1. The bacterium Micrococcus luteus lives on mammalian skin where it feeds on amino acids and lactic acid found in sweat. Answer the following questions about carbohydrate metabolism[1] in M. luteus.

1. M. luteus lacks any hexokinase orthologs (e.g. any enzyme catalyzing the reaction glucose + ATP ⇌ glucose-6-phosphate + ADP) as well as any phosphohexose isomerase homologs (e.g. any enzyme catalyzing the reaction glucose-6-phosphate ⇌ fructose-6-phosphate), but they express all other enzymes involved in glycolysis. Are M. luteus bacteria capable of catabolizing glucose via glycolysis? (1 point)

2. M. luteus expresses glycogen phosphorylase as well as phosphoglucomutase; i.e. these bacteria can convert glycogen to glucose-6-phosphate. Assuming M. luteus bacteria can transport glycogen into their cytoplasm, can M. luteus catabolize glycogen (e.g. via glycolysis) and, if so, how many ATP molecules can M. luteus produce (via glycolysis) for each 6 carbons of glycogen? (3 points)

3. Given your answer to the previous question, how many ATP molecules can an M. luteus bacterium produce (via glycolysis) from one 30,000 carbon molecule of glycogen? (2 points)

Which pathway enables M. luteus to produce sugars (e.g. for oligosaccharide biosynthesis) from glucogenic amino acids: glycolysis, gluconeogenesis, the Calvin cycle or the pentose phosphate reactions?

in response to comment: ok..so take time then

Question 7

A strain of E. coli is grown under aerobic conditions. However, this strain has an inactivating mutation in the enzyme that converts Pyruvate to Acetyl-CoA. What is the consequence of this mutation?

1. The organism cannot fully oxidize glucose, but can metabolize fats and some amino acids

2. The organism can metabolize as normal

3. The organism cannot carry out glycolysis

Question 4

Which of the following organisms are directly beneficial to vascular plants?

(1). Rapidly growing cancers generally exhibit increased glycolysis for ATP generation (the Warburg effect). Do you think targeting glycolysis could be a good strategy for cancer therapy? If your answer is YES, which enzyme could be a good anti-cancer drug target? If your answer is NO, please explain why

(2). Please discuss the process of making beer, or wine, or bread. What ingredients in these items participate in the fermentation pathways? How are the end products of fermentation utilized?

(3). You eat a hamburger that has polysaccharides, proteins and lipids. Using your knowledge of the integration of biochemical pathways, explain how the amino acids in the proteins and glucose in the polysaccharides can end up as fats.

Match the following statements with the description of what level of structure in a protein?
1. The sequence of amino acids is Asp-Asp-Arg-Asn-Met-Met- etc.
2. The chain of amino acids coils into a helix.
3. Several separate proteins link together to form an active enzyme.
4. The set of linked amino acids folds repeatedly and creates a large globular shape.​

1. The active site of an enzyme usually consists of a pocket on the enzyme surface lined with the amino acid side chains necessary to bind the substrate and catalyze its chemical transformation. Carboxypeptidase, which sequentially removes the carboxyl-terminal amino acid residues from its peptide substrates, consists of a single chain of 307 amino acids. The two essential catalytic groups in the active site are furnished by Arg¹⁴⁵ and Glu²⁷⁰ .

a. How many amino acid residues apart are these two amino acids?

b. Explain how it is that these two amino acids, so distantly separated in the sequence, can catalyze a reaction occurring in the space of a few tenth of a nanometer?

c. If only these two catalytic groups are involved in the mechanism of hydrolysis, why is it necessary for the enzyme to contain such a large number of aa residues?

2. What level of protein structure would be disrupted by the following below

a. heat

b. strong acid

c. saturated salt solution

d. organic solvents such as alcohol and chloroform

1. Glycolysis is an almost universal pathway for extraction of the energy available from carbohydrates, shared among prokaryotes and eukaryotes, aerobes and anaerobes alike. Base on what you have learnt and your best understanding towards the mentioned process, investigate the direct and indirect glycolysis as well as give concrete examples, where possible.

4. Why does human body require a certain amount of carbohydrates in daily diet? Exemplify case by case.

5. The citric acid cycle is a central metabolic pathway that completes the oxidative degradation of fatty acids, amino acids, and monosaccharides. Base on your understanding, clarify the above statement.

6. Show your understanding and figuring out the oxidative phosphorylation of utilizing the chemical energy of those reduced molecules from glycolysis and Citric Acid Cycle to produce ATP.

7. Show your understanding and exemplifying the roles of NADPH in the all related issues of concern.

B. PROTEINS

1. Chemical digestion of proteins by enzymes first begins in the stomach. Name the gastric enzyme that initiates protein digestion. Explain how this enzyme is activated.

2. Pancreatic juice contains enzymes which digest proteins including trypsin and chymotrypsin. Name the ducts in the pathway by which pancreatic juice flows from the pancreas to the duodenum.

3. The products of chemical digestion of dietary proteins are amino acids (protein subunits), which are then absorbed into the bloodstream. Describe 3 ways the body uses these amino acids. In other words, name 3 important proteins (needed by the body to maintain health) which are synthesized using dietary amino acids.

1. The 21st and 22nd amino acids found in proteins are the rare amino acids ______________ and ______________.
2. ________________ are nonviral genetic elements that have reverse transcriptase activity.
3. An example of retrotransposons in the human genome is the ____ family of sequences.