Bio 110 Exam 2 Matkin

What is a enzyme?

Part of catalysts in living organisms which help speed up chemical reactions

what is ribozymes?

catalytic RNA

what does enzyme made up of?

protein catalysts

why are catalysts necessary to speed up a reaction?

enzyme helps stretching or straining of the bonds so the 2 molecules can interact with each other

activation energy

energy required to start a reaction by breaking bonds in the reactant molecules

transition state

unstable state where bonds are stretched (activation energy lowered)

how to overcome activation energy?

heat and enzymes by stretch and strain

what type of reaction is burning glucose?

exergonic reaction

what are the products of burning glucose?

CO2 and H2O

does burning of glucose required additional energy?

no

how does enzyme speed up chemical reaction?

by lowering the activation energy

does enzymes affect free energy?

no

enzyme only speed up reactions that would occur without them

true

how does enzyme lower activation energy?

1. positioning reactants together to facilitate bonding

2. straining bonds in reactants to achieve transition state

enzymes are ________ for the reactions they catalyze

specific

substrates

The reactants that bind to the enzyme

active site

Region on enzyme where substrate binds.

enzyme + substrate =

enzyme-substrate complex

results from the fit between the shape of the active site and the substrate

specificity

enzyme only bind with the right shape and fit with the substrate

lock and key metaphor

can enzyme changes shape? why?

yes, because of the chemical interactions with the substrate.

induced fit

confirmational changes and bring chemical groups of the active site together due to enzyme and substrate

catalyst reaction

stretching and straining on the bond

steps of an enzyme-catalyzed reaction

1. Substrate Binds

2. enzyme undergoes conformation change that binds the substrates more tightly

3. substrates are converted to products

4. products are released

affinity

attraction of enzyme

enzyme with high affinity

conduct catalyst

enzyme with low affinity

more substrate needed

velocity

amount of product produced per second

what would happen if the velocity of the reaction is high?

the substrate will be higher. producing more product (with max velocity)

Saturation

all active site is filled and cannot go faster. enzymes have to wait in line till its turn

V max

Enzyme is working at it's maximum rate.

What is the Michaelis constant (Km)?

The concentration of substrate at which an enzyme works at half its maximum velocity.

What does the Michaelis constant (Km) measure?

It measures how tightly the substrate is bound to the enzyme.

competitive inhibition

Inhibitor competes with substrate for active site.

competitive inhibitor enzyme reaction

Km increase = more substrate needed

noncompetitive inhibition

binds at allosteric site.

noncompetitive inhibitor enzyme reaction

lowers V max without affecting Km

factors that affect enzyme activity

temperature and pH

metabolism

All of the chemical reactions that occur within an organism

metabolic pathway

begins with a specific molecule and ends with a product

what does each step of metabolic catalyzed by?

a specific enzyme

catabolic reaction

exothermic reaction in organisms

how does catabolic pathway release energy?

by breaking down complex molecules into simpler compounds

Anabolic reaction

endothermic reaction in organisms

why does anabolic pathway consume energy?

to build complex molecules from simpler ones

does anabolic pathway must coupled to exergonic reaction?

yes

what does building blocks use to recycle building blocks

catabolic reaction

what does catabolic reaction use to store energy?

ATP and NADH

how to make ATP?

substrate level phosphorylation and chemiosmosis (oxidative phosphorylation)

how substrate-level phosphorylation make ATP?

- enzyme directly transfers phosphate from one molecule to another molecule

- oxygen not needed

how does chemiosmosis create ATP?

energy stored in an electrochemical gradient is used to make ATP from ADP and P

what reaction transfer electrons between reactants?

redox

Oxidation

loss of electrons

reduction

gain of electrons

how are energy intermediates create?

by the oxidation of organic molecules

NAD+

oxidized

NADH

reduced

where does electrons from organic compounds usually transferred to first?

NAD+

what are the functions of NAD+ during cellular respiration?

oxidizing agent

what does NADH do during synthesis reaction? Why?

donate electrons to energize them

what is another name for anabolic reactions?

biosynthetic reactions

what happen in anabolic reactions?

make large macromolecules or smaller molecules not available from food

does anabolic reaction require energy?

yes, from catabolic ATP

gene regulation

the turning on and off of genes

Cellular Regulation

cell-signaling pathways like hormones

biochemical regulation

feedback inhibition- product of pathway inhibits early steps to prevent over accumulation of product

what does feedback inhibition do?

prevents a cell from wasting chemical resources by synthesizing more product that it is needed

allosteric regulation

a regulatory molecule binds to a protein at one site and affects the protein's function at another site, may either inhibit or stimulate an enzyme activity

half life

time it takes for 50% of the molecules to be broken down and recycled

what does the expression of genome allow cells to do?

respond to changes in their environment

why is mRNA degradation important?

Conserve energy by degrading mRNAs for proteins no longer required;

Remove faulty copies of mRNA;

Proteasome

complex that breaks down proteins using proteases enzyme

large proteases ______ bonds between _____ _____

cleave; amino acids

Ubiquitin

tags target proteins to the proteasome to be broken down and recycled

what does ubiquitin do?

- degrade improperly folded proteins

rapidly degrade proteins to respond to changing cell conditions

lysosomes contains what and what does it do?

hydrolases to breakdown proteins, carbohydrates, nucleic acids, and lipids

Autophagy

recycling worn out organelles using an autophagosome. breakdown into macromolecules

cellular respiration

- process by which living cells obtain energy from organic molecules and release waste products

- make ATP

- aerobic respiration

- O2 consumed and CO2 released

when glucose is broken down, energy is ________

released

Glycolysis

breakdown of glucose (6c) into 2 molecules of pyruvate (3c)

stage 1 of cellular respiration

glycolysis

Where does glycolysis occur?

cytoplasm

does glycolysis need oxygen to function?

with or without oxygen

how many steps is in glycolysis and how many phase?

10 and 3 phases

3 phases of glycolysis

1. energy investment

2. cleavage

3. energy liberation

Energy Investment Phase

requires 2 ATP in order to create fructose-1, 6 bisphosphate

what are the molecules produced during glycolysis

- 2 pyruvate (3c)

- 2 net of ATP

- 2 molecules of NADH

enzymes used in glycolysis

- hexokinase

- aldolase

- isomerase

hexokinase (glycolysis)

- transfer phosphate from ATP to glucose = more reactive

- trap atp

Aldolase (glycolysis)

- split sugar molecule in 2 diff. 3c sugars

- create DHAP & G3P

isomerase (glycolysis)

conversion between DHAP and G3P to energy liberation phase

Cleavage Phase

Splitting of glucose into two 3-carbon molecules.

Energy Liberation Phase

2 G3p molecule broken down into 2 pyruvate = 2 NADH and 4 ATP

how does ATP created in glycolysis?

substrate level phosphorylation

How does ADP become ATP?

It gains a phosphate from enzyme (2 to 3)

inputs and outputs of glycolysis

Inputs: Glucose, ATP; Outputs: Pyruvate, ATP, NADH.

second stage of cellular respiration

breakdown of pyruvate

where does breakdown of pyruvate occur?

mitochondrial matrix

Inputs and outputs of breakdown of pyruvate

input: pyruvate (3c)

Outputs: 2NADH, 2 CO2, 2 Acetyl CoA

enzyme used in breaking down of pyruvate

pyruvate dehydrogenase