Biomolecules Flashcards
Who is (1) Aleksander Oparin, (2) John Haldane, and (3) Stanley Miller?
1+2: Theorized about life forming on prehistoric earth through water, hydrogen, ammonia and methane
3: combines H2O, H, NH3, CH4 as well as electricity to stimulate lightning and created organic molecules
What is the difference between an organic molecule and a biomolecule?
Organic molecule: molecule containing carbon (said to have been derived from plants animals)
Biomolecule: type of organic molecule associated with an organism existing in units or polymers
What are the 4 classes of biomolecules and what they’re made of?
Carbohydrates: CHO (CH2O)
Lipids: CH
Proteins: CHON(S)
Nucleotides: CHONP
What are examples of conjugated biomolecules?
Conjugated proteins (e.g. lipoproteins)
Glycosylated molecules (e.g. glycoproteins, glycolipids)
What are lipids? What are the two kinds?
Nonpolar biomolecules made of C and H that typically have a glycerol backbone and 1-3 fatty acids. Divided into fats and oils.
What are the roles of lipids and lipid-related molecules?
1) Structure of cells/membrane (waterproof and pliable)
2) Energy source/storage
3) Communication (Within cells and between cells)
Whats the difference between fats and oils?
Fats: solid at room temp, typically derived from animal sources
Oils: liquid at room temperature, typically derived from plant sources
What are fatty acids? How are they divided?
Long chains of carbon atoms bound to hydrogens with a carboxyl (-COOH) or acid at the end of the chain. Divided into saturated, monounsaturated, polyunsaturated
What is the difference between the three fatty acid types?
Saturated: no double bonds in carbon chain, solid at room temp
Monounsaturated: one double in carbon chain, less solid at room temp
Polyunsaturated: more than one double bond in carbon chain, liquid at room temp
What is a glycerol?
3 carbon molecule that makes up the backbone of most lipids, including monoglycerides (1 FA), diglycerides (2 FA), triglycerides (3 FA)
what are three types of lipid-related molecules and examples?
Eicosanoids (Prostaglandin E2), Steroids (Cholesterol, Cortisol), Phospholipids
What are eicosanoids?
Lipid related molecule made of 20C with two tails connected to a complete/partial carbon ring
What are steroids?
Lipid related molecules with four linked carbon rings, typically found as a cholesterol in the human body.
What are phospholipids?
Lipids made of 2 fatty acid tails, glycerol, and a phosphate group (H2PO4) that are important components of animal cell membranes.
What is a carbohydrate?
Most abundant biomolecule that is polar with the form CH2O and are used mainly in energy storage and structure.
What is the difference between pentoses and hexoses and examples of each?
Pentose: five carbon sugar (e.g. ribose and deoxyribose)
Hexose: six carbon sugar (e.g. Fructose, Glucose, Galactose)
What are the different disaccharides and what monosaccharides make them?
Maltose: Glucose + Glucose
Sucrose: Glucose + Fructose
Lactose: Glucose + Galactose
What are the types of storage and structure polysaccharides?
Storage: glycogen (A) starch (P)
Structure: Chitin (A) Cellulose (P)
What are nucleotides’ structure and function?
Structure: one or more phosphate groups, a pentose, and a carbon-nitrogen “nucleobase.”
Function: major component of genetic material, energy metabolism, and signalling.
What is the difference between a nucleotide and a nucleoside?
Nucleotide: Nucleobase + Phosphate + Pentose
Nucleoside: Nucleobase + Pentose
What are the four nitrogenous bases?
Purines: Adenine, Guanine
Pyrimidines: Cytosine, Thymine, Uracil
What are types of adenine molecules, and their structure and functions?
Adenosine Triphosphate (ATP) ; Adenine + Ribose + 3xPO4 ; energy carrier
Adenosine Diphosphate (ADP) ; Adenine + Ribose + 2xPO4 ; Energy carrier
NAD ; Adenine + 2xRibose + 2xPO4 + Nicotinamide ; Energy carrier
FAD ; Adenine + Ribose + 2xPO4 + Riboflavin ; Energy carrier
cAMP ; Adenine + Ribose + PO4 ; intracellular communication
What is a nucleic acid?
Polymers of nucleotides that store and transmit information. They link via PO4 and sugar, creating the backbone of these chains.
What is the difference between the 3’ and 5’ end?
3’ end: unbound sugar
5’ end: unbound phosphate
What are types of guanine molecules?
Guanosine Triphosphate (GTP): Energy source in many physiological chemical reactions
cGMP: intracellular singalling
What are amino acids?
Structure: alpha carbon connected to a Hydrogen, Amine group, Carboxyl group, and R group
Function: subunits of polypeptides
How is a peptide bond formed?
The hydroxyl of the C terminus of one AA fuses with the H of the N terminus, causing a dehydration reaction and the production of H2O
What are the one letter symbols of the following amino acids: Arginine, Aspartic acid, cysteine, glutamic acid, glutamine, glycine, tryptophan, and tyrosine?
Arg = R
Asp = D
Cys = C
Glu = E
Gln = Q
Gly = G
Trp = W
Tyr = Y
What is homocysteine?
sulfur containing AA, in excess is associated with heart diesase
What is gamma-amino butyric acid (GABA)?
chemical made by nerve cells
What is Creatine?
Molecule that stores energy when it binds to a phosphate group?
What are the different levels of structure of peptides?
Primary structure: linear sequence of amino acids
Secondary structure: Formation of alpha helices or beta pleated sheets due to hydrogen bonds
Tertiary structure: 3D shape created via interactions of R groups
Quaternary structure: combination of multiple protein subunits
What are important roles that proteins play in cell function?
- Enzymes: speed up chemicals to aid in metabolism
- Transport: move substances within the intra and extra cellular space
- Signal molecules: proteins and small peptides may act as hormones
- Receptors: bind signal molecules and initiate cellular responses
- Binding proteins: transport molecules throughout the body
- Immunoglobulins: antibodies that aid in immune response
- Regulatory proteins: turn cell processes on and off
What is the difference between a binding site, ligand, and substrate?
binding site: area in a protein that a molecule will bind via (H-bonding, ionic bonding, and van der waals forces)
ligand: any molecule that binds to another molecule
substrate: Ligands that bind to enzymes and membrane transporters
What is the induced-fit model of protein-ligand binding?
binding site shape doesnt exactly match that of the ligand(s), but rather change shape (conformation) to accommodate the ligands
What is binding affinity? How does the dissociation constant indicate affinity?
Degree to which a protein is attracted to a ligand.
Higher Kd = greater [P][L] = less affinity
Lower Kd = greater [PL] = more affinity
What is the law of mass action?
When protein binding is at equilibrium, ratio of bound and unbound components remain constant. When equilibrium is disturbed, reaction rates will change to restore equilibrium.
What is the difference between an agonist and an antagonist?
Agonist: a ligand that binds to a protein and alters the state of it, resulting in a biological response
Antagonist: a ligand that binds to a protein and causes no biological response, may be reversible or irreversible
What kinds of factors alter protein binding?
Isoforms: closely related proteins whose function is similar but affinity for ligands differs
Activation: pro- proteins must be activated via proteolytic activation or aid of cofactors
Physical factors: pH and temp may cause structural changes to the protein
Modulation: chemical modulators that change the protein’s ability to bind, or changes the protein’s activity/ability to create a response
What is the difference between allosteric modulators and competitive modulators?
Allosteric: reversibly bind to regulatory site or binding site to change the shape of the site and activate/inhibit binding.
Competitive: block an agonist at its normal binding site
What is up-regulation and down-regulation?
Up-regulation: programmed production of new proteins
down-regulation: programmed removal of proteins.
What is protein saturation?
When there are no more binding sites available for ligand binding
What are the functions of kinases and phosphatases?
kinases: phosphorylation
phosphatases: dephosphorylation
How was phosphorylation discovered?
19th century scientists discovered phosphoproteins casein (milk) and phosvitin (eggs) and were thought to provide phosphorus as a nutrient and a consequence of metabolic reactions. 1954 observed phosphorylation of casein via liver enzyme now known as kinase.
What are 4 ways (de)phosphorylation is important?
- increases biological activity of an enzyme
- aids in movement of proteins
- allows protein interaction
- labeling proteins for degradation.
How does phosphorylation work?
Negatively charged phosphate is added to a protein’s amino acid side chain and changes tertiary structure.
What are the most common amino acids kinases target for phosphorylation? What are the most common proteins kinases target?
AA: hydroxyl groups of serine, tyrosine, histidine
Proteins: enzymes, structural proteins, cell receptors, ion channels, signalling molecules
What is a phosphorylation cascade?
A kinase is activated by phosphorylation upon reception of a signal and then phosphorylates the next kinase which phosphorylates the next in the cascade until a phosphatase activates and shuts off transmission.
What kinases mediate cascades in animal cells?
Serine/theronine kinases (phosphorylate serine and theronine amino acids)
