BIO EXAM 3

Hormone

signaling molecule // chemical messenger

Gap junction

tiny tunnels that connect cells and let them share molecules and signals

Plasmodesmata

plant version of gap junctions

Autocrine

self signaling communication between cells

Juxtacrine

direct contact communication between cells

Paracrine

local signaling communication between cells

Endocrine

long distance signaling between cells

Reception

- binding of a signal molecule with a specific receptor on a target cell

- specific receptor recognizes signaling molecule outside the cell and binds to it

Transduction

- changes a signal into a form that causes a cellular response

- cell translates the received signal into a form that it can understand and act on, signaling cascade happens here

Response

- caused by a transduced signal

- pre programmed, cell specific responses that depend on the signal

Kinase

adds phosphate groups

Phosphatase

removes phosphate groups

First messenger

Binding of the extracellular signal molecule activates the G-protein-coupled receptor

Second messenger:

The activated effector generates internal, nonprotein

signal molecules

Autophosphorylation

:each phosphorylates trysones on the other receptor

G protein:

Large glycoproteins with 7 segments that zigzag back and forth across the membrane

Amplification

increases the magnitude of each step as a signal transduction pathway proceeds

Cross talk

- inter pathway interaction, leads to modifications of the cellular responses controlled by pathways

- instances in which one or more components of one signal transduction pathway affects another. Leads to activation or inhibition of another signal transduction pathway

be able to describe direct contact - cell to cell communication

- Animal cells with specific membrane bound cell surface molecules interact, initiating contact

- Juxtracrine

- Plasmodesmata = plants

- Gap junction = humans

Be able to describe local signaling communication

cell releases molecule that diffuses through the aqueous fluid surrounding the cells and causes a response in nearby target cells

- Signal molecule: local regulator

- Process: paracrine regulation

describe the stages involved in long distance cell signaling

- Endocrine

- Cell uses hormone to signal far away

- A controlling cell secretes a signaling molecule (hormone) which produces a response in target cells that may be far from the controlling cell

- Animal: secreted cells enter the circulatory system and travel to target cells elsewhere in the body

- Plants: most hormones travel to target cells by moving through cells or plant conductive tissues

- Some plant hormones are gasses that diffuse through the air to target tissues

what is signal reception

specific receptor recognizes signaling molecule outside the cell and binds to it

what is signal transduction

cell translates the received signal into a form that it can understand and act on, signaling cascade happens here

what is signal response

pre programmed, cell specific responses that depend on the signal

what is meant by signal amplification

- Signals intensity is increased as it is passed through the signaling cascade

- First molecule activates 10 first molecules, each of those 10 activate 100 second molecules, each 100 activate 1000 third molecules and so on

list examples of second messengers

- Cyclic AMP

- Inositol triphosphate

- Diacylglycerol

how is cyclic AMP (cAMP) made

- adenyl cyclase converts ATP to cAMP by attaching a phosphate to the 3rd and 5th carbon of the ribose in adenosine

- cAMP diffuses through cytoplasm and activates protein kinases

- phosphate added to ATP making it cAMP and activating PKA

How is inositol triphosphate (IP3) made?

- IP3 regulated Calcium channels

- phospholipase C (PLC) makes it by the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2)

- DAG

how is diacylglycerol (DAG) made?

phospholipase C (PLC) makes it by the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2), functions in plasma membrane bc it is hydrophobic

protein kinase does, and how this relates to signaling

- enzymes that transfer a phosphate group from ATP to one or more sites on particular proteins

- add phosphate

- act in chains to catalyze the phosphorylation cascade during transduction

- reversed by protein phosphatase

Be able to give examples of cellular responses to signaling pathways

- protein synthesis

- change in cell metabolism

- cell division, growth, or death

Be able to explain the link between the cell signaling pathway and cancer

Cells ignore signal molecules telling them to stop growing or die, causing cancer

- Receptor thinks it is constantly having a signal molecule binding to it

- Cell misinterprets signal during transduction leading to an incorrect response

- Continuously responds due to false activation

DRAW IT

- glucose

- amino acid

- phospholipid

- nucleotide

- g-coupled protein receptor pathway

- tyrosine kinase pathway

- steroid hormone pathway

- free energy equation

- energy change for exergonic and endergonic reaction

how do internal (steroid) receptors work?

- molecules derived from cholesterol with two domains

- Combine with hydrophilic carrier proteins

- They pass through the nonpolar portion of the plasma membrane and bind to its internal receptor on in the cytoplasm

- One part of the steroid receptor (internal) can bind with the steroid. This process allows the other part of the receptor to change shape

- The other part then activates the DNA to control genetic function

Metabolism

the biochemical modification and use of organic molecules and energy to support the activities of life

Anabolism

energy is used to build complicated molecules from the simpler ones, ΔG is positive

Catabolism

energy is released by the breakdown of complex molecules to simpler compounds ΔG is negative

Energy

the capacity to do work

Kinetic

energy of an object in motion

Potential

stored energy

Exothermic

reactions that release energy

Endothermic

reactions that absorb energy

Entropy

total disorder of a system and its surroundings

Enthalpy

- potential energy in a system

- energy not in use, stored

Free energy:

the portion of a systems energy that is available to do work

Endergonic

free energy is gained, products have more free energy than reactants and the reaction is not spontaneous

Exergonic

free energy is released, products have less free energy than reactants, and the reaction proceeds spontaneously

Enzyme

a biological catalysts that is a protein

Substrate

the reaction that an enzyme acts on

Product

the end result of a reaction

Cofactor

a nonprotein group that binds to the enzyme for catalytic activity

Coenzyme

small organic molecules which are often derived from vitamins

Active site

the substrate interacts with a small pocket or groove in the enzyme molecule

Reversible reaction

reaction that can be reversed, written with a double arrow

Activation energy

makes bonds unstable and ready to be broken

Competitive inhibitor

inhibitors bind to the active site, blocking access for the normal substrate - slowing or stopping the reaction

Noncompetitive inhibitor

inhibitors bind at a location other than the active site - reducing the ability of the active site to bind the substrate

Allosteric regulator

enzyme activity is controlled by the reversible binding of a regulatory molecule to the allosteric site

Feedback inhibition

excess accumulation of a product often inhibits the enzymatic reaction producing it

isolated system

does not exchange matter or energy with its surroundings

closed system

exchanges energy with its surrounding

Open system

all living organisms, exchanges both energy and matter with its surroundings

ex. humans

What does the first law of thermodynamics state?

Energy can be transformed from one form to another, or transferred from one place to another, but it cannot be created or destroyed

second law of thermodynamics

- The total disorder (entropy) of a system and its surroundings always increases (although the total energy in the universe does not change)

- the measure of a system's thermal energy per unit temperature that is unavailable for doing useful work

What determines whether or not a reaction will be spontaneous?

- The change in energy content of a system and its change in entropy

- No input of energy = spontaneous reaction

- When products have less potential energy and are less ordered (entropy = order) than reactants, it's usually spontaneous

- negative ∆G is spontaneous

What is the equation to calculate free energy, and what does each term mean?

ΔG=ΔH - TΔS

ΔH - change in enthalpy

T - absolute temperature in Kelvin

ΔS - change in entropy

What is meant by the term homeostasis ("dynamic" equilibrium)?

- A state of balance between the opposing factors pushing the reaction in either direction

- when the forward and reverse processes occur at the same rate, resulting in no observable change in the system

- I think this is when the reaction can go both ways? The arrow can point both ways?

explain degradative pathway (how it works + example)

- Catabolic pathways that involve the degradation (or breakdown) of complex molecules into simpler ones

- has -∆G

- EX: both the receptor and its bound signal molecule may be degraded in lysosomes after entering the cell, or receptors can be reused (sent back to cell surface) while the signal molecule is degraded (broken down)

- Lysosome breaks down receptor and signal molecule after used

explain biosynthetic pathway (how it works + example)

- anabolic

- Positive ∆G

- Energy is used to build complicated molecules from simpler molecules

- EX: production of lipids and nucleotides

what is ATP and its function in the cell

- Consists of five-carbon sugar ribose linked to the nitrogen base adenine and a chain of three phosphate groups

- Negative charges of the phosphate groups repel each other strongly, making the bonding arrangement high energy

ATP/ADP Cycle

- the continual hydrolysis of resynthesis of ATPs

- Addition of water turns ATP into ADP+Pi (endergonic)

- When phosphate is added ADP becomes ATP and water is released (exergonic)

How does coupling reactions to hydrolysis of ATP change reaction energetics?

- The terminal phosphate group is transferred to a reactant molecule involved in an endergonic reaction

- The ATP is ending with more energy than it started with (ADP). Therefore its endergonic

general structure of enzymes and how they affect reaction kinetics

- amino acids linked together in one or more polypeptide chains

- enzymes are proteins, so remember the primary, secondary, tertiary, and quaternary structures

- Enzyme increase the rate of reaction by lowering the activation energy of the reaction

role of cofactors

- these are nonproteins required for an enzymes role as catalyst

- they aid in biochemical transformations

- includes inorganic ions and coenzymes

- some are metallic ions, including iron, copper, magnesium, zinc, and manganese

- They just help

what are coenzymes (definition and function)

- small organic cofactors derived from vitamins. Some bind loosely to enzymes others (prosthetic groups) bind tightly

- aid in substrate recruitment

What mechanisms do enzymes use to lower the activation energy?

- Enzymes reduce the activation energy of a reaction by reducing the amount of energy required for reactants to join/react

- Enzymes bring the reactants together so they don't use energy moving around until they randomly collide in the right formation

- this doesn't alter ΔG

Be able to explain how changes in enzyme or substrate or inhibitor concentration affects reaction kinetics

- Enzymes bring the reacting molecules together

- Enzymes expose the reactant molecules to altered charge environment that promote catalysis

- Enzymes change the shape of the substrate molecules

What are conditions/ factors that affect enzyme activity?

- pH

- temperature

- enzyme inhibitors

- allosteric regulation

- cofactors and coenzymes

- enzyme compartmentalization

- feedback inhibition

- control mechanisms

what are enzyme inhibitors (define + name the two types)

- non substrate molecules that bind an enzyme and decrease its activity

- competitive inhibitors

- noncompetitive inhibitors

what is competitive inhibition

- binds to the active site and blocks the access for the normal substrate

- This slows/stops the reaction

- Added substrate

what is noncompetitive inhibition

- binds to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively

- Substrate unaffected

what are control mechanisms

modify enzyme activity, adjusting reaction rates to meet a cells requirements for chemical products

what is enzyme compartmentalization

- Storing enzymes in specific compartments (like organelles)

- makes sure enzymes only function under the proper conditions, allows them to easily find their substrates, and prevents damage to the cell

Mitochondria

They are essential, powerhouse of the cell, cannot survive without them

Cellular respiration:

collection of metabolic reactions that break down food molecules to produce energy in the form of ATP

Aerobic respiration

forms of cellular respiration in eukaryotes and many prokaryotes, oxygen is a reactant in the ATP producing process

Anaerobic respiration

form of cellular respiration in some prokaryotes, a molecule other than oxygen, such as sulfate or nitrate, is used in the ATP producing process

Oxidation

the removal of electrons from a substance

Reduction

the addition of electrons to a substance

Glycolysis

enzymes break a 6-carbon molecule of glucose into two 3-carbon molecules of pyruvate

NAD+/NADH

The most common electron carrier

FAD/FAD H2

high energy electron carrier

Phosphorylation

The addition of a phosphate group to a molecule

Chemiosmosis

movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient

cytochromes

proteins with a heme prosthetic group that contains an iron atom that accepts and donates electrons

proton motive force

- stored energy produced by proton and voltage gradient

- energy is used for ATP synthesis and cotransport of substances to and from mitochondria

fermentation

- enzymes break down of sugar into simpler compounds without oxygen to produce substances that can be used in making chemical energy

- begins with glycolysis: breakdown of glucose into two pyruvate molecules and produces two ATP (net) and two NADH.

- Fermentation allows glucose to be continuously broken down to make ATP due to the recycling of NADH to NAD+

what are redox reactions

- chemical reaction involving both reduction (gain in electrons) and oxidation (loss of electrons)

- Oxidation is when there is an increase in oxidation number, while reduction is when there is a decrease in oxidation number.

how is an oxidation reaction identified

- Reactions that remove electrons from a donor molecule and simultaneously add them to an acceptor molecule

- Oxidation and reduction reactions are always coupled

what general role does NAD+ have in metabolism

redox reactions - carrying electrons from one reaction to another. Found in 2 forms: NAD+ is an oxidizing agent, accepting electrons from other molecules and becoming reduced; with H +, this reaction forms NADH can can be used as a reducing agent to donate electrons