Chapter 3: Carbon and the Molecular Diversity of Life

Isomers

• Isomers are compounds that have the same number of atoms of the same elements but different structures and properties 

  • Structure determines function → Biologists would be more interested in structural formulas

Structural isomers

• differ in the covalent arrangement of their atoms

  • The number of possible isomers increases as the carbon skeletons increase in size

Cis-trans isomers

•  carbons have covalent bonds to the same atoms, but the atoms differ in their spatial arrangement due to the inflexibility of double bonds

  • Single bonds allow the atoms they join to rotate freely about the bond axis 

  • The subtle differences in shape between cis-trans isomers can greatly affect the activities of organic molecules

Enantiomers

• are isomers that are mirror images of one another (left and right-hand versions)

  • They differ in shape due to the presence of an asymmetric carbon 

  • Usually, only one isomer is biologically active

Functional groups

the chemical groups attached to carbon skeletons that affect molecular function by being directly involved in chemical reactions → can replace hydrogens or hydrocarbons

Each functional group

• Hydroxyl group → ( -OH or HO- )

• Carbonyl group → ( >C ═ O )

• Carboxyl group → ( -COOH )

• Amino group → ( -NH2 )

• Sulfhydryl group → ( -SH )

• Phosphate group → ( —OPO3^2– )

• Methyl group → ( -CH3 ) Hydrophobic

• Most except methyl are hydrophilic, and increase the solubility of organic compounds in water 

  • Methyl is not reactive and serves as a tag on biological molecules

Condensation synthesis 

• when two monomers, or a monomer and a polymer, are covalently bonded together through the loss of a small molecule

Dehydration synthesis

• When condensation synthesis occurs with a loss of a water molecule  

  • When one monomer joins another/a polymer, an OH (hydroxyl group) is removed from one item and an H from another, which forms water and opens up room for the bond that joins the two items together.

Hydrolysis

•  breaking down a polymer → polymers are disassembled to monomers, a reaction that is essentially the reverse of the dehydration reaction 

  • A water molecule is added, breaking a bond → the OH gets bonded to one item and the H gets bonded to another

Organic

to contain carbon 

Carbon

•  is unparalleled in its ability to form large, complex, and varied molecules

• Has 4 valence electrons and can form 4 covalent bonds -- usually single or double bonds

  • Serves as an intersection point, and each can branch off in as many as 4 directions → creates large molecules

  • Carbon can covalently bond with a variety of atoms, including hydrogen, oxygen, phosphorus, and nitrogen, to form compounds with different chemical properties

• Living organisms depend upon these compounds

• Carbon can also bond to itself, giving it the ability to form chains that are almost unlimited in length

  • Carbon chains form the skeletons of most organic molecules 

  • Carbon chains vary in length and shape

• This enables carbon to form large, complex molecules

Hydrocarbons

•  are organic molecules consisting of only carbon and hydrogen 

• Many organic molecules, such as lipids (fats), have hydrocarbon components

• Hydrocarbons can undergo reactions that release a lot of energy

Macromolecules

•  Large molecules that have a lot of atoms in them, including carbon

  • Most macromolecules are produced by a process known as polymerization, in which larger compounds are built by joining smaller ones together

  • The structure of macromolecules determines properties

ATP

• Adenosine triphosphate: an organic phosphate molecule that provides energy for the cell 

• Consists of organic molecules called adenosine attached to a string of three phosphate groups

  • Modified nucleotide: has an adenine base, ribose, and 3 phosphate groups

    • Adenosine: adenine + ribose (nucleoside)

  • Becomes adenosine diphosphate if it loses a phosphate group due to a reaction with water

• ATP stores the potential to react with water, releasing energy that can be used by the cell

  • Reforming the bond after it has been broken is what releases energy

    • The bond between the 2nd and 3rd phosphate groups

    • These bonds are very strong as the energy in the bonds is what is repelling the negatively charged oxygens (keeping them close together) 

      • Due to this, they hold a lot of energy 

Monomers

• Monomers are building blocks or repeating subunits that make up polymers

  • Monomers do not need to be identical, but they do need to be similar.

  • Some molecules that serve as monomers also have functions of their own

Polymers

• Long chains/molecules consisting of many identical building blocks (monomers) linked by covalent bonds

Carbohydrates

Functional groups: Carbonyl group and multiple Hydroxyl groups 

Function: 

• Main sources of energy

• Quick access to energy

  • Bonds are easy to break, so they can be quickly accessed

• raw/building materials 

Atoms: C, H, O 

Monomer: monosaccharides (sugars)

Covalent Bonds: glycosidic bonds 

• α and β glucose ring structures

  • These two interconvertible forms of glucose differ in the placement of the hydroxyl group attached to the number 1 carbon 

  • α → below 

  • β → above 

Each level of carbohydrates

Simple sugars: monosaccharides (monomers) 

• have molecular formulas that are usually multiples of CH2O

  • Ex: glucose, fructose, and ribose

• classified by the number of carbons in the carbon skeleton and the placement of the carbonyl group

Double sugars: disaccharides (two monosaccharides)  

• formed when a dehydration reaction joins two monosaccharides covalently 

• Must be broken down into monosacharides to be used as energy

  • Ex: Glucose and Fructose → Sucrose 

    • Lactose and maltose are also examples

Macromolecule (many monosaccharides): polysaccharides

• The polymers of sugars have storage and structural roles 

• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages

  • Ex: Starch, glucose, cellulose

Starch, Glycogen, and cellulose

• Starch → energy storage in plants

  • The synthesis of starch enables plants to create a surplus of glucose

  • a configuration 

• Glycogen → energy storage in animals

  • Stored in liver and muscle cells 

  • Breakdown of glycogen releases glucose when energy demand increases

  • a configuration

• Cellulose → component for tough cell walls (referred to as fiber)

  • Glycosidic linkages differ → ring structure  

  • B configuration

Proteins

structure: proteins are biological functional molecules made up of one or more polypeptides, folded and coiled into a specific three-dimensional structure

Function

• more than 50% of the dry mass of most cells

• Functions include 

  • defense (protect against diseases)

  • storage (of amino acids)

  • transport substances

  • cellular communication

  • Movement

  • Controls rate of reaction (enzymes)

  • structural support

Atoms: C, H, O, N

Monomers: amino acids (only 20)

• Amino acids are organic molecules with carboxyl and amino groups 

• Amino acids differ in their properties due to differing side chains, called R groups

  • Categories: Nonpolar hydrophobic, polar hydrophilic, electrically charged hydrophilic

Covalent bonds: Amino acids are linked by peptide bonds

• Two amino acids join by a dehydration reaction 

Examples of each level:

• Four levels 

4 levels of structure in proteins

• Primary - appears as a line 

  • amino acids are “beads on a string”

  • The sequence of amino acids determines what the protein will eventually look like

  • Not a functional protein. 

• Secondary - primary folds into beta sheets, alpha helices, or both

  • Result of hydrogen bonds

  • Also not a functional protein

• Tertiary structure - specific 3D shape

  • Hydrophobic aspects should be on the inside of the protein, hydrophilic on the outside. May or may not be a functional protein, depending on whether one polypeptide chain is enough for function 

  • Disafide bridges

• Quaternary structure - an interaction between multiple different tertiary polypeptide chains

  • Hemoglobin is a great example

  • Functional protei

Denaturing in Proteins

• Unraveling of protein structure due to changes in the environment; prevents function. Acidity, alkalinity, high temperature, and increased salt concentration can all cause denatured proteins

  • Misfolding can also cause many issues such as alzheimers or Parkinson's disease

5 components of an amino acid

• Center (alpha) carbon (Cα): This is the central carbon atom to which all other groups are attached.

• Amino group (-NH₂): This is a nitrogen atom bonded to two hydrogen atoms. It acts as a base and can accept a proton.

• Carboxyl group (-COOH): This is a carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group (-OH). It acts as an acid and can donate a proton.

• Side chain (R group): This is a variable group attached to the central carbon. The nature of this side chain differs among amino acids and determines the chemical properties of the amino acid.

• Hydrogen atom (H): A single hydrogen atom attached to the central carbon.

The side chain (R group) determines which amino acid it is. This R group can be anything from a simple hydrogen atom (like in glycine) to more complex structures (like aromatic rings in phenylalanine), and it gives each amino acid its unique characteristics.

Lipids

Function: 

• Hydrophobic

• Store energy (long term)

  • Bonds are harder to break

• Part of biological membranes and coverings

• Waterproofing

Atoms: C, H, O

Monomers: Do not form polymers → not big enough to be considered macromolecules

• Not made up of monomers

covalent bonds: ester linkage 

Lipids examples at each level 

Fats (triacylglycerol or triglyceride): composed of a glycerol molecule joined to three fatty acids by ester linkages 

• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon

• A fatty acid consists of a carboxyl group attached to a long carbon skeleton

• Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats 

Phospholipids: two fatty acids attached to a glycerol 

• The third hydroxyl group of glycerol is joined to a phosphate group -- a negative charge 

Steroids: 

• Steroids are lipids characterized by a carbon skeleton structure consisting of four fused rings

• Cholesterol, an important steroid, is a component in animal cell membranes

Makeup of the phospholipid bilayer 

• Hydrocarbon tails are hydrophobic 

• The phosphate group forms a hydrophilic head

• When phospholipids are added to water, they self-assemble into a double-layered sheet called a bilayer to protect hydrophobic tails from water → the hydrophobic tails pointing toward the interior

• This feature of phospholipids results in the bilayer arrangement found in cell membranes

• The phospholipid bilayer forms a boundary between a cell and its external environment

What do all lipids have in common

Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds

Saturated vs unsaturated fats

• Saturated fatty acids have the maximum number of hydrogen atoms possible and only single bonds between their carbon atoms

  • Fats can be packed together tightly, becoming solid at room temperature 

    • Ex: butter

• Unsaturated fatty acids have one or more double bonds, decreasing the amount of hydrogen 

  • The double bonds prevent the molecules from packing together, making them liquid at room temperature

  • Exceptions to the rules → coconut oil is solid at room temperature

Nucleic acids

Function: stores and transmits hereditary information

• Deoxyribonucleic acid (DNA): DNA is your genetic material, which controls everything in the cell

  • Sugar: deoxyribose

  • DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix 

  • In the DNA double helix, the two backbones run in opposite 5’ → 3’ directions from each other, an arrangement referred to as antiparallel 

  • Most DNA molecules are very long, with thousands or millions of base pairs - the sequence is unique for each gene

• Ribonucleic acid (RNA): RNA is used for protein synthesis (gene expression) 

  • Sugar: ribose

  • Single stranded

• ATP 

Atoms: C, H, O, N, P 

Monomers: nucleotides

• Polymer: polynucleotides

• Nucleotides: 

  • a nitrogenous base

  • a pentose (five carbon) sugar

  • and one or more phosphate groups

  • The portion of a nucleotide without the phosphate group is called a nucleoside

covalent bonds: phosphodiester linkage

• Bonds formed in a dehydration reaction 

• Create the sugar phosphate backbone

  • Nitrogenous bases are appendages

  • Hydrogen bonds between bases 

Purines vs Pyrimidines

• Each nitrogenous base has one or two rings that include nitrogen atoms 

• There are two families of nitrogenous bases

• Pyrimidines have a single ring and include cytosine (C), thymine (T), and uracil (U)

• Purines have a double ring and include adenine (A) and guanine (G) 

  • Thymine is found only in DNA

  • Uracil is only found in RNA

  • The rest are found in both DNA and RNA

AT and GC rule

• Purines and pyrimidines must be paired together 

• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) • This is called complementary base pairing

Differences and similarities between RNA and DNA

• Differences 

  • DNA is a double helix; RNA is single-stranded. 

  • DNA has deoxyribose as the sugar, RNA has ribose. 

  • DNA has thymine, RNA has uracil. 

• Similarities

  • Both have adenine, guanine, and cytosine. 

  • Both have phosphate groups. 

  • Both are examples of polynucleotides or nucleic acids. 

  • Both are involved in creating proteins.