chapter 4/5 (carbon life, biological molecules)

What are the two types of Nucleic Acids?

DNA and RNA (Deoxyribonucleic Acid and Ribonucleic Acid)

What is the monomer of a Nucleic Acid?

A Nucleotide

What does a Nucleotide consist of?

A Phosphate (PO4 with 2 negative charges), a Ribose Sugar (in RNA) or Deoxyribose Sugar (in DNA), and a Base

What are the two types of Bases found in Nucleic Acids?

Purines and Pyrimidines

Describe a Purine and list its members.

2X ringed and includes Adenine (A) and Guanine (G)

Describe a Pyrimidine and list its members.

Single ringed and includes Cytosine (C), Thymine (T) in DNA, or Uracil (U) in RNA

What process links nucleotides to form a single strand?

Dehydration Synthesis

How does Dehydration Synthesis link nucleotides?

It links the number 3 carbon of one nucleotide to the phosphate of the next nucleotide

What is the bond that links nucleotides into a strand?

A Phosphodiester Bond (located between the phosphate and sugar)

Why are the ends of a single strand designated as 3 prime and 5 prime?

The numbers refer to the carbon atom on the sugar at that end of the strand

What links the two strands to form the DNA double helix shape?

Hydrogen Bonds link the bases of each strand per the Base pairing Rules

What are the Base pairing Rules?

Cytosine (C) and Guanine (G) form 3 hydrogen bonds, and Adenine (A) and Thymine (T) form 2 hydrogen bonds

What term describes the orientation of the two DNA strands relative to each other?

Antiparallel

What is the "twisted ladder" analogy for DNA?

The rungs are the base pairs, and the rails of the ladder are the sugar-phosphate ribbons or "backbone"

Where are double bonds found in fatty acids and what do they provide?

In the fatty acid chains of unsaturated fats; they free up spaces (fewer H atoms) providing for movement and wiggling room

What are Omega 3 and Omega 6 Fats?

Types of polyunsaturated fats defined by the location of the double bonds

Describe the structure and examples of Omega 3 Fats.

C-C-C-C

Describe the structure and examples of Omega 6 Fats.

C-C-C-C-C-C

What is the required ratio of Omega 3:6?

Should be about 1:3, instead of the typical 1:20

What are Trans Fats?

Unsaturated fats that result from food processing, where associated chemical groups are catercorner above and below a double bonded C to C in the fatty acid chain

What is the status of Trans Fats in the US?

They have been banned in foods as of July 2018

What are Hydrogenated fats?

Fats (like peanut butter and margarine) where H atoms are added to fatty acid chains, creating saturated fats from unsaturated fats like seed oils

How much energy do fats contain compared to carbohydrates or proteins?

Fats contain about 2X as much energy

What is a Phospholipid?

A second kind of Lipid and the major constituent of every cell membrane

What does it mean that a Phospholipid is amphipathic?

It has a hydrophobic tail and a hydrophilic head

What is the implication of the amphipathic nature of phospholipids?

It forms the basic structure of the cell membrane (a lipid bilayer)

What are Steroids?

A third kind of lipid consisting of 4 fused rings, such as cholesterol

What are Steroids a precursor to?

Sex hormones like estrogen and testosterone

What are Proteins?

Large Biological Molecules whose monomers are Amino Acids

What are the monomers or building blocks of Proteins?

Amino Acids (there are 20)

What is the structure of an Amino Acid?

A central carbon bonded to a hydrogen, a carboxyl group, an amino group, and an R group or sidechain

What determines the type of Amino Acid?

The R group or sidechain

What are the functions of Proteins?

Acting as enzymes, providing structural support (like keratin and collagen), transport, signal transduction, attachment, receptor, muscle contraction (like actin and myosin)

If there are 20 amino acids, how many different combinations are there in a polypeptide chain of length N?

There are $20^N$ different combinations

What process forms Polypeptide Chains and what is the resulting bond?

Dehydration synthesis forms peptide bonds

How many levels of protein structure are there?

4 levels

Describe Primary or 1st degree or order protein structure.

The simplest, determined by the **number and order

sequence** of amino acids. An example is Transthyretin

Describe Secondary or 2nd degree or order protein structure.

The formation of Beta Pleated Sheets or Alpha Helices, relying on Hydrogen bonding

Describe Tertiary or 3rd degree or order protein structure.

Formed with H bonds, ionic bonds, disulfide bridges, hydrophobic interactions and present a 3-dimensional structure, such as ovalbumin or egg white

Describe Quaternary or 4th degree or order protein structure.

Here, protein subunits are combined to form the largest proteins such as hemoglobin and collagen

What can cause **Protein Denaturation

destruction**?

High heat (frying an egg) or non-polar solvent exposure

What can result from misfolded proteins?

Madcow Disease and Alzheimer Disease, Parkinson Disease

What is Acid Rain?

Precipitation with a pH less than 5.2

What is Ocean Acidification?

Occurs when an excess of CO2 from the atmosphere reduces the pH of the oceans

What is the effect of Ocean Acidification on marine organisms?

It causes carbonate ions to be less abundant, reducing the carbon needed to build marine organisms like corals; this makes building calcium carbonate shells difficult as well

What does Chapter 4 cover?

Carbon + Diversity of Life

What is Organic Chemistry?

The study of compounds and molecules containing carbon (Organic)

What are some examples of Organic molecules?

Methane, CH4

Why is Carbon so central to Organic Chemistry?

It is Tetravalent, potentially forming 4 covalent bonds with 4 other atoms

What does Carbon's tetravalency lead to?

A diverse number of forms and shapes of organic molecules, which can be polar or non-polar and able to bond with oxygen and hydrogen

What was the Miller Experiment (1953)?

Demonstrated that organic compounds could spontaneously arise from inorganic materials under the early Earth's atmospheric conditions

What is the significance of the Miller Experiment?

A paradigm shift occurred in the US from Vitalism to Mechanism within Biology

What are hydrocarbons?

Consist of H plus C compounds

Where are hydrocarbons found?

They are fossil fuels and vary in length, branching and placement of double bonds

Who first described the ring structure of Benzene?

Kekule

What are Isomers?

Molecules that have the same molecular formulas but a different arrangement of their atoms

What are the three types of Isomers?

Structural, Cis-Trans (Geometric), or Enantiomers

What are examples of Enantiomers?

Thalidomide and Ibuprofen and Albuterol

What are the 7 Biologically Important Functional Groups?

Groups that when added to a relatively inert carbon skeleton they impart a function to the compound and get it involved in a biochemical reaction

List the 7 Biologically Important Functional Groups and their structure

function.

1. Hydroxyl -OH: forms an alcohol such as ethanol

2. **Carbonyl -C

O**: forms a *ketone* when added to the middle of a carbon chain, or an aldehyde when added to the end of a carbon chain**

3. **Carboxyl -C

O-OH**: forms a *carboxylic or organic acid* such as acetic acid in vinegar

4. Amino -NH2: which forms an amine like glycine, an amino acid

5. Sulfhydryl -SH: which forms a thiol such as cysteine

6. Phosphate -PO4 or PO3: which forms an organic phosphate like glycerol phosphate

7. Methyl -CH3: which forms a methylated compound

How is the power and importance of Functional Groups illustrated?

By comparing testosterone to estradiol in animals, in the determination of secondary sexual characteristics as well as sexual dimorphism

What is ATP (Adenosine triphosphate)?

A molecule that, when functioning as ATP + water, releases one high energy phosphate functional group and becomes ADP (adenosine diphosphate). The released phosphate carries with it 7.3 kcals of energy to perform work in the cell

What are the Large Biological Molecules which build life's structure?

Carbohydrates, Proteins, Lipids, Nucleic Acids

What are the Macromolecules which weigh in excess of 100,000 Daltons?

**Carbohydrates, Proteins, and Nucleic Acids (DNA

RNA)** (Lipids are NOT macromolecules)

Why are Lipids not technically macromolecules?

They do not form polymer precursors

What are Polymers?

Long molecules consisting of many repeating units called Monomers (like cars on a train)

How are Polymers made and what is the process called?

Made or synthesized by a process called Dehydration Synthesis, where a water molecule is lost and a covalent bond is formed as each monomer is added

How are Polymers broken down and what is the process called?

Broken down by a reverse process called Hydrolysis, where a water molecule is added and a covalent bond is broken

What is the difference between Dehydration Synthesis and Hydrolysis?

Dehydration Synthesis is a processive enzyme-facilitated reaction that builds polymers, and Hydrolysis is a digestive enzyme-facilitated reaction that breaks them down

What are Carbohydrates?

Their monomers are called monosaccharides or simple sugars

What is the general chemical formula for Carbohydrates?

C H2 O or multiples thereof

What are examples of Monosaccharides?

Trios sugars, Pentose and Hexose sugars

What is Glucose?

A Hexose sugar with the molecular formula C6 H12 O6

How are the carbons of Glucose typically numbered?

To indicate a **short term fuel

energy source** and cell structure

What two monosaccharides combine to form Maltose?

Glucose + Glucose

What two monosaccharides combine to form Sucrose?

Glucose + Fructose (Table sugar)

What two monosaccharides combine to form Lactose?

Glucose + Galactose

What is the key covalent bond linking two monosaccharides?

A Glycoside Bond or Linkage

What are Polysaccharides?

May include several hundred to thousands of monosaccharides linked by glycoside bonds

What are examples of Polysaccharides and their function?

Starches, Glycogen and Cellulose

What is Glycogen?

The storage polysaccharide in animals found in the liver and muscles

What is Cellulose?

The structural polysaccharide in chitin (in insect and crustacean exoskeletons) and the structural polysaccharide in plants found in the cell walls

What is Starch?

The storage polysaccharide in plants found in **seeds and tubers

roots

bulbs**

What is the difference between unbranched and branched Starches?

Amylose is unbranched and amylopectin is branched

What are Lipids?

Highly Hydrophobic and include Fats (triglycerides), Phospholipids and Steroids

What do Lipids mainly consist of?

Fats (Water resistant)

What is a Fat (Triglyceride) composed of?

A Glycerol molecule (a 3 -carbon compound with 3 -OH added) and 3 Fatty Acid Chains attached to the glycerol molecule via 3 covalent Ester Bonds