Week 7 Flashcards
Anabolism
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
Organic and Inorganic carbon sources
Organic carbons are usually peptides like sugars and lipids.
Inorganic carbons is almost always Co2.
What cycles do autotrophs use to fix CO2 ?
Most common:
- Calvin cycle
- Reductive TCA cycle
Depends on type of bacteria:
- Hydroxypropionate bi-cycle
- Reductive acetyl-CoA pathway
- 3-hydroxypropionate/4-hydroxybutyrate pathway
Steps of the Calvin Cycle
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.
- CO2 is combined with RuBP using the rubisco enzyme. A 6 carbon molecule is created.
- This 6 carbon molecule is broken down into 2 3 carbon chains called PGA.
- ATP is used as an energy source and NADPH is used to add protons to PGA making it G3p.
- The G3P are and 2 of them make glucose, the other G3P are left to make RuBP and the cycle continues.
Bacterial Carboxysome and the Calvin Cycle
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.
What are the 3 phases of the carbon cycle ? What are reactants ?
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)
What is the reductive TCA Cycle ?
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
How do inorganic molecules become organic ones ?
by assimilation
Assimilation is the incorporation of inorganic molecules into organic ones.
What is nitrogen assimilation and why is it important ?
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.
What enzyme is used in ammonia synthesis ?
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.
Where does ammonia come from ?
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.
Why does Nitrogenase need protection ? How is it protected ?
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.
Phosphorous Assimilation
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
Sulfur Assimilation
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
How does sulfur become useful ?
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.
What carbohydrates are found in Bacteria ?
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
Bacteria vs eukaryotic carbohydrates
Bacteria have more diverse monosaccharides than eukaryotes
What is gluconeogenesis? what is it the reverse of ?
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
What is the pentose phosphate pathway ?
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)
Unique Monosaccharides
Special pathways are required to make unusual sugars.
Are unique to bacteria that make a specific polysaccharide
Need specific enzymes to make these polysaccharides
Amino acid Biosynthesis
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.
Nucleotide Biosynthesis
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
What is needed in purine biosynthesis ?
- Aspartate
- Glutamine
- Glycerine
- Folic acid
- Co2
- Ribose
- ATP
Deoxyribonucleotides are formed by reduction of nucleoside diphosphates or nucleoside triphosphates.
precursor- inosinic acid
What is needed in pyrimidine biosynthesis ?
- Aspartate
- NH3
- Co2
- Ribose
- ATP
Deoxyribonucleotides are formed by reduction of nucleoside diphosphates or nucleoside triphosphates.
precursor- uridyrate
Lipid Biosynthesis
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
Fatty Acid Biosynthesis
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
Phospholipid Biosynthesis
Synthesized from phosphatidic acid by forming CDP-diacylglycerol, then adding the head group
CTP is used to activate, similar to ATP
Fatty acid Biosynthesis steps
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.
