Biol 241 Midterm 1 Review

Flashcards of vocabulary terms extracted from lecture notes on molecular energy transformations and biological systems.

Information Flow

The use of genetic material such as DNA and how it is passed through organisms.

Evolution

The process by which organisms are preserved and continue to evolve, influenced by their properties and environment.

Cells

The basic unit of life, not life itself, but a fundamental component of living organisms.

ATP

The basic unit of energy used by cells for various functions.

DNA

The basic unit of heredity, storing and passing on genetic information.

Falsifiable

The ability to be proven false; new data tends to change conclusions.

Great Chain of Being

• An ordering organisms, along with the Earth and the soul, into levels of complexity

• Humans would often get special treatment, with most other lifeforms being positioned to be below them in a sort of hierarchy, with divine beings such as angels and a supreme being at the top of the chain

• In this chain, Humans are being pulled down towards the devil and strive to move up to the divine

Taxonomic Hierarchy

A hierarchical system used to classify organisms, from broad categories to specific species.

Kingdom

The broadest and most inclusive category in the taxonomic hierarchy.

Genus Species

The combination of genus and species names that uniquely identifies an organism.

Protista

A group of single-celled organisms that exhibit plant and animal-like behaviors.

Motile

An organism that is able to move on its own.

Photosynthetic

Organisms that use light energy to synthesize organic compounds.

Ribosome DNA Sequence Comparison

A technique used to compare the nucleotide sequences of ribosome genes among species. This is very useful as it can tell us truly how similar or how different species can be.

Bacteria

• All Prokaryotes (before nucleus)

  • Does not have a nucleus

• Unicellular

  • Fully functional lifeforms as a single cell

• Cell Walls of peptidoglycan

  • Way of protecting itself

  • “Peptido” refers to amino acids while “glycan” refers to sugar

• Small

  • 1-10 micrometers long

  • Can also have various shapes

Archaea

• Very similar to bacteria so it was a kind of surprise to discover that they are different enough on a molecular level to be their own domain

• Archaea seem to grow in very extreme regions

• Prokaryotes

• Unicellular

• Cell walls made of pseudomurine

  • Slightly different mix of peptides and sugars from peptidogylcan

• Small

  • 1-10 micrometers

• These traits are why it was so hard to tell the difference between Archaea and Bacteria, as the only real noticeable difference is their cell wall material

Prokaryotes

• Cells that do not have a nucleus.

• Possess a single, circular double-stranded DNA genome

• No membrane-bound organelles

• 70S (seventy-es) ribosomes

• Are incredibly small as to have enough surface area:volume ratio.

• All metabolism occurs in the cytosol and on the plasma membrane

Eukaryotes

Cells that possess a nucleus. Are typically 10x larger than that of prokaryotes because the rate of diffusion and energy generation are the same. Possess multiple, linear double-stranded DNA genome with 80S (eighty-es) ribosomes.

Cell Membrane

A biological membrane that surrounds all cells, separating the internal environment from the external one. It's a dynamic structure composed of a phospholipid bilayer with embedded proteins and carbohydrates. It acts as a barrier, regulating the passage of substances into and out of the cell, and plays a vital role in cell-cell communication and recognition. The surface area of a cell is the surface area of its cell membrane.

Cytosol

The fluid inside of a cell.

Endomembrane system

A membrane system within the cell membrane

Diffusion

The tendency of molecules to move from areas of high concentration to low concentration.

Horizontal Gene Transfer

Occurs when a gene from one species becomes part of the genome in another species

Endosymbiotic Theory

The theory that eukaryotic organelles were originally prokaryotes, which survived digestion of the larger cell and formed a mutual relationship where the smaller prokaryotic cell would have a safe place and the larger cell would receive the excess energy generated from the prokaryotic cell.

Phototroph

Organisms that get their energy from light sources.

Chemotroph

Organisms that extract energy from redox reactions

Organotroph

Organisms that get their carbon from organic molecules (Molecules with 2 or more C atoms)

Lithotroph

Organisms whose carbon source comes from inorganic molecules (Molecules with no C atoms)

Autotrophs (Self-eater)

Organisms that fix C atoms to make organic molecules from which it can sustain itself.

Heterotrophs

Organisms that must consume other sources of organic carbon, usually plants or animals.

System

Anything of interest in the study of biological systems.

Surroundings

Everything outside the system that interacts with it.

Isolated System

A system that has no interaction with its surroundings.

Closed system

A system that exchanges energy with its surroundings but not matter.

Open System

A system in which both energy and matter can cross the boundaries between the system and its surroundings.

Energy

The ability to cause change, essential for life to grow, replicate, and survive.

Potential Energy

Energy that is stored due to position.

Kinetic Energy

Energy of motion or change; energy doing work.

Enthalpy (H)

The sum of the potential and kinetic energy of a system. Measured in kJ/mol.

Exothermic

A reaction where the products have less enthalpy than the reactants, releasing heat.

Endothermic

A reaction where the products have greater enthalpy than the reactants, absorbing heat.

Spontaneous Reactions

A reaction that can occur under specific conditions. It is important to know that these reactions are not instantaneous.

Entropy (S)

How dispersed energy (matter) of the system and surroundings becomes. Measured in J/molK.

Second Law of Thermodynamics

The total entropy of the universe must always increase.

Free Energy (G)

• Is a measure of the energy in a system that is “free” (available) to do work

• For work to occur (for something to change), energy must be available to carry out the change

  • The reactants must have more free energy than the products

• The change in free energy, before a reaction to after, is ΔG

• Measured as the amount of energy that was used to make the change

  • If energy is available, then ΔG is negative

  • If energy is not available, then ΔG is positive

Exergonic

A reaction that releases free energy, products have less free energy than reactants. Spontaneous reactions fall into this category.

Endergonic

A reaction that free energy is gained, so products have more free energy than reactants. Non-spontaneous reactions fall into this category.

Chemical Equilibrium

The state where the rate of the forward and reverse reactions are the same, resulting in constant reactant and product proportions. This is not when the reaction has come to completion.

Standard Free Energy Change (ΔG^∘)

Measurements are made under specified “standard” conditions to determine standard free energy changes for reactions.

Metabolism

The sum of all reactions in a cell.

Catabolism

The breaking down of complex molecules, which is done in a series of exergonic reaction to carry out an exergonic process.

Anabolism

Anabolism is a series of exergonic reactions, which overall, are carrying out an endergonic process

Connected Reactions

If the product of the first reaction is the substrate for the second reaction

Coupled Reactions

Allows exergonic reactions to power endergonic processes

Lipids

• Water insoluble (hydrophobic) molecules composed mostly of carbon and hydrogen atoms (hydrocarbons)

• Three types we’ll discuss:

  • Triglycerides (triacylglycerol)

  • Phospholipids

  • Sterols

Fatty Acids

• Building blocks of lipids

• Hydrocarbons with a carboxyl group at one end

• Fatty acid molecules vary in the:

  • Number of carbon atoms in the hydrocarbon chain

    • E.x C6, C24, C32

  • Presence (and number) of carbon-carbon double bonds

    • Saturated has no carbon-carbon double bonds

    • Unsaturated has carbon-carbon double bonds

Triglycerides

• Used as energy storage molecules

  • Hydrocarbons have lots of non-polar covalent bonds

• 3 fatty acid “tails” bound to a glycerol “anchor”

  • Glycerol is a 3C alcohol, which is linked through the carboxyl group

Fluid Mosaic Model

• Current model on membranes

• Mosaic: Lipids, proteins + carbohydrates all mixed together

• Integral proteins

  • Cross and are exposed on both sides of the membrane

  • Also referred to as transmembrane proteins

• Peripheral proteins

  • Sits on one side or the other of the membrane

• Glycolipid

  • Has a sugar attached to it

• Glycoprotein

  • Has a sugar attached to it

Integral proteins

• Are exposed on both sides of the cell membrane

• Also referred to as transmembrane protein

• Transports molecules across the membrane

Peripheral proteins

Sits on one side or the other of the membrane

Glycolipid

Has a sugar attached to it

Glycoprotein

Has a sugar attached to it

Sterols

Animal cells insert cholesterol into bilayer

Membrane Permeability

• Affected by the fluidity of the membrane

• Fluid membranes are “leaky”

  • More molecules can pass from one side to the other

• Viscous membranes are better barriers

  • Few molecules can cross the membrane

Aquaporins

Only allows water to pass through. These have amino acids that are hydrophobic as the exterior with hydrophilic amino acids as the interior, allowing water to pass

Diffusion

• The tendency of dissolved molecules to evenly distribute themselves in a solution

  • Molecules move from areas of high concentration to areas of low concentration

  • Equilibrium will eventually be reached

    • [gradient] has been eliminated

    • Will occur when solutes are equally spread out

Tonicity

• The relative solute concentration difference across a lipid bilayer

• Differences affect diffusion/osmosis across the membrane

• There are three major categories

  • Isotonic solution

    • The concentration is the same as the solute

  • Hypotonic Solution

    • Less than the solute

  • Hypertonic solution

    • Greater than the solute

Passive Transport

The ability of molecules to cross a membrane without the use of energy via diffusion with two types: Simple and Facilitated DIffusion.

Simple Diffusion

• Small hydrophobic and small polar solutes diffuse by themselves

• Potential energy in a concentration gradient is what allows  molecules to diffuse

• Is reversible; things can move in but can also move out should there be a concentration gradient

• Increases at a linear rate as the concentration difference increases (the greater the [ ], the faster it will occur)

Facilitated Diffusion

• Facilitated Diffusion

  • Large/charged/polar molecules require assistance

    • A transporter

      • Proteins shaped like tunnels across the membrane

      • Facilitate the diffusion of these types of molecules down their concentration gradient

      • This is not active as it is relying on the potential energy from the concentration gradient

      • Substrate-specific i.e every molecule needs a specific transporter to aid it

      • As the concentration difference increases, the rate of transport increases until eventually reaching a plateau

Channel Proteins

• Handles diffusion of Ions and Water

• Form hydrophilic channels in the membrane

• Aquaporin

  • Creates a hydrophilic channel for water tor diffuse

• K+ voltage-gated channel

  • Are able to change their shape to close or open

Carrier Proteins

• Moves larger molecules i.e glucose and amino acids

• Binds to a single, specific solute and move it through the membrane, unlike how channel proteins rely on diffusion to move it

• Acts similar to the K+ voltage-gated channel as it will as open and close when transporting molecules

25

What percent of a cell’s ATP is used to establish a concentration gradient by moving solutes away from equilibrium through transporters that use energy?

Active Transport

• Concentrates molecules (like sugars and amino acids) inside cells

• Also used to push ions in or out of cells

• Two types: Primary and Secondary

Primary Active Transport

• There are substrate-specific proteins called “pumps” that cross the membrane and

  • Move solutes up their concentration gradient

  • Transporters use ATP to power the movement

  • Often generate concentration gradients

    • Electrical

    • Chemical

• ATP is used to change the shape of carrier proteins to match the molecule

Symporters

Moves two solutes as one is moved to provide energy for the other solute in the same direction

Antiporters

Similar to symporters but instead, the solutes are moved in opposite directions

Enzymes

• Remember that proteins are polymers of amino acids

• Amino acids consist of an amino group (NH3), an alpha carbon, a carboxyl group and an R group, which is a side chain of molecules

• Amino acids can be either polar or non-polar

• Amino groups and carboxyl groups are generally on the outside of molecules, which allow them to interact with water

polypeptides

Chains of peptides, which tend to be chains of 10+ amino acids

Activation Energy

Energy needed to trigger reactions

Reversible Competitive Inhibitor

Inhibitor is chemically like the substrate

Reversible Noncompetitive Inhibition

Is not chemically like the substrate, Rather than binding to the active site, it binds to a different spot on the enzyme, the Allosteric site

Regulator (Allosteric) Enzymes

• Some enzymes have these sites that allow other molecules to bind to it but not to inhibit the enzyme

• These enzymes have quaternary structures (more than one active site)

• Activators

  • Binds to the enzyme which changes the shape to a more active form to catch substrates

• Inhibitors

  • Binds to the enzyme which changes the shape to a less active form

• Feedback inhibition

  • The final product of a pathway inhibits an enzyme early in the pathway

Aerobic Respiration

• A series of coupled redox reactions that release the free energy of glucose and transfers some of the released energy to other molecules

• Generally where glucose is “burned” in oxygen (combustion) to produce CO2 and H2O with the release of heat

  • However, if this were done in a single step, our cells would literally blow up from the immense amount of energy and so this process actually occurs in a series of reactions

Coupled Redox Reactions

Chemical reactions in which one species is reduced while another is oxidized, allowing for the transfer of electrons and energy between them.

Electron Carrier (Redox) Coenzymes

Biological redox reactions generate reduction potential that is stored in electron carriers

What are reduced electron carriers

We can think of reduced electron carriers as energy transport molecules that move electrons from one reaction to another

Glycolysis

• Glucose (6 carbons) which will end up into 2 pyruvate (3 carbons)

• Glucose requires 2 molecules of ATP, which will result in 2 ADP

  • This is done because glucose is a stable molecule so by adding phosphate groups to glucose, this will destabilize it into glucose-6-P

• Afterwards, 2NAD+ go in and 2 NADH come out

• 4ADP go in, 4ATP goes out

  • Since we consumed two molecules of ATP and created four molecules of ATP, we say that we net gained 2 molecules of ATP

• The ATP alone isn’t enough, so we also use the NADH generated

• Is NOT a part of fermentation

Electron Carriers are Reduced

We used a electron carrier to reduce NAD+ to get NADH + H+

Fermentation

• The anaerobic reduction of pyruvate

  • Reduced by using NADH

  • Pyruvate + NADH —> Organic Acid + NAD+

  • Acts as an emergency pathway as ATP is not produced here if no oxygen is being available

  • Will end there is a supply of oxygen again

  • Two types: Lactate and Alcoholic

Electron Transport Chain (ETC)

• Consists of four protein complexes named Complex I - Complex IV.

• Is embedded or associated with the inner membrane of the mitochondrion.

• The work done by it is to move protons with pumps.

Electronegative Final Electron Acceptor

O2 is highly electronegative and is the final electron acceptor

Ubiquinone

A hydrophobic electron taxi. Is often abbreviated as UQ and is often found with the hydrophobic tails of lipids. UQ taxis electrons of NADH from Complex I to Complex III and electrons of FADH from Complex II to Complex IV. When it is reduced, it grabs H+ protons from the matrix and releases H+ into the Intermembrane System when oxidized.

Proton Motive Force (PMF)

• An electrochemical gradient that makes the matrix positively charged

• [H+] is lowered in the matrix when they are

1. Pumped or moved across the membrane to the Intermembrane Space

2. Used to reduce O2 to H2O

• Since it is a concentration gradient, it also possess a lot of potential energy

ATP Synthase

• ATP Synthase catalyzes ATP synthesis using energy from the H+ gradient across the membrane

• Fnot - the proton channel

• F1 - the catalyst

  • The part where ATP is made as energy is gained here and the

• A coupled reaction occurs as ADP + Pi would never happen on its own so its coupled with H+ to lead to an overall negative ΔG

Aerobic Respiration - Prokaryotes

• Prokaryotic organisms do NOT have membrane-bound organelles i.e no mitochondria

  • As such, all of their metabolism occurs in the cytosol

  • They have no internal membranes so they use the cell membrane

  • Otherwise, it is “the same”

Anaerobic Respiration

• Does not use O2 but rather, inorganic molecules such as NO3, PO4

  • NO3 → NO2 (Reduction)

  • PO4 → PO3 (Reduction)

Light reactions

• First Process in photosynthesis

• Thylakoid is needed here

Calvin Cycle

• Other half of photosynthesis

• Where carbon fixation occurs

• All ATP and NADPH formed from the light reaction is used in the Calvin Cycle

Pigment

• Molecules that are efficient in absorbing photons

• Their chemical structure allows their electrons to absorb solar energy

• Pigments absorb photons of specific wavelength i.e pigments don’t all absorb the same photons

  • The wavelength must EXACTLY match the energy needed to raise an electron to a higher orbital

  • If the wavelength isn’t exact, nothing happens