Biology - Chapter 3 An Introduction to Metabolism

metabolism

the sum of all chemical reactions in a cell or organism

the ability of a living organism to do work (move, grow, digest, transport sucrose across a cell membrane) requires

energy

2 main types of energy in biology

1. kinetic

2. potential

kinetic energy

occurs as a result of motion

potential energy

stored within an object

• in biochemistry, this is often energy stored in chemical bonds

the total amount of energy in any closed system is

constant

energy cannot be _______ or _______. it can only be converted from _________ into _______

created, destroyed, one form, another

if a physical system gains an amount of energy, another physical system must

experience a loss of energy of the same amount

eg. photosynthesis converts light energy to chemical potential energy (carbs). this chemical energy is then consumed by animals and converted into high energy molecules (ATP), which is converted to other types of energy (thermal and kinetic)

however, the above example depends on chemical reactions where bonds are broken, and bonds are formed

when chemical bonds break

energy is absorbed

when chemical bonds form

energy is released

bond energy

the minimum amount of energy that is required to break a particular type of bond

every time energy is converted from one form to another, some of that energy is

lost (becomes unusable)

therefore, energy transfer is not 100% efficient

entropy

a measurement of disorder in a system

astronomers tell us that the Universe is continually increasing in entropy

what entropy means in terms of biology

• when large particles are broken down into smaller particles (digestion)

• when particles spread out (diffusion)

what entropy means in terms of chemistry

• when solids react to form liquids or gases

• when liquids react to form gases

• when the total number of product molecules is greater than the total number of reactant molecules

spontaneous reactions

• happens without requiring the input of energy from the cell

• can only happen if the total amount of entropy increases

non-spontaneous reactions

• whenever cells use energy (endocytosis), entropy decreases

• cells use this energy to maintain order/organization

as spontaneous reactions proceed, __________ is released

free energy

free energy

available to perform work

spontaneous example

a brick wall ages and crumbles and falls apart into a random pile

in biology, this could be carbs being broken down into monosaccharides. this makes energy available to the cell (catabolic reaction)

entropy ______ because disorder _______

increases, increases

non-spontaneous example

a random pile of bricks. these bricks will not just build themselves into a wall. that will require energy.

in biology, this could be monosaccharides being built into carbohydrates (anabolic reaction)

disorder to order will _______ entropy

decrease

energy in sunlight for plants, food for animals maintains cell in a highly ordered state — the exact opposite of entropy. does this mean living organisms do not obey the second law of thermodynamics?

• no, because the release of by-products such as thermal energy and CO₂ increases the entropy of our surroundings, while the organisms themselves maintain order

  • in other words, the entropy of the organism decreases while the overall entropy of the Universe increases

ATP

adenosine triphosphate

ATP is the _____ for _________

• energy carrier, almost all energy-driven actions in every cell on Earth

  • eg. mechanical work (beating of cilia or the contraction of muscle fibres)

  • transport work (pumping substances across membrane against a concentration gradient)

  • chemical work (protein synthesis)

what is ATP made of

• nitrogenous base called adenine is linked to:

• a 5-carbon sugar called ribose is liked to:

• a chain of 3 phosphate groups

what does the 3 phosphate groups being crowded together do?

• their close proximity creates a mutual repulsion of their electrons

• similar to the potential energy in a compressed spring

• the last phosphate wants to split off from the others and the result is a release of the potential energy stored in the bond

• the terminal phosphate is easily broken off by a hydrolysis reaction to form ADP (adenosine diphosphate) and inorganic phosphate

why is energy released when a bond is broken?

• breaking off the terminal phosphate is energetically favourable because of the repulsion between the phosphates

• the entropy of the system is increased

  • 1 molecule split into 2 molecules

• the H and the OH from the water molecules form 2 new bonds with the ADP and the inorganic phosphate

overall the reaction releases energy, about 7.3 Kcal/mol of energy is released

ATP is _______ to form ______ and ______

• hydrolysed, ADP, inorganic phosphate

  • energy is released during this reaction

to convert ADP back into ATP, _________ reaction is used and the ________ is _________

• the opposite, a phosphate is added back onto the ADP

  • requires energy

    • energy comes from the food we eat, carbs, fats, proteins

why is ATP called the universal energy ‘currency’

it directly supplies the energy that powers nearly every cellular function

the types of work carried out by ATP includes ______, ______, and ______

mechanical, transport, and chemical work

mechanical work

• beating of cilia or movement of flagella

• contraction of muscle fibres

• movement of chromosomes during mitosis/meiosis

transport work

• process of pumping substances across membranes against their concentration gradient

chemical work

• process of supplying chemical potential energy for non-spontaneous, endergonic reactions, including protein synthesis and DNA replication

phosphorylation

the transfer of a phosphate group, usually from ATP, to another molecule

how is ATP regenerated

the P_i is synthesized back onto the ADP with the addition of free energy

why is ATP used as the universal energy currency rather than cells using the energy, for example, from food?

• cells use ATP as an immediate source of energy because it has specific properties that are important for the biochemical reactions that allow proper cell functioning

• complex food molecules also require numerous reactions to release their energy, but ATP can be created and accessed immediately

enzyme

a biological catalyst (usually a protein) that speeds up a chemical reaction

approximately how many enzymes are present in a typical cell

about 4000 different enzymes in a typical living cell

what must happen for a chemical reaction to move forward

it must overcome an energy barrier

what do enzymes do to help this process

enzymes bind a specific reactant (or reactants), called a substrate; in doing so, they lower the energy barrier so that the reaction proceeds at a faster rate than it would without the enzyme

substrate

a substance that is recognized by and binds to an enzyme

active site

a pocket or groove in an enzyme that binds its substrate

induced fit model

a model of enzyme activity that descries how an enzyme changes shape to better accommodate a substrate

why are enzymes able to change shape in order to make the active site even more precise

because they are not rigid objects but are flexible

catalytic cycle

cofactors

• non-protein group that binds precisely to an enzyme

• often nonmetals (iron, copper, zinc, manganese)

• essential for catalytic activity

• eg. an enzyme that is essential for providing one of the key components of the chemical pathway within mitochondria for the production of energy requires a magnesium cofactor to function properly

coenzyme

• organic cofactors

• derive from water-soluble vitamins

• many coenzymes shuttle molecules from one enzyme to another

• ex. NAD⁺ , a derivative of vitamin B₂ acts as a electron carrier during a number of biochemical pathways

enzyme inhibitors

molecules that bind to an enzyme and decrease its activity, lowering the rate at which an enzyme catalyzes a reaction

competitive inhibition

• a situation in which a competitor substance binds to a normal substrate binding site to block enzyme activity

• the inhibitor actually competes with the normal substrate for access to the active site of the enzyme

noncompetitive inhibition

• a situation in which molecules bind to an enzyme at a site that is not the active site, thus blocking enzyme activity

• non-competitive inhibitors bind to an enzyme at a location other than the active site. this changes the shape of the enzyme, reducing the ability of the substrate to bind efficiently

molecules that naturally regulate enzyme activity in a cell often behave like

a noncompetitive reversible inhibitor

these molecules bind to a special site on the enzyme called an

allosteric site

this causes a change in

the shape of the enzyme, thus affecting the active site

this type of regulation is called

allosteric regulation

feedback inhibition

the regulation of a pathway by one of the products of this pathway

what happens in feedback inhibition

the regulation of the pathway by one of the products in the pathway

feedback inhibition happens in the pathway that produces ________ from _________.

isoleucine, threonine

product of the feedback inhibition pathway

isoleucine

what happens if isoleucine accumulates in excess

it slows or stops the pathway by acting as an allosteric inhibitor of the enzyme that catalyzes the first step in the pathway

enzyme activity is significantly altered by changes in

pH and temperature

what happens when there are deviations from an enzyme’s optimal conditions

leads to decreased activity, often represented by a peaked curve in activity graphs

each enzyme has an optimal pH for peak efficiency, usually around ____ for cellular processes

pH 7.5

what happens when an enzyme’s pH deviates from it’s optimal amount?

the enzyme’s activation site is severely impacted, and potentially reduces reaction rates to 0

enzymes secreted from cells may have ________ pH optima

varying

pepsin optimal pH level

1.5 (stomach acidity)

trypsin optimal pH level

8 (alkaline intestinal environment)

temperature influences enzyme activity through __ main processes

2

general reaction rate

higher temperatures increase reaction rates due to increased molecular motion and collision frequency

protein structure

higher temperatures enhance the kinetic motion of amino acid chains in structures, but excessive heat leads to denaturation, breaking the enzyme’s 3D structure

enzyme activity generally ______ for every ___ increase in temperature from ____ to _____

doubles, 10°C, from 0°C to 40°C

what happens when the temperature in an enzyme’s environment goes beyond 40°C

it begins to denature, leading to a decrease in activity

for most enzymes, the peak in activity lies between

40°C to 50°C

for most enzymes, activity sharply declines at ____ and reaches 0 around _____

55°C, 60°C

effects of enzymes on animal feed

degradation of the components to feed to improve nutrient digestion and uses of the feed

effects of enzymes on brewing

faster maturation of beer; removal of carbohydrates in lighter beer

effects of enzymes on dairy

cheese making; removal or conversion or lactose in milk

effects of enzymes on detergent

breakdown of starch and fatty stains as an active biological component of powder and liquid detergents; colour brightening and softening of cotton garments

effects of enzymes on leather

unhairing, batting, and defatting; soaking to soften hides and skins

effects of enzymes on starch

production of glucose, dextrose, fructose, and special syrups for baking and soft-drink production

wine and juice

degradation of the protein pectin for clarification and increase in juice yield