Chemical Reactions and Organic Chemistry

Hydrocarbons

Compounds composed only of carbon and hydrogen

Carbon skeleton

The chain of carbon atoms in an organic molecule. Branched: example isobutane, Unbranched: example butane

Determining molecules unique properties

The size, shape, and the chemical groups that are attached to an organic molecule

Functional groups

Chemical groups that are polar and affect a molecules reactivity. These are polar because oxygen or nitrogen present within the group has a very strong pull on the electrons that are shared in a covalent bond

Functional groups are…

Water loving or hydrophilic (synonymous as polar) because of their polarity. Key characteristic that they are water soluble > important for life function

The Methyl Group (CH3)

#6 on the chart, non-polar and non-reactive, it still affects molecular shape and thus function

Hydroxyl group (OH)

Composed of a hydrogen atom bound to an oxygen atom. This group is then bound to a carbon skeleton. Example: ethanol - fuel source. Groups containing this are called alcohols

Carbonyl Groups

Consist of a carbon atom joined by a double bound to an oxygen atom. This is apart of something else (not isolated) If it is at the very end of the chain it is called an aldehyde, the middle of the chain is a ketone.

What groups do sugars have?

They have one carbonyl groups and several hydroxyl groups

Carbonyl Group

Have carbon double bonded to an oxygen and single bonded to a hydroxyl group. OH group behaves as an acid, ionizing and donating H+ to solution. Compounds with this group are called carboxylique acids

Amino Groups

Composed of a nitrogen bonded to two hydrogen atoms and a carbon skeleton, acts as a base by picking up H+ from solution. Organic compounds containing this group are called amines.

Amino acids

These acids which are the protein building blocks contain both an amino group and a carbonyl group

Phosphate group

Consists of phosphorous atom (PO4) bound to four oxygen atoms. Attached to carbon skeleton by 1 of 4 Oxygen atoms. Involved in energy transfers from the ATP molecule

Organic phosphates

Compounds containing the phosphate group

Polymers 4 main classes…

…of biological molecules referred to as macromolecules:

1. Carbohydrates

2. Proteins

3. Lipids

4. Nucleic acids

Polymers

When larger molecules are formed by joining smaller molecules together, the larger molecules are called this. Large molecules consist of many identical or very similar building blocks > monomers

How are polymers made?

These are made Via dehydration reactions. 2 monomers are joined to one another by the removal of water. 1 of unlinked monomers has free OH group, other unlinked has free H group.

H and Oh removed from polymers form

A water molecule

A covalent bond between the two monomers

Breaking polymers occurs via a

Hydrolysis reaction > addition of water to molecule. Occurs when carbohydrates you eat are broken down to sugars. Reverse reaction of dehydration reaction. Hydroxyl group joins to 1 monomer, hydrogen to the other.

Carbohydrates are a class of

Molecules that include small sugars found in things that we drink and large sugars such as starch in foods such as potatoes.

Monosaccharides

Carbohydrate monomers (ex: glucose). Generally have the formula CnH2n0n - n=6 for glucose. Can be linked by a dehydration reaction to form more complex molecules. Ex: honey - mix of ____ glucose and fructose

Disaccharides

Are constructed from a dehydration reaction between 2 monosaccharides - Maltose formed from dehydration of 2 glucose monomers.

Sucrose is made by

Joining a glucose monomer and a fructose monomer together via a dehydration reaction. (Table sugar)

Polysaccharides

Cellulose is a ____ found in plant cell walls. Made entirely from glucose but are linked to one another in a distinct fashion

Cellulose

Referred to as dietary fibre. It passes through the human digestive tract undigested, some animals such as cows though are able to digest it because they have the necessary enzymes.

Lipids

Grouped together because they mix poorly (or not at all) with water. As a consequence lipids are hydrophobic. Ex: salad dressing > oil separates from vinegar

Oils are…

Liquid fat. Fat is a large lipid made of glycerol and fatty acids

Difference between lipids and carbohydrates

(And most other organic molecules) because they are composed mainly of non-polar carbon-hydrogen bonds

Glycerol is…

An alcohol with 3 carbons each bearing a hydroxyl group

A fatty acid has a…

Carbonyl group and a hydrocarbon chain. Hydrocarbon chain > 16-18 carbons in length (hydrophobic chain). Carbons are bound to one another and to hydrogens by non-polar covalent bonds.

Fats primarily function to store..

Energy. 1 gram of fat stores twice as much energy as one gram of carbohydrate (ex: starch) Also functions to cushion vital organs and insulates the body

Fatty acids are linked to…

Glycerol via a dehydration reaction. Fat is produced when 3 fatty acids are linked to glycerol > fat is called triglyceride (3 fatty acids in fat often all different from one another)

Fatty acids can sometimes contain a…

Double bond. This adds a kink or a bend to the carbon chain. These double bonds prevent max # of hydrogen atoms from binding to the carbon skeleton. This can be done by forming 4 single bonds (4×1=4), forming 2 single bonds and 1 double bond (2×1 + 1×2=4), or forming 2 double bonds (2×2=4)

Fatty acids (containing double bonds) are referred to as…

Unsaturated (having fewer than max # of hydrogen bonds) most plant fats are unsaturated. Fatty acids WITH max # are saturated. Most animal fats are saturated.

Kinks present in unsaturated fatty acids prevent…

Molecules from packing tightly together in the solid state at room temp and as a result unsaturated fats are often liquid at room temp. Ex: oil.

Hydrogenated fats have…

Hydrogen added to the double bonds of the fat. Allows the fat to be solid at room temp. Downside: also gives way to trans fats which have been found to associate with heart disease.

Phospholipids

These are major component of the cell membrane. Structurally similar to fats but rather than 3 fatty acids, these only have 2 attached to glycerol. A negative charged phosphate group replaces the 3rd fatty acid in these.

What associates to form a balayer in phospholipids?

Hydrophilic regions and hydrophobic regions. Hydrophilic: these regions face to the inside and the outside (both areas are full of water) Hydrophobic: face to the inside of the bilayer (inside areas lack water)

Steroids

These are lipids. The carbon skeleton contains four fused rings > each point of a diagram represents a carbon atom. Hydrogen atoms are also omitted but bound to each carbon atom > satisfies required 4 bonds to carbon

What is cholesterol?

A steroid, commonly found embedded in the cell membrane. It is used as a starting point to build other hormones (estrogen, testosterone)

Different functional groups attached to the steroid ring…

Change its chemical properties which in turn affects the molecules function

Anabolic steroids

These are synthetic variants of the male hormone testosterone. Testosterone causes a build up of muscle and bone mass in males during puberty and maintains male sex traits throughout life.

Anabolic steroids can be produced to…

Correct the loss of muscle mass and general anemia.

Side effects of anabolic steroids

Overdose: violent mood swings (steroid rage) & deep depression. Liver damage > liver cancer. Alter cholesterol levels > high blood pressure & cardiovascular problems. Slows down testosterone production = shrunken testicles, reduced sex drive, infertility and breast enlargement.

Proteins are..

Polymers made from amino acid monomers. Each individual ____ has a unique 3 dimensional structure. ___ are structurallly important to cells and whole organisms.

Enzymes are..

Proteins. ___ are chemical catalysts that speed up and regulate all cellular chemical reactions

Structural proteins are found in…

Hair and fibres that compose connective tissues, ligaments, tendons and muscles. Muscles are specifically made up of contractile proteins.

Defensive proteins are produced by…

The immune system. Ex: antibodies

Signal proteins are…

Hormones and other messengers necessary for communication between different cells in the body. Receptor proteins are usually located in the cell membrane and bind to _____

Proteins are the most diverse…

Biological molecules in terms of structure and function. ____ are based on differing arrangements of amino acids. 20 amino acids known, different combos = different proteins.

Amino acids consist of an…

Amino group and a carbonyl group. Carbonyl group makes amino acid an acid. R group makes each amino acid different from one another + determines chemical properties of the acid.

Proteins

A dehydration reaction between the carboxyl group of one amino acid and the amino group of another amino acid occurs.

What is a dipeptide? What is a polypeptide?

1. 2 amino acids linked together

2. Many amino acids linked together

Peptide bonds

Formed by removing water. A water molecule can be added to the ______ in order to break it apart (hydrolysis reaction)

Proteins shape determines….?

The proteins function. Proteins found in hair and tendons are usually fibrous (long and thin)

Globular

Most enzymes and other proteins are this

Dénaturation of protein indicates

The importance of the protein shape on protein function. This ruins the protein shape resulting in a loss of function

What changes can denature proteins?

Heat, salt and pH changes. Ex: frying an egg and the visible changes in the egg white from the heat.

Reasoning behind the danger of fevers which can denature key bodily enzymes.

Amino acid sequence of a protein is determined by…

The gene sequence of the gene. Genes > made of DNA > DNA is a nucleic acid.

DNA is not directly made into….

Protein. Must first be converted into RNA.

DNA > transcription > RNA > translation > protein

What is made up of nucleotide monomers?

Nucleic acid polymers (DNA and RNA)

Each nucleotide is composed of…

Three parts.

1. A five carbon sugar (deoxyribose in DNA and ribose in RNA)

2. A phosphate group

3. A nitrogenous base (structure containing carbon and nitrogen)

Nitrogenous base names (DNA vs RNA)

Adenine, guanine, thymine and cytosine in DNA

adenine, guanine, cytosine and uracil in RNA

Nucleic acid polymers are joined to one another by…

Covalent bonds via a dehydration reaction. Phosphate group of one nucleotide bond to the sugar of the next nucleotide (monomer) Results in repeating sugar-phosphate backbone in the polymer

DNA is always double stranded and

Is found as a double helix. 2 polynucleotides are wrapped around one another. (RNA is always single stranded)

Nitrogenous bases on one…

Strand, always pair with nitrogenous bases of the second strand according to the following rule A::T, C::G

Adjacent strands are held together by..

Hydrogen bonds

Most DNA molecules have 1000s or..

Even millions of base pairs

What are enzymes?

Protein molecules that act to increase the rate of a chemical reaction.

All chemical reactions have a…

Particular activation energy that must be overcome in order for the reaction to proceed. (Enzymes function to decrease this activation energy)

If heat were added to increase the rate of a reaction would it work?

Yes, however heat is non-specific and would act to simultaneously increase the rate of ALL chemical reactions

Enzymes act to increase the rate of a

Chemical reaction > They are not consumed during a chemical reaction. They work to lower the activation energy of the reaction. They are specific to a particular chemical reaction.

Shape of enzymes

Unique three dimensional shape

Enzymes acting on specific reactants is called what?

Substrates. They fit into a particular region on the enzyme called the active site

What is the active site?

A groove on the surface of the enzyme. Remainder of the protein maintains the ______ shape. Enzymes act specifically on a particular target because the shape of the ____ caters to the shape of the specific substrate.

The enzyme sucrase catalysés the breakdown of what?

The disaccharide sucrose. Enzymes usually have the ending ase and are named after their substrate > EX: maltase catalysés breakdown of disaccharide maltose

Sucrose begins with….

An empty active site. Once it enters, attaches with weak bonds

The induced fit hypothesis refers to…

The fact that the active site changes shape slightly in order to fit the substrate more closely. Also functions to strain substrate bonds making them easier to break & places amino acids of the active site in proper position to catalyze the reaction

Strained substrate bond reacts with

Water converting sucrose to glucose and fructose

Enzymes releases the newly formed products and is…

Released unchanged from the reaction ready to catalyze a new reaction. (Single enzyme may act on 1000s or millions of substrate molecules per one second)

What is critical to an enzyme to function?

The shape. The Environment of an enzyme may act to alter the enzyme shape and therefore alter its _____.

Certain parameters of an environment affect its function if they are not optimal what?

Temperature: optimal temp for particular enzy. maxes contact between active site and substrate molecules

pH: most human enzymes function best near neutral pH (pH=7) At pH value higher and lower than 7 may impair enzyme function

What happens if the temperature is higher than optimal?

Functions to denature the enzyme rending it non-functional. Most human enzymes function best at 37 degree Celsius.

In order to function, most enzymes require…

Non-protein molecules called cofactors. Cofactors can be either organic or Inorganic.

Inorganic cofactors vs Organic cofactors

1. Usually ions of zinc, copper or iron

2. Are called coenzymes, Vitamins that are essential dietary components often function as coenzymes.