Biochem Exam 2 to End

What are the 3 classes of lipids and what do they commonly do

Free fatty acids which are a common fuel, triacylglycerol which are a storage form, and membrane lipids which are phospholipids (membranes), glycolipids (membrane lipids w carbs), and steroids (polycyclic hydrocarbons w a variety of functions)

What is the definition of fatty acid

Hydrogen bearing carbon chain with a carboxylic acid at one end and methyl on the other

Saturated vs unsaturated fatty acid

Unsaturated has double bond, saturated is made of all single bonds

How is nomenclature of fatty acids achieved (numbering, alpha beta, double bond, and naming)

The numbering starts at the carbon of the carboxylic group. Atom 2 is the alpha carbon and atom 3 is the beta carbon. Triangle indicates double bond. Ionized is usually the name as this is the physiological form.

Fatty acids even/odd and what config are they

Usually there is an even number of carbon atoms w double bonds, usually cis config

What are polyunsaturated fatty acids separated by

At least one methylene group

How do double bonds and chain length affect polyunsaturated fatty acids

Cis double bonds increase fluidity as well as short chain length

Why are cis polyunsaturated fatty acids important

They are precursors to hormones and therefore essential in our diet

What are triacylglycerol composed of

Three fatty acids and glycerol backbone

Where are triacyclglycerols housed in the body and why do they hold more energy than glycogen

Adipose tissue, and it is because they are anhydrous

What is meant when you say that membrane lipids are amphipathic

The fatty acids are the hydrophobic part and the alcohol/phosphate are hydrophilic

What are phospholipids made of

Fatty acids (2 or more), a platform (glycerol or sphingosine), phosphate, and an alcohol

What is a phospholipid that uses glycerol and a phospholipid that uses sphingosine called

Glycerol is called phosphoglycerates and sphingosine is called sphingolipids

What is the importance of sphingomyelin

Sheath in nerve cells

What are glycolipids and what do they do

Glycolipids contain carbohydrates and play a role in cell/cell recognition on the extracellular surface

What are steroids

Tetracyclic platform with three cyclohexane rings fused with cyclopentane

What is the most common steroid and what does it do

Cholesterol is the most common and it is a precursor to hormones

What are the three ways that glycerol 3-phosphate can be obtained

Dihydroxyacetone phosphate getting and glycerol being phosphorylated

How does glycerol 3-phosphate turned into phospholipid or triacylglycerol

Glycerol 3-phosphate has two fatty acids added to make phosphatide. Then phosphatidate can react with triacylglycerol synthase on the ER to make triacylglycerol or they can react w an alcohol to make a phospholipid

What is the significance of Phosphatidic acid phosphatase

Main regulator enzyme converting between phosphatidate and diacylglycerol

How is cholesterol synthesized

Mevalonate is turned into isopentyl pyrophosphate, six molecules of isspentyl pyrophosphate is turned into squalene, then squalene cyclized and is turned into cholesterol

Expand on how mevalonate is made then 3-isopentyl pyrophosphate

Three acetyl CoA molecules make the Mevalonate (2 NADPH + 2H → 2NADP+ + CoA). Then Mevalonate gets turned into 3-isopentyl pyrophosphate by three phosphorylations and one decarboxylation

Expand on how six 3-isopentyl is turned into squalene

C5 → C10 → C15 (Farnestyl pyrophosphate) which combines the two molecules to make squalene

Where is the main site of cholesterol synthesis

The liver is the main site where synthesis HMG CoA reductase

What are the three stages of fatty acid processing

1. Degradation of the TAG into blood for transport, 2. Activation of the fatty acids and transport into the mitochondria, 3. Degredation to Acetyl CoA for processing

How are triacyclglycerols degraded and into what

Lipases cleave triacyclglycerols into three fatty acids and glycerol

What happens to the glycerol in the triacylglycerol degradation

Glycerol is not wasted, it enters the liver and can be metabolized by glycolytic or gluconeogenic pathways. Can be turned into dihydroxyacetone phosphate which can easily be turned into glyceraldehyde 3 phosphate

How do epinephrine and glucagon play a role in TAG degredation

Glucagon and epinephrine activate a g coupled protein that turns ATP → cAMP, activating protein kinase A, furthermore turns on lipase (phosphorylates) and perilipin which helps mobilize

How does the hormone-mediated degradation of TAG’s get coordinated with metabolism

At the same time as TAG degradation, glycogen gets broken down

How are fatty acids activated and what is special about the reaction

Fatty acids are joined with CoA to make Acyl CoA. This happens by first Acyl adenylate being made by breaking down ATP → AMP, then CoA displacing the AMP making Acyl CoA. This reaction is made irreversible by pyrophosphatase

How does the fatty acid get transported into the mitochondria

The fatty acid (acyl) gets transferred to carnitine to make acyl carnitine, and the acyl carnitine translocase allows for penetration into the membrane

Describe how the acyl carnitine translocase works

Oxidation of the beta carbon of acyl CoA (generating FADH), then this resulting molecule is hydrated and the DB is broken, then the resultant molecule is oxidized again (producing NADH), then the resulting molecule is cleaved by THIOLASE to make Acetyl CoA and Acyl CoA

What is an alternate fuel source synthesized by fatty acids and what are they

Ketone bodies which are made from acetyl CoA in the liver mitochondria and secreted into the blood

How are ketone bodies formed?

Two acetyl CoA’s make acetoacetyl CoA which gets another acetyl CoA to make an intermediate which quickly gets turned into acetone which spontaneously turns to acetoacetate and the formation of D-3-hydroxybutyrate by breaking up NADH

Describe diabetic ketosis

No insulin causes fats to be released from adipose tissue. Fats are degredated by the liver but cannot process acetyl CoA. Excess ketone bodies form, lowering pH, causing coma and death.

What happens to fuel sources during starvation

Protein degredation is the initial source of carbs, and after a few days ketone bodies are used as fuel for the brain. The ketones prevent the substantial degredation of tissues.

How does D-3-hydroxybutyrate get used as fuel

D-3-hydroxybutyrate reacts with a dehydrogenase to make acetoacetate (and NADH) which gets turned into acetoacetyl CoA (generating succinate), then 2 Acetyl CoA’s by thiolase.

What are the three stages of synthesis of fatty acids

Transfer of acetyl CoA out of mitochondria to cytoplasm, acetyl CoA activation into malonyl CoA, and then the repetitive addition and reduction of two carbon units to synthesize C16 fatty acid, with synthesis occurring on an acyl carrier protein.

How is Acetyl CoA taken out of the mitochondria

Acetyl CoA is turned into citrate, which moves out into the cytoplasm, the acetyl CoA gets removed and this creates oxaloacetate, then malate is made with NADH, which then turns to pyruvate with the removal of NADPH.

What does fatty acid synthesis use for reducing power and how is it produced

NADPH is used for reducing power and it can be produced by the oxidation of oxaloacetate

How Malonyl CoA is synthesized and what’s the significance

It is the committed step and is done by Malonyl CoA carboxylase.

What are the two steps of malonyl CoA synthesis

The first step is biotin-enzyme complex using ATP to make CO2 Biotin complex, then the CO2 Biotin works on acetyl CoA to make malonyl CoA and revert biotin-enzyme

What is the enzyme that catalyzes the formation of fatty acids and how does it work

Fatty acid synthase catalyzes the formation on acyl carrier proteins, making Acyl ACP and Malonyl ACP.

Expand on the condensation, reduction, dehydration, and final reduction steps

Acetyl ACP + Malonyl ACP combine to make Acetoacyl ACP, then this is reduced w NADPH, then a dehydration, and another reduction using NADPH.

How does the fatty acid synthesis terminate

The cycle will be continued until a C16 body is formed. The ACP is cut off at the end, leaving palmitate

What is the structure of the enzymes that work in fatty acid synthesis

Animals have entire enzyme on a single polypeptide chain. They are two identical chains (a homodimer). There are two distinct components with one selecting and condensing, and the other modifying part which reduction/dehydration

Where are longer fatty acids synthesized and how does this work

They are made by enzymes on the endoplasmic reticulum. These enzymes extend palmitate by adding two c units, using malonyl CoA.

How are double bonds introduced into saturated fatty acids and how does this play into essential fatty acids

Enzymes bound to the ER add the double bonds. Mammals lack the agbility to add double bonds past carbon 9, making essential fatty acids

How is Acetyl CoA carboxylase regulated

One way is phosphorylation with AMP Activated kinase, citrate activates by facilitating active polymers

How specifically does citrate work to promote active carboxylase

Inactive dimers get combined with the help of citrate to make active filaments, palmitoyl CoA inhibits carboxylase by depolymerization,

How is Acetyl CoA carboxylase regulated

Glucagon and epinephrine enhance AMPK activity (AMP activated kinase). Insulin stimulates the dephosphorylation of carboxylase.

How are amino acids turned into ammonium ions

Amino groups are transferred onto alpha ketoglutarate by aminotransferases which then is deaminated to make NH4

What enzyme is responsible for the deamination and what does it make

Glutamate dehydrogenase releases the NH4 (mitochondrial) also producing NADH or NADPH

Which amino acids can be directly deaminated

Serine makes pyruvate + NH4 while Threonine makes alpha ketobutyrate and NH4

What happens to the NH4 and where does this occur in humans

The excess ammonia ions are ultimately converted to urea in the urea cycle. This occurs within the liver of humans

What is the committing step of the urea cycle

This is the first step where ammonia is coupled with bicarbonate to make carbamoyl phosphate, and is facilitated by carbamoyl phosphate synthetase (CPS I)

What happens to carbamoyl phosphate once it is formed

Carbamoyl phosphate combines with ornithine to make citrulline, which is transported out of the mitochondria

What happens to citrulline after it is brought into the cytoplasm and then the next step followed by restarting the cycle

Citrulline is combined with aspartate to make arginosuccinate. Arginosuccinate is cleaved into fumarate and arginine. The arginine is cleaved into urea which is excreted and ornithine is transported back into the mitochondria to restart the cycle

How is the urea cycle, citric acid cycle, and transamination of oxaloacetate linked and how

Fumarate and aspartate. Fumarate can be converted into oxaloacetate by the citric acid cycle and then glucose by the gluconeogenic pathway

What happens with liver in the site of urea synthesis

Defects in any of the urea cycle enzymes increase NH4 in the blood, which is fatal

What is a ureotelic organism vs ammoniotelic organism

Ureotelic organisms excrete nitrogen as urea while ammoniotelic organisms excrete directly as NH4

What is phenylketonuria

A lack of phenylalanine hydroxylase, and excess phenylalanine is turned into phenylpyruvate, leading to impaired mental ability.

Whats the difference between plants/bacteria and animals in terms of amino acid synthesis

Plants and bacteria make all amino acids themselves while animals need to get some from their diet

Where do the carbon skeletons of amino acids come from

Intermediates of pentose phosphate pathway, glycolytic pathway, and the citric acid cycle

What are the two types of bacteria that can fix nitrogen (and third natural way)

Free-living bacteria which are non symbiotic and mutualistic bacteria which are symbiotic. Lightning can also fix nitrogen.

What enzyme is responsible for nitrogen fixation and how does it work

Nitrogenase enzyme complex is responsible. There are two parts, the reductase provides high energy electrons (ferredoxin) for reducing power while the nitrogenase uses the electrons to reduce N2 into NH3

What is the industrial process that fixes nitrogen

The Haber Process

Why does nitrogenase need ATP

N2 reduction is thermodynamically favorable but breaking the double bonds requires a ton of energy.

What is gluconeogenesis and where does it occur

Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors occurring primarily in the liver and some in the kidney

Which enzymes are not located in the cytoplasm

All enzymes are located in the cytoplasm other than pyruvate carboxylase (mitochondria) and glucose 6-phosphate (bound to the ER)

What are the three irreversible steps that have to be bypassed

Glucose + ATP to Glucose 6 phosphate, Fructose 6 phosphate + ATP to fructose 1,6 bisphosphate, and phosphoenolpyruvate + ADP to pyruvate

How does pyruvate get turned into phosphoenolpyruvate

Uses two enzymes; pyruvate carboxylase which is in the mitochondria, turning the pyruvate into oxaloacetate (which is tuned into malate to leave the mitochondria then back) as well as phosphoenolpyruvate carboxykinase which turns the oxaloacetate to phosphoenolpyruvate (using GTP)

How does fructose 1,6 bisphosphate turned into fructose 6 phosphate

This reaction is catalyzed by fructose 1,6 bisphosphatase

How is glucose 6 phosphate turned into glucose in the final step

Glucose 6 phosphate is transported into the lumen of the ER with glucose 6 phosphatase catalyzing the reaction. G6P is transported in with one transporter, with two more transporters for pi and glucose respectively.

What determines if gluconeogenesis or glycolysis prevails?

Energy charge. ATP needed? then glycolysis. Glucose needed? then gluconeogenesis

What are the specific molecules that regulate glycolysis vs gluconeogenesis

For glycolysis, there is ATP, citrate, and H+ which negatively regulate then AMP and F-2,6-BP which positively regulate. The opposite is true for gluconeogenesis. For glycolysis, alanine is a negative regulator along with F-1,6-BP as a positive regulator. For gluconeogenesis, acetyl coa is a positive regulator and ADP as a negative regulator.

What is the significance of fructose 2,6 bisphosphate

Stimulated PFK and inhibits fructose 1,6 bisphosphatase

What is interesting about the enzyme that makes and hydrolyzes fructose 2,6 bisphosphate

The PFK (synthesis) and fructose bisphosphatase (hydrolyzes) are ont he same polypeptide chain meaning that it is a bifunctional enzyme

What does glucagon do in terms of gluconeogenesis

Glucagon stimulates PKA, activating FBPase which increases gluconeogenesis. High F 6-phosphate stimulates phosphoprotein phosphatase which removes the phosphate, stimulating glycolysis through PFK2.

What is the significance of lactate in the muscle in terms of gluconeogenesis

The lactate is brought to the liver where glucose is made and brought back into the muscle for use

How does signal transduction work

Signal gets received, then amplified to transduction, which them leads to response (s)

What is the difference between fast and slow response

Fast response immediately creates an altered protein response while slow response goes though DNA to make a protein product

What are the 5 parts of signal transduction that are in common

1. Release of a primary message as a response to a physiological circumstance. 2. Reception of the primary message by a receptor, often an integral membrane protein. 3. Relay of the detection of the primary message to the cell interior by the generation of a intracellular second message. 4. Activation of effector molecules by the second messenger that result in a physiological response. 5. Termination of the signal cascade!

What are the three major classes of surface receptor proteins

Ion-channel-coupled receptors, g protein coupled receptors, and enzyme coupled receptors

What are the ways that extracellular signals can act short or long distances

They can be close and contact dependent w/membrane bound signaling, long distance by synaptic, paracrine with local mediators through signaling cells, and Endocrine through hormones in the bloodstream

What are the three steps in the lifecycle of a hormone

Biosynthesis, secretion of the hormone, transport of the hormone, recognition, relay/amplification, degradation and reset

What is a second messenger and some examples

A non protein molecule in the cell that act to transmit signals from a receptor to a target. Some examples are calcium and cyclic AMP/GMP