Molecular Bio: Cellular Respiration Flashcards
B-pleated sheet
A beta pleated sheet is a secondary structure of a protein in which the single polypeptide chain of the primary structure “lies alongside itself.” Connecting segments of the two strands of the sheet can lie parallel or anti-parallel. Like alpha helices, beta sheets are reinforced by hydrogen bonds between the carbonyl oxygen and the hydrogen on the amino group.
Alpha helix
An a-helix is a secondary structure of a protein. It twists the single chain of polypeptides of the primary structure into a helix. Alpha helices are reinforced by hydrogen bonds between the carbonyl oxygen and hydrogen on the amino group.
Water
Water is the solvent in which the chemical reactions of living cells take place. It makes up 70 to 80% of a cell’s mass. Water is a small, polar molecule that can hydrogen bond.
Water maintains its liquid state in a cell because it can hydrogen bond. Hydrogen bonding also provides strong cohesive forces between water molecules. These forces squeeze hydrophobic molecules away.
Hydrophobic molecules
These “water-hating” molecules are squeezed away from water, which causes them to aggregate elsewhere.
Hydrophilic molecules
These “water-loving” molecules dissolve easily in water. Their negatively charged ends attract the positively charged hydrogens of water, while their positively charged ends attract the negatively charged oxygen on water. Water molecules surround a hydrophilic molecule, separating it from the group.
Lipids
A lipid is any biological molecule with low solubility in water, and high solubility in nonpolar organic solvents.
Lipids are hydrophobic and make excellent barriers separating aqueous environments.
The six major groups of lipids are: fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, and terpenes.
Fatty acids
Fatty acids are lipids. Fatty acids are also the building blocks for most, but not all, complex lipids.
Structure is a long chain of carbons, truncating in a carboxylic acid.
Fatty acids can be saturated or unsaturated.
Oxidation of fatty acids liberates large amounts of chemical energy, which can be used by the cell. Most fats reach the cell as fatty acids, not as triacylglycerols.
Saturated vs. unsaturated fatty acids
Fatty acids can be saturated or unsaturated. Saturated fatty acids possess only single carbon-carbon bonds. Unsaturated fatty acids contain 1+ carbon-carbon double bonds.
Triacylglycerols
Triacylglycerols are a type of lipid that, along with phospholipids and glycolipids, are sometimes called fatty acids.
Triacylglycerols a.k.a. triglycerides, fats, or oils.
Structure: 3-carbon backbone called glycerol attached to three fatty acids.
Function: They store energy in cells, provide thermal insulation, and padding.
Glycerol
Glycerol is the three carbon backbone that makes up triacylglycerol
Adipocytes
Adipocytes are also called fat cells. They are specialized cells who cytoplasm contains almost nothing but triglycerides.
Phospholipids
Phospholipids also have a glycerol backbone, but a polar phosphate group replaces one of the fatty acids.
This phosphate group lies opposite the fatty acids on the glycerol. This makes phospholipids amphipathic.
The amphipathic nature of phospholipids makes them good components of membranes.
Steroids
Steroids are four-ring structures. They include: hormones, vitamin D, and cholesterol.
Proteins
Proteins are built from chains of amino acids linked together by peptide bonds. Proteins are a.k.a. polypeptides.
Digested proteins reach the cells of the human body as single amino acids.
Proteins have four levels of structure.
Proteins can be divided into two types-globular and structural.
Globular proteins can be enzymes, hormones, membrane pumps and channels, membrane receptors, intercellular and intracellular transport, storage, regulators, immune response, etc.
Structural proteins are made from long polymers, and adds strength to cellular and matrix structure. An example is collagen, the most abundant protein in the body.
“Essential”
Something being essential means that the body cannot manufacture it and it must be ingested directly. Examples of essential nutrients are 10 of the 20 amino acids.
Amino acids
There are 20 amino acids. Amino acids have the general structure: amine group directly across from a carbonyl group, both attached to a central carbon with an R group (“side chain”) on top.
Each amino acid in a polypeptide chain is called a residue. Very small polypeptides are sometimes called peptides.
Tertiary structure
Tertiary structure refers to the three-dimensional shapes formed when the peptide chain curls and folds.
Five forces create the tertiary structure: 1. Covalent disulfide bonds between two cysteine amino acids on different part of the chain
- Electroststatic (ionic) interactions between acidic and basic side chains
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic side chains pushed away from water toward the center of the protein
The amino acid proline induces turns in the polypeptide that will disrupt both Alpha helix and beta-pleated sheet formation
Secondary structure
The alpha helix and the beta pleated proteins are the secondary structure and contribute to the conformation of the protein. All proteins have a primary structure and most have a secondary structure. Larger proteins (globular, fibrous/structural, etc.) can have a tertiary and quaternary structure.
Quaternary structure
When two or more polypeptide chains bind together, they formed the quaternary structure of the protein.
Larger proteins- like globular, fibrous, structural etc., have tertiary and coronary structure.
Five forces create the quaternary structure: 1. Covalent disulfide bonds between two cysteine amino acids on different part of the chain
- Electroststatic (ionic) interactions between acidic and basic side chains
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic side chains pushed away from water toward the center of the protein
Denaturing proteins
When confirmation is disrupted, the protein is said to be denatured. A denatured protein has lost most of it’s secondary, tertiary, and quaternary structure. Very often, once the denaturing agent is removed, the protein will spontaneously refold to its original confirmation.
Urea denatures hydrogen bonds.
Salt or change in pH denatures electrostatic bonds.
Mercapthoethanol denatures disulfide bonds.
Organic solvents denature hydrophobic forces.
Heat denatures all forces.
Carbohydrates
Carbohydrates are also called sugars or saccharides, and are made from carbon and water. Five and six carbon carbohydrates are the most common in nature. The six carbon carbohydrate glucose is the most commonly occurring six carbon carbohydrate.
Glucose
Glucose accounts for about 80% of the carbohydrates absorbed by humans. Glucose exists in aqueous solution in an unequal equilibrium that favors its ring form over its chain form.
If the cell has sufficient ATP, glucose is polymerized to the polysaccharide glycogen, or converted to fat.
Only certain cells in the digestive tract and kidney can absorb glucose against a concentration gradient. This uses a second transport mechanism. All other cells use facilitated diffusion to absorb glucose.
Insulin increases the rate of facilitated diffusion for glucose and other monosaccharides. In the absence of insulin, only neural and hepatic cells are capable of absorbing enough glucose using facilitated transport.
Plants form starch and cellulose from glucose.
Anomers
The ring form of glucose has two anomers. In the first anomer, alpha glucose, the hydroxyl group and the methoxy group are on opposite sides of the carbon. In beta glucose, the hydroxyl group and the methoxy group on the same side of the carbon. The cell can oxidize glucose - transferring its chemical energy to a more usable form, ATP.
Glycogen
When a cell has sufficient ATP, glucose is polymerized to the polysaccharide glycogen.
Glycogen is a branched glucose polymer with alpha linkages. Glycogen is found in all animal cells, with especially large amounts in muscle and liver cells.
