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UMD / Biology / BIOL 5666 / What is a transport protein that have a hydrophillic channel through w

What is a transport protein that have a hydrophillic channel through w

What is a transport protein that have a hydrophillic channel through w

Description

School: University of Maryland - College Park
Department: Biology
Course: Principles of Biology I
Professor: Michael keller
Term: Winter 2016
Tags: Biology, Bio, bsci105, Study Guide, exam, membrane, structure and function, Lipids, Proteins, Molecules, Energy, Enzymes, reactions, reaction coupling, activation energy, ATP, glycolysis, and cells
Cost: 50
Name: Biology Exam Study Guide II
Description: This study guide covers all class and reading material from February 10 - March 2. It includes all key concepts on the study guide, important ideas explained, and vocabulary.
Uploaded: 03/02/2016
9 Pages 54 Views 1 Unlocks
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Biology Exam Study Guide


What is a transport protein that have a hydrophillic channel through which certain molecules or atomic ions can use as a tunnel to get through the membrane?



I. Membrane Structure and Function

Key concepts:

A. All cells are defined by a cell membrane that establishes “inside” versus “outside”. - The cell membrane is a “fluid mosaic” of two types of molecules:

- Protein molecules

- Fluid bilayer of phospholipids

B. Membrane lipids compose the structural parts of the membrane.  

• Amphipathic phospholipids arrange in a bilayer with hydrophobic tails oriented  inward.

• Phospholipids that make up the membrane each contain one head and two tails. • Amphipathic: the tails of the phospholipids are hydrophobic and the head is  hydrophilic, so the head attracts water and the tails repel water, sending the tails  in towards each other and creating the bilayer with heads on the outside and tails  on the inside.


What is the movement of material into the cell ?



If you want to learn more check out What is the expression of 0 derivative?

C. The degree of movement and space in-between molecules in a membrane is a function  of membrane fluidity, which is determined by the saturation and length of fatty acid tails • Saturated fatty acids: the tails are straight, so the membrane is more viscous • Unsaturated fatty acids: the tails are more curved, so the membrane is more fluid. • Cholesterol can be added to the membrane to modulate fluidity: If you want to learn more check out What is dna replication?

• It keeps more fluid membranes from becoming too fluid

• Also keeps less fluid membrane from becoming too viscous If you want to learn more check out What are victimless crimes?

D. Membrane proteins are largely responsible for determining the functions of a cell  membrane.

• Functions of protein:

• Transport


What is cell engulfing?



• Enzymatic activity

• Signal transduction We also discuss several other topics like What is the state of the evidence for emotional disclosure in the pennebaker study?

• Cell-cell recognition

• Peripheral membrane proteins associate with the membrane on one side but don’t  enter the membrane

• Integral membrane proteins insert into the lipid bilayer and penetrate the  hydrophobic interior of the bilayer, either partially (monotopic) or passing all the way  through (transmembrane)

• Transmembrane proteins provide mechanisms for the transport of solutes across  the cell membrane in a regulated fashion, which makes membranes selectively  permeable.

• Selective permeability allows cells to protect themselves from unwanted  elements and to allow for wanted items in the cell

• 2 kinds of transport proteins allow for some ions and polar molecules to enter the  membrane:

1. Channel proteins have a hydrophillic channel through which certain  molecules or atomic ions can use as a tunnel to get through the membrane. • Aquaporins are a kind of channel protein that allow 2 billion water  If you want to learn more check out What do motor maps really represent?

molecules to pass into the cell every second.

2. Carrier proteins hold onto their passengers and change shape in a way that  the movement of particles of any substance so that they spread out into the  available space. shuttles them across the membrane.We also discuss several other topics like What is the study of death?

E. Passive transport requires no energy investment

• Occurs when solutes are moving “down” a concentration gradient. • Concentration gradient: the region along which the density of a chemical  substance increases or decreases. Every substance diffuses down its  concentration gradient.  

• The cell uses facilitated diffusion: the movement of particles of any substance so  that they spread out into the available space.

• Through channel proteins or carrier proteins to allow them to cross the  membrane without expanding energy

F. Active transport requires the cells to spend energy to move solutes “up” a  concentration using protein pumps.

• Uses energy to move solutes against their gradients

• 3 kinds of protein pumps:

• Uniport: moves one solute through the membrane

• Antiport: moves two solutes across the membrane in opposite directions • Symport: moves two solutes across the membrane in the same direction G. Bulk transport — moves large or abundant molecules or groups of molecules across  a membrane, using endocytosis and exocytosis.

• Endocytosis: the movement of material into the cell

• 3 Main mechanisms:

• Phagocytosis: the cell engulfs a particles by extending pseudopodia  around it and packaging it within the vacuole

• Pinocytosis: the cell continuously “gulps” droplets of extracellular fluid  into tiny vesicles so that the cell can obtain molecules that are  

dissolved in the droplets. It is nonspecific for the substances it  

transports. The vesicles are often lined with a protein coating called  clathrin.

• Receptor mediated endocytosis: a specialized type of pinocytosis that  allows the cell to acquire bulk quantities of things, but is more specific  than the other mechanisms. The receptor proteins in the plasma  

membrane cluster in coated pits and each pit forms a vesicle that  

contains the molecules. These proteins are very selective about what  enters and exits the cell.

• Exocytosis: the movement of material out of the cell,

• In exocytosis, a transport vesicle from the Golgi apparatus moves along the  microtubules of the cytoskeleton to the plasma membrane, where plasma and  vesicle membranes come in contact and the proteins rearrange the lipid  molecules of the membranes so that the two membranes fuse together.  When the vesicle becomes part of the plasma membrane the contents of the  vesicle spill outside of the cell.

II. Energy, Enzymes, and Reaction Coupling

Key concepts:  

A. Metabolism is the sum of all anabolic and catabolic reactions in an organism. • Metabolism is the sum of all biochemical reactions in every cell (the broad definition) • It is assembled into pathways that intersect different networks, called metabolic  pathways.  

• The metabolic pathways break the process of metabolism down into multiple  steps, dividing small jobs up for different enzymes.

• Allows for complex, interconnected systems.  

• Anabolic reactions (aka biosynthetic) refer to the body making things. • Catabolic reactions (aka degradative) refer to the body breaking things down.  B. Energy is the capacity to do work.  

• There are two main kinds of energy:

• Kinetic energy is transferred between objects in motion

• Potential energy is stored in an object and must be released

• For example, a ball at the top of a hill has potential energy.

• Free energy: the released potential energy that is available to do work. • In molecules, free energy is stored in covalent bonds. When the bonds break the  energy is released. This reaction occurs, for example, when two logs are rubbed  against each other hard enough to break the bonds that release heat that start a fire.  C. The First Law of Thermodynamics: conservation of energy — energy can be transferred but  cannot be created nor destroyed

• The Second Law of Thermodynamics: entropy in the universe always increases • Entropy = the drive for energy to spread out evenly throughout the universe • Measure of disorder

• Unusable energy

• Energy is made available to do work

• Energy can be used to increase order in the system.

D. Free energy = chemical energy that is available to do work

• It’s expressed as the difference between enthalpy and entropy

• Enthalpy = total energy

E. Any reaction involves change in free energy (delta G) between reactants and products. • The positivity or negativity of delta G determines whether it is spontaneous  (exergonic) or non spontaneous (endergonic)

• If the change in G is negative, meaning that the free energy of the reactant is  lower than the energy of the product, the reaction is exergonic.

• If the change in G is positive, meaning that the free energy of the reactant is  higher than the energy of the product, the reaction is endergonic.

F. Enzymes are proteins that reduce activation energy of a reaction to speed up the reaction. • They are the “catalysts of biological systems”

• Activation energy is the free energy of activation; the energy that is required for a  chemical reaction to start  

• Enzymes speed up reactions without changing thermodynamics

G. Enzyme specificity and function are the result of the shape of the protein. • Most enzymes are proteins, and proteins’ shape determine their function. • The shape also determines the specificity of the active site

• Shape change causes activity change

• A substrate is a reactant that the enzymes act on

• The substrate binds to an active region of the enzyme called the active site. The  active site is a small pocket or groove on the surface of an enzyme that binds to the  substrate.

• Enzyme + substrate —> Enzyme-substrate complex —> Enzyme + products • When the active site and the substrate bind they form an enzyme-substrate complex  with a close interaction through induced fit. Induced fit is the way that the binding  between the substrate and the enzyme gets tighter as the enzyme shape shifts,  which brings chemical groups of the active site into positions that enhance their  ability to catalyze the chemical reaction.

H. Environmental factors interfere with the tertiary or quaternary structure of an enzyme will  impact its activity.

• If protein structure is changed, the activity is also affected.

• Factors that could interfere:

• Temperature: when temperature increases, molecules move faster causing  substrates to collide with active sites more often. Past a certain temperature  the activity will decrease because the thermal agitation will cause the weak  bonds to break. Optimal temperature for most humans is 35-40 C

• pH: a neutral or almost neutral pH provides the best environment for  

enzymes (between 6-8, with a few exceptions)

I. Cofactors: nonprotein helpers that can be bound tightly to the enzyme as permanent  residents or loosely and reversible with the substrate.  

• Sometimes inorganic, such as zinc, iron, and copper

• Sometimes organic (coenzymes), such as vitamins  

J. Optimal conditions refer to environment that process the most favorable active shape for  the enzyme to work. Enzymes adapt, evolve, and diversify over generations, and enzymes have  different optima.

K. Enzyme activity can be reduced by competitive inhibitors that compete with substrates for the  active site.  

• Inhibitors are chemicals that selectively inhibit the action of specific enzymes • Competitive inhibitors mimic normal substrates and compete for admission into the active  sites.

• Noncompetitive inhibitors do not directly compete with the substrate to bind to the active  site — they bind to another part of the enzyme causing the enzyme moleculed to change  and to function less effectively.

L. Enzymes can be regulated by allosteric effectors.

• Allosteric effectors are noncompetitive inhibitors that bind somewhere not on the active  site and change the shape of the protein.

• Can either inhibit, activate, or stabilize the enzyme function

M. Metabolic pathways can be regulated at different steps depending on the demands of the  cell.  

• Feedback inhibition: when a metabolic pathway is halted by the inhibitory binding its end  product to enzyme that acts early in the pathway

• Negative feedback (aka feedback inhibition) loops use the product of a pathway to inhibit an  enzyme at the beginning of the pathway.

• Substrates are usually competitive, so as the product increases in concentration, it will bring  the reaction back up.  

• When the inhibitor changes the shape of the enzymes, the substrate is not  competitive. This is an exception to the rule of adding more to a substance to  increase the reaction.

N. Positive ∆G reactions are driven by reaction coupling with negative ∆G reactions to give a net  overall negative ∆G for the combined reactions.  

• Energy coupling: an enzyme causes an endergonic reaction to be driven by an exergonic  one.  

O. The most common energy couple is ATP/  

• ATP has stress bonds between oxygen-rich phosphate groups that are weak (easy to  break).  

• Yields -.73 kcal/mole (∆G)  

• The exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a  phosphate group to specific reactants, forming a phosphorylated intermediate that is more  reactive.  

P. ATP is recycled.  

• ATP is used and regenerated from ADP as they exchange a phosphate.  • The cell gains the free energy required to phosphorylate ADP from the exergonic breakdown  reactions, and then ATP becomes regenerated with the repeated addition of an inorganic  phosphate.  

Q. ATP is made by enzyme driven substrate-level phosphorylation or by redox driven  oxidative phosphorylation.  

• Oxidation: the loss of electrons from one substance  

• Reduction: the addition of electrons to another substance  

• Oxidation-reduction (redox) reactions: the transfer of one or more electrons from one  reactant to another  

• Substrate-level phosphorylation: the enzyme-catalyzed formation of ATP by direct  transfer of a phosphate group to ADP form an intermediate substrate in catabolism.  • Redox driven oxidative phosphorylation: the production of ATP using energy derived  from the redox reactions of an electron transport chain  

• The three steps of aerobic respiration include (1) glycolysis, (2) pyruvate oxidation and  the citric acid cycle, and (3) redox driven oxidative phosphorylation.  

R. NADH (or NADPH) is an important energy couple.  

• It shuttles electrons between redox reactions  

• During aerobic respiration (aka cellular respiration), electrons are usually passed to NAD+,  reducing it to NADH, and then from there to an electron transport chain.  

S. The energy from redox reactions is extracted in small amounts by electron transport chains.  • Electron transport chains: a number of molecules (mostly protein) that are built into the  inner membrane of the mitochondria of eukaryotic cells  

• The ETC conducts them to O2 in energy-releasing steps.  

• It also captures H+, and forms water.  

• That energy is used to make ATP.

Vocabulary:

Bulk transport

the transportation of large molecules or a group of molecules from the cell at  the same time

Endocytosis

the process of bringing things into the cell

Exocytosis

reversed endocytosis; the secretion of molecules from the cell

Phagocytosis

“cell eating”, the form of endocytosis that allows the cell to consume large  things at once

Pinocytosis

"cell drinking”, the form of endocytosis that brings in water by fusing the  vesicle membrane with the plasma membrane

Receptor-mediated  endocytosis

A more specific version of pinocytosis that uses both peripheral and receptor  proteins.

Metabolism

the sum of all biochemical reactions in every cell

Anabolic reactions

Biosynthetic; the body making things

Catabolic reactions

Degradative; the body breaking things down

Metabolic pathways

reactions that occur one after another, in a specific order; they allow for  complex metabolic systems, and break down the process into small steps

Energy

the capacity to do work

Kinetic energy

energy that goes from motion to something else

Potential energy

non-kinetic energy that is stored in bonds and released by the movement  from higher concentration to a lower one

1st Law of  

Thermodynamics

Conservation of Energy: energy can be transferred, but it cannot be created  nor destroyed

2nd Law of  

Thermodynamics

Entropy in the universe is always increasing

Entropy

the drive for energy to spread out evenly throughout the universe; a measure  of randomness/disorder

Fluid mosaics

The model that shows the constructs of a plasma membrane; a mosaic of  protein molecules bobbing in a fluid bilayer of phospholipids; called mosaic  because membranes within each cell have a unique collection of membrane  functions

Amphipathic

the characteristic of the phospholipids that make up a plasma membrane:  they have hydrophilic heads and two hydrophobic tails that lead to the  bilayer formation of the membrane.m

Phospholipid bilayer

The two-layered membrane arranged with hydrophilic tails on the inside and  hydrophobic heads on the outside.

Viscous

the opposite of fluidity; when the lipid tails are packed more tightly together  and allow for less to enter the membrane

Integral proteins

proteins that penetrate the hydrophobic interior of the lipid bilayer

Peripheral proteins

proteins that are not embedded in the lipid bilayer and are just loosely bound  to the surface of the membrane; held down by the cytoskeleton or attached  to fibers of the extracellular matrix

Glycolipids

the membrane carbohydrates that are covalently bonded to lipids

Selective permeability

a property of the membrane that allows only some substances to exit and  enter the cell

Transport proteins

proteins that help move some ions and polar molecules into the membrane

Channel proteins

a kind of transport protein that have hydrophilic channels through which  certain molecules or atomic ions can use as a tunnel to get through the  membrane

Aquaporins

a kind of channel protein that allow water through the membrane

Carrier proteins

hold onto their passengers and change shape in a way that shuttles them  across the membrane

Passive transport

diffusion of a substance across a membrane with no energy investment  needed

Diffusion

the movement of particles of any substance so that they spread out into  available space

Concentration gradient

the region along which the density of a chemical substance increase or  decreases; every substance diffuses down one; substances move from high  to low gradients in diffusion

Osmosis

the diffusion of water molecules through the pores of a membrane

Tonicity

the ability of surrounding solution to cause a cell to gain or lose water,  depending on the solute concentration and membrane permeability (if  concentration is high water leaves, if it’s lower, water enters)

Isotonic

when there is no net movement of water in or out of the cell because water  diffuses in and out of the membrane at the same rate

Hypertonic

a solution that does not maintain enough water because the water leaves the  cell faster than it enters; could result in shrivel and death

Hypotonic

solution that has too much water because the water enters the cell faster  than it leaves; could cause swelling and bursting

Osmoregulation

the control of solute concentrations and water balance; usually achieved by  rigid cell walls

Turgid

very firm, created by turgor pressure in a hypertonic cell

Flaccid

very limp, created when the cell is isotonic

Plasmosys

when the cell shrivels up it develops this, which can be deathly

Facilitated diffusion

when polar molecules and ions diffuse passively with the help of transport  proteins on the membrane

Ion channels

the channel proteins that function as gated channels and open or close in  response to stimulus

Active transport

the pumping of a solute across a membrane that requires work, undergone  by carrier proteins

Sodium-potassium  pump

a pump that exchanges sodium for potassium across the membrane in order  to maintain higher concentrations of potassium ions and lower concentration  of sodium ions in the cell

Voltage

electrical potential energy; all cells have it

Membrane potential

voltage across a membrane, which is negative on the cytoplasmic side and  positive on the extracellular side because of unequal distribution of anions  and cations

Electrochemical  

gradient

the combination of two forces that drive diffusion of ions across a membrane

Electrogenic pump

the transport protein that generates voltage across a membrane

Cotransport

when transport protein couples the “downhill” diffusion of the soul to the  “uphill” transport of a second substance against its own concentration  gradient

Clathrin

the peripheral protein with a coated pit that helps with receptor-mediated  endocytosis

Cellular respiration

a major pathway of catabolism where sugar glucose and other organic  molecules become available to do the work of the cell

Bioenergetics

the study of how energy flows through living organisms

Thermal energy

kinetic energy associated with random movement of atoms or molecules

Heat

thermal energy that transfers from one object to another

Chemical energy

potential energy that is available to be released in a chemical reaction

Spontaneous process

the process that leads to an increase in entropy and can proceed without  requiring an input of energy; notated by a negative delta G

Free energy

the portion of a system’s energy that can perform work when temperature  and pressure are uniform throughout the system

Exergonic reactions

reactions propelled forward by a net release of free energy (G is negative);  usually random

Endergonic reactions

absorbs free energy from its surroundings (G is positive)

Enthalpy

total energy (marked by H in the delta G equation)

Activation energy

free energy of activation, the energy required to start a reaction

Enzymes

the biological catalysts; speed up reactions by lowering activation energy

Cell’s 3 kinds of work

chemical, transport, and mechanical work

Chemical work

pushing of endergonic reactions that would occur as the synthesis of  polymers from monomers (like dehydration or hydrolysis - the breaking down  of molecules)

Transport work

the pumping of spontaneous movement (like diffusion or pumping an ion)

Mechanical work

any physical movement in the cell (like arrangement of the cytoskeleton or  muscle contraction)

Energy coupling

the use of exergonic processes to fuel an endergonic one

ATP

adenosine triphosphate, a nucleotide that is used to drive endergonic  reactions in cells

Inhibitors

block the active site to inhibit a reaction

Allosteric control

turns on, off, or stabilizes enzymes with the use of noncompetitive

Oscilation

the active site going back and forth from bad shape to good shape on its  own (adding an inhibitor keeps it in bad shape and adding an activator keeps  it in a good shape)

Substrate

a reactant that an enzyme acts on

Oxidation

the loss of electrons

Reduction

the gaining of electrons

Electron transport  

chain

a number of molecules (mostly proteins) that are built into the inner  membrane of the mitochondria of eukaryotic cells

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