Chapter 2 - Chemical Components of Cells

Chemical Components of Cells

Learning Objectives

• Chemical Bonds: Understand the types of chemical bonds.

• Atoms: Identify atoms of interest and their structure and interactions.

• Small Molecules: Identify small molecules in cells.

• Electrons: Understand the role of electrons in forming molecules.

• Water: Understand the importance of water to life, including its properties and functions.

• Macromolecules: Understand how macromolecules are made in cells.

• Review: Review BIOS100-level material and inorganic and organic chemistry.

• Reading: Read Chapter 2 of the Open Stax eBook or any cell biology book on chemistry (e.g., Alberts et al., "Essential Cell Biology" 6th edition, Chapter 2).

Elements and Atoms

• Elements: Substances that cannot be chemically interconverted or broken down into simpler substances.

• Atoms: Building blocks of molecules, composed of protons and neutrons in the nucleus, surrounded by electrons in orbitals.

• Common Atoms in Organic Molecules: Carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and phosphorus (yellow) are typical colors used to denote these atoms.

Atomic Number and Isotopes

• Carbon: Atomic number of 6, with stable isotopes of mass numbers 12 and 13. Relative atomic mass is 12.11.

Atomic Structure

• Atom: Consists of a nucleus (positively charged due to protons and possibly containing neutral neutrons) surrounded by orbiting electrons.

• Atomic Number: Determined by the number of protons in an atom.

Bohr Diagrams and Electron Configuration

• Bohr Diagrams: Illustrate how many electrons fill each principal shell.

• Group 18 Elements: (Helium, neon, argon) have a full outer, or valence, shell, which is the most stable electron configuration.

• Other Elements: Have partially filled valence shells and gain or lose electrons to achieve a stable electron configuration.

• Electron Vacancies: Depict possible atomic interactions for bonding.

Electron Interactions and Chemical Reactions

• Outermost Electrons: Determine how an atom will interact with other atoms.

• Chemical Reactions: Electrons can participate in chemical reactions with other atoms, facilitating bonding.

Bond Types in Cells

• Covalent Bonds: Formed by atoms sharing electrons.

• Ionic Bonds: The difference between covalent and ionic bonds is significant in cellular processes.

Elements in Living Cells

• Key Elements: Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen (N) constitute approximately 96% of living cells, with Phosphorus (P) and Sulfur (S) also being important.

Covalent Bonds

• Formation: Covalent bonds form by atoms sharing electrons.

• Double Bonds: If two pairs of electrons are shared, a double bond is formed.

• Molecules: When two or more atoms are held together by covalent bonds, they form a molecule.

• Strength: Covalent bonds are strong enough to survive a range of conditions inside cells.

• Electron Sharing: Electrons in covalent bonds can be shared equally or unequally.

Water Molecule Formation

• Water Molecule: Formed when two hydrogens and an oxygen atom share electrons via covalent bonds.

Double Bond Example

• Oxygen Molecule (O2): An example of a double bond joining two oxygen atoms.

Ionic Bond Formation

• Ionic Compound Formation: Metals lose electrons, and nonmetals gain electrons to achieve an octet.

Ionic Bond Example

• Sodium Chloride (NaCl): Sodium (Na) reacts with chlorine (Cl) to form NaCl.
  *How does water dissolve this ionic bond?

Hydration Spheres

• Dissolving NaCl in Water: When table salt (NaCl) is mixed in water, it forms spheres of hydration around the ions.

Polarity and Molecular Shape

• Polarity: Whether a molecule is polar or nonpolar depends on both bond type and molecular shape.

• Water and Carbon Dioxide: Both have polar covalent bonds, but carbon dioxide is linear, so the partial charges cancel each other out.

Polarity of Water

• Electronegativity: Polarity of water is due to differing electronegativities of hydrogen and oxygen.

• Hydrogen Bonds: Formed when the slightly negative oxygen on one water molecule is attracted to the slightly positive hydrogen of another water molecule.

Hydrogen Bonds and Water Properties

• Hydrogen Bonds: Important noncovalent bonds for many biological molecules.

• Cell Composition: Cells are 70% water by weight.

• Polarity: Water molecules are polarized, allowing two water molecules to form a noncovalent linkage called a hydrogen bond.

• Electron Attraction: Oxygen atoms have a greater attraction for shared electrons, imparting a slight negative charge on the oxygen side and a slight positive charge on the hydrogen side of the water molecule.

• Water Properties: Water is an excellent solvent; it has high cohesion to other water molecules, adhesion to non-water materials, high specific heat, high tensile strength, and high surface tension, making it a perfect molecule to support living cells.

Ice Density

• Ice vs. Liquid Water: Hydrogen bonding makes ice less dense than liquid water.

• Lattice Structure: The lattice structure of ice makes it less dense, allowing it to float on water.

Hydrophilic and Hydrophobic Molecules

• Hydrophilic Molecules: Substances that dissolve readily in water, including ions and polar molecules that attract water molecules through electrical charge effects.
  *Example: sodium chloride, urea

• Hydrophobic Molecules: Substances that contain a preponderance of nonpolar bonds are usually insoluble in water.
  Example: hydrocarbons

Water as a Solvent

• Solvent Properties: Many substances, such as sucrose, dissolve in water; their molecules separate from each other, each becoming surrounded by water molecules.

• Solution: When a substance dissolves in a liquid, the mixture is termed a solution.

• Components: The dissolved substance is the solute, and the liquid that does the dissolving is the solvent.

• Water as a Solvent: Water is an excellent solvent for hydrophilic substances because of its polar bonds.

Surface Tension of Water

• Surface Tension: A needle's weight pulls the surface downward, while surface tension pulls it up, suspending it on the water's surface.

Cohesion and Adhesion

• Capillary Action: Adhesive forces exerted by the glass' internal surface exceeding cohesive forces between water molecules causes capillary action in a glass tube.

Water Strider

• Cohesive and Adhesive Properties: Allow water striders to stay afloat.

Methane and Carbon Bonds

• Methane Geometry: Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart.

Carbon Bonding

• Tetrahedral Shape: When carbon forms single bonds with other atoms, the shape is tetrahedral.

• Planar Shape: When two carbon atoms form a double bond, the shape is planar, or flat.

• Rotation: Single bonds can rotate, while double bonds cannot, locking atoms on either side in place.

Carbon Rings

• Ring Formation: Carbon can form five- and six-membered rings. Single or double bonds may connect the carbons in the ring, and nitrogen may be substituted for carbon.

Isomers

• Isomers: Molecules that have the same number and type of atoms arranged differently.

  • Structural Isomers: Have a different covalent arrangement of atoms.

  • Geometric Isomers: Have a different arrangement of atoms around a double bond.

  • Enantiomers: Mirror images of each other.

Cis and Trans Fatty Acids

• Cis vs. Trans: Space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. The cis configuration causes a bend in the molecule.

Enantiomers

• Mirror Images: Enantiomers are molecules that are mirror images of each other and are non-superimposable.

• L/D Naming System: From the Latin words for left and right: laevus and dexter, respectively. Example: L and D isomers of the amino acid alanine.

Functional Groups

• Functional Groups: Occur in many different biological molecules; R-group signifies a carbon or hydrogen atom attached to the rest of the molecule, often with bioactivity significance.

DNA Structure

• Double Helix: Hydrogen bonds connect two strands of DNA together to create the double-helix structure.

Weak Interactions

• Noncovalent Bonds:

  1. Hydrogen bonds: Commonly form between molecules containing oxygen or nitrogen.

  2. Electrostatic attraction.

  3. Van der Waals attraction.

  4. Hydrophobic forces: Not true bonds, but they bring molecules together.

Chemical Bond Length and Strength

Table 2-1: Length and Strength of Some Chemical Bonds

*The bond lengths and strengths listed are approximate, because the exact values will depend on the atoms involved.

**Values in brackets are kcal/mole. 1 kJ = 0.239 kcal and 1 kcal = 4.184 kJ .

Noncovalent Interactions

• Protein Binding: A large molecule (e.g., a protein) can bind to another protein through noncovalent interactions on the surface of each molecule.

pH Scale

• pH Scale: Measures the concentration of hydrogen ions (H^+) in a solution.

Acids and Bases

• Hydroxyl Ions: In aqueous solutions, the concentration of hydroxyl (OH^–) ions increases as the concentration of H_3O^+ (or H^+) ions decreases.

Buffering in Blood pH

• Blood Buffering: The body buffers blood pH levels. Blue arrows indicate raising pH as more CO_2 is made; purple arrows indicate lowering pH as more bicarbonate is created.

Acids and Bases in Water

• Polar Molecules: Some polar molecules form acids and bases in water, playing a role in proton dynamics.

Small Molecules in Cells

• Cell Formation: A cell is formed from carbon compounds.

• Major Families: Cells contain four major families of small organic molecules.

  • Simple sugars (monosaccharides, disaccharides): Energy sources; subunits of polysaccharides, providing structure.

  • Fatty acid chains: Components of cell membranes.

  • Amino acids: Subunits of proteins.

  • Nucleotides: Subunits of DNA and RNA.

Four Major Families of Small Organic Molecules

• Lipids: Fatty acids are one type of lipid. Lipids, as a group, have no true “monomer,” unlike large sugar polymers, proteins, and nucleic acids. Other lipids include triacylglycerols, phospholipids, isoprenoids, glycolipids, and steroids.

Macromolecule Subunits

*Each macromolecule contains a specific sequence of subunits.
*Reminder: note there is no monomeric subunit that applies to all types of lipids

Chemical Composition of a Bacterial Cell

Table 2-2: The Chemical Composition of a Bacterial Cell

*There are four classes of phospholipids, each of which exists in many varieties (discussed in Chapter 4).

Glucose Structure

• Glucose: Structure of glucose, a monosaccharide and monomer of larger molecules.

Monomers and Polymers

• Polymer Formation: Polymers are made from simple subunits.

• Sugars: Can be a source of energy and can be structural molecules (polysaccharides).

Condensation and Hydrolysis

• Reverse Reactions: Condensation and hydrolysis are reverse reactions.

  • Condensation:
    A-H + HO-B \rightarrow A-B + H_2O

  • Hydrolysis:
    A-B + H_2O \rightarrow A-H + HO-B

  • Condensation is energetically unfavorable; hydrolysis is energetically favorable.

Lipids

• Lipids: Fatty acids are one type of lipid. Lipids, as a group, have no true “monomer,” unlike large sugar polymers, proteins, and nucleic acids. Other lipids include triacylglycerols, phospholipids, isoprenoids, glycolipids, and steroids.

Fatty Acid Chains

• Cell Membranes: Fatty acid chains are components of cell membranes.

Phospholipid Structure

• (A) Phospholipid structure:

  • hydrophilic head

  • polar group

  • phosphate

  • glycerol

  • two hydrophobic fatty acid tails

• (B) phospholipid bilayer:

  • phospholipid bilayer

  • water

Lipids (continued)

• Lipids: Fatty acids are one type of lipid. Lipids, as a group, have no true “monomer,” unlike large sugar polymers, proteins, and nucleic acids. Other lipids include triacylglycerols, phospholipids, isoprenoids, glycolipids, and steroids.

Amino Acid Structure

• (A) Nonionized form: Amino acid structure: amino group, carboxyl group, α-carbon, side chain (R)

• (B) At pH 7: Amino Acids are the Subunits of Proteins (ionized form).

• H_3N-C-COO

• |

• CH_3

• (C)

Amino Acids and Proteins

• Proteins: The most versatile and diverse group of macromolecules.

• Amino Acids: 20 main amino acids compose cellular proteins.

• Polypeptide Chain: The length can vary greatly.

• Protein Mass: Proteins can constitute up to 50% of the dry mass of a cell.

Lipids (revisited)

• Lipids: Fatty acids are one type of lipid. Lipids, as a group, have no true “monomer,” unlike large sugar polymers, proteins, and nucleic acids. Other lipids include triacylglycerols, phospholipids, isoprenoids, glycolipids, and steroids.

ATP

• ATP: Adenosine triphosphate (ATP) is the most common energy carrier in cells.

ATP Synthesis and Hydrolysis

• ATP Synthesis: Synthesized from ADP and inorganic phosphate.

• ATP Hydrolysis: Releases energy when hydrolyzed to ADP and inorganic phosphate.

Nucleotides

• Nucleotides: The subunits of DNA and RNA.

Macromolecule Composition

• Dry Mass: The majority of dry mass of a cell is composed of macromolecules.

Macromolecule Subunits (revisited)

*Each macromolecule contains a specific sequence of subunits.
*Reminder: note there is no monomeric subunit that applies to all types of lipids

Polymer Formation

• Polymer Sequence: The sequence of subunits determines the unique functions.

Macromolecule Shape

• Noncovalent Bonds: Specify the precise shape of a macromolecule.

Macromolecule Binding

• Noncovalent Bonds: Allow a macromolecule to bind other selected molecules.

Macromolecular Assembly

• Covalent and Noncovalent Bonds: Both are needed to form a macromolecular assembly such as a ribosome.

Macromolecules details

• The following slides are panels from the text that show details of each macromolecule group—these are background which will help with future material

Monosaccharides

Monosaccharides

• Monosaccharides usually have the general formula (CH2O)n, where n can be 3, 4, 5, or 6, and have two or more hydroxyl groups.

• They either contain an aldehyde group (-CHO) and are called aldoses, or a ketone group (=O) and are called ketoses.

Aldoses

• 3-carbon (Trioses):

  • Glyceraldehyde

• 5-carbon (Pentoses):

  • Ribose

• 6-carbon (Hexoses):

  • Glucose

Ketoses

• 3-carbon (Trioses):

  • Dihydroxyacetone

• 5-carbon (Pentoses):

  • Ribulose

• 6-carbon (Hexoses):

  • Fructose

Ring Formation

• In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of the same molecule, thereby closing the molecule into a ring.

Isomers

• Many monosaccharides differ only in the spatial arrangement of atoms—that is, they are isomers. For example, glucose, galactose, and mannose have the same formula (C6H{12}O_6) but differ in the arrangement of groups around one or two carbon atoms.

α and β Links

• The hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one position to the other. These two positions are called α and β.

• As soon as one sugar is linked to another, the α or β form is frozen.

Disaccharides

• The carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide. Three common disaccharides are:

  • Maltose (glucose + glucose)

  • Lactose (galactose + glucose)

  • Sucrose (glucose + fructose)
    The reaction forming sucrose is shown here:
    +fructose -> sucrose + water

Sugar Derivatives

• The hydroxyl groups of a simple monosaccharide, such as glucose, can be replaced by other groups.
  *Glucosamine, N-acetylglucosamine, glucuronic acid

Ligosaccharides and Polysaccharides

• Large linear and branched molecules can be made from simple repeating sugar subunits. Short chains are called oligosaccharides, and long chains are called polysaccharides. Glycogen, for example, is a polysaccharide made entirely of glucose subunits joined together.

Complex Oligosaccharides

• In many cases, a sugar sequence is nonrepetitive. Many different molecules are possible. Such complex oligosaccharides are usually linked to proteins or to lipids, as is this oligosaccharide, which is part of a cell-surface molecule that defines a particular blood group.

Panel 2-5 Lipids images the next 4 slides

Triacylglycerols

*Triacylglycerols
Fatty acids are stored in cells as an energy reserve (fats and oils) through an ester linkage to glycerol to form triacylglycerols.
*Carboxyl group
If free, the carboxyl group of a fatty acid will be ionized.
C^-
But more often it is linked to other groups to form either esters or amides.

Glycercol

Phospholipids

*Phospholipids
Phospholipids are the major constituents of cell membranes.

• In phospholipids, two of the -OH groups in glycerol are linked to fatty acids, while the third -OH group is linked to phosphoric acid.

• The phosphate, which carries a negative charge, is further linked to one of a variety of small polar groups, such as choline.

Other lipids

*OTHER
LIPIDS
Lipids are defined as water-insoluble molecules that are soluble in organic solvents. Two other common types of lipids are steroids and polyisoprenoids. Both are made from isoprene units.
CH 3\C-CH=CH2\CH2
Isoprene
*Steroids have a common multiple-ring structure.
Cholesterol and testosterone are examples

Glycolipids

*Glycolipids
Like phospholipids, these compounds are composed of a hydrophobic region, containing two long hydrocarbon tails, and a polar region, which contains one or more sugars. Unlike phospholipids, there is no phosphate.

Amino Acids

*Amino acids the next slides

Families of Amino Acids

The common amino acids are grouped according to whether their side chains are
*BASIC SIDE CHAINS
Lysine
Arginine
Histidine
*ACIDIC SIDE CHAINS
Aspartic acid
Glutamic acid
*NONPOLAR SIDE CHAINS
Alanine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan
*UNCHARDGED POLAR SIDE CHAINS
Asparagine
Glutamine
Serine
Threonine
Tyrosine
Glycine
Cysteine

The Amino Acid

The general formula of an amino acid is:
-a-carbon atom amino group, carboxyl group, -side chain
Proteins contain exclusively L-amino acids.

Peptide Bonds

In proteins, amino acids are joined together by an amide linkage, called a peptide bond.
Proteins are long polymers of amino acids linked by peptide bonds, and they are always written with the N-terminus toward the left.
Peptides are shorter, usually fewer than 50 amino acids long.

Nucleotides

Bases:
*Pyrimidine - Uracil, Cytosine, Thymine
*Purine - Adenine, Guanine

Phosphates

The phosphates are normally joined to the C5 hydroxyl of the ribose or deoxyribose sugar (designated 5'). Mono-, di-, and triphosphates are common.

Nucleotides

A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups.

Nomenclature

The names can be confusing, but the abbreviations are clear.

Nucleic Acids

To form nucleic acid polymers, nucleotides are joined together by phosphodiester bonds between the 5' and 3' carbon atoms of adjacent sugar rings. The linear sequence of nucleotides in a nucleic acidchain is abbreviated using a one-letter code, such as AGCTT, starting with the 5' end of the chain.

*NUCLEOTIDES AND THEIR DERIVATIVES HAVE MANY OTHER FUNCTIONS
As nucleoside di- and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds.
They combine with other groups to form coenzymes.
They are used as small intracellular signaling molecules in the cell.

Comprehension Test

• Atoms: What are their main composition? (protons, electrons, neutrons)

• Atom Interactions: What part of the atom determines interactions and types of bonds? (electrons)

• Atoms in Living Cells: What atoms are involved in living cells – CHONPS is a nonsense word, but helps to remember which atoms are most representative in building blocks

• Bonding: Define covalent, ionic, and hydrogen bonding

• Electron Sharing: Equal and unequal sharing of electrons—what is the impact? Please review 100 level chemistry, and if you took organic chemistry, review that too