Prelim 1 Biog1440 Flashcards
Cell membrane
membrane that separates the cell from its environment
Phospholipids
Synthesized from glycerol & two fatty acid side chains in ester linkage. The third alcohol (-OH) functional group is linked to a phosphate containing head group.
Amphipathic
Contain both hydrophobic and hydrophilic molecules
Hydrophobic
Not soluble with water
Hydrophilic
Polar, soluble with water
4 major phospholipids
Phosphatetidylcholine, phosphateidylethanolamine, phosphatidylserine, sphingomyelin *additional: Phosphatidylinositol
Entropy
The measure of randomness of a system
High entropy: high disorder & low energy
Low entropy: Lower disorder & greater energy
Hydrophobic effect
Hydrophobic molecules mix well in hydrophobic solvents & hydrophilic molecules with hydrophilic solvents (water) LIKE MIXES WITH LIKE
Phospholipids will spontaneously assemble into bilayers due to hydrophobic effect. Hydrophobic molecules with water tend to form cage like shells (altercate) separating water which forms an ice like layer.
Which is chaotic=entropy which is favorable though it goes against thermodynamics
Fluid mosaics
Phospholipids are not covalently linked to one another, they’re held together by weak hydrophobic forces. So these phospholipids can diffuse around in the plane of the membrane from side to side.
Chemical composition can change to maintain membrane fluidity. A model of membrane structure in which proteins are inserted in a fluid phospholipid biolayer
Fluidity
Controlled by the introduction of a double bond into a fatty acid side chain which leads to bends or kinks in the fatty acid chain which weakens the intra & intermolecular packing interactions (ex. cholesterol)
Cholesterol
At warm temperatures (37 degrees) it limits excess fluidity. At cool temperatures cholesterol maintains fluidity, prevents tight packing of FA chains.
Laterally
Lipids and proteins can drift laterally but the size of the proteins & their interactions often limit their movement.
Peripheral membrane
Surface of the membrane but don’t actually extend into the membrane. Operationally defined as proteins that dissociate from the membrane following treatments with polar reagents, such as solutions of extreme pH or high salt concentration that DO NOT disrupt the phospholipid bilayer
Integral membrane
Extends through the bilayer and usually peaks out of both sides. Proteins can be released only by treatments that disrupt the phospholipid bilayer (ex. detergents)
Outer leaflet
Mainly phosphatidylcholine & sphingomyelin
Inner leaflet
Phosphatidylethanolamine & phosphatidylserine
Why is the phospholipid important?
- The interior phospholipid bilayer uses hydrophobic fatty acid chains which makes it impermeable to water
- Bilayers of phospholipids are fluid so the fatty acids of phospholipids have one or more double bonds which introduce kinks into the hydrocarbon chains & makes them difficult to pack together; therefore the long hydrocarbon chains move freely in the interior of the membrane so its flexible.
Cells can vary the properties of their membranes in two ways:
- They can change the type of polar head group (chlorine-serine-glycerol-ethanolamine) which changes the charge & properties of the membrane
- Change the length & shape of fatty acids
Homeoviscous Adaptation
Cells actively regulate membrane fluidity by changing the shape of their fatty acids depending on the temp they are grown
Transmembrane Proteins
Typically require assistance to integrate into membranes
SecYEG Translocon
Proteins that help other proteins cross or move into the membrane where they become integrated into the membrane. Once the protein is integrated, it can be modified.
Osmosis
The net movement of water (solvent) across a selectively permeable membrane into a region of higher solute concentration.
Facilitated diffusion
Speeds the passive movement of solutes across the membrane.
When transport proteins speed the passive movement of molecules across the plasma membrane (down a concentration gradient).
Active transport
Requires the energy of ATP or the energy available in other gradients (e.g. PMF) & leads to the accumulation of solutes against their gradients.
Uses energy to move solutes against (up) their gradients.
Can also use energy stored in chemical gradients
Six Major Functions of Membrane Proteins
- Transport - water & solutes
- Cell-cell recognition
- Intercellular joining
- Attachment to the cytoskeleton & extracellular matrix (ECM)
- Enzymatic activity
- Signal transduction
Cell-cell recognition
This type of intermolecular recognition helps cells adhere to each other & recognize each other. Protein complex spanning red blood cell membrane, the carbohydrate types give rise to the ABO blood groups.
Intercellular joining
Many cells are joined together by gap junctions (plasmodesmata in plant cells), made up of the protein connexin. So proteins can play important functions in helping cells join & communicate with each other.
Attachment to the cytoskeleton & extracellular matrix
Many eukaryotic cells are surrounded by a complex environment which may include an extracellular matrix. This matrix may include a variety of polymers, proteins & carbs. This matrix provides a substrate for the interaction of many different cell types.
Enzymatic activity & signal transduction
Proteins are important in cell signaling bc many proteins have an enzymatic function & some of these enzymes are important in signal transduction (GPCRs)
GCPRs
Largest family of cell surface receptors in humans
Activate the “G proteins”
G proteins affect the production of “second messenger” molecules
Passive transport
Is diffusion of a substance across a membrane with no energy expenditure
Osmosis
Diffusion of free water across a selectively permeable membrane, like a plasma membrane (more technically, it is the movement of solvent across a selectively permeable membrane into a region of higher solute concentration).
Isotonic solution
Solute concentration is the same as that inside the cell; no net water movement across the plasma membrane
Hypotonic solution
Solute concentration outside is less than that inside the cell; therefore. H20 concentration is higher… cell gains water
Hypertonic solution
Solute concentration is greater outside than inside; cell loses water.
Plant cells turgid
Plant cells are normally “swollen”; this is turgor pressure and is constrained by the cell wall.
Hypotonic: turgid
Flaccid: Isotonic
Hypertonic: Plasmolyzed
Aquaporins
Facilitate the diffusion of water (Aquaporins are integral membrane proteins)
Have a water channel that allows water to pass
Cotransport
Also called secondary active transport uses the energy of ATP directly as in the proton pump.
Couples H+ with sucrose [needed molecules]
Membrane potential
The voltage difference across a membrane
Voltage is created by differences in the distribution of positive & negative ions across a membrane.
Electrochemical gradient
Two combined forces, collectively called the electrochemical gradient, drive movement of ions across a membrane.
- -> A chemical force (the ion’s concentration gradient)
- -> An electrical force (the effect of the membrane potential on the ion’s movement)
Plants and microbes use
Proton pumps that are powered by ATP. The gradient of protons is an energy source for cells.
Bulk transport
Uses exocytosis; cell transports molecules out of the cell (uses energy)
Endocytosis
Phagocytosis, Pinocytosis, Receptor-Mediated Endocytosis
Phagocytosis
A process in which particles present in the environment can be engulfed into a vacuole. Some cells may use this to feed.
Pinocytosis
A process in which vacuoles may be used by the cell to drink (water)
Receptor-Mediated Endocytosis
Whereby compounds binding to the surface of the cell can trigger an engulfment reaction
Model for a cell membrane
Ideally we want a cell that is -Abundant & easy to isolate -Has a typical eukaryotic membrane -Lacks internal membranes Therefore, Red Blood Cells
O2, CO2, H20
Can diffuse into the membrane without a carrier
Uniporters
A uniporter carries one molecule or ion
Symporter
A symporter carries two different molecules or ions, both in the same direction
Antiporter
An antiporter also carries two different molecules or ions, but in different directions.
Metabolism
The totality of an organism’s chemical reactions. Much of metabolism is organized into pathways that utilize enzymes to convert a substrate to a desired product or products.
Enzymes
Proteins that speed up metabolic processes by acting as catalysts mainly by lowering the energy of activation of a reaction.
Speed up reactions by reducing Ea. However, delta G is unaffected, enzymes speed up kinetics, does not affect thermodynamics
Delta G
The favorability of reactions or pathways is given by delta G, Gibbs free energy.
Negative G are energetically favorable and can do work
G=0 cannot be used to do work
The free-energy change of a reaction is the free energy difference between the reactants and products (free energy of the products minus free energy of the reactants). The energy change is the sum of the changes in enthalpy.
Delta G= Delta H - T(Delta S)
ATP’s importance in enzymatic activity
ATP is a critical energy coupling molecule since its hydrolysis has a large negative delta G.
Eukarya
- More complex cells
- Made for multicellular organisms
- Rely on chemistry invented early in evolution
Unity if biochemistry
The biochemistry that underlies life evolved early and it has been retained throughout the many branches of life
*aerobic prokaryote and photosynthetic prokaryote as the early mitochondria and chloroplast
Endosymbiosis
Describes the process of “taming” of a bacterial cell after engulfment by an ancestral Eukaryote (over many, many generations)
Mitochondria
(respiration) evolved from an aerobic, O2 respiring bacterium. Generates ATP and is known as the powerhouse of a cell.
Chloroplast
(photosynthesis) evolved from a photosynthetic (O2 generating) bacterium. Responsible photosynthesis.
A+B kf kf AB
Keq= [AB]/[A][B]
A and B are reactants (enzyme substrates).
AB is the product
Keq
The equilibrium constant. Determines the equilibrium
kf and kr
Rate constants kf and kr are used when calculating reaction rates
Keq>1
Reaction favors the product
Keq<1
Reactions that are unfavorable
Negative Delta G
Reactions with a negative delta G are spontaneous, require no energy input. Spontaneuous energy can perform work. E.g. active transport?*
Positive Delta G
Reactions with a positive delta G are not spontaneous, require energy input to proceed.
e.g. ATP Production
Delta G=-RTInKeq
When Keq is <1, ex. -1, and you plug it into the formula, the delta G will be positive which means that the reaction is not spontaneous and requires energy input. This is true because when Keq<1, the reaction is unfavorable energetically
Exergonic Reactions
-Releases energy
-Spontaneous
-Delta G<0
- Large negative delta G = irreversible reaction
Memorize exergonic and endergonic graphs
Endergonic reaction
-Requires input of energy
-Not spontaneous
-Delta G>0
Memorize exergonic and endergonic graphs
What if delta G is zero?
It will lean more towards the negative side.
Kinetics
Measures how fast a reaction proceeds. Defined by rate constants [k]
Forward Reaction
Rate=kf[A][B]
Reverse Reaction
Rate=kr[AB]
At equilibrium…
The forward and reverse reactions are equal, and the relative concentrations of products and reactants stop changing
- the reaction is still going on, but there is no net effect on the concentrations of reactants and products
- equilibrium does not mean that the concentration of reactants and products are equal, but only that their concentrations have stabilized at a particular ratio
The more reactants there are…
The more rapidly the reaction will proceed, as reactants are used up, it will slow down
The reverse rate reaction…
occurs at a very slow rate. As the reaction proceeds and AB accumulates in the system, the reverse reaction will begin to occur more rapidly.
Reactions will proceed until they reach…
Equilibrium
Keq=kf/kr
Therefore, Keq=ratio of the forward and reverse rate constants
Transition State
Determines kinetics or how rapidly the reaction occurs
- unstable
- high energy
- thermodynamically unfavorable
(Ea)
The activation energy for the forward reaction. Determines kf under a given set of conditions.
Spontaneous reactions (in terms of energy requirements)
Can also be initiated by an input of energy or by lowering the activation energy
Cofactors
Enzymes may also require cofactors for their function
- -> metalloenzymes
- Use metal ions as cofactors
- All cells require metals for life
- Cofactors aid enzymes so they can lower activation energy
Organic cofactors
NADH, NADPH, FAD
Concentration
Creates high local concentration of substrates (next to each other)
Orientation
Holds them in a precise orientation
Facilitation (please watch this explanation again when you come across this card)
Speeds reactions using active site “acids” and “bases” or other functional groups and cofactors
Uses side chains of amino acids to regulate pH.
Stabilization of transition state
Uses binding energy energy to stabilize the transition state, thereby increasing the probability of reaction
Active site
The binding of substrates to enzymes occurs at a specific pocket on the surface of an enzyme
Induced fit
substrate binding changed shape of enzyme
Competitive
Molecules structurally similar to the substrate can bind to the active site; block substrate binding
Substrate increases its abundance to increase its probability of binding at the active site.
Non-competitive
Molecules bind to a separate site (allosteric site); do not block substrate binding, but block enzyme function (e.g. prevent “induced fit”)
Allosteric regulation
A regulatory molecule binds a proteins at one site, affects the protein’s function at another site, can either inhibit or stimulate enzyme activity
Feedback Inhibition (look at diagram from slides/videos)
A special case of negative, allosteric regulations, The product of a pathway acts as a negative allosteric regulator of the first step in the pathway. An example of non-competitive enzyme inhibition
Allows chemical flow (flux) through the pathway to respond to cellular needs (when product is high, pathway turns off) - mechanism of homeostasis.
How can endergonic reactions become more energetically favorable?
- Energy from exergonic ATP hydrolysis can drive an otherwise endergonic reaction (coupling the reaction)
- Drain the product to be less than one
What can affect enzymatic activity?
Temperature, pH, and chemicals that specifically influence the enzyme
Catabolism
Breakdown of organic compounds to simpler components.
- Often oxidation reaction
- Importance: can yield energy and detoxify reactions
Anabolism
Buildup of complex molecules from simpler ones
- usually requires energy
- Common precursors (from central metabolism)
- Phospholipids
- Macromolecules (proteins, nucleic acid)
Key Steps in Cellular Respiration
- Glycolysis
- Pyruvate Oxidation
- TCA Cycle
- Oxidative Phosphorylation
Results of Cellular Respiration
Oxidation of glucose all the way to carbon dioxide and water, generation of ATP, & generation of many precursor molecules that can be used to build up other molecules important for the cell
Redox reactions
Oxidation-reduction reactions (redox): Transfer electrons between reactants - Loss of Electrons, Oxidation (LEO) - Gain of Electrons, Reduction (GER) Xe- + Y --> X + Ye- Oxidation: Xe- loses an electron, becomes X X is the reducing agent for Y. Reduction: Y gains an electron, becomes Ye- Y is the oxidizing agent for x
Why is oxygen so important in respiration?
Oxygen happens to be one of the most powerful oxidizing agents in biology. It has the highest redox potential of any electron acceptor.
Cellular Respiration
Formula:
C6H12O6 + 6O2 –> 6CO2 + 6H2O
Source of most cellular energy
Glycolysis (catabolic)
The lysis or breaking apart of the sugar. This yields 2 molecules of pyruvate.
C6H1206 + 2NAD+ + 2ADP = 2Pi –> 2 pyruvate (C3H4O3) + 2ATP + 2NADH + 2H+
Key inputs: Glucose, 2 ATP (in), 2NAD+
Outputs: 2 pyruvate, 2 NADH, 4 ATP
Pyruvate oxidation
Pyruvate is then oxidized into acetyl-CoA and CO2
2 pyruvate +2NAD+ + 2CoA –> 2acetyl-CoA + 2NADH +2H+ + 2CO2
Key inputs: 6 Carbons (per glucose). 2NAD+, 2CoASH (free CoA)
Key outputs: 2CO2, 2NADH, 2Acetyl-CoA,
Tricarboxylic acid cycle (TCA)
Pyruvate is transferred into the TCA cycle where it is further oxidized with the generation of reducing equivalent electrons carried by carrier cofactors in the cell. Oxidizes acetly-CoA making NADH, FADH2, and ATP.
2Acetyl-CoA +4H20 +6NAD+ +2FAD + 2ADP + 2pi –> 4CO2 + 6NADH + 2FADH2 + 2CoASH + 2ATP + 6H+
Each turn of the cycle:
Key steps:
-2 carbons in as acetyl-CoA per glucose, turns the cycle twice
-2 carbons out as CO2 through oxidation
-3 NAD+ reduced to NADH, and 1 FAD reduced to FADH2
Output: 1 ATP per cycle
Oxidative Phosphorylation
Electrons are transferred through what’s called the electron transport chain to generate a proton gradient that can then be used to generate ATP. Accounts for most of the ATP synthesis makes a proton gradient from NADH, FADH2, oxidation by O2.
10NADH + 25ADP + 25Pi –> 10NAD+ + 10H+ + 25ATP
* reoxidizes NADH and FADH2
Key inputs: NADH & FADH2
Outputs: NAD+, FAD+, H2O and ATP (mainly)
-As NADH oxidized, the electrons are transported down a chain of protons (ETC) to O2
-As they pass electrons, they produce a H+ gradient (PMF) across the membrane (10 H+ per NADH)
- H+ ions flow by chemisomosis through to generate ATP from the H+ gradient
-The ATPase is an “active transporter” that can use ATP hydrolysis to transport, BUT during chemiosmosis it runs in reverse
Glycolysis is in the ____ of the cell and the rest of the breakdown occurs in the
Mitochondria
Coenzyme A
Example of an enzyme cofactor
Synthesized in 5 steps from 4 ATPS, Pantothenate, and Cysteine
Important because it carries the acetyl groups into the next stage
Chemiosmosis
H+ flowing back through F1F0 synthase
Provides energy to make ATP
Movement of ions across semipermeable membrane, down their concentration gradient
Electron Transport Chain
- Electrons from NADH flow to acceptors with increasingly larger redox potential (change E)
- Means accceptors have increasing tendency to accept electrons; like molecules flowing down a concentration gradient, from high to low
Redox potential increases…
As electrons flow which means electron donor < electron carrier < electron acceptor (O2)
Q= coenzyme Q (ubiquinone)
A lipid soluble, diffusible electron carrier
Proton Motive Force
Proton gradient used to drive ATP synthesis
Basal Metabolic Rate
The rate of O2 consumption when a person is totally at rest in a constant temperature environment can be used to establish the BMR, this is the minimum amount of energy needed, in calories, to support life.
Q10
Equation: Q10 = (R2/R1)^(10/T2-T1)
Is a quotient describing the sensitivity of a process to temperature. Tells us how sensitive an enzyme is to change in temperature.
Anaerobic respiration
Respiration without oxygen. Instead of O2 being the oxidizing agent, other electron acceptors have this role.
ex. Sulfate, nitrate
Production of methane
In certain archaea, a specialized form of anaerobic respiration occurs in which H2 gas is the electron donor and CO2 is the electron acceptor, resulting in methane.
Fermentation
respiration without oxygen or a proton gradient. The first sets of reactions are the same as glycolysis, where the oxidizing agent is NAD+ which becomes reduced to NADH, enabling the oxidation of glucose to pyruvate
- pyruvate can be reduced to lactate or ethanol
- no regeneration of NAD+
- glycolysis would stop when NAD+ is depleted
Photosynthesis
Uses light energy to generate ATP, and the reduced compound, NADPH
-organic molecules produced by photosynthesis support both catabolic and anabolic metabolism
~50% is used for growth and assembly of macromolecules (anabolism)
~50% is used for respiration to provide energy (catabolism)
Photons are absorbed by…
pigments and electrons are shifted to an excited state
PS II
Excited electrons are transferred from the reaction center (P680 special pair of chlorophyll molecules) to the primary electron acceptor (phophytin)
The electron then enters an ETC which allows a pumping of protons (to establish a proton gradient)
The proton gradient is used to make ATP by chemiosmosis (this is called photophosphorylation) rather than ox phos
Photophosphorylation and Ox Phos are examples of..
Chemiosmosis
PS I
The electrons lost from the P680 reaction center are replaced with electrons generated by the spitting of H2O in the oxygen-evolving complex (OEC), which results in protons (H+), oxygen atoms that combine into O2 & electrons.
Contains the P700 reaction center, and excited electrons enter a second ETC where they are ultimately captured as the reduced NADPH
What is produced from the z scheme?
ATP, NADPH
Heterotrophs
Rely on complex carbon sources
Autotrophs
Can obtain carbon from inorganic sources CO2; plants and photosynthetic microbes
Photo
Light
Chemo
Chemical energy
Phototrophy
Energy from light
Chemotrophy
Energy from chemicals
Methanogenesis
Methane gas can be generated and released into the atmosphere, and also in livestock (particularly cattle) where, as they graze on food stuffs (these are chemoheterotrophs, of course) the biomass that they’ve consumed ends up undergoing a complex fermentation in the cow rumen. And in this environment, these fermentation end-products support methanogenesis. leading to the production of methane.
Branched respiratory
Bacteria will happily use O2 if its available but can adapt to anaerobic conditions by using alternative electron acceptors
ex. nitrate, sulfate, fe, mn (metals)
Nitrogen fixing bacteria
Bring nitrogen from the atmosphere into a fixed form that can be used by other organisms
Respiratory dehydrogenases
Methanogens
The roles of plants and cyanobacteria in this cycle by fixing carbon dioxide into organic matter, the roles of plants/animals/microbes in recycling that fixed organic matter by aerobic oxidation, respiration, to regenerate CO2
Great Oxidation Event
Cyanobacteria invented oxygenic photosynthesis and is responsible for the O2 in the atmosphere.
Thylakoid membrane
Inside the chloroplast and harvests light. The output of the light reactions in the thylakoid is reducing equivalence.
Calvin Cycle
Carbon dioxide is going to be fixed into organic carbon and ultimately into sugars. This requires the ATP and NADPH generated by the light reaction.
Light Reactions
Convert light energy to ATP and NADPH
Inputs: light, H20
Outputs= ATP, NADPH, O2
Z scheme
Two photosystems in sequence
Photosystem II
Photosystem 2 is going to use light energy to generate an electron that is not and has high reduction potential
The connection between the two systems is an electron transport chain where generating a proton motive force can then be harvested as ATP.
Photosystem I
The electron delivered from photosystem two can again be accelerated to a very high-energy state using energy input from a photon.
That very high energy electron can then be used to create a reducing molecule, NADPH
Action spectrum
The amount of oxygen being released by photosynthetic cells when you shine them on different wavelengths (there isn’t much activity on green which is why plants reflect a green color)
Carotenoids
They can absorb light energy very well and transfer the energy through a non radiative energy transfer process. They can transfer energy to other chlorophyll molecules. They provide photo-protection by absorbing excessive light.
Donor energy transfer
Energy transfer between molecules does not depend upon transfer of light or electrons but is due to donor energy transfer that requires direct interaction between the molecules.
Oxygen Evolving Complex
Oxidizes H20 to replenish electrons.
2H20 –> O2 +4H+ 4 electrons
Reducing equivalent
Any of a number of chemical species which transfer the equivalent of one electron in redox reactions
Cyclic photosynthesis
- Involves one photosystem
- There is no terminal electron acceptor
- Makes ATP through chemiosmosis
- Cyclic electron flow; does not make NADPH
Sensor Proteins
Detect if the membrane fluidity is too low in cold temperatures.
NarGHI
The NarGHI in the inner membrane will accept electrons from reduced quinone carriers. The electrons are transferred through a series of carriers, hemes that have a central iron atom and iron sulfur clusters all the way to nitrate, where nitrate is reduced to nitrite. In the process, two protons are released into the periplasm to help generate PMF and sustain ATP generation.
Active when O2 isn’t available
