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1.6Problems

 

 

List the four characteristics that define an organism, and describe the cellular structural differences between prokaryotes and eukaryotes.

 

Draw a phylogenetic tree that includes animals, plants, fungi, archaea and bacteria. Name one species of eubacterium and one species of fungus.

 

 

In an ideal environment, E. coli bacteria multiply every 20 minutes. Assuming that no bacteria die, calculate the time taken for one E. coli bacterium in a medium (1 ml) to reach 10 billion/ml.

Respond to the following protein-related tasks:

1)

Explain the primary, secondary and tertiary structures.

2)

Name some typical examples of secondary structures.

3)

Identify the forces that contribute to the stabilization of secondary and tertiary structures.

4)

Explain the quaternary structure.

 

List the three main functions that proteins perform within cells.

Mark the following with ○ (Yes) or × (No). If your answer is ×, give one or two lines explaining the reason.

1)

A hydrogen bond is a bond between hydrogen atoms formed on the surface of protein molecules in a solution.

2)

Glucose is a constituent of nucleic acid.

3)

When a translated protein forms a higher-order structure, a structural change occurs so that the hydrophobic residues of the protein are positioned on its inner side.

4)

The peptide tyrosine-glycine-glycine-phenylalanine-leucine is known as an enkephalin. A peptide whose amino acid sequence is opposite to this (i.e., leucine-phenylalanine-glycine-glycine-tyrosine) has the same functions as an enkephalin.

5)

DNA consists of four bases: A, G, U and C.

 

 

List the four characteristics that define an organism, and describe the cellular structural differences between prokaryotes and eukaryotes.

Organisms are defined as: consisting of cells, having the ability to replicate themselves, responding to external stimuli and using the energy of adenosine triphosphate - the currency of energy transfer - to grow.
The difference between prokaryotes and eukaryotes lies in whether they have a nucleus that contains DNA. Prokaryotes are classified into eubacteria and archaea; E. coli and salmonellae belong to the former, with methane bacteria, halobacteria and Archaeoglobus belonging to the latter. Eukaryotes are descended from archaea. It should be noted that yeasts are classified as eukaryotic fungi (which include mushrooms).

 

Draw a phylogenetic tree that includes animals, plants, fungi, archaea and bacteria. Name one species of eubacterium and one species of fungus.

See Figure. 1-1 for the phylogenetic tree. Eubacteria: E. coli, Bacillus subtilis, cyanobacteria, etc. Fungi: yeasts, Dictyostelium, etc.

 

 

In an ideal environment, E. coli bacteria multiply every 20 minutes. Assuming that no bacteria die, calculate the time taken for one E. coli bacterium in a medium (1 ml) to reach 10 billion/ml.

To make the calculation, the number of cell divisions necessary must be ascertained.
Consider the common logarithm of 2n = 1010 (nlog2 = 10). Since log2 = 0.3010, n is 33.2, so 34 divisions are needed.
The time taken is therefore 11.3 hours (or around half a day).

Respond to the following protein-related tasks:

1)

Explain the primary, secondary and tertiary structures.

Primary structure: the sequence of amino acids that constitute a protein. Secondary structure: the folding structure of a protein often seen in tertiary protein structures. Tertiary structure: the three-dimensional structure of a protein made of polypeptide chains.

2)

Name some typical examples of secondary structures.

α-helix, β-sheet

3)

Identify the forces that contribute to the stabilization of secondary and tertiary structures.

Hydrogen bonds, S-S bonds, hydrophobic interaction, etc.

4)

Explain the quaternary structure.

If multiple polypeptide chains form a protein complex (i.e., an oligomer protein), the resulting structure is called the quaternary structure.

 

List the three main functions that proteins perform within cells.

The first is involvement in "in vivo" chemical reactions as enzymes. Enzymes in glycolysis, RNA polymerase (which is involved in DNA transcription) and trypsin (a digestive enzyme) are examples of this. The second is involvement in the formation of organisms as structural proteins. Examples include myosins in muscles, actins that form the cytoskeleton, collagens in the stromata, and crystallins that form the crystalline lens. The third is transport, and transport proteins include hemoglobin (which transports oxygen) and albumins (which transport various substances in the blood). Other protein types include immune proteins (e.g., γ-globulins) and receptors that receive external stimuli (hormones, growth factors and transmitters) on the plasma membrane.

Mark the following with ○ (Yes) or × (No). If your answer is ×, give one or two lines explaining the reason.

1)

A hydrogen bond is a bond between hydrogen atoms formed on the surface of protein molecules in a solution.

×. A hydrogen bond is a weak interaction that exists in biological molecules such as DNA and proteins, and is a bond between hydrogen and nitrogen and between hydrogen and oxygen (represented by the dotted lines in the figure below).
?N?H-----N?
?N?H-----O?
?O?H-----N?
?O?H-----O?

2)

Glucose is a constituent of nucleic acid.

×. Glucose contains ribose or deoxyribose.

3)

When a translated protein forms a higher-order structure, a structural change occurs so that the hydrophobic residues of the protein are positioned on its inner side.

○. In eukaryotes, protein folding takes place while translation is being performed in a ribosome, but in prokaryotes it occurs after the translation of the protein is complete. In the former case, folding is initiated from the N-end, and proteins are generally folded with hydrophobic amino acids facing inward and hydrophilic ones facing outward. The molecules that accelerate this process are called chaperones.

4)

The peptide tyrosine-glycine-glycine-phenylalanine-leucine is known as an enkephalin. A peptide whose amino acid sequence is opposite to this (i.e., leucine-phenylalanine-glycine-glycine-tyrosine) has the same functions as an enkephalin.

×. Proteins are long linear chains of amino acids joined together by peptide bonds, and one amino-acid difference results in a protein with different properties. Reversing the amino acid sequence of enkephalin results in a peptide with wholly different properties. As an example, dipeptides - alanine-histidine and histidine-alanine - are different. Hereditary disease is an example of one amino acid change in a protein consisting of hundreds of amino acids resulting in different functions of the protein. Replacement of the sixth amino acid in the hemoglobin β-chain (i.e., glutamic acid) with valine causes sickle-cell anemia.

5)

DNA consists of four bases: A, G, U and C.

×. DNA has Ts (thymines) instead of Us (uracils).

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