Chapter 3 Flashcards
Valence electrons
The electrons in the outer most shell of an atom that are available for chemical bonding.
Hydrogen = 1 valence e-
Oxygen = 6 valence e-
Nitrogen = 5 valence e-
Carbon = 4 valence e-
Carbon
All organic life is based on carbon and all organic molecules contain carbon.
- It is the 4th most abundant element in the universe
- easily forms and breaks bonds with O (crucial to respiration/photosynthesis)
Isomers
Organic compounds with the same molecular formula, but different structures.
3 kinds:
1) structural
2) geometric
3) enantiomers
Structural isomers
The molecular formula for these molecules are identical, but the arrangement of the atoms is different which leads to different chemical properties.
Geometric isomers
Cis = a functional groups on the same side of the molecule
Trans = have functional groups on opposite sides of the molecule.
The difference is the location of the functional groups, but the molecular formula stays the same.
Enantiomers
Mirror images of each other
Monomers
A very small atom or molecule that serves as a building block for a polymer
(Mono =1)
Polymer
A large molecule, consisting of many identical or similar monomers.
(Poly = many)
Dehydration synthesis
The formation of larger molecules from smaller reactants, accompanied by the loss of a water molecule.
(Puts things together!)
Catalyst
A substance that increases the rate of a chemical reaction without being permanently changed.
(Should also be reusable)
Carbohydrates
- Contain carbon, hydrogen, oxygen : basic formula = CH2O
- functional groups: hydroxyl (OH) and carbonyl (C=O)
- Tend to be hydrophilic due to the OH groups
3 classes: mono/di/poly-saccharides
Function: energy-storage molecules
Monosaccharides
Single unit sugars, (aka monomers)
The basic ratio is 1:2:1 in C:H:O
(i.e. CH2O)
Ex. Glucose
(If C=O is at the end of molecule it’s a Aldehyde group, if C=O is not at the end it’s a ketone group)
Disaccharides
Two monosaccharides join together via dehydration synthesis.
Ex. Glucose + glucose - H2O (=maltose)
Polysaccharides
Could contain hundreds to thousands of monosaccharides joined together via dehydration synthesis.
4 most common:
1) Starch (plant)
2) Glycogen (animal)
3) Cellulose (plant)
4) Chitin (animal)
Starch
The simplest polysaccharide; used for an energy-storage in plants.
Made by sticking several glucoses together via dehydration synthesis.
Glycogen
A storage polysaccharide of animals; highly branched, and most often found in muscle and liver cells.
Chitin
A modified polysaccharide of animals that contains nitrogen.
It is an important structural material in the exoskeleton of insects, crabs, and lobsters.
Cellulose
The most abundant organic molecule on earth; it is the principal component of plant cell walls.
It is just a polymer of glucose, but our body cannot break it down to get the glucose out for use. (Only cows and termites can)
Proteins
Polymers made from various combinations of 20 amino acids.
Each protein contains a carbon, a carboxyl group (COOH), an amine group (NH2), and a R group
Organized by levels: primary, secondary, tertiary, quaternary.
Primary structure of protein
The sequence of amino acids in the polypeptide chain.
(In order for a protein to function, it must have the correct amino acids are arranged in a precise order)
Secondary structure of protein
Only a small portion of the protein.
The chain of amino acids either makes an alpha helix or beta pleated sheets. This is due to the hydrogen bonding of the amino acids next to each other.
Tertiary structure of proteins
Refers to the entire protein made up of chains, alpha helix, beta pleated sheets
The R groups of amino acids will interact and create covalent bonds with each other. This will shape the protein, allowing for a 3-D shape.
Quaternary structure of protein
2 or more tertiary proteins and putting them together to form a larger protein.
Denatured protein
When a protein loses its tertiary 3D shape, which is accompanied by loss of function as well.
Proteins can be denatured by acids, salts, or heat
What are some functions of proteins?
- Act as enzymes to catalyze reactions
- Molecular transport across the cell membrane
- Defend against antibodies
- Be structural support in connective tissue
Nucleic acids
Found in nucleus of eukaryotic cells. Responsible for gene transferring.
2 types:
1) DNA
2) RNA
Made up of repeating monomers called nucleotides
Nucleotides
Backbone / Ladder:
Made up of a 5 carbon sugar (ribose or deoxyribose) and a phosphate group (PO4)
Not backbone/ Steps:
Nitrogen bases (adenine, thymine…)
Nucleotides join via dehydration synthesis, this joins the sugar of one nucleotide to the phosphate group of the next nucleotide
RNA
Tends to be a single-stranded helix. Can leave the nucleus and interact with ribosomes to make proteins.
4 nucleotides involved:
- Adenine (A)
- Uracil (U)
- Cytosine (C)
- Guanine (G)
DNA
A double-stranded helix that codes for everything the cell makes and does. Responsible for coding the primary structure of proteins.
Since it can’t escape the nucleus it transcribes code to RNA
4 nucleotides involved:
- Adenine (A)
- Thymine (T)
- Cytosine (C)
- Guanine (G)
Triglycerides
Contain a glycerol “head” (3 carbon alcohol), and 3 fatty acid chains (carboxyl group COOH and hydrocarbon chain usually 16-18 carbons long).
The carboxyl end of the fatty acid joins with the OH of the glycerol head. This creates an ester bond via dehydration synthesis.
Functions:
- long term energy storage‼️
- cushioning organs
- make up cell membranes
Saturated fatty acid
A fatty acid chain with the max amount of hydrogens attached to it since it doesn’t have a double bond.
Often solid at room temperature
Unsaturated fatty acid
Do not contain the max amount of hydrogens since there are double bonds of carbon.
Tend to be less solid at room temp
Phospholipid
Made up of a (polar) glycerol “head” , and 2 (nonpolar) fatty acid chains, and 1 negatively charged phosphate group.
Polar head is hydrophilic, but the fatty acids are hydrophobic
2 layers of phospholipids form cell membranes -> phospholipid bilayer
Or
a micelle is formed which is a circle of phospholipids
Steroids
Lipids with a carbon skeleton of 4-fused rings.
Cholesterol is a building block for steroids, and steroids are formed in the smooth ER
Cholesterol
Extremely nonpolar meaning it won’t dissolve in water.
HDL = high density lipoproteins (more protein than fat/cholesterol; will pick up cholesterol and fat)
LDL = low density lipoproteins (more fat/cholesterol than protein; drops off cholesterol/fat
Too much LDL will build up in arteries and harden into plaque = high blood pressure
Hydrolysis
To break or dissolve with water; breaking polymers into smaller molecules by adding water back into them
The 6 primary functional groups
Polar:
- Hydroxyl group (OH) - alcohols
- Carbonyl group (C=O) - aldehydes/keystones
- Carboxyl group (COOH) - carboxylic acids
- Amino group (NH2) - amines
- Phosphate group (PO4) - phosphates
Nonpolar:
- Methyl group (CH3) - Methylated compound
Amino acids
The “building blocks” of proteins.
Contains a central (alpha) carbon. On one side is an amino group (NH2), on the other side is a carboxyl group (COOH). On top is a hydrogen, on the bottom is an R group.
(R = addition functional group that determine how the amino acid will act)
R groups
Means that there is an additional functional group attached to an protein determining how it will act.
Could be hydrophobic (more insoluble) or hydrophilic (soliable)
Note: typically anything bonded with oxygen will be slightly polar and more soluble in water
How are proteins formed?
Amino acids are linked via dehydration synthesis between the carbon of the carboxyl group of a molecule, and the amino group of another.
The bond between the carbon and the amino group is called a peptide bond
Lipids
Smaller molecules NOT made from monomers. They vary in structure and function, but they are all very hydrophobic
3 main kinds:
- triglycerides
- phospholipids
- steroids
Lipoproteins
Contains proteins, triglycerides, phospholipids, and cholesterol each of these components varying in amount.
Used to package cholesterol in order to make it soluble in your body.
If lipoprotein has more protein than fat, it is HDL if it contains more fat than protein it is LDL
Hydroxyl group
OH
(Alcohols)
Polar
Carbonyl group
C=O
Aldehydes (on the end)
Ketones (in the middle)
Polar
Carboxyl group
COOH
(Carboxylic acid)
Polar
Amino group
NH2
(Amines)
Polar
Phosphate group
PO4
(Phosphates)
Polar
Methyl group
CH3
(Methyls)
Nonpolar
