Biology Hwk - Proteins

1. Explain the four levels of protein structure, indicating the significance of each level. The primary structure is the basic order of amino acids in the polypeptide protein chain, before any folding or bonding between amino acids has occurred. Proteins are usually not functional on the primary level, and all proteins have a primary structure.

The secondary structure is the repeated, regular structure protein chains take due to hydrogen bonding between amino acids. The secondary structure is usually in the form of an alpha helix (similar to a DNA chromosome) or a beta- pleated sheet (similar in form to the corrugations of cardboard). Alpha helix is due to hydrogen bonding within one polypeptide chain:

While the beta pleated sheet is due to hydrogen bonding between separate polypeptide chains:

The third structure is the tertiary structure. It is the complex, three-dimensional protein shape resulting from the folding of the polypeptide due to different types of bonds between the amino acids. These bonds include hydrogen bonds, disulphide linkages and electrovalent bonds. A disulphide linkage is where one of the amino acids, cysteine, contains sulfur. Two of these can have a bond between their sulfur atoms which results in a disulphide linkage which leads to a folding in the chain. An electrovalent bond is between the negative and positive molecules or amino acid groups along the chain.

The quaternary structure is the most complicated form of a protein. It encompasses the primary, secondary and tertiary, and then adds another level: the quaternary is one or more peptide chains bonded together. This is the functional form of many proteins, but again, just as not all proteins have secondary or tertiary structure, not all proteins have a quaternary structure. For a common example of a quaternary-structured protein, see hemoglobin.

2. Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type, where they are used and how their structure is related to their function. Fibrous proteins are in their secondary structure, which could be in the alpha helix or beta pleated forms. They are made of a repeated sequence of amino acids that can be coiled tightly around in a pattern that makes it a very strong structure. Two examples are keratin (in hair and skin) and collagen (in tendons, cartilage, and bones).

Globular proteins are in their tertiary or quaternary structure, which is folded, creating a globular, three-dimensional shape. Two examples are all enzymes and microtubules (form centrioles, cilia, flagella, and cytoskeleton).

3. Explain the significance of polar and non-polar amino acids. How do they affect bonding and structure of the protein? Non-polar amino acids have non-polar (neutrally charged) R groups. Polar amino acids have R chains with polar groups (charged either positive or negative). Proteins with a lot of polar amino acids make the proteins hydrophyllic and therefore able to dissolve in water. Proteins with many non-polar amino acids are more hydrophobic and are less soluble in water. With these abilities, proteins fold themselves so that the hydrophilic ones are on the inner side and allow hydrophilic molecules and ions to pass in and out of the cells through the channels they form. These channels are vital passages for many substances in and out of the cell.

4. State four functions of proteins, giving a named example of each. Transportation. An example is hemoglobin, which transports oxygen around the body within a blood cell.

Enzymes and catalyse reaction. Some examples are trypsin and amylase.

Hormones. An example is insulin, a hormone secreted by the pancreas which is used to regulate blood sugar levels.

Contraction of muscles. An example is actin and myosin which are involved in the contraction of muscles.

Heat makes molecules in proteins to vibrate. The bonds linking the amino acids in chains are strong covalent bonds that withstand the heat. However, most of the bonds that stabilises the three-dimensional structure of proteins are hydrogen bond, which is weak; hence, when heated, these hydrogen bonds will break, allowing the proteins to unravel. When two unraveled proteins make contact, they form new bonds with each other. A large net of interconnected proteins forms and the proteins harden to its new shape.

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7. Give an example to explain how correlation does not indicate or prove causation. Very infants develop the symptoms of autism shortly after the normal time in childhood when the MMR inoculation is administered. Some parents of these autistic children came to blame the vaccination for the child’s condition. This confusion lasted for several years and the numbers of children received vaccination felt to dangerously low levels. Fortunately, detailed studies then was able to convince the majority of parents that MMR inoculation and the onset of autism were not causally linked. Therefore, even if we have applied statistical tests that indicate the possibility of a correlation, we cannot then assert that one event is the cause of the other.

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6. Explain what the T-test is, why it is useful and when you would use it. T-test provides a way of measuring the overlap between two sets of data; hence using T-test, you are able to tell how significant the difference between two data sets. For instance, a small value of t indicates large overlap; hence the difference between two data sets are highly unlikely to be significant. The t-test is normally applied to sample sizes of between 5 and 30 of normally distributed data.

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5. Show a picture and explain what 1 and 2 standard deviations from the mean are and what this means for normally distributed data in terms of how many of the values lie in this range.

Standard deviations can be used to decide whether the differences between two related means are significant or not. If standard deviations are much larger than the difference between the means, then the differences in the means are highly unlikely to be significant. On the other hand, when standard deviations are much smaller than the differences between the means, then the differences between the means is almost certainly significant.

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4. Explain what normally distributed data is and compare it to skewed or unequally distributed data. Give an image or two to help you explain. Normally distributed data is the data values that group symmetrically around a central value, when the data is plotted into a curve. Here, as you can see, in the normal distribution curve, the mode, median and mean coincide.

Whereas, in the skewed or unequally distribution curve, values reduce in frequency more rapidly on side of the most frequently obtained value than the other. Hence, the measurement of inequality of the data is the difference between the mean and mode.

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3. What does it mean if data has a small standard deviation? If the data has a small standard deviation, this indicates that the data is clustered closely around the mean value.

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2. What is the measure of how much readings in a sample vary from the mean called? How do you calculate it? Why is it useful? The measure of how much readings in a sample vary from the mean is called standard deviation. In order to calculate standard deviation, you need the equation:

Or you can follow these steps: 1. Calculate the mean (x) 2. Measure the deviations (x-x) 3. Square the deviations (x-x)2 4. Add the squared deviations (x-x)2 5. Divide by the number of samples (n) Standard deviation is useful because it tells us how spread out are the readings; hence, this will give you a better picture of the data than just the mean alone (i.e. by using standard deviation we have a ‘standard’ way of knowing which data is normal and which is not).