Week 7

Question 1

Anabolism

Answer 1

A lot of energy is required for making molecules
• There is a lot of turnover
• Cell breaking down materials and resynthesizing
new ones
• Possibly due to potential damage
• Certainly due to adaptations in changing
environments
• NADPH tends to be the electron carrier
• Sometimes biosynthetic pathways are segregated to
avoid mixing - allows both to occur with some
specificity in the molecules being synthesized/broken
down

Question 2

Organic and Inorganic carbon sources

Answer 2

Organic carbons are usually peptides like sugars and lipids.

Inorganic carbons is almost always Co2.

Question 3

What cycles do autotrophs use to fix CO2 ?

Answer 3

Most common:

• Calvin cycle
• Reductive TCA cycle

Depends on type of bacteria:

• Hydroxypropionate bi-cycle
• Reductive acetyl-CoA pathway
• 3-hydroxypropionate/4-hydroxybutyrate pathway

Question 4

Steps of the Calvin Cycle

Answer 4

The Calvin cycle is occurring at 6 different times so that there is enough carbon to make glucose and more RuBP.

Calvin cycle is also known as the reductive pentose phosphate pathway.

1. CO2 is combined with RuBP using the rubisco enzyme. A 6 carbon molecule is created.
2. This 6 carbon molecule is broken down into 2 3 carbon chains called PGA.
3. ATP is used as an energy source and NADPH is used to add protons to PGA making it G3p.
4. The G3P are and 2 of them make glucose, the other G3P are left to make RuBP and the cycle continues.

Question 5

Bacterial Carboxysome and the Calvin Cycle

Answer 5

Calvin cycle occurs in the carboxysome of some bacteria ( Cyanobacteria, nitrifying bacteria, and thiobacilli. It is also found in the stroma of chloroplasts in eukaryotes.

Question 6

What are the 3 phases of the carbon cycle ? What are reactants ?

Answer 6

Three phases
• Carboxylation
• Reduction
• Regeneration

3 ATP and 2 NADPH are used during the incorporation of one CO2.

3 phosphoglycerate is an intermediate in glycolysis its used to make glucose (glycogenesis)

Question 7

What is the reductive TCA Cycle ?

Answer 7

Citric acid cycle in reverse. The use of ATP, FADH2 and NADH to fix carbon.

This is used by some chemolithoautotrophy.

3 CO2 will make glyceraldehyde 3 - phosphate
6 CO2 will make fructose 1,6-bisphosphate

Question 8

How do inorganic molecules become organic ones ?

Answer 8

by assimilation

Assimilation is the incorporation of inorganic molecules into organic ones.

Question 9

What is nitrogen assimilation and why is it important ?

Answer 9

Nitrogen is a major component of proteins, nucleic acids, co enzymes and other cell constituents. The potential nitrogen sources are ammonia, nitrogen gas and nitrate.

Ammonia is the easiest to incorporate into organic compounds and nitrogen gas is turned into ammonia for use.

Question 10

What enzyme is used in ammonia synthesis ?

Answer 10

Glutamine synthase.

A 6 monomer ring, stacked to create a 12 monomer dodecomer. Used in ammonia synthesis. Turns glutamate to glutamine by adding a second ammonia side chain.

Using ATP glutamate gets an extra phosphate added to its sdie chain, ammonia comes along and attacked the phosphate group kicking it out and the ammonia gets attached.

Question 11

Where does ammonia come from ?

Answer 11

Ammonia can come from:
• Other organisms
• The environment
• And from nitrogenase
○ This is found in bacteria and archaea
○ Need high amounts of ATP
○ Once reduced NH3 can be incorporated into organic compounds
• 16 ATP are needed
• 4 pyruvate turn into one nitrogen gas which creates two ammonia.

Question 12

Why does Nitrogenase need protection ? How is it protected ?

Answer 12

Nitrogenase is sensitive to oxygen, it wont work when oxygen is present.
To protect the nitrogenase from oxygen the bacteria and archaea use a thick glycocalyx to keep oxygen out or they make a heterocyst which is a thick walled cell that doesn’t use aerobic respiration.

Question 13

Phosphorous Assimilation

Answer 13

Phosphorus found in nucleic acids as well as
proteins, phospholipids, ATP, and some coenzymes
• Most common phosphorus sources are inorganic
phosphate and organic phosphate esters
• Inorganic phosphate (Pi) incorporated through the
formation of ATP by
• oxidative phosphorylation
• substrate-level phosphorylation
• Organic phosphate esters
• present in environment in dissolved or particulate
form
• hydrolyzed by phosphatases, releasing Pi

Question 14

Sulfur Assimilation

Answer 14

Sulfur needed for:
• synthesis of amino acids cysteine and methionine
• synthesis of several coenzymes
• Sulfur obtained from
• external sources
• intracellular amino acid reserves
• Sulfate = inorganic sulfur source
• comes from oxidation of reduced sulfur (S0 or HS-)
• assimilatory sulfate reduction
• sulfate reduced to H2S and then used to
synthesize cysteine
• cysteine can then be used to form sulfur
containing organic compounds

Question 15

How does sulfur become useful ?

Answer 15

sulfur is turned to cysteine

APS and PAPS are used to help form cysteine, cysteine is used to make organic sulfur containing compounds

Serine is used to make cysteine. This occurs in most bacteria. An acetyl group from acetyl coA is added to serine to make it a cysteine.

Question 16

What carbohydrates are found in Bacteria ?

Answer 16

Glycoproteins (S-layer, pilin/flagellin, adhesins, etc)
• Variable (Man, Glc, GlcNAc, Gal, Xyl, Pse, Fuc, Bac)

Peptidoglycan
• GlcNAc, MurNAc

(Lipo)teichoic acid
• ribitol, mannitol, + others

Lipopolysaccharide
• Kdo, heptose, Glc, GlcNAc, Gal, O-antigen
• E. coli O157 [,4)-β-Glc-(1,3)-α-PerNAc-(1,4)-α-GalNAc-
(1,3)-α-Fuc-(1,]n

Capsule
• Variable

DNA/RNA
• deoxyribose/ribose

Question 17

Bacteria vs eukaryotic carbohydrates

Answer 17

Bacteria have more diverse monosaccharides than eukaryotes

Question 18

What is gluconeogenesis? what is it the reverse of ?

Answer 18

It is the reverse of glycolysis. It is the formation of glucose from pyruvate.

6 enzymes are shared, 4 are unique to gluconeogenesis

Unique steps:

1. Pyruvate becomes oxaloacetate using pyruvate carboxylase 
2. Oxaloacetate becomes phosphoenolpyruvate using PEP carboxykinase  
3. Fructose 1-6, bisphosphate to fructose 6-phosphate using the enzyme fructose 1,6  bisphosphatase. 
4. Glucose 6 phosphate becomes glucose using glucose 6- phosphatase

Question 19

What is the pentose phosphate pathway ?

Answer 19

it generate pentoses from other sugars and is used in pentose catabolism.

Makes Ribulose 5- phosphate, which becomes Ribulose 1,5- phosphate which is used in the Calvin cycle.

Ribulose 5- phosphate also becomes Ribose 5 phosphate which is a key intermediate of nucleotides (ATP, UTP, RNA, DNA)

Question 20

Unique Monosaccharides

Answer 20

Special pathways are required to make unusual sugars.

Are unique to bacteria that make a specific polysaccharide

Need specific enzymes to make these polysaccharides

Question 21

Amino acid Biosynthesis

Answer 21

Glycolysis and the citric acid cycle products can be used in the biosynthesis of amino acids

In glycolysis:
Pyruvate becomes the Alanine family of amino acids ( Valine and Leucine)

3-phosphoglycerate becomes the serine family of amino acids Glycine and cysteine

Phosphoenolpyruvate turns into chorismate (pentose phosphate pathway) which forms the aromatic family of amino acids phenylalanine, tyrosine and tryptophan

Carbon skeleton is remodeled
Amino groups and sometimes sulfur are added.

A single precursor metabolite can give rise to several amino acids.

Question 22

Nucleotide Biosynthesis

Answer 22

Most microbes can synthesize their own
purines and pyrimidines
• Purines
• cyclic nitrogenous bases consisting of 2
joined rings
• adenine and guanine
• Pyrimidines
• cyclic nitrogenous bases consisting of
single ring
• uracil, cytosine, and thymine
• Nucleoside = nitrogenase base-pentose sugar
• Nucleotide = nucleoside-phosphate

Question 23

What is needed in purine biosynthesis ?

Answer 23

• Aspartate
• Glutamine
• Glycerine
• Folic acid
• Co2
• Ribose
• ATP

Deoxyribonucleotides are formed by reduction of nucleoside diphosphates or nucleoside triphosphates.

precursor- inosinic acid

Question 24

What is needed in pyrimidine biosynthesis ?

Answer 24

• Aspartate
• NH3
• Co2
• Ribose
• ATP

Deoxyribonucleotides are formed by reduction of nucleoside diphosphates or nucleoside triphosphates.

precursor- uridyrate

Question 25

Lipid Biosynthesis

Answer 25

Lipids
• major required component in cell
membranes
• most bacterial and eukaryal lipids contain
fatty acids
Fatty acids
• synthesized then added to other molecules
to form other lipids such as triacylglycerols
and phospholipids

Question 26

Fatty Acid Biosynthesis

Answer 26

Synthesized from acetyl-CoA, malonyl-CoA, and NADPH by fatty acid synthase system
• Produces CO2
During synthesis the intermediate are attached to acyl carrier protein (ACP)

Double bonds are formed by desaturation of the intact fatty acid chain

Question 27

Phospholipid Biosynthesis

Answer 27

Synthesized from phosphatidic acid by forming CDP-diacylglycerol, then adding the head group

CTP is used to activate, similar to ATP

Question 28

Fatty acid Biosynthesis steps

Answer 28

Fatty acids are made by 2 carbon atoms at a time by the protein acyl carrier protein (ACP). ACP hold the growing fatty acid as it is being made and releases it once it has reached the final length.

Each 2 carbon unit come from the 3 carbon compound malonate. Malonate is attached to ACP to form malonyl ACP.