Biology Midterm 2

Amphipathic

A molecule that has both a polar and non poplar part

ex: phospholipid (non polar tail, polar phosphate head)

Functoon: they allow for the plasma membrane to create a shield so that not all molecules can come in (they need to be transported instead)

Selective permeability

Only certain molecules are let in; the cell membranes ability to control the flow of substances in and out of the cell

Function: pH balance, maintains internal environment, pressure, ion concentration)

Bulk transport

Large particle moved across a cell membrane

Ex: a macraphage engulfs a pathogen in a sphere membrane called a food vacuole

• allows cells to obtain nutrients ad grab certain particles out of the extra cellular fluid

Contra sport

• The energy stored in the electrochemical gradient by the movement of a driving ion (usually Na or H) to move another ion (the driven ion)

• The coupled movement of one molecule going against its concentration gradient with another molecule going down its concentration gradient

• 2 types symport and anti port

• Ex of symport: there’s more sodium outside the cell and more glucose in the cell; two sodium’s move down its concentration gradient and that powers 1 glucose to move against its concentration gradient alongside the sodium

• Ex of antiport: there’s more sodium outside the cell and more calcium outside the cell; 3 sodiums move down its concentration gradient and that energy allows for a calcium to move against t concentration gradient in the opposite side of sodium

Membrane potential

The voltage across a membrane (-50 to -200 mV)

The negative indicates the inside of the cell is more negative compared to the outside

• it is an energy source

• It prefers passive transport into the cell for cations

• It prefers passive transport out of the cell for anions

Integral

Most are Transmembrane proteins that span the membrane, and others only enter halfway into the hydrophobic interior

• the hydrophobic region contains non polar amino acids

• Some proteins have hydrophilic channels that allow the passage through the membrane of hydrophilic substances

Peripheral proteins

Not imbedded in the lipid belayer

• they ar loosely bond to the surface of the membrane and exposed to parts of integral proteins

• Function: act as receptors, enzymes, give the cell its shape and offer support

Transport proteins

• some ions and polar molecules can’t move through the cell membrane on their own so they use transport proteins to help them pass

• Some transport proteins have a channel that is hydrophilic that allows certain molecules and ions to use as a tunnel

Osmoregulation

The control of solute concentration and water balance

Facilitated diffusion

The passive diffusion of ions and polar molecules through transport proteins (that span the cell membrane)

• does not require energy because it goes down the gradient

Endocytosis

• the process of capturing a particle and engulfing it into the plasma membrane

• Phagocytosis: cellular eating

• Pinocytosis: cellular drinking

• Receptor mediated Endocytosis: receptor proteins on the cell’s surface are used to capture a specific particle

• The receptors, transmembrane proteins, cluster in regions of the plasma membrane called crated pits

Glycolipids

• cells recognize other cells by binding to molecules which usually have carbohydrates (on the outer surface of the plasma membrane)

• Membrane carbohydrates bond to lipids and are known as glycolipids

• Functions: provide energy to cells

• Help determine blood type

• Help fight pathogens

• Act as a receptor at the surface ed of. Red blood cell

Glycoprotein

• carbohydrates that bond to proteins

• Help cells attach and bind to each othe

Osmosis

• water diffuses across a membrane from a region of high free water concentration and low solute concentration to a place of high solute concentration until the solute concentration on both sides of the membrane are the same

Passive transport

The movement of a solute down its concentration gradient

• does not need energy

Active transport

• pumps a solute across a membrane against the gradient

• Needs energy

• The transport proteins that move solutes against the gradient are carrier proteins

• Active transport helps the cell maintain internal concentrations of solutes that differ from the concentration of the environment

Electrochemical gradient

• 2 forces drive the diffusion of ions across a membrane: a chemical force (the ion’s concentration gradient), an electric force (the effect off the membrane potential- moves cations into the cell, and anions out of the cell-on the ion’s movement)

• The combination of these forces is the electrochemical gradient

Solute

The substance getting mixed

Solvent

The substance that the solute is getting mixed into

Hypotonic

Hypertonic

Isotonic

Metabolism

The entirety of an organisms chemical reactions that change food into energy

Kinetic energy

• energy associated with the relative motion of objects

Moving objects that perform work by imparting motion to other matter

Chemical energy

The potential energy available for release in a cemca reaction

Spontaneous process

If a given process, by itself, leads to an increase in entropy, the process can proceed without the input of energy

Equilibrium

The forward and the reverse reactions cur at the same rate, there is no further net change in the concentration for products and reactants

ATP

Contains sugar ribose with the nitrogenous base adenine and a chain of 3 phosphate groups bonded to it

Activation energy

The minimum amount of energy require to convert a reactant into a product

• the minimum amount of energy required for atoms to undergo a chemical reaction.

Cofactor

• enzymes need non protein helpers fo catalytic activity like electron transfers that only amino acids cannot carry out

• They can be bound tightly to the enzyme or they can be bound loosely and reversible along with the substrate

Coenzyme

• a cofactor that is an organic molecule

• Vitamins act as coenzymes or are raw material for coenzymes

Cooperativity

The substrate molecule binding to one active site triggers a shape change in all the sites which increase catalytic activity at the other active sites

Catabolic pathways

Energy release by breaking down complex molecules into simpler compounds

Thermal energy

Kinetic energy associated with random movement of atoms or molecule

Thermodynamics

The study of the energy transformations that occur in a collection of matter

Delta g=delta h-T(delta S)

• how free energy (portion of a system’s energy that can perform work when temp and pressure are uniform) change is determined

• Delta h: change in systems enthalpy

• Delta s: change in a systems entropy

• T: absolute temperature in kelvin

• Once delta G is found we can know whether the process will be spontaneous

• For delta G to be -, delta h has to be negative or T(deltaS) has to be positive

• Delta g+ = +delta H, —delta s

• When delt h and t(delta S) are tallied, delta g has a negative value

• Spontaneous processes decrease the system free energy

• Systems with a positive or 0 delta g are not spontaneous

Exergonic

• proceeds with net released free energy (g decreases)

• Delta g is negative, so it is spontaneous (does not require energy) process

Endergonic

• absorbs free energy from its surrounds

• Because it stores free energy, g increases, and delta g is positive

Phosphoralyzation

The addition of a PO3 group to a molecule

• it is vital for free energy transferring of molecules and cellular storage

Substrate

The reactant an enzyme acts on

• an enzyme binds to a substrate

Non competitive inhibitor

Do not directly compete with the substrate to bind to the enzyme at the active site

• they bind to another part of the enzyme and this causes the enzyme to change its shape in a way that the active site becomes less effective

Competing inhibitor

Block the substrates from entering the active sites

• this can be overcome by increasing the concentration of substrates so that the active site become available

Feedback inhibition

Metabolic enzymes that are inhibited by the end product of the pathway thy control

Anabolic pathways

Consume energy to build complicated molecules from simplier ones

Potential energy

Energy that matter possesses because of its position

Entropy

Measure of molecular disorder (the more the disorder, the higher the entropy)

Free energy

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

Energy coupling

The use of an exergonic process to drive an Endergonic one

Enzyme vs catalyst

Enzyme is a molecule that acts as a catalyst, a chemical agent that speeds up a reaction

• enzymes allow for chemical raffles through the pathways of metabolism to be cleared

Active site

A pocket or a groove on the surface of the enzyme where catalysis occurs

• a restricted region of the enzyme molecule that binds to the substrate

Allosteric inhibitor

The protein function at one site is affected by the binding of a regulatory molecule to a separate site

Fermentation

A partial degradition of sugars and other organic fuels that occur without oxygen

Reducing agent

The electron donor which reduces the electron acceptor which accepts the electron

Electron transport chain

Consists of molecules but mainly proteins that is built into the inner membrane of the mitochondria of eukaryotic cells and th plasma membrane of repirating prokaryotes

• electrons removed from glucose are moved by the NADH to the top, high energy end of the chain

• At the bottom, low energy end, O2 captures these electrons with H+ to make water

• Anaerobically respiring prokaryotes have an electron acceptor at the end of the chain that is different from O2)

Phosphorylation

Oxidative phosphorylation: the energy released at each step of the chain is stored in a form the mitochondrion can use to make atp from adp (90% of atp generated by respiration)

• it is powered

Cytochromes

• Proteins that are electron carriers between ubiquinone (electron carrier that is not a protein) and oxygen

• Heme group: has an iron atom that accepts and donates electrons

NADH

• a coenzyme that is an electron carrier that helps hydrogen atoms transfer to O2

Lactic acid fermentation

• pyruvate is reduced directly by NADH to form lactate as an end product

• This regenerates nad+ with no release of co2

Aerobic respiration

Oxygen is consumes as a reactant along with organic fuel

Anaerobic respiration

Respiration that occur in a similar process as aerobic respiration but use substances other than oxygen

Oxidizing agent

Te electron acceptor that oxidizes by removing its electron

Glycolysis

• occurs in the cytology

• A catabolic pathway that breaks down glucose

• Begins the process by breaking glucose into 2 molecules of a compound called pyruvate

• In eukaryotes pyruvate enters the mitochondrion and is oxidized to a compound called acetyl CoA

• In the end of glycolysis left with 2 pyruvates, 2 NADH, and 2 ATP

Pyruvate

A 3 carbon atom that is formed during glycolysis

ATP synthase

The enzyme that makes ATP from ADP and inorganic phosphate

• it works like an ion pump running in reverse instead of using atp as an energy source to pump ions against the concentration gradient, it uses energy of an existing gradient to power atp synthesis

FADH

An electron carrier that carries electrons generated in the citric acid cycle or glycolysis to the electron transport chain

Kinase

An enzyme that adds phosphate groups to other molecules

Reduction/oxidation (redox

The transfer of one or more electrons from one reactant to another

NAD+

The oxidized form of NADH

• as an electron acceptor, nad+ function as an oxidizing agent

• - dehydrogenase enzyme remove a pair of hydrogen atoms (2e- and 2+) from the substrate and oxidize them

• The enzyme delivers the 2 e- and 1 proton to NAD which forms NADH

• The other proton is released as a h+ ion into the surrounding solution

Citric acid cycle

• pyruvate is broken own into 3 co2 molecules, including the molecule of co2 released during the conversion of pyruvate to acetyl coA

• This generates 1 atp per turn from substate level phosphorylation but most energy is transferred to NAD+ and FAD which become NADH and FADH

• NADH and FADH transport the Hugh energy electrons they are carrying into the etc

Eight steps:

1) with each turn of the citric acid cycle, 2 carbons enter the acetyl group

Citrate synthase

• To put energy into the system, citrate synthase links to oxaloactate which then binds to acetyl coA’s acetyl group

• This allows for coenzyme a to be released which creates citric acid or citrate

  2)

Acetyl coA

Pyruvate is converted to a compound called acetyl coenzyme A

An enzyme called coenzyme a is attached via its sulfur atom to the 2 carbon intermidiate, forming acetyl coA

• acetyl coa has a high potential energy which is used to transfer the acetyl group to a molecule in the citric acid cycle (high exergonic reaction)

Chemiosmosis

Movement of ions across a semipermeable membrane, down their electrochemical gradient

• Refers to the flow of H+ across a membrane

• Important example is the movement of H+ ions across a membrane to form ATP during cellular respiration or photosynthesis

Alcohol fermentation

• pyruvate is converted into ethanol in 2 sets

• CO2 is released from the pyruate which is then converted into the 2 carbon acetadehyde

• Then acetaldehyde is reduced by NADH to ethanol

• This regnrats nad+ needed for the continuation of glycolysis

Substrate level phosphorylation

Substrate level phosphorylation- when an enzyme transfers a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ATP

• substrate is the organic molecule generated as an intermediate during the break down of glucose

Autotrophs

Self feeders, they sustain themselves

Photosynthesis

• the use of sunlight for energy

• 6co2, 12h20+light=c6h12o3+6o2

Grand

Transmission

Spectrum

A graph plotting a pigments light absorbs ion verses wavelength

Action spectrum: profiles the relative effectiveness of different wavelengths of radiation in driving the process

Cartenoids

• hydrocarbons that are yellow and orange because they absorb blue-green and violet light

• They protect chlorophyll from taking in excess light energy which could damage the chlorophyll by absorbing it

Linear electron flow

the transfer of electrons that drives photosynthesis

1) a photon of light strikes the pigment molecules and boosts one of is electrons to a higher energy level

• when that electron falls back to ground state, an electron in a nearby molecule is raised to an excited state

• This happens until it reached p680 pair of chlorophyll

  2) electron is transferred from the p680 to the primary electron acceptor

  3) an enzyme catalyses the splicing of water into 2 electrons, 2 h+ and an oxygen

• The h+ are released to the thylakoid space and the oxygen combines with an oxygen generated by the splitting of another molecule to make o2

  4) each photoexcited electron passes from the primary electron acceptor of ps 2 to ps1 via etc; each component carries a redox reaction that releases energy that pumps h+ to the thylakoid space (makes a proton gradient)

  5) the potential energy stored in the proton gradient makes atp through chemiosmosis

  6) light energy has been transferred via light harvesting c

3 phosphoglycerate

Glycerakdehyde 3 phosphate

The carbohydrate produced from he Calvin cycle is g3p for 1 g3p the cycle has to happen 3 times

CAM vs C4 plants

• during the night desert plans take up co2 and incorporate it into organic acids

• They store it n their stroma and use it in the morning when they can supply atp and NADPH from the Calvin cycle with co2 from the night before

C4

• Co2 is incorporated first before t enters the Calvin cycle

• In c4 the initial steps of carbon fixation are separated structurally from the Calvin cycle

Heterotrophs

Unable to make their own food and live on compounds produced by other organisms

Chloroplasts

Absorbs energy from the sun and uses it to drive te synthesis of co2 and water

Thylakoid

Separates the stroma from the thylakoid space in the sacs

Light reactions

• convert solar energy to chemical energy

• Water splits which provides electrons and protons and given O2

• Light absorbed by the chlorophyll drives a transfer of electrons to NADP+

• The light reactions use solar energy to reduce nadp+ to NADH by adding a pair of electron and h+

• The light reactions also generate atp using chemiosmosis to power the adding of a phosphate group to ADP

• Light reaction results in NADPH and ATP

Wavelength

The distance between the cress of electromagnetic waves

Fluorescence

Carbon fixation

• the Calvin cycle incorporates each co2 molecule one at a time by attaching it to RuBP

  • The product of the is a 6 carbon intermediate that is short lived bc it is energetically unstable and slits in half

RuBP

The Calvin cycle incorporates each co2 molecule by attaching it to RuBP

Decomposers

Take food from animals and plants that are already dead

Stroma

A dense fluid n the chloroplast which is surrounded by 2 membranes

Absorption

The

Calvin cycle

— begins by taking co2 from the air into organic molecules in the chloroplast

• reduces carbon to carbohydrate by adding electrons which is powered by NADPH

• It also requires energy to convert co2 to carbohydrate which is given by the light reactions

Chlorophylls

Green ligament that gives eaves its color

• the light energy absorbed by them drives photosynthesis

Photo system 1

Provides energy to reduce nadp to NADPH

Photosystem 2

• Reaction center is called p680 because it is best at absorbing light having a wavelength of 680 nm

RuBisCo

The most abundant protein which catalyzes the reaction between RuBP and co2

Cytochrome complex