Cell and Molecular Biology BIO 2210: Midterm 2

DNA

Essential need of a cell: has information to guide activities

Macromolecules

Essential need of a cell: molecular building blocks

Enzymes

Essential need of a cell: chemical catalysts

ATP

Essential need of a cell: energy to drive reactions and processes essential to life

Activation energy

Molecules need enough of this to react

Enzymes

Protein catalysts that overcome the activation energy barrier

Phosphoanhydride bonds

Free energy is released from this type of bond when ATP is hydrolyzed to ADP

Exergonic

Hydrolysis of ATP to ADP is _____

Properties shared by catalysts

Increase reaction rates by lowering activation energy, form complexes with substrate molecules, and change the rate at which equilibrium is achieved

Ribozymes

Enzymes made of RNA

Enzyme nomenclature

Named for substrate or function, often ends with “-ase”

Active site

Where substrates bind and catalysis occurs; results from 3D folding of the enzyme

Prosthetic groups

Necessary for enzyme function, often function in electron transfer

Coenzymes

Organic prosthetic groups

Metal ions

Inorganic prosthetic groups

Holoenzyme

An enzyme + prosthetic group

Affinity

___ between active site and substrate; based on size, shape, and strength of intermolecular interactions

Group specificity

Some enzymes recognize multiple similar substrates

Induced-fit model

Current model for active site/substrate. Random collision of substrate with the active site, substrate binding induces a conformational change (tightens fit)

Allosteric regulation

Regulation by binding of an activator or inhibitor at a site that is not the active site

Covalent modification

Regulation by the addition or removal of covalent chemical modifications

Regulatory domain

The allosteric site is found in the ___

Catalytic domain

The active site is found is the ___

Feedback inhibition

The final product of an enzyme pathway negatively regulates an earlier step in the pathway

Allosteric inhibitor

Isoleucine is a(n) ____ of threonine deaminase

Glycogen phosphorylase

____ catalyzes a reaction that promotes release of glucose monomers from glycogen

Covalent modification

Addition or removal of phosphate groups. Regulates glycogen phosphorylase

Kinase

Adds a phosphate group

Phosphatase

Removes a phosphate group

Phosphotransferase

any enzyme that catalyzes the covalent addition of a phosphate group to another molecule

Phosphorylases

Phosphotransferase that uses inorganic phosphate as its phosphate source

Kinase

Phosphotransferase that uses ATP as its phosphate source

Zymogens

Inactive, newly synthesized enzymes

Proteolytic cleavage

Cuts the inactive zymogen, irreversibly activating its enzymatic activity

Metabolism

The sum of chemical reactions in a cell

Anabolic metabolism

Build cellular components, requires energy

Catabolic metabolism

Break down cellular components, this is the main way our cells make energy

Phototrophs

Convert energy from light into chemical energy

Chemotrophs

Oxidize chemical compounds to make energy

Photosynthesis

Using light energy to make chemical energy, and then synthesize organic molecules

Energy transduction reactions

Light energy is captured and converted into chemical energy

Cellular respiration

Using hydrocarbons as fuel sources, movement of electrons powers production of ATP

Cellular respiration

Oxidation-driven flow of electrons from reduced coenzymes to an external electron acceptor, usually accompanied by the generation of ATP

External electron acceptor

A molecule that is not a byproduct of metabolism

Aerobic respiration

exergonic process using oxygen as the ultimate electron acceptor, with a significant portion of the released energy conserved as ATP

Glycolysis

How cells make ATP from glucose

Glycolysis

The first step in using glucose to generate energy, and does not require oxygen. Requires energy input, net gain of 2 ATP molecules per glucose. Also produces 2 NADH and 2 pyruvates

Coenzymes

Electrons and hydrogens removed in enzyme-catalyzed oxidations are transferred to coenzymes

NAD+

Oxidized form of nicotinamide

NADH

Reduced form of nicotinamide

Aerobic respiration

Pyruvate from glucose can be used for ____. Has a high ATP yield of about 30 ATP per glucose

Fermentation

Follows glycolysis in anaerobic conditions

Fermentation

Metabolism of pyruvate that recycles NADH. This makes NAD+ available for continued glycolysis

Lactic acid fermentation

During exertion, muscles are deprived of oxygen and undergo ______, results in pain

Alcoholic fermentation

Pyruvate loses a carbon (as CO2), forms acetaldehyde. Acetaldehyde reduction by NADH gives rise to ethanol.

Miller’s simulation

Early earth contained hydrogen, methane, ammonia, and water vapor

Cellular respiration

Uses an external electron acceptor to oxidize substrates completely to CO2, allowing more efficient generation of ATP

External electron acceptor

An electron acceptor that is not a byproduct of glucose catabolism

Respiration

The flow of electrons from reduced coenzymes to an external electron acceptor, usually accompanied by the generation of ATP

Anaerobic respiration

Molecules other than oxygen (sulfur, nitrates) are the terminal electron acceptors

Aerobic respiration

The terminal electron acceptor is oxygen, and the reduced form is water

Mitochondria

Where does aerobic respiration occur

Aerobic respiration

System for efficient extraction of energy from nutrients

Glycolysis

The first stage of aerobic respiration: glucose is converted to pyruvate

Oxidation

The second stage of aerobic respiration: pyruvate or fatty acids to generate acetyl CoA

Citric acid cycle

The third stage of aerobic respiration: acetyl CoA is completely oxidized

Electron transport chain

The fourth stage of aerobic respiration: from coenzymes to oxygen, coupled to proton transport

Oxidative phosphorylation

The fifth stage of aerobic respiration: diffusion of protons drives ATP synthesis

Outer membrane

Where in the mitochondrion do small molecules (

Inner membrane

Where in the mitochondrion does the electron transport chain and oxidative phosphorylation occur

Matrix

Where in the mitochondrion does pyruvate oxidation, beta oxidation of fatty acids, citric acid cycle, and ATP synthesis occur

FoF1 complexes

What structure protrudes into the matrix of the mitochondrion

H+ diffusion

what drives ATP synthesis

Polypeptides

H+ channels are composed of multiple ____

Pyruvate oxidation and the TCA cycle

Results in: 5 reduced coenzymes, 1 ATP, and 3 CO2

Acetyl CoA

made from glucose and fatty acids; has a high energy thioester bond

Electron transport

Creates a non-equilibrium proton gradient across the inner membrane

Electron transport chain

Electrons are transferred (from NADH and FAD) to oxygen via a series of energetically favourable steps; each complex is composed of multiple proteins and coenzymes

Intermembrane space

The movement of electrons drives movement of protons from the matrix into the _____

Signals

Cells need to generate, detect, and respond to ____

Ligands

Term for signalling molecules; mostly organic molecules such as proteins

Source of the signal

What releases a signalling molecule

Receptors

How do cells listen to their environment

Autocrine

Signal sent from one cell to itself

Paracrine

Signalling and the target cells are distinct

Endocrine

Long distance signalling, often mediated by hormones

Hormones

Signalling molecules released from specialized endocrine cells

Bloodstream

How do hormones travel long distances?

Epinephrine

What hormone is a tyrosine derivative, sends a “fight or flight” signal, and signals to many cell types

Adrenal gland

What gland secretes epinephrine

Signal transduction

Receptors convert extracellular signals to intracellular signals/the transmission of a signal that results in a cellular response

Protein phosphorylation

The process used to transmit signals in cells

Kinase

Enzyme that adds a phosphate group

Phosphatase

Enzyme that removes a phosphate

Protein Kinase A

What does cAMP activate?

cAMP response elements (CRE)

cAMP signalling leads to activation of genes that have _____ (7 nucleotide sequence)

cAMP Response Element Binding protein (CREB)

What is the protein that binds CRE sequences? Is considered a regulatory transcription factor

Binding site

Each receptor has a ____ for its ligand

G-protein coupled receptor (GPCR)

Receptor with 7 transmembrane alpha helices, each with a unique extracellular ligand-binding site. Also important in medicine as many drugs activate or inhibit these receptors.

G-protein

What does a ligand binding to a GPCR activate? It is a guanine nucleotide binding protein, with 3 subunits.