Biology 330 - Organic Molecules

Based on the study guide

What are simple sugars called?

Monosaccharides

What are complex sugars called?

Polysaccharides

In cells, which sugars are most common?

3 and 5 carbon sugars

How many carbons are in sugars that form ring structures in a cell?

5 or more carbons

Identify the structures of both α-glucose and β-glucose

Both are cyclic, 6-carbon sugars, but they differ at the anomeric carbon. In α-glucose, the C-1 hydroxyl group points downward. In β-glucose, the C-1 hydroxyl group points upward.

What is a disaccharide made of, and what type of bond is found in this sugar (e.g. maltose)?

A disaccharide is made of two monosaccharides linked with an α-1,4 glycosidic bond.

Explain why maltose is a reducing sugar

One of the anomeric carbons (C-1) of maltose remains unbound and reactive, meaning it is a reducing sugar. Maltose can be used in glycogen or starch synthesis.

What are oligosaccharides and the role they play when linked to proteins in the plasma membrane?

Oligosaccharides are short chains of sugar molecules that are attached to proteins to mark them for transport to the cell surface. They play a role in cell surface recognition.

What type of glucose is used in the synthesis of maltose, starch, and glycogen?

α-glucose

What is the unbranched starch called, and what type of linkages or bonds are found in this type of starch?

Unbranched starch is called amylose. It is made entirely of α-1, 4 glycosidic bonds.

What is branched starch called? What types of bonds are found in this type of starch?

Branched starch is called amylopectin. Amylopectin has α-1, 4 glycosidic bonds like amylose, but there are also α-1, 6 glycosidic bonds at branching regions.

What type of glucose is used in cellulose synthesis? What type of linkages or bonds are found in cellulose?

Cellulose is made of β-glucose linked together with β-1, 4 glycosidic bonds.

What are lipids made of?

A glycerol backbone and fatty acids

What are saturated and unsaturated fatty acids?

Saturated fatty acids are fatty acids with no double bonds in the hydrocarbon chain. Unsaturated fatty acids have one or more double bonds. Fatty acids can be described by ratio of carbons to double bonds (ex. 12:0 represents lauric acid).

Which molecule is a precursor of the phospholipids? What is its structure?

Phosphatidic acid - Has two fatty acids esterified at C-1 and C-2 of the glycerol, and C-3 has a phosphate group.

Name the phospholipid with a choline head group

Phosphatidylcholine

Name the phospholipid with a serine head group

Phosphatidylserine

Name the phospholipid with an inositol-4,5-biphosphate head group

Phosphatidyl-inositol-4,5-biphosphate

What type of fatty acids are frequently found at C-1 and C-2 of phospholipids respectively?

Saturated fatty acids tend to occur at C-1, and unsaturated fatty acids tend to occur at C-2

Explain what amphipathy means with regard to phospholipids

Phospholipids are amphipathic, meaning that they have a polar (hydrophilic) head group and nonpolar (hydrophobic) fatty acid tails.

What are triglycerides made of, and what is their function?

Made of a glycerol backbone and three fatty acids; one attached to each carbon. Triglycerides are not a part of plasma membranes because they are hydrophobic. They are mainly used for energy, because one fatty acid yields 2x more ATP than glucose.

Which amino acid forms the backbone of sphingolipids?

Serine

What is cholesterol made of, and which two hormones are derived from it?

Cholesterol is made of four hydrocarbon rings, which are strongly hydrophobic. The end ring has a hydroxyl group, which is weakly hydrophilic. The steroid hormones testosterone and estrogens are derived from it. It is also a component of cell membranes.

Presume a phospholipid is cut by only PLA₁ What would be the products of PLA₁ activity?

1 fatty acid (expressed in name and ratio) + lysophosphatidyl—(head group)

What happens when PLA₂ cuts a phospholipid already cut by PLA₁ ?

PLA₂ cannot cut a lysophospholipid. Both fatty acids must be esterified to the glycerol for either PLA₁ or PLA₂ to function.

If PLC cuts phosphatidylinositol 4,5-biphosphate, what water-soluble product is released into the cytoplasm? What role does this play in the cell?

IP₃ will be released into the cytoplasm. IP₃ mobilizes Ca²⁺ from the ER, which is used for muscle function.

In the general structure on an amino acid, what is bonded to the α-carbon?

The α-carbon is at the center, with the amino group, carboxyl group, side chain, and hydrogen all bonded to it.

Which property of amino acids is used in classifying them into 4 to 5 categories?

The R group, or side chain, is used to classify an amino acid as nonpolar, polar charged, polar non-charged, or aromatic (has a ring).

How many amino acids are used in protein synthesis?

20 different amino acids

What are the 10 nonpolar amino acids? Hint: remember GAVLIP CMPT.

Glycine, alanine, valine, leucine, isoleucine, proline, cysteine, methionine, phenylalanine, and tryptophan.

Which nonpolar, cyclic amino acid introduces rigidity in protein structure? How?

Proline. Its side chain is bonded to the nitrogen of its amino group, which gives it a cyclic structure that makes the protein more rigid.

Where are nonpolar amino acids usually located in a folded protein?

Nonpolar amino acids are located inside of the folded protein, minimizing interaction with water.

Name 2 sulfur containing amino acids. Which of these 2 amino acids is strongly nonpolar and why?

Methionine and cysteine both contain sulfur. Methionine is strongly hydrophobic compared to cysteine due to cysteine’s ending SH group.

Name the 3 aromatic amino acids? Which one is slightly polar and why?

Phenylalanine, tryptophan, and tyrosine are aromatic. Tyrosine is slightly polar due to its OH group.

Name 3 polar amino acids that contain hydroxyl groups on their side chain

Tyrosine, serine, and threonine,

Name 2 polar amino acids with amide groups in their side chain

Asparagine and glutamine

Name the 3 basic or positively charged amino acids.

Lysine, arginine, and histidine

Which basic amino acid has an ionizable side chain and is found in the active sites of many enzymes where it is involved in enzyme catalysis?

Histidine.

Name 2 amino acids that have their side chains termination in carboxyl groups and are therefore acidic.

Aspartic and glutamic acid

What type of bond links amino acids in a protein?

Peptide bond

How many molecules of ATP are used in activating an amino acid, and how many GTPs are used in peptide bond formation?

1 ATP; 2 GTP

Name the 4 levels of protein structure

Primary, secondary, tertiary, quaternary

Name two types of protein secondary structure and how they are formed.

α-helixes: hydrogen bonds link the carbonyl and amino groups every 4th amino avid. This causes the polypeptide to coil. β-sheets: occur when hydrogen bonds connect two adjacent parts of the polypeptide, creating a zig-zag shape.

In a folded protein, what type of bond is formed when sulfhydryl groups of cysteine interact?

Disulfide bond - very strong

What did Christian Anfinsen do in his experiment? What was the conclusion drawn from the data?

Heated RNase with heat, causing it to denature. When less heat was applied, RNase was able to refold into its functional shape. Conclusion: polypeptides self assemble into functional, 3D proteins.

Describe protein quaternary structure

Occurs when multiple fully folded proteins interact to form a protein complex with polypeptide subunits.

What are homodimers and heterodimers?

Homodimer: protein complex made of the same polypeptide subunits. Heterodimer: Protein complex made of different polypeptide subunits