Chapter 2: Chemical Components of Cell

The chemistry of life is organic. What does that mean?

Carbon

Chemical reactions in aqueous solutions react in

very limited temperatures

Most polymers are

small molecules linked in long chains

Chemical reactions are tightly regulated meaning

they only happen in the proper place and time

The characteristics of cellular molecules are dependent on

1. Atoms comprising them

2. Chemical bonds linking atoms together into molecules

Element

Cannot be broken down any further

• Examples that are important to cells: Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, Phosphorus

Atom

Smallest unit of an element that still retains distinct chemical properties

An atoms nucleus is _____ charged

positively

_____ in cloud surrounds the nucleus, which are ______ charged

electrons, negatively

In an uncharged atom, the charge of protons is equal and opposite to

change of electrons

Atoms are held together by

Electrostatic attractions

The nucleus of an atom contains (particles)

protons (positive charge) and neutrons (neutral)

Atomic number is equal to

the number of protons or neutrons in an uncharged atom

Isotope

Physically distinctive, chemically identical, with the same number of protons but a different number of neutrons

What is the exception to the rule that protons and neutrons always are equal in an uncharged atom?

Hydrogen, which is the smallest element and lightest atom with 1 proton, 1 electron, and 0 neutrons

In chemistry, atomic weight is

Mass of protons + mass of neutrons in an atom

In the cell, weight is relative to the

mass of a hydrogen atom in daltons

• 1 da defined as 1/12 amu of carbon = ~1

• = mass of all protons + all neutrons in a molecule

Avogadro’s number

6 × 10²³

• Weight proton/neuron = 1/(6 × 10²³)g

• 1 g H = 6 × 10²³

• Mole = # grams of substance containing 6 × 10²³ molecules or atoms of substance

Molar solution

1 mole of substance in 1 liter solution (mol/L)

CHONSP

• Carbon

• Hydrogen

• Oxygen

• Nitrogen

• Sulfur

• Phosphorous

Composes majority all organisms weight and participates in the composition of DNA, RNA, proteins, lipids, and carbohydrates

Neutrons are not usually involved in bonding except in

• radioactive decay

• inside sun

• inside nuclear reactor

Octet Rule

Outer shell of electron shell can have up to 8 electrons, except in the first electron shell

Electron Rules

Move in shells and are filled in certain ways

• 1st shell = 2 electrons

• 2nd and 3rd shell = 8 electrons

• 4th and 5th shell = 18 + 32 (Not CHONSP)

Atoms are most stable when the outer electron shell is full

Inert atoms

Atoms with full electron shells prior to forming a chemical bond

Examples: noble gases such as helium, neon, argon

Oxidation

Giving up an electron in biological systems

Reduction

Gaining an electron in a biological system

Ionic bond

Transferring electrons to another atom

Covalent bond

Sharing electrons between 2 atoms

• CHONSP usually

Close in electronegativity

Valence electrons

Number of electrons gained, lost, or shared

Valence shell

Outer most shell of electron shells

Molecules are a cluster

of atoms covalently bound, meaning they are shared

Shared electrons complete outer shells of both atoms, why?

1. They form “permanent link” between atoms making it more than thermal energy to break them apart

2. Electron could is densest between 2 nuclei

3. Lower temperature for covalent bonds (low and stable) vs ionic bonds (high, not stable)

How many bonds can CHONSP make?

• Hydrogen: 1 bond

• Sulfur, Phosphorous, Oxygen, Nitrogen, and Carbon: More than 1 bond

Covalent Single Bond

Shares 2 electrons

• Longest bond length

• Allows for rotation around bond

Covalent Double Bond

Shares 4 electrons

• Shorter bond length

• Less flexible, but stronger than single bond

Both single/double Covalent bond

Highly stable and bonding of electron is evenly distributed

Polar Covalent Bond

• Has net dipole

• Usually involved O or N bonded to H

Noncovalent bond

• No net dipole

• Usually between same atoms and C and H

Bond energy

Stronger than thermal energy of collisions. This is important because molecules are always hitting each other

Bond strength

Amount of energy required to break a bond

• expressed in kJ or Kcal/mol

• Kcal = amount of energy needed to raise temperature of 1L of water at 1 degree celsius

1 Kcal of energy is needed to break 6 × 10²³ bonds of a specific type

Noncovalent bonds in cells are much weaker in strength but

there is strength in numbers. They are simultaneously occurring and they are strong enough to provide tight bonding

Ionic bond

Transferring electrons between atoms

Have

• Cations

• Anions

Held together by electrostatic interactions

Ionic Bond - Cations

1 more proton than electrons

Ionic bond - Anion

1 more electron than proton

Salts (Ionic Bond)

• Tend to have a higher melting temp

• Will dissolve in water

• High difference in electronegativity

Partially charged molecules polarity rules

• Negatively charged have higher electrostatic energy

• Higher electrostatic energy, higher interactions that hold molecules together in unique ways

Hydrophilic molecules

• Water - loving

• Really dissolve/associate

• Ionic compounds

• Polar molecules can H-bond with water

• In cells

  • Sugars

  • RNA and DNA

  • Proteins

Hydrophobic Molecules

• Do not easily dissolve

• Uncharged molecules (hydrocarbons) cannot form H-bonds

• H covalently linked to C is non polar

• In cells, lipid membranes (they don’t mix with water)

Hydrogen bonds

• Non covalent, weak bonds between

  • Positively charged H on one polar molecule and a negatively charged atom of a second molecule (usually N or O)

• Can occur within the same molecules

  • in and between proteins for stability

Hydronium Ion

• Occurs in molecules with highly polar covalent bonds

• Positively charged hydrogen gave up an electron, so it is a naked proton

• H+ jumps between adjacent O’s of H2O or other polar molecule —> H3O+

• Acidic

Hydroxyl ion

• H+ lost from H2O —> OH-

• Basic

pH measures ________ in cells

H+

H3O+ defines cell ______ ←→ H+

acidity

The pH scale is ______ meaning for 1 unit increase/decrease PH, get 10-fold increase/decrease in H+

logarithmic

Acids in Cell Biology

• Strength depends on ease of acid to release protons to H2O

• Strong acids lose H+ easily

  • Happens if H3O in solution is low

• Weak acids don’t easily give up H+

  • COOH

    • This is important in buffering systems

Homeostasis

Molecules self regulating

Bases in Biology of Cells

• Solutes accept H+ (protons) from H2O when dissolved in water

• Also called Alkaline

  • Increases OH- in water

• Strong - readily forms ions in solution

• Weak - low tendency to reversiby accept protons from H2O

  • many contain NH3 groups

Buffers

Cell neutrality = weak bases and weak acids

Dehydration Synthesis/Condensation

Creating a macromolecule by losing water and using energy

Hydrolysis

Breaking apart a macromolecule using water and energy

Precise Shape of Macromolecules

Conformation

______ are important in maintaining conformation

Non covalent bonds such as ionic, hydrogen, van der walls, hydrophobic

Van der Waals Attraction

Electrical attraction due to fluctuating electric charges as 2 atoms approach each other; weaker than H bonds

Hydrophobic Forces

Force driving hydrophobic molecules together to exclude water

Atoms held by covalent bonds are

monomers

Monomers held together by covalent bonds are

polymers (macromolecules in cells)

Atoms within macromolecules held by noncovalent interactions are

conformations (shapes)

Macromolecules held by noncovalent bonds are

macromolecule complexes

4 Major families of small organic molecules or Macromolecules

• Sugars- Energy sources and subunits of Polysaccharides

• Fatty Acid Chains- components of Cell Membranes

• Amino Acids- subunit of proteins

• Nucleotides- subunits of DNA and RNA