2-8 Summary

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Everything we can see, touch, taste or experience in any other way is made of matter. Matter is made of atoms and they consist of the subatomic particles, protons, neutrons and electrons. Biological compounds are made of matter, just like everything else, but living systems tend to be made of the lighter elements, with C, N, O, H, P and S being the majority. These elements are part of cell structures, and many of theses structures are formed by making polymers. These polymers are made from just a few basic types of molecules: amino acids, sugars, nucleic acids and fatty acids. Sugars are used in structures in the cell, and sometimes decorate proteins and lipids. Nucleic acids are more complex polymers having a backbone made of sugar and phosphorus, with the base giving the nucleic acid its identity. Proteins are polymers of 20 assorted amino acids and they are the biological catalysts of the cell. The sequence of the polymers dictates their structure and subsequently their function, especially for proteins. Finally, lipids are made from glycerol, a polar head group and two long-chain fatty acids. The amphipathic nature of lipids encourages them to assemble into a lipid bilayer and forms the foundation of the cell. In subsequent chapters we will discuss how this chemistry comes together to form the diversity of living organisms we call microbes.

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1. Why are the noble gases so stable?


2. Carbon is a unique element when it comes to orbitals. Why?


3. Explain the difference between a hydrogen bond and a covalent bond.


4. Which weighs more, a mole of table sugar or a mole of oleic acid.


5. Define pH. Why do cells normally maintain a neutral pH in their cytoplasm?


6. Why do you think D-amino acids don't work in enzymes? (Hint: Think about your hands, they are mirror images of one another. Now thing about gloves)


7. Draw the chemical reaction of water being split into oxygen and hydrogen gas.


8. Compare and contrast the DNA polymer and the RNA polymer.


9. Think about an α helix and a zinc-finger. Which one could be a subset of the other?


10. List the roles that small molecules play in the cell.


11. An element can exist with only protons and no neutrons?

True
False


12. Which of the following is an important property of water?

A. Water repels most things
B. Water is an excellent solvent
C. Water changes temperature quickly
D. Water has a high boiling point

13. You are trying to grow a microbe that requires histidine, an amino acid. You add D-histidine to the plate, yet your microbe won't grow. This is because..

A. histidine is not an amino acids cells use.
B. D-histidine cannot be transported into cells.
C. this should have worked, something is wrong with your technique
D. D-histidine is the wrong stereoisomer, L-histidine is what cells need.

14. In the redox reaction in Figure 2.12

A. glyceraldehyde 3-phosphate is oxidized and NAD+ is reduced
B. glyceraldehyde 3-phosphate is oxidized and NAD + is oxidized.
C. NADH is reduced and glyceraldehyde 3-phosphate is reduced
D. glyceraldehyde 3-phosphate is reduced and NAD + is oxidized.

15. The conversion of glyceraldehyde 3-phosphate to 1,3 bisphophoglycerate releases free energy. This reaction is favorable

True
False


16. If you change the sequence of sugars in a polymer, you will not change the properties of the polymer.

True
False


17. If you change the sequence of amino acids in a protein, you will not change the properties of the protein.

True
False


18. What structural group of amino acids get buried in proteins, dictating a significant amount of their structures?

A. hydrogen bonding amino acids
B. charged amino acids
C. non-polar amino acids
D. polar amino acids
E. acidic amino acids

19. Lipids are made from

A. glycerol, phosphates and fatty acids
B. glycerol, ribose sugars and phosphates
C. glycerol, amino acids and ribose sugars
D. glycerol, phosphates and amino acids

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