Chapters 1 and 2: Part 1

What is the fundamental unit of life and is the smallest thing that has all the properties of life?

The cell

What are cells made of and what separates a cell from its environment?

Made up of a core set of organic and inorganic molecules/macromolecules and is separated by at least one membrane

How are a cell’s internal and external environments (milieux) linked?

Cells transport nutrients and waste and also sense and respond to their environment

How do cells obtain and use energy?

They convert external energy or carbon into more complicated molecules and waste through energy-requiring (endergonic) reactions

How do catabolic and anabolic pathways work together?

Catabolic pathways provide energy that power anabolic pathways

What molecules allow cells to use their genetic information and how does it help? What does a cell’s genetic program control?

A genetic program made of DNA that helps the cell reproduce and direct cellular activities

RNA and proteins

What is another fundamental property of life that cells have?

The ability to evolve

What does “All cells descend from earlier cells,” mean?

Cells come from pre-existing cells, meaning there was no spontaneous generation and they share common ancestors

How do eukaryotic cells generally compare in size to prokaryotic cells?

Eukaryotic cells are generally larger

What sets the lower limit on cell size?

A cell cannot be too small because it needs enough room for the genes and enzymes required for life.

what sets the upper limit on cell size?

• Gene copy number

• metabolic requirements

• Surface area-to-volume ratio

• Takes longer to adapt to new conditions

How does gene copy number limit cell size? Are there any exceptions?

A single nucleus may not be able to transcribe and translate enough proteins to support a very large cell.

The only exception is some fungal cells and embryos of certain species

How do metabolic requirements limit cell size?

A large cell must produce enough nutrients, cytoskeleton, organelles, structures, and other materials to fill and maintain the cell

What is the surface-area-to-volume (SA:V) ratio?

The amount of surface area available relative to the cell’s internal volume

How does cell size affect passive diffusion?

In a larger cell with a lower SA:V ratio, passive diffusion throughout the cell takes longer

Why does diffusion take longer in larger cells? How does cell size affect intracellular transport?

Molecules have farther to travel to reach their destinations

Transporting materials throughout a larger cell takes more time and/or energy

How does prokaryotes higher surface to volume ratio, despite being smaller than eukaryotes, affect it?

In prokaryotes, things coming from outside the cell are evenly spread throughout the cell rapidly

In eukaryotes, nutrients don’t diffuse as quickly to regions farther from the surface - so they need a lot of extra structure and transport machinery

Characteristics of Eukaryotic cells

• Have a nucleus and other membrane-bound organelles

• Generally larger and more complex than prokaryotic cells

• Contain mitochondria for energy production

• Use the endomembrane system for transport and protein processing

• Can be single-celled or part of multicellular organisms

• Exhibit compartmentalization to increase efficiency of cellular processes

Characteristics of prokaryotic cells

• Lack a nucleus and membrane-bound organelles

• Generally smaller and simpler than eukaryotic cells

• Reproduce quickly binary fission

• Have a cell wall that provides shape and protection

• Contain ribosomes for protein synthesis

• Exhibit high surface-to-volume ratio for efficient nutrient and waste exchange

Why are not all eukaryotes multicellular organisms?

Not all eukaryotes are multicellular because some, like protozoa and certain algae, have evolved to live and function as single cells, performing all essential life processes independently.

What are the key cellular components of the eukaryotic cell?

• Endomembrane system

• Mitochondria

• Glyoxysomes

• Peroxisomes

• Chloroplasts

• Cytosol

• Plasma membrane

Why is water considered the universal solvent?

Its polar molecules can dissolve a wide variety of substances, allowing essential nutrients and chemicals to be transported and participate in biological reactions.

What does the polarity of water allow it to interact with?

Water interacts with itself and with solutes

What is a hydration shell?

A layer of water molecules surrounding a solute

Why do water molecules form hydration shells around solutes?

Their polar nature allows them to interact with and surround the solute

What bonds are formed when water interacts with polar solutes?

Hydrogen bonds

What two things are needed to form a hydrogen bond?

An electronegative atom = hydrogen acceptor

A hydrogen atom covalently bonded to another electronegative atom = hydrogen donor

What is the difference between hydrogen acceptor and hydrogen donor?

Acceptor: An electronegative atom that attracts the hydrogen in a hydrogen bond

Donor: A hydrogen atom covalently bonded to an electronegative atom

When are hydrogen bonds strongest?

When the acceptor atom is in line with the covalent bond between the donor atom and H - which maximizes the electrostatic interaction between the donor and acceptor

What is the ideal arrangement for a strong hydrogen bond?

Donor atom — H — acceptor atom

• all in a straight line

When do hydrogen bonds not occur?

When hydrogen atoms covalently bond to carbon atoms

What are examples of hydrogen bonding?

• Alcohols

• Aldehydes

• Ketones

• Compounds containing N—H bonds

What can determine how strongly two molecules bind?

Their on-rate and off-rate, represented by Ka and Kd

What is Ka? What is Kd?

Ka: The association constant, which reflects how strongly two molecules associate/bind

Kd: The dissociation constant, which reflects how accessible the binding site is to water

How does water affect binding strength?

Binding strength is often regulated by how accessible the binding site is to water, especially when ionic interactions are involved

What happens to water when molecules form a tight interaction? What does this do ti an interaction?

Water is excluded from the interaction area and it can produce a stronger and longer-lasting interaction

How can the same transcription factor bind one gene more strongly than another?

One DNA sequence may be a better match to the consensus sequence, resulting in tighter binding

What does tighter binding mean for a transcription factor?

The transcription factor has a stronger interaction and lower tendency to dissociate

Does pure water contain ions?

Yes, water undergoes a slight, reversible ionization to produce hydrogen ions and hydroxide ions

What happens when water ionizes?

H₂O ⇌ H⁺ + OH^—

What happens to H⁺ immediately after it forms?

It is immediately hydrated, forming a hydronium ion (H₃O⁺)

What is proton hopping and what does it result in?

Proton hopping: The rapid transfer of a proton (H⁺) from one water molecule to another through hydrogen-bonded water molecules

Results: Gives hydrogen ions high ionic mobility, allowing them to move rapidly through water

What is an acidic solution?

A solution where a compound dissolved in water releases an excess of H⁺ ions

What determines whether an acid is strong or weak?

The proportion of acid molecules that releases H⁺

What does a stronger acid have a greater tendency to do?

Lose its proton (H⁺)

Are most organic acids strong or weak?

Most organic acids are weak acids

What does the equilibrium constant (Keq) tell us about an acid?

It describes the tendency of the acid to lose H⁺ and form its conjugate base

What is a conjugate acid-base pair?

An acid (proton donor) and its corresponding conjugate base (proton acceptor)

In the reaction HA ⇌ H⁺ + A⁻, what is HA?

In the reaction HA ⇌ H⁺ + A⁻, what is HA?

The acid (proton donor)

The conjugate base (proton acceptor).

What is a basic solution?

A solution where a compound removes protons (H⁺) from the solution

What substances commonly act as bases?

Substances containing or producing OH^- or NH₃, although bases do not always contain these

What is the pH scale and what does it say?

Range of acidity to basicity.

• 0 (most acidic) to 14 (most basic); 7 is neutral

What happens to acidity when pH decreases by 1 unit?

What happens to acidity when pH increases by 1 unit?

The H⁺ concentration increases by 10×, so the solution is 10 times more acidic.

The H⁺ concentration decreases by 10×, making the solution 10 times less acidic.

What is the equation for Ka?

Ka = [H⁺][A⁻] / [HA]

What does a high Ka mean?

The acid dissociates more readily, so it is a stronger acid

What is pKa?

A measure of acid strength defined as: pKa = −log Ka

How are Ka and pKa related?

They are inversely related:
High Ka → low pKa
Low Ka → high pKa

What does a low pKa indicate? What does a high pKa indicate?

Low: A stronger acid with a greater tendency to donate H⁺

High: A weaker acid with a lower tendency to donate H⁺

How does pH affect amino acid side chains?

pH affects whether their side chains are protonated or deprotonated, which changes their charge

Stronger acid →

Stronger acid → more H⁺ released → higher Ka → lower pKa

What is the function of charged regions on the outside of many proteins?

They often serve as interaction surfaces for interacting with other molecules

What happens to the arrangement of charged and nonpolar regions in transmembrane proteins?

Their roles are generally reversed because the protein must interact with the hydrophobic interior of the membrane

What is the function of the hydrophobic core of a protein?

It helps stabilize the protein and give it its shape

Why are nonpolar/hydrophobic amino acids often found inside proteins?

They avoid water and pack together to form a stable hydrophobic core

What are internal salt bridges?

Electrostatic interactions between oppositely charged groups within a protein that can help stabilize its structure

What is the general arrangement of a soluble protein?

Charged/polar regions → outside → interact with water and other molecules

Hydrophobic/nonpolar regions → inside → stabilize the protein

Why are biological processes sensitive to pH?

Changes in pH can change protein structure and function

How does a change in pH affect protein structure?

It can change the charge of amino acid side chains, which can alter intramolecular ionic bonds and therefore change protein structure

What happens when amino acid charges change?

Intramolecular ionic bonds can change, potentially altering the protein’s shape and function

What are buffers? What are they generally made of?

Substances that resist changes in pH, that are made up of acid/base pairs that can absorb or release H⁺

What is the main buffer system in blood discussed here?

The bicarbonate/carbonic acid buffer system

What does the bicarbonate buffer system help maintain? What buffer system is important inside cells and what does it maintain?

Blood at approximately pH 7.4

The phosphate buffer system, involving H₂PO₄^- and HPO₄^2- , maintains pH 7.6

How does increased CO₂ affect ocean pH? Why is increasing ocean acidity a problem for coral reefs?

More CO₂ leads to lower ocean pH (increased acidity), dangerous because lower pH can decrease reef stability

How can Streptococcus mutans affect tooth enamel?

Acids produced by S. mutans can lower the pH around teeth, contributing to damage of tooth enamel

Energy is the capacity to?

• Do work

• Change something

• Move something

Thermodynamics is?

The study of the changes in energy that accompany events in the universe

Thermodynamics does and doesn’t do?

• Tell if energy is required

• Hints to which direction reaction will go

• Don’t tell how fast a specific rxn occurs

• Don’t tell which mechanism is used

What does the First Law of Thermodynamics state?

Energy can neither be created nor destroyed. It can only be transferred or transformed

What are the two parts of the universe in thermodynamics?

System: The subset of the universe being studied

Surroundings: Everything that is not part of the system

What is internal energy (E)?

The energy contained within the system

What is ΔE?

The change in the system’s internal energy during a transformation or reaction

What equation describes the change in internal energy?

ΔE = ΔQ + ΔW

What does ΔQ represent? What does ΔW represent?

ΔQ: Heat energy added to or released by the system

ΔW: Work energy done on or by the system

What does a negative ΔEsys mean? What does a positive ΔEsys mean?

+ΔEsys: The system’s internal energy increased

-ΔEsys: The system’s internal energy decreased

What does ΔEsys = 0 mean?

There is no net change in the system’s internal energy

If the system gains energy, what happens to the surroundings?

If the system loses energy, what happens to the surroundings?

The surroundings lose an equivalent amount of energy

The surroundings gain an equivalent amount of energy

What is the relationship between changes in system and surroundings?

Energy is conserved, so changes in the system are balanced by changes in the surroundings: ΔEₛᵧₛ + ΔEₛᵤᵣᵣ = 0

If the system gains energy →
If the system loses energy →

surroundings lose energy

surroundings gain energy

What is the second law of thermodynamics?

Events in the universe move from state of higher energy to a state of lower energy

Characteristics of the second law of thermodynamics?

• Everything is going downhill

• Movement is spontaneous

• Occurs without the input of external energy

pH + pOH = ?

14

Finding pH ? Finding pOH ?

pH = -log₁₀(H₃O⁺)

pOH = -log₁₀(OH^-)

Finding [H₃O⁺] ? Finding [OH^-] ?

[H₃O⁺] = 10^-pH

[OH^-] = 10^-pOH

What happens when one hydrogen gets charged?

All the hydrogens attached to the molecule will also become charged and become hydrogen bonds

What is entropy?

A measure related to the randomness/disorder and energy dispersal of particles or matter

What is free energy?

G, the energy available to do work

In free energy what does <0 mean?

The rxn is exergonic

• gives off energy (usually as heat)

• move toward lower free energy state

In free energy, what does >0 mean?

The rxn is endergonic

• requires energy input

• moves toward higher free energy state

Forward rxn vs Backward rxn

F: k[A][B]

B: k[C][D]

Keq <1 = ?

Keq >1 = ?

Rxn moves toward reactants

Rxn moves toward products