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Human Physiology (BIOL 2410/2420) > Biomolecules > Flashcards

Biomolecules Flashcards

1
Q

Who is (1) Aleksander Oparin, (2) John Haldane, and (3) Stanley Miller?

A

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

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2
Q

What is the difference between an organic molecule and a biomolecule?

A

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

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3
Q

What are the 4 classes of biomolecules and what they’re made of?

A

Carbohydrates: CHO (CH2O)
Lipids: CH
Proteins: CHON(S)
Nucleotides: CHONP

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4
Q

What are examples of conjugated biomolecules?

A

Conjugated proteins (e.g. lipoproteins)

Glycosylated molecules (e.g. glycoproteins, glycolipids)

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5
Q

What are lipids? What are the two kinds?

A

Nonpolar biomolecules made of C and H that typically have a glycerol backbone and 1-3 fatty acids. Divided into fats and oils.

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6
Q

What are the roles of lipids and lipid-related molecules?

A

1) Structure of cells/membrane (waterproof and pliable)

2) Energy source/storage

3) Communication (Within cells and between cells)

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7
Q

Whats the difference between fats and oils?

A

Fats: solid at room temp, typically derived from animal sources

Oils: liquid at room temperature, typically derived from plant sources

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8
Q

What are fatty acids? How are they divided?

A

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

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9
Q

What is the difference between the three fatty acid types?

A

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

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10
Q

What is a glycerol?

A

3 carbon molecule that makes up the backbone of most lipids, including monoglycerides (1 FA), diglycerides (2 FA), triglycerides (3 FA)

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11
Q

what are three types of lipid-related molecules and examples?

A

Eicosanoids (Prostaglandin E2), Steroids (Cholesterol, Cortisol), Phospholipids

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12
Q

What are eicosanoids?

A

Lipid related molecule made of 20C with two tails connected to a complete/partial carbon ring

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13
Q

What are steroids?

A

Lipid related molecules with four linked carbon rings, typically found as a cholesterol in the human body.

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14
Q

What are phospholipids?

A

Lipids made of 2 fatty acid tails, glycerol, and a phosphate group (H2PO4) that are important components of animal cell membranes.

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15
Q

What is a carbohydrate?

A

Most abundant biomolecule that is polar with the form CH2O and are used mainly in energy storage and structure.

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16
Q

What is the difference between pentoses and hexoses and examples of each?

A

Pentose: five carbon sugar (e.g. ribose and deoxyribose)

Hexose: six carbon sugar (e.g. Fructose, Glucose, Galactose)

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17
Q

What are the different disaccharides and what monosaccharides make them?

A

Maltose: Glucose + Glucose

Sucrose: Glucose + Fructose

Lactose: Glucose + Galactose

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18
Q

What are the types of storage and structure polysaccharides?

A

Storage: glycogen (A) starch (P)

Structure: Chitin (A) Cellulose (P)

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19
Q

What are nucleotides’ structure and function?

A

Structure: one or more phosphate groups, a pentose, and a carbon-nitrogen “nucleobase.”

Function: major component of genetic material, energy metabolism, and signalling.

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20
Q

What is the difference between a nucleotide and a nucleoside?

A

Nucleotide: Nucleobase + Phosphate + Pentose

Nucleoside: Nucleobase + Pentose

21
Q

What are the four nitrogenous bases?

A

Purines: Adenine, Guanine

Pyrimidines: Cytosine, Thymine, Uracil

22
Q

What are types of adenine molecules, and their structure and functions?

A

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

23
Q

What is a nucleic acid?

A

Polymers of nucleotides that store and transmit information. They link via PO4 and sugar, creating the backbone of these chains.

24
Q

What is the difference between the 3’ and 5’ end?

A

3’ end: unbound sugar

5’ end: unbound phosphate

25
Q

What are types of guanine molecules?

A

Guanosine Triphosphate (GTP): Energy source in many physiological chemical reactions

cGMP: intracellular singalling

26
Q

What are amino acids?

A

Structure: alpha carbon connected to a Hydrogen, Amine group, Carboxyl group, and R group

Function: subunits of polypeptides

27
Q

How is a peptide bond formed?

A

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

28
Q

What are the one letter symbols of the following amino acids: Arginine, Aspartic acid, cysteine, glutamic acid, glutamine, glycine, tryptophan, and tyrosine?

A

Arg = R
Asp = D
Cys = C
Glu = E
Gln = Q
Gly = G
Trp = W
Tyr = Y

29
Q

What is homocysteine?

A

sulfur containing AA, in excess is associated with heart diesase

30
Q

What is gamma-amino butyric acid (GABA)?

A

chemical made by nerve cells

31
Q

What is Creatine?

A

Molecule that stores energy when it binds to a phosphate group?

32
Q

What are the different levels of structure of peptides?

A

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

33
Q

What are important roles that proteins play in cell function?

A
  1. Enzymes: speed up chemicals to aid in metabolism
  2. Transport: move substances within the intra and extra cellular space
  3. Signal molecules: proteins and small peptides may act as hormones
  4. Receptors: bind signal molecules and initiate cellular responses
  5. Binding proteins: transport molecules throughout the body
  6. Immunoglobulins: antibodies that aid in immune response
  7. Regulatory proteins: turn cell processes on and off
34
Q

What is the difference between a binding site, ligand, and substrate?

A

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

35
Q

What is the induced-fit model of protein-ligand binding?

A

binding site shape doesnt exactly match that of the ligand(s), but rather change shape (conformation) to accommodate the ligands

36
Q

What is binding affinity? How does the dissociation constant indicate affinity?

A

Degree to which a protein is attracted to a ligand.

Higher Kd = greater [P][L] = less affinity

Lower Kd = greater [PL] = more affinity

37
Q

What is the law of mass action?

A

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.

38
Q

What is the difference between an agonist and an antagonist?

A

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

39
Q

What kinds of factors alter protein binding?

A

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

40
Q

What is the difference between allosteric modulators and competitive modulators?

A

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

41
Q

What is up-regulation and down-regulation?

A

Up-regulation: programmed production of new proteins

down-regulation: programmed removal of proteins.

42
Q

What is protein saturation?

A

When there are no more binding sites available for ligand binding

43
Q

What are the functions of kinases and phosphatases?

A

kinases: phosphorylation

phosphatases: dephosphorylation

44
Q

How was phosphorylation discovered?

A

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.

45
Q

What are 4 ways (de)phosphorylation is important?

A
  1. increases biological activity of an enzyme
  2. aids in movement of proteins
  3. allows protein interaction
  4. labeling proteins for degradation.
46
Q

How does phosphorylation work?

A

Negatively charged phosphate is added to a protein’s amino acid side chain and changes tertiary structure.

47
Q

What are the most common amino acids kinases target for phosphorylation? What are the most common proteins kinases target?

A

AA: hydroxyl groups of serine, tyrosine, histidine

Proteins: enzymes, structural proteins, cell receptors, ion channels, signalling molecules

48
Q

What is a phosphorylation cascade?

A

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.

49
Q

What kinases mediate cascades in animal cells?

A

Serine/theronine kinases (phosphorylate serine and theronine amino acids)

Human Physiology (BIOL 2410/2420) (8 decks)

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