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KIN 217 - Human Biochemistry > Chapter 15 > Flashcards

Chapter 15 Flashcards

1
Q

Three Stages of Energy Generation from Food

A
  1. Large molecules in food are broken down into smaller molecules
  2. The many small molecules are processed/converted into key molecules of metabolism, mainly acetyl CoA
  3. ATP is produced from complete oxidation of acetyl CoA
  • Energy in form of ATP is essential for cell growth, cellular functions, and information processing
  • ATP is also essential for whole organism growth and development, daily activities and movements, and response to injury and repair
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2
Q

The three main things energy is needed for is _________

A

Movement: need muscle contraction to take place in cell

Active transport: involving molecules and ions

Biosynthesis: building complex molecules from simple ones (otherwise, growth and repair of damaged cells and tissues couldn’t occur)

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3
Q

Phototrophs

A

An organism that can meet its energy needs by converting light energy into chemical energy

  • Ex. plants
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4
Q

Chemotrophs

A

An organism that obtains energy by the oxidation of foodstuffs (through oxidation of carbon fuels)

  • Ex. humans
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5
Q

Energy Currency

A
  • All life uses ATP as ultimate energy currency
  • Carbon fuel oxidation generates ATP
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6
Q

Basic Principles that Govern Energy Manipulation in all Cells

A
  1. Molecules are degraded or synthesized stepwise in a series of reactions called metabolic pathways
  2. ATP is the universal energy currency of life
  3. ATP can be formed by the oxidation of carbon fuels
  4. Although many reactions occur inside cell, a limited # of reaction types that involve particular intermediates are common to all metabolic pathways
  5. Metabolic pathways are highly regulated
  6. The enzymes involved in metabolism are organized into large complexes
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7
Q

Metabolic pathways: general overview

A
  • Metabolism consists of two main types of reactions: energy yielding and energy requiring
  • The two main types of reactions will be linked such that energy liberated in one series of reactions will be channeled into another series of reactions that require energy
  • Metabolic pathways = stepwise reactions breaking down or synthesizing molecules
  • Overall reactions are actually limited and will often involve common intermediates
  • Metabolic reactions are defined as a specific substrate converted into a specific end point
  • Example: Glucose into pyruvate; glucose into acetyl-CoA; glucose into CO2, H2O, and ATP
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8
Q

Intermediary metabolism

A
  • There will be a multitude of metabolic pathways in a cell, which can be linear, branched, circular and/or interconnected
  • Pathways interact w/ other pathways
  • All reactions within a cell are considered “intermediary metabolism”
  • “Systems biology” is an emerging field that attempts to study the pathways all at once
  • Typically, isolated pathways are studied. Then link different components to different pathways together
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9
Q

Types of metabolic pathways

A

Catabolic:
- Convert energy from fuel (from carbon sources) to ATP (Ex. glycolysis)
- set of metabolic reactions that transform fuels into cellular energy
- using energy to breaking down complex molecules
- big structures to small (= uses/releases energy)

Anabolic:
- Requires energy for synthesis (Ex. gluconeogenesis, synthesis of DNA, glucose, or fats)
- set of metabolic reactions that require energy to synthesize molecules from simpler precursors
- needs energy to create big complex molecules from small ones
- small structures to big (= needs energy)

 Catabolic and anabolic pathways often share reactions (ex. enzymes) and there may be shuttling of molecules between these two types of pathways

 There will be key, regulated irreversible reactions and steps for distinct pathways

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10
Q

Thermodynamics of Pathways

A
  • Reaction coupling  couple unfavorable endergonic reactions w/ a favorable exergonic reaction and it will be spontaneous and favorable moving forward
  • For reaction coupling…
  1. Each reaction must be SPECIFIC in the pathway
  2. The overall pathway MUST be thermodynamically favorable
  • Exergonic = releases energy, negative G, WILL be spontaneous
  • Endergonic = requires energy, positive G, WON’T be spontaneous
  • thermodynamically unfavorable reaction CAN be converted into a favorable reaction by coupling it to the hydrolysis of ATP
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11
Q

ATP: High Energy Phosphates

A
  • ATP = universal energy currency, attributed to the high energy phosphates the molecule has
  • Hydrolysis of ATP is exergonic b/c triphosphate unit contains 2 unstable phosphoanhydride bonds
  • Energy is released upon ATP hydrolysis and used to power cellular functions
  • Hydrolysis of ATP to ADP and Pi will liberate -30.5 kJ/mol (-7.3 kcal/mol)
  • Hydrolysis of ATP to AMP and pyrophosphate will liberate -45.6 kJ/mol (-10.9 kcal/mol)
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12
Q

Properties of ATP

A

Factors that contribute to ATP being an ideal energy currency:
1. Electrostatic repulsion
2. Resonance stabilization
3. Increase in entropy
4. Stabilization due to hydration

Electrostatic repulsion:

 at pH 7.4, phosphates have negative charges

 Triphosphate of ATP carries 4 negative charges

 negative charges repel each other, creating electrostatic repulsion. Repulsion is reduced when ATP is hydrolyzed

 ester bond in AMP displays less repulsion (= less energy) then anhydride bonds between phosphate groups

 ADP will contain one anhydride bond
 ATP will contain two anhydride bonds (cleavage of bonds = more energy)

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13
Q

High Phosphoryl-transfer potential

A
  • The high phosphoryl-transfer potential of ATP provides further explanation of the utility of ATP as the universal energy currency
  • The greater energy yield from ATP hydrolysis provides evidence for the unique molecular structure of ATP and its utility as energy currency

 AKA, presence of phosphate group and associated bond cleavage is not enough to generate high levels of free energy

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14
Q

High Phosphoryl-transfer potential and important molecules

A
  • Phosphoryl transfer potential = important form of cellular energy transformation
  • Phosphoryl transfer potential refers to transfer of phosphate groups
  • Molecules (including ATP) w/ phosphate groups are carries of phosphoryl groups
  • Biologically important molecules w/ high phosphoryl transfer potential include:

 1, 3-BPG (1,3-biphosphoglycerate)

 PEP (phosphoenolpyruvate)

 Creatine phosphate

  • Phosphoryl transfer potential of ATP is LESS than the three molecules above but GREATER than glucose-6-phosphate or glycerl-3-phosphate

 Thus, ATP has intermediate phosphoryl transfer potential amongst biologically important molecules

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15
Q

Resonance Stabilization

A

Resonance stabilization - where ability to share electrons across molecule will lead to lower energy state, especially where there’s more sharing of electrons

  • Orthophosphate has 4 possible resonance states due to electron sharing
  • In ATP, w/ two anhydride bonds, electron sharing and possible resonance states are limited to only 3 possible states - limitation contributes to higher energy contained within ATP
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16
Q

Phosphoanhydride bonds

A
  • bonds between phosphate molecules
  • high energy bonds linking phosphate groups
  • phosphate-phosphate bonds formed when compounds like ATP or ADP are created
17
Q

Phosphates in Biochemical Processes

Phosphates and their esters are prominent in biology b/c…..

A
  1. Phosphate esters are thermodynamically unstable, yet kinetically stable
  2. Phosphate esters are stable b/c the inherent negative charges resist hydrolysis
  3. Since phosphate ester are kinetically stable, they are ideal regulatory molecules: can be added to molecules by kinases and removed by phosphatases = covalent modification
18
Q

ATP: Other Roles & Signal Transduction

A
  • ATP has other roles and may be involved in signal transduction
  • Intracellularly, cells maintain very high concentration of ATP
  • ATP may function as a biological hydrotope w/ hydrophilic and hydrophobic characteristics
19
Q

Hydrotrope

A

Amphipathic molecule w/ hydrophobic and hydrophilic component, but unlike fatty acids, hydrophobic part is too small to self-aggregate

 Hydrophobic component would be attributed to adenine and less prominent

 Hydrophobic nature is thought to contribute to its ability to prevent formation of protein aggregates within cytoplasm, thus maintaining protein solubility

20
Q

ATP (adenosine triphosphate)

A

ATP = immediate donor of free energy for biological activities and systems

  • Amount of ATP in the body is 100g
  • Amount of ATP in a system is limited
  • ATP must be constantly recycled to provide energy to power cells and organisms
21
Q

Oxidation-Reduction Reactions

A
  • key to understanding metabolic reactions and pathways
  • Oxidation reactions = loss of electrons. Must be paired w/ reduction to gain electrons
  • Paired reactions are called oxidation-reduction reactions (redox reactions)
  • Carbon atoms in fuels are oxidized to yield CO2, and electrons are accepted by O2 to form H2O
  • The more reduced a carbon atom is, the greater the amount of more free energy that will be released upon oxidation
  • Fats = more efficient food sources than glucose b/c fats are more reduced
22
Q

Reduced vs. oxidized

A
  • Reduced compounds can oxidize to release electrons
     These released electrons power ETC to make energy (ATP)
  • Oxidized compounds have already lost electrons
     Have limited ability to power ETC

More reduced compounds will liberate more energy than more oxidized compounds

23
Q

Oxidation-reduction reactions & high phosphoryl transfer potential

A

Compounds w/ high phosphoryl potential can be coupled to carbon oxidation for ATP synthesis

 Essence of catabolism is capturing the energy of carbon oxidation as ATP

 Oxidation of carbon atom may form a compound w/ high phosphoryl transfer potential that can then be used to synthesize ATP

24
Q

Glyceraldehye-3-phophsate oxidation into 3-phosphoglyceric acid:

A
  1. Carbon oxidation of glyceride-3-phosphate generates an acyl phosphate, which is coupled to the capture of electrons in the reduction of NAD+ to NADH

 This generates 1,3-BPG

  1. The high phosphoryl-transfer potential of 1,3-BPG is utilized to generate ATP w transfer of phosphoryl group to ADP

** This reaction demonstrates carbon oxidation couple to ATP-synthesis AND pairing of oxidation-reduction reaction**

25
Q

Two common characteristics of activated carriers

A
  1. Carriers are kinetically stable in absence of specific catalysts
  2. Metabolism of activated groups is accomplished w/ small # of carriers
26
Q

4 Activated carriers: General overview

A

NADH and FADH2 - activated electron carriers for fuel oxidation

NADPH -activated electron carrier for biosynthesis

Coenzyme A - activated 2-carbon carrier molecule

27
Q

NAD+

A

Structure:
- An adenine
- 2-ribose sugars
- 2-phosphates
- A nicotinamide ring
 The reactive part
 derived from vitamin niacin (B3) (panel A)

  • Nicotinamide adenine dinucleotide (NAD+) = major electron carrier in oxidation of fuel molecules
  • Redox reaction involving NAD+ = hydrogenation reaction w/ protons accompanying electrons
  • Reduction of NAD+ to NADH occurs at nicotinamide ring, which accepts protons and electrons
  • In oxidized state, positive change of NAD+ resides on nitrogen atom within nicotinamide ring
27
Q

FAD

A

Structure:
- An adenine
- 1-ribose sugar
- 2-phosphates (ADP)
- A flavin moiety w/ an isoalloxazine ring
 The reactive part
 Derived from vitamin riboflavin (B2) (panel A)

  • Flavin adenine dinucleotide (FAD) = second major electron carrier in oxidation of fuel molecules
  • Redox reaction involving FAD = hydrogenation reaction w/ protons accompanying electrons (panel B)
  • Reduction of FAD to FADH2 occurs at N atoms of isoalloxazine ring which accept protons and electrons
28
Q

NADP+

A
  • Activated carrier nicotinamide adenine dinucleotide phosphate (NADP+) = major electron carrier for biosynthetic pathways
  • NADP+ differs from NAD+ by a phosphoryl group (arrow), which is how cellular enzymes can distinguish between an anabolic pathway and a catabolic pathway
  • In biosynthetic pathways, NADP+ serves as an electron donor and gets reduced to generate NADPH

Example:
- For the biosynthesis of fatty acids, reduction of an acetyl carbon atom to a methylene group requires four electrons, which are supplied by 2-molecules of NADPH + (H+) (each donating 2-protons)

29
Q

CoA

A
  • Coenzyme A (CoA or CoA-SH) = activated carrier of acyl groups, such as acetyl groups
  • Acyl groups contain a carbonyl and an alkyl group (w/ only C and H’s)
  • Acetyl group = specific type of acyl group w/ a carbonyl and methyl group
  • Acyl groups are linked to the sulfhydryl group of CoA by thioester bonds
  • Hydrolysis of thioester bonds is thermodynamically favorable
  • Acetyl-CoA has high transfer potential since transfer of acetyl group will be exergonic
30
Q

Other carriers

A

Many activated carriers are derived from vitamins

B vitamins function as coenzymes

Vitamins A, C, D, E and K play a variety of roles but DO NOT serve as coenzymes
- Instead, these vitamins have integral roles in immunity, digestion, or as hormones

31
Q

Metabolic processes are regulated w/ three common themes

A
  1. Amount of enzymes
  • Prescence or absence and quantity of an enzyme will determine whether an enzyme catalyzed reaction will proceed
  • Enzyme concentration will be regulated at the level of gene expressions and through proteases that target enzymes
  • Gene expression can be upregulated to increase amount of enzyme available
  1. Regulate Enzyme Activity
  • This level of regulation is through the regulation of catalytic activity
  • This level of regulation is through allosteric regulation or by reversible covalent modification
  • Hormone pathways can be involved in the reversible covalent modification

 Ex. in the epinephrine pathway, hormone epinephrine regulates that catalytic activity of protein kinase C through a series of reactions that involve secondary messengers, most notably cAMP

  1. Substrate accessibility
  • This will also be a form of regulating metabolic processes
  • Compartmentalization of reactions allows for control of substrate accessibility to certain enzymes, especially when reactions are compartmentalized to different locations in the cell

 Ex. fatty acid oxidation takes place in mitochondria, while fatty acid synthesis takes place in cytoplasm
Metabolic processes are regulated w/ three common themes

32
Q

Metabolic Processes are Regulated

A
  • Many reactions in metabolism will be controlled by the energy status of the cell
  • Energy status = energy charge
  • Energy charge = the concentration of ATP plus half the concentration of ADP over sum total of all the adenine nucleotide molecules, ATP, ADP, and AMP
  • Energy charge is on scale from 0 to 1, with zero representing high levels of AMP and 1 representing high levels of ATP
  • W/ high amounts of ATP within a cell, the ATP-generating pathways will decrease and ATP utilizing pathways will increase
  • Energy potential of most cells is between 0.8-0.95
  • Another way to determine energy status of a cell is w/ phosphorylation potential

 phosphorylation potential is directly related to the available free energy on the concentration of inorganic orthophosphate plus the concentration of ADP relative to the conception of ATP

33
Q

Orthophosphate

A
  • kind of phosphate
  • composed of one phosphate unit per molecule
  • has 4 possible resonance states due to electron sharing
34
Q

Phosphatases

A

enzymes that removes phosphate groups from proteins

35
Q

Kinase

A

enzyme that catalyzes the attachment of a phosphoryl group to a substrate by using ATP as a phosphoryl donor

attaches phosphate group to a protein

36
Q

Feedback inhibition

A
  • first member of an entire series of polyphosphates

KIN 217 - Human Biochemistry (34 decks)

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