Graphing enzymes and metabolic pathways

Graphs

Used as visual representation

Help you see patterns or relationships

Several kinds of graphs depending on which data

What are the two ways a graph title can be written

Effect of dependent variable on independent variable

or

dependent variable vs independent variable

How to label your axis

X = horizontal, independent

Y = vertical dependent

Make sure to include units

How to graph a scale

Count # of lines on graph → Take highest data point value and divide by the # of lines available and round up your answer to the nearest whole #

What is constantly happening in our cells so that we can carry out activities we do on the daily.

Biochemical reactions → which are also used for homeostasis

Each one must happen very fast so = all cells involved = out put necessary energy required to live

How is it possible for cells to constantly covert chemicals from one form to another to produce usable energy

Thanks to enzymes

Metabolism

Many chemical reactions occur in our cells is collectively called metabolism

Metabolism = maintaining homeostasis

A + B → C + D

What are AB and what are CD

AB = reactants

CD = Products

Metabolic pathway

A series of conversions that is orderly and step wise series of chemical reactions

One reactions becomes the reactant next recaction

A → B → C→ D → E → F →

Explain this sequence

A = reactant

B = product, but reactant for C

C = product, but reactant for D

Whats not efficient/ not possible in biological systems

to have on reactant and one product in a linear fashion

To hace single reaction that can produce complex molecules from simple reactants

Metabolic pathwys (multiple)

One path way can lead to several others

One intermediate product of one pathway can be the starting reactant of another pathway

What does having more than one step mean for Metabolic Pathway (Multiple)

It means reactions can be controlled overall in multiple structures

Our bodies cannot with stand high heat required for some reactions so what does our body use

Our bodies use enzymes as catalysts to over come that barrier

Enzymes

Proteins created by protein synthesis

Enzymes act as catalysts that speed up chemical reactions without being consumed or changed

Wh

What do enzymes not determine

If a reaction goes forward, they simply increase the rate of reactions En

Enzymes are highly __________ and speed up _________ reaction(S)

Specific, One

How do enzyme names usually end

“ase” = Lactase, Amylase, Nuclease, Lipase

'“sin” Trypsin, pepsin

What are molecules that react with enzymes called

Substrate

Whats another word for substrate

Reactant

Why are enzymes considered very specific

Enzymes = specific bc each enzymes binds only to a particular substrate forming an enzyme substrate complex

What determines an enzyme can form a complex with a substrate

The substrate must have the correct shape to fit the enzymes active site

What role does the presence or absence of an enzyme play in a reaction

Determines wether specific reaction will take place, as enzymes = catalysts

What is activation energy

Required energy for a chemical reaction to occur

Why is Ea important

There are many pathways in the cell, and we cannot heat up our bodies to the point for the reactions to happen

If Ea isnt high enough then reactions would trigger all the time

Dont want it too low or reactions wont happen

Energy of activation (no enzyme)

If no enzyme is present and conversion of substrate to product requires a higher Ea

Energy of activation (with enzymes)

Enzyme is present and conversion of substrate to product requires lower Ea

Whats important to note about Ea

Product of a reaction is the same wether an enzyme is present or not

Depending on the reaction conditions, more products may form or the rate may be altered

What do delt G and delta H represent

(delta energy) and (heat energy) represent net change or net difference of energy / heat

What something all enzymes do regardless of the specificity

They all function the same way

What is the central dogma of the enzyme complex

1 enzymes

1 function

Why are there many different enzymes

B/c each enzyme is specific to one substrate and one type of chem reaction

How do all enzymes function

they bind to a specific substrate, lower activation energy, speed up the reaction, release the products and remain unchanged

What happens to an enzyme after a reaction

it is not used up and can be reused again

How many reactions does an enzyme usually catalyze

one specific chemical reaction

What is the main function of an enzyme

to speed up chemical reactions by lowering activation energy

WHat is the active site of an enzyme

the specific region of an enzyme where the substrate binds and the chemical reaction takes place

What is an enzyme substrate complex

Temporary compled formed when a substrate binds to the enzyme active site before the reaction occurs

When does the enzyme substrate complex form

It forms after substrate binds to the enzyme and before the products are released

Where does the chemical reaction occur

At the enzymes active site while the enzyme substrate complex is formed

What happens in a degradation reaction

One substrate is broken down into two or smaller products

What happens in a synthesis reaction

Two or more substates join together to form one larger products

What happens to the enzyme after the products are released

The enzyme remains unchanged and can catalyze another reaction

What are enzymes made of

Enzymes and proteins

Why does each a enzyme have a unique active site

B/c proteins have different combos of R groups (side chains) from their amino acids

What properties can an enzymes active have

Large or small

Acidic or basic

Hydrophilic hydrophobic

Positively charged, negatively charged or neutral

Why are enzymes specific to their substrate

Bc the acrive sites unique shape and chemical properties only fit certain substrates

What happens when a substrate binds to the active site

An enzyme substrate complex forms the reactions occurs products are released and the enzyme unchanged

What happens to enzyme activity as temp increases

The reaction rate increases bc molecules move faster up to the enzymes optimum temp

Do enzymes work at all temp

No each enzyme = specific range of temp and pH where it functions

S.H.A.P.E

S = Specific active site

H = heat increases reactions (to a point)

A = Active site is formed by amino acid R groups

P = Protein (Enzymes are proteins)

E = Extreme conditions cause denature

What determines how an enzyme works

The shape of its active site determines which substrate it can bind to and what reaction it can catalyze

What is the enzyme equation

Enzyme + substrate → Enzyme Substrate complex → Enzyme + product

(E + S → ES → E + P)

What is a cofactor

A non protein helper often an inorganic ion, that helps an enzyme function properly

What are some inorganic cofactors

Metal ions = (Iron, Zinc, Copper)

How do cofactors help enzymes

They can:

Activate enzymes

Help stabilize the enzyme

Donate or accept atoms or ions (Such as H+)

Help the reaction occur Ar

Are cofactors proteins

No they are non protein molecules or inorganic ions Wh

What is a co enzyme

Organic, non protein molecule that helps enzymes functions. Most coenzymes are vitamins or made from vitamins

What is the difference between a coenzyme and a cofactor

Cofactors = Usually an inorganic ion

Coenzyme = Organic molecule often a vitamin

Why are vitamins important for enzymes

Many vitamins are part of co enzymes that are essential for enzyme activity

Give an example of a vitamin used as a coenzyme

Riboflavin (Vitamin B) part of coenzyme FAD → helps with metabolic reactions

What happens if the body lacks vitamins

Enzymes cannot function properly leading to vitamin deficiency symptoms

What is an apoenzyme

the protein portion of an enzyme that is inactive until a cofactor or coenzyme binds

What is a holoenzyme

The active enzyme formed when an apoenzyme binds to its cofactor or coenzyme

Why is an apoenzyme inactive

BC it needs a cofactor or coenzyme attached before it can function

What does a coenzyme do

It binds to an inactive enzyme (apoenzyme) and helps activate it so it can catalyze a reaction

What happens when a coenzyme binds to an apoenzyme

An active holoenzyme is formed

What is the active site

The part of an enzyme where the substrate binds and the chemical reaction occurs

What is the LOCK AND KEY model

A model stating that an enzyme active site and its substrate fit together perfectly from the beginning like a lock and its matching key

Why is it called the lock and key model

Bc only the correct substrate fits into the enzyme active site just as only the correct key fits a lock

What does the lock and key model explain

Explains the specificity of enzymes = each enzyme binds to specific substrate

What is the induced Fit model

A model in wich the enzyme changes its shape slightly when the substrate binds allowing a better fit

What happens when a substrate binds to an enzyme in the induced fit model

The enzyme undergoes a slight conformational change (Shape change) to fit the substrate more closely

Why is it called the induced Fit model

BC the substrate induces (causes) the enzyme to change shape for a tighter fit

What happens after the reaction is complete in the induced Fit model

The products are released and the enzyme returns to its original shape

Does the enzyme permanently change shape in the induced fit model

No the shape change = temprorary

What is conformational change

A temp change in the shape of an enzyme that improves binding to the substrate

What is the advantage of the induced fit model

It allows the enzyme to bind the substrate more tight = reaction more effecient

What happens if an enzymes shape changes

Its activity decreases or stops bc the substrate no longer fits the active site

What are the five main factors that affect enzyme activity

Temp

pH

Substrate concentration

Enzyme concentration

presence of inhibitors

What is an inhibitor

is a substance that slows down or completely stops a specific chemical reaction or biological process.

How does increase in temp affect enzyme activity

Increases molecular movement = more collisions btwn enzymes and substrates = increased reaction rate

What is the optimum tmep

The temp at wich an ezyme works at its maximum rate

What happens to human enzymes above 45 degrees

usually denature losing shape and function

What happens to an enzyme at low temps

They become inactive bc molecules move more slowlu resulting in fewer collisions with substrates

Are enzymes denatured at low temps

No = inactive but = active when warmed

Why does enzyme activity decrease after the optimum temp

High temp = denatures enzyme changing → shape

What happens to denatured enzymes

Lose secondary and tertiary protein structure → changing shape of active site

What is the optimum pH for most human enzymes

6-8 (near neutral)

Why do most human enzymes work best at pH 6-8

bc most body tissue have close to neutral pH

What is the optimum pH for pepsin

About pH 2 bc it works in the acidic environment of the stomach

Why cab pepsin function at pH 2

bc the stomach = hydrochloric acid creating a highly acidic environment

What is the optimum pH for trypsin

Ph of 8 bc it works in small intestine

What happens if the pH is too high or too low

The enzyme denatures changing the shape of its active site so it can no longer form an enzyme substrate complex

What happens when substrate concentration increases

The reaction rate increases bc more enzymes substrate complexes can form

Why does increasing substrate concentration increase the reaction rate

More substrate molecules collide with enzyme active sites

What is enzyme saturation

The point where all enzyme active sites are occupied so the reaction cannot go any faster

What happens after the enzyme saturation is reached

Increasing substrate concentration no longer increases the reaction rate

What happens if the substrate concentration decreases

The reaction rate decreases bc fewer enzyme substrate complexes form

On a substrate concentration graph what does the plateau represent

Enzyme saturation all active sites are occupied