
  • d) condensation and hydrolysis – condensation loses water, hydrolysis uses water
  • e) hydrophobic and hydrophilic – hydrophobic things are water-fearing, hydrophilic things are water-lovin’

2. Write a word equation for each of the following.

  • a) hydrolysis of maltose: maltose + H2O = glucose + glucose 
  • b) the condensation reaction that forms a triglyceride: (glycerol * 3) + (H2O *3) + (fatty acids * 3) = triglyceride
  • c) hydrolysis of starch to remove a single molecule: (starch made up of n monomers) + H2O = (starch made up of n – 1 monomer) + monomer

3. Explain the importance of the transparency of water to life.

The transparency of water is important to life firstly because many aquatic organisms (plants) need it to do photosynthesis for their food. Following this need for food, without the ability to do photosynthesis, the aquatic organisms will die off, leaving no food for their predators, or the animals that need to eat them to survive. Also, water needs to be transparent for aquatic organisms to see underwater in order to identify their prey.

4. Hemoglobin is a protein composed of two pairs of globin subunits. During the process of development from conception through to 6 months after birth, human hemoglobin changes in composition. Adult hemoglobin consists of two alpha- and two beta-globin subunits. Four other polypeptides are found during development: zeta, delta, epsilon and gamma.

  • a) State which two subunits are present in highest amounts early in gestation. —> epsilon-globin and zeta-globin
  • b) Compare changes in the amount of the gamma-globin gene with beta-globin. —> While gamma-globin shows up in the first weeks of gestation, beta-globin shows up only after the tenth week. By then (10 weeks), gamma-globin is at 50% while beta-globin is at the very bottom (0%). At 44 weeks of gestation, gamma- and beta-globin intersect taboo 23%. After that, beta-globin continues to increase while gamma-globin continues to decrease. 
  • c) Determine the composition of the hemoglobin at 10 weeks of gestation and at 6 months of age. —> At 10 weeks of age, the hemoglobin is made up of 49% alpha-globin and 48% gamma-globin. At 6 months of age, the hemoglobin is composed of 50% alpha-globin, 46% beta-globin, and 4% delta-globin. 
  • d) State the source of oxygen for the fetus. —> The fetus’s source of oxygen alpha-globin.
  • e) The different types of hemoglobin have different affinities for oxygen. Suggest reasons for the changes in hemoglobin type during development and after birth. —> During birth, the fetus doesn’t require as much oxygen. Of course it requires oxygen, just not as much as the baby will when it’s born. Once out and cut off from it’s mother’s supply of food, the baby might (might?) need more food and oxygen supply because it’s no longer being looked after and provided for by its mother’s womb. Based on this, we can assume that the types of hemoglobin after birth are the types that have a higher affinity for oxygen. 

5.

  • a) State one type of secondary structure of a protein. —> α-helices
  • b) Outline the differences between globular and fibrous proteins, giving a named example of each. —> Globular proteins, like hemoglobin (notice the -globin), are compact and rounded and are soluble in water. Fibrous proteins, like collagen, are long and narrow and are insoluble in water.
  • c) Explain the significance of polar amino acids for membrane proteins. —> Polar amino acids are responsible for determining the function and position of a protein in a membrane. A polar amino acid on the surface of a membrane, for example, may tell an integral protein to jut out of the membrane a little bit.
  • d) Distinguish between a secondary and tertiary structure using examples. While secondary structures like α-helices and β-pleated sheets are the interactions between the different groups in the polypeptide (specifically the amino group, the acid group, and the lone hydrogen atom), tertiary structures are the interactions between the R group, the variable group. The bonds between the R group include hydrophobic interactions, disulfide bridges, ionic bonds, etc. 

6. The protein content of harvested wheat grain depends on the water content in the soil at the time of sowing. In an experiment carried out in semi-arid soil in Queensland, Australia, over several years, researchers measured the protein obtained from wheat sown in different soil conditions.

  • a) Outline the relationship between water content at planting time and protein content. —> Generally, the relationship between the water content at sowing time (x-axis) and protein content (y-axis) is that the less the amount of water at planting time, the more grain protein %. As the content of water increases, the grain protein % decreases. We see that between 150 – 200 mm of water (towards the very right of the graph), the % of grain protein is at its lowest, below 10%. 
  • b) Suggest why this relationship exists. —> Perhaps past a certain amount of water (mm), the optimum level of water is surpassed. Also, the grain protein, instead of remaining in the water, will have gone into the plants or into the soil.

7. Lipase is a digestive enzyme that accelerates the breakdown of triglycerides in the small intestine. In the laboratory the rate of activity of lipase can be detected by a decline in pH. Explain what causes the pH to decline.

The decline of pH is caused by the presence of the fatty acids (three!) that originally came from the triglycerides. pH is affected by these fatty acids.

 

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