Bis 2A Midterm 1

Great Oxygenation Event

• Oxygen was initially toxic (highly reactive) to everyone

• When cyanobacteria became the first to split water and produce oxygen, everyone was NOT vibing

• Organisms began to adapt to an oxygenated atmosphere - including oxygen-dependent plants!

• Eukaryotes took much longer to evolve

  • Much more complex

Energy

• Energy comes from facilitating chemical reactions → which supports life

  • EX: Cellular respiration

• Early Life used H₂ as a fuel (like how we use sugars, lipids, proteins)

  • Reaction between “fuel” and O₂

  • High H₂ concentrations → reducing atmosphere

  • High O₂ concentration → oxidizing atmosphere

• Life uses more stable sources of energy!

• Eukaryotes require oxygen to live/evolve 

• Energy is inherent in structure of molecules additional energy is present in the motion and vibration of molecules

Entropy

• Disorder or randomness

• EX:

  • Room that gets increasingly messier with no work from you

  • Throwing something off of a building

  • Cracking an egg into a pan to cook it

• Very difficult to decrease entropy (Can you put the egg back in the shell and seal it up?)

• Easier to increase entropy!

• Things will spontaneously move in the direction of increasing entropy

Gibbs Free Energy

Potential energy used to do work (including the reduction of local entropy).

• When the change in Gibbs free energy is negative (ΔG < 0), a given reaction is spontaneous and exergonic

• The reaction will proceed in the forward direction

• When the change in Gibbs free energy is positive (ΔG > 0), a given reaction is non-spontaneous and endergonic

• • The reaction will need an input of energy from somewhere else in order to proceed in the forward direction •

• Life is powered by spontaneous chemical reactions

• There is no correlation between the sign of ΔG and the speed of a reaction

2nd Law of Thermodynamics

For any spontaneous process, total entropy of the universe increases

Equilibrium vs. Steady State

• Equilibrium: when reactants and products are formed at the same rate, looks like nothing is happening

  • Can’t harvest useful energy

  • Your cells are cooked.

• Steady state: nonequilibrium (think: water flowing)

  • Concentrations of reactants and products constantly change

  • Chain of reactions where we feed reactants and extract products

CHONPS

Carbon —> 4 bonds

Hydrogen —> 1 bonds

Oxygen —> 2 bonds

Nitrogen —> 3 bonds

Phosphorus —> 5 bonds

Sulfur —> 2 bonds

Valence Electrons and Bonds

• Full octet = 8 valence electrons (for most atoms! But we don’t care as much about elements that can have expanded octets)

• Carbon, for example, has 4 valence electrons

  • Needs 4 more electrons to have full octet

  • 4 electrons can be from 4 different atoms

• Each bond (covalent) is made up of two electrons shared between atoms!

Electronegativity 

• The ability of an atom to attract electrons to itself

  • Most electronegative atoms are towards the top right of the periodic table – the ones we will worry about are O, N, S (electropositive are C, H, P)

• Each element is associated with an electronegativity value

• The types of bonds between atoms are determined by the difference between the EN values of the two atoms involved

Hydrogen Bonds

1. Hydrogen bonds: type of electrostatic attraction that occurs between partially positive and partially negative charged atoms

   1. Hydrogen Bond acceptor: atom with partial negative charge (O, N)

   2. Hydrogen bond donor: atom with partial positive charge (H)

Functional Groups

FGs give biomolecules (i.e. proteins, lipids, carbohydrates, drugs) their properties and determines how they interact with each other

Carbohydrates

• Have C, H, O (fixed ratio of 1:2:1)

• Have a lot of -OH groups

• Rings and long chains

Nucleic acids

Has a nitrogenous base, a pentose sugar, and a phosphate group

Lipids

• Contain many C-H bonds, no fixed ratio

• More carbon atoms than oxygen

• Has long chains of C-H bonds (“tail”)

Proteins

• Have C, H, N, O

• Have amino and carboxylic acid groups (can be in P/D state)

• Have the N-C-C backbone pattern (can also show up as C-C-N depending on orientation)

Equilibrium

The state in a reversible chemical reaction where the rate of the forward reaction is equal to the rate of the reverse reaction

• [reactants] ≠ [products], but the concentrations are constant

• Life is constantly fighting equilibrium—it likes to keep a non-equilibrium steady state (via homeostasis)

• This is because life derives its energy from the flow of high potential energy to low potential energy

• High concentration = high potential energy

• Low concentration = low potential energy

Le Chatelier’s Principle

when a system is disturbed, then the reaction will proceed in the direction that brings the system back to an equilibrium state

• Ex. Adding more A to A + B ⇌ C + D will force the reaction in the forward direction

Transition State Energy

• the state of a molecule during a reaction (“at the top of the hill”)

• •The transition state for biochemical reactions has a higher potential energy than the reactants/products

• This is because the transition state is unstable — lots of breaking and forming of bonds

• In order to reach the transition state, you will need an input of energy from somewhere

Activation Energy

• the minimum amount of energy needed start a chemical reaction

• If the activation energy is very large, it may be impossible for a reaction to ever occur

Catalysts

• enzymes that lower the amount of energy needed to begin a reaction by

•  Bringing substrates together

•  Creating a favorable environment for a reaction to occur

•  Holding substrates in a favorable orientation

• Catalysts DO NOT change the ΔG of a reaction, they only reduce the activation energy barrier

•  They enable reactions to take an alternate pathway that uses a lower energy transition state

• Lower AE to increase reaction speed 

• Changes transition state energy

Heat & Rxn

• Lowers AE but doesn’t change energy of the transition state

Glycolysis (Metabolism)

• Overall exergonic

• Some energonic (highly unfavorable)

Electron Tower

Shows reduction-oxidation half reactions

• Oxidized/Reduced

• Increasing reduction potential (E0’) as we move

down the tower

Calculating ΔE

• Relationship between ΔG and ΔE

• +ΔE —> -ΔG (spontaneous, exergonic)

• -ΔE —> +ΔG (non-spontaneous,

endergonic)

Paradigm

A dominant way of thinking

True

T/F: Science works entirely with ideas that are consistent with observations and have some probability of being right. There’s often no solid answer. The theories are not certainties.

Diversity of life

Explained in principle by 3 random processes (mutation, recombination and drift) plus 1 directed process (selection)

True

T/F : We (optimally) maintain steady-state levels of fuel (glucose) and O2, to burn the fuel in our bloodstream.

Direction of Rxn

molecules in a population are undergoing forward and reverse reactions all the time
(provided there’s enough vibrational/kinetic energy) regardless of whether the reaction’s already at equilibrium, or instead has a net flow going backward or forward

Determinants of the flow of rxn

• The innate (molecular) nature of the reactants and products. Affects the probability they’ll react IF they bump into each other. Big
  PF (and small PR) pushes rx to the right.

• The concentration of each reactant and product (which affects the
  frequency with which they bump into each other). Increasing the
  concentration of reactants A+B means the reactants will bump into
  each other more frequently, pushing the rx to the right. 

• When these two equal each other, they reach equilibrium

True

T/F: Life takes advantage of existing disequilibria to harvest energy. Energy can’t be derived from a system at equilibrium

Homeostasis

In living things, open systems, most reactants and products are kept
at a nonequilibrium steady state (called homeostasis), which
determines the direction of metabolite flow.

• A nonequilibrium steady state suggests a continuous flow

True

T/F: Concentration also affects reaction direction increasing the concentration of product increases the likelihood of the reverse reaction

True

T/F: While individual molecules may be participating in the forward or reverse reaction. The net direction of a reaction depends on the relative potential energies of the reactants and products.

True

T/F: potential energy is determined by both the structure and the concentration of the molecules

Good Fuel

• Release energy when burned (negative ∆G)

• Being lightweight (more bang per ounce) would be nice too, if you need to carry it around.

• Not burn unless you want it to

• Have a high potential energy

True

T/F: A reaction can’t proceed- in either direction- if none of the molecules have the
vibrational/kinetic energy required to reach the transition state.

Enzymes

• Life reduces barriers for some reactions without
  affecting others... using proteinaceous catalysts
  called _____ that have very specific substrates (=
  reactants) and products

• Reduce activation energy barriers- this
  makes both the forward and reverse reactions
  faster- or in most cases, possible on a biological
  time scale

• Can be switched on and off, and act as
  stopcocks or lockable doors to regulate the flow of
  energy and materials

• Like all catalysts, ________ regulate the rate, but not
  the direction/energetics (∆G), of a reaction.