Micro - Chapter 5 Lecture

-All chemical rxns in a cell, both catabolic and anabolic. 

-It is the chemical rxns that organisms used to break down substances to release energy, and well as used that energy to build new substances

-catabolic: pathways that break down substances and release energy. usually hydrolytic and exergonic

-anabolic: pathways that combine energy and molecules to build new substances (think anabolic steroids) usually dehydration synthesis and endergonic

-amphibiolic: they can be used for breaking down and building substances

• ATP=Adenosine triphosphate
• all cells need ATP to do cellular work. If they don't have ATP they die.

it is made by catabolic reactions and provides energy for anabolic reactions

• DTP- guanosine triposphate
• UTP- uridine triphosphate

ATP: adenosine, ribose, and 3 phosphate groups

ADP: adenosine, ribose, and 2 phosphate groups

-when ATP is dephosphorylated it releases energy and ADP. when the cell needs more energy it phosphorylates ADP and adds back the phosphate to made ATP. 

*ATP-ADP cycle

AMP- adenoside monophosphate 

cells dephosphorylate ADP to make AMP

An enzyme is a protein catalyst that helps chemical rxns happen. 

A catalyst is something only needed in small amounts to speed up the reaction rate. Keep in mind they are utilized, not consumed or changed by the rxn. 

In fact, they help hold the reactions into their proper place and lower the amount of energy needed for the rxn.

When atoms and molecules constantly move around they collide. Energy is transferred during these collisions chemical bonds are either made or broken. In order for bonds to be made or broke, they must fit together properly with the help of enzymes.

the molecule that an enzyme acts upon. most enzymes are named after their substrate

enzymes have specificity. 

lock and key model: the enzyme is the lock that can only be opened by the key (substrate) at the active site, where chemical rxns happen.

the enzyme will struggle to interact with the substrate and there enzyme activity will be decreased.

substances required by some enzymes for full activity

-coenzymes: organic molecules like NAD+, FAD, crytochromes. they are often formed from vitamins. 

-cofactors: inorganic molecules like magnesium, calcium, zinc, etc work to improve the fit of substrates in the active site

apoenzyme- an enzyme that must be activated by a cofactor/coenzyme 

holoenzyme- an enzyme that doesn't need to be activated because it already has a cofactor/coenzyme

• 1.  the enzyme is available with empty active site
• 2. the substrate binds to active site forming the enzyme-substrate complex
• 3. the substrate is converted to the product after going through transition state
• 4. products are released and enzyme is available to interact with other substrates

• NAD+: nicotinamide adenine dinucleotide
• -exergonic rxns usually

• NADP+: nicotinamide adenine dinucleotide phosphate
• - endergonic rxns usually

*B vitamin niacin derivates

• FMN: flavin mononucleotide
• FAD: flavin adenine dinucleotide
• *derivatives of B vitamin riboflavin

• CoA: coenzyme A
• *derivative of B vitamin pantothenic acid

• Temperature- the rate of the rxn speeds up with the increase in temperate. If the temperature goes beyond the optimal temperature, denaturation occurs and the rxn rapidly slows. 
• Denaturation is when there is a loss of 3D tertiary structure of the protein. It's hydrogen and covalent bonds are broken. 
• *optimal temp for disease causing bacteria is 35-40 degrees C in human body

• PH- extreme changes can cause denaturation because the H+ and OH- compete with hydrogen and ionic bonds in the enzyme
• *most pathogens like neutral ph

Substrate concentration- when there is a high substrate concentration, the enzyme active site is saturated either by the substrates or the products. When the active sites are saturated, more substrates will not make a difference. Normally enzymes aren't saturated, so the empty ones are inactive until they are filled. 

Presence/absence of inhibitors- inhibitors prevent the enzyme from functioning and the cell dies. this is a way that we can prevent the spread of bacteria. there are competitive, noncompetitive, and allosteric inhibitors.

competitive: compete with the normal substrates for the active site. it is able to do this because its chemical structure and shape is similar to the normal substrates. however, it doesn't undergo any changes to turn into a product. some competitive inhibitors are reversible, some are not. 

• non-competitive/allosteric
• non-competitive: they interact with another part of the enzyme other than the active site. so they do not compete with substrates. they reduce the enzyme activity because they are linked to the enzyme at the same time as the substrate. some are reversible, some are not. 
• allosteric: they activate or inhibit the enzymes activity (increase or decrease) by binding the the allosteric site. these are reversible.

inhibition- When the end product of a reaction "end-bound product" is released and binds to the active/allosteric site thereby halting the reaction. This prevents overuse and wasted energy. Ex: Blood pressure and body temp. regulation

• they stop the cell from making more of a substance so that it doesn't waste chemical resources. 
• feedback inhibition generally acts on the first enzyme in the process.

they cut and splice RNA and are involved in protein synthesis at ribosomes

the removal of electrons from an atom or molecule. its a reaction that releases energy. 

the addition of electrons from another atom or molecule. it is generally endergonic.

substrate level phosphorylation: the high energy phosphate from a substrate combines with ADP to generate ATP

oxidative phosphorylation: electric transport chains powered by nutrients recharge ADP to ATP

photophosphorylation: solar energy causes electric transport chains to recharge ADP to ATP

• SLP- glycolysis, krebs cycle, and fermentation
• - eukaryotes and prokaryotes

• Oxid- anaerobic and anaerobic ETCs of cellular respiration 
• -eukaryotes and prokaryotes

• Photo- used in light-dependent reactions of photosynthesis
• -photosynthetic eukaryotes and prokaryotes

glycolysis breaks down glucose and turns it into 2 pyruvic acid (pyruvate), 2 NADH (after being reduced from NAD), and 2 ATP. 

the purpose is to create ATP from glucose

*there is a net gain of 2 ATP per every glucose that is oxidized

happens in the cytoplasm of prokaryotes and eukaryotes

eukaryotes, bacteria (prokaryotes) use it in addition to glycolysis. (this pathway is more common)

it starts with glucose to produce various precursors: nucleotides, amino acids, and NADPH (from reduced NADP+). 

its purpose is to create synthetic precursors 

• *there is a net gain of only 1 ATP per oxidized glucose
• *e.coli use this

G6PD deficiency- this is when NAD+ is not able to be reduced to NADPH anymore, which causes glutathionine to no longer be reduced. glutathionine protects cells from oxidative stress (oxygen on a cell for too long is damaging). the RBCs can't repair themselves and they get hemolytic anemia 

hemolytic anemia can also be triggered by henna, infections, sulfa drugs, etc. 

*this deficiency also protects from malaria

only used by prokaryotes

it starts with glucose and produces 1 ATP, 1 NAD, and 1 NADPH, but most importantly yields a KDPG. 

this KDPH product is important for clinical diagnostic purposes, if found in patient. its significant because this pathway is only found in gram-negative bacteria. this means it is antibiotic resistant.

• *Pseudomonas aeroginosa is a bacteria that infects people with severe burns or cystic fibrosis
• *Enterococcus faecalis is found in endocarditis and cystitis patients

• 1. the intermediate step (acetyl CoA synthesis)
• 2. the Krebs cycle
• 3. the electric transport chain

• glycolysis produces a lot of pyruvate, which is a good source of chemical energy that can be used. however, the Krebs cycle only accepts 2 carbon molecules instead of 3 carbon molecules (pyruvate). 
• So, this intermediate step turns pyruvate into 2 acetyl CoA, 2 NADH, and 2 CO₂. 
• Now, the 2-carbon molecules can be used in the Krebs

Since there is still a lot of chemical energy in the bonds of Acetyl CoA (from the intermediate step).

Krebs cycle begins when oxaloacetic acid (OAA) joins with acetyl CoA to reduce NAD+ and FAD into NADH and FADH₂. ATP and CO₂ is also produced. 

The Krebs cycle takes 2 cycle to use up 1 glucose molecule

The Krebs cycle ends with oxoloacetic acid (OAA) 

The purpose is to get as much ATP out of the oxidized glucose as possible (think of it as squeezing out that last little bit)

the purpose is to make a lot of ATP from oxidizing the previously reduced electron carriers.

• the process starts with reduced NADH and FADH₂ and oxidizes them into NAD, FAD, a LOT of ATP, and H₂O. 
• *regenerates reducing power from electron carriers such as cytochromes, flavoproteins, ubiquinones and coenzyme Q
• *eukaryotes- mitochondria
• *prokayotes- plasma membrane

after glycolysis, pyruvate can enter respiration or can be broken down into various organic products with fermentation. 

the purpose of fermentation is to regenerate reducing power for glycolysis, oxidizing NADH into NAD. NAD needs to be regenerated so that glycolysis can continue. 

*fermentation offers a way to oxidize NADH anaerobically. it is energetically inefficient because most of the potential energy remains in the various products.

vitamin B deficiency 

poor people that eat too much corn, malnourished because they don't have vitamin B

the patchy, scaly, dry skin

deficient in vitamin B1

the enzyme is not folding properly. Bruce aims put a ton of thiamine (B1) into their system and it fixed it. 

if not treated it causes retardation