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Princeton Review MCAT Biology Book > Chapter 3: Biologically Important Molecules > Flashcards

Chapter 3: Biologically Important Molecules Flashcards

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1
Q

What roles do proteins have in the cell?

A

Proteins act as enzymes, hormones, receptors, channels, transporters, antibodies, and support structures inside and outside cells.

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2
Q

What are proteins made of?

A

Composed of 20 amino acids linked together in polymers

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3
Q

What makes each protein unique?

A

Composition and sequence of amino acids in the polypeptide chain is what make each protein unique/ play a special role in the cell.

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4
Q

All 20 amino acids have the same ___ ___ ___ backbone

A

nitrogen-carbon-carbon

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5
Q

What makes an amino acid unique?

A

Side chain (variable R group) which gives it hte physical and chemical properties that distinguish it from the other 19.

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6
Q

What are the two common types of covalent bonds between amino acids in protein?

A

Peptide bonds and disulfide bridges

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7
Q

What are peptide bonds?

A

Link amino acids together into polypeptide chains

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8
Q

What are disulfide bridges?

A

covalent links between the sulfur atoms of two cysteine amino acids (cysteine R groups)

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9
Q

What is residue?

A

Individual amino acids part of the polypeptide chain

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10
Q

The ___ terminus is the first end made during polypeptide synthesis and the ___ terminus is made last.

A

amino, carboxyl

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11
Q

In the oligopeptide The-Glu-Gly-Ser-Ala which residue has a free alpha-amino group and which residue has a free alpha-carboxyl group?

A

Amino terminus: Phe
Carboxyl terminus: Ala
Amino end is always written first so it begins with exposed Phe amino group and ends with exposed Ala carboxyl

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12
Q

What is proteolysis/proteolytic cleavage?

A

Hydrolysis of another protein (proteolytic cleavage is a specific method of cutting peptide bonds. Many enzymes only cleave the peptide bond adjacent to a specific amino acid.

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13
Q

What does the proteolytic enzyme/protease do?

A

Protein that does the cutting

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14
Q

Based on the following: H2N-Ala-Phe-Ser-Lys-Gly-Leu-COOH. If the following peptide bond is cleaved by trypsin what amino acids will be on the new N-terminus and how many fragments will result in this sequence: Ala-Gly-Lys-Phe-Phe-Lys ^2?

A

Trypsin will cleave on the carboxyl side of the Lys residue with Phe on the N-terminus of the new Phe-Phe-Lys fragment. There will be two fragments after trypsin cleavage: Phe-Phe-Lys and Ala-Gly-Glu-Lys.
The carboxyl group is the end of the amino acid chain terminated by COOH.
The N terminus is the one with the free amino group (H2N).

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15
Q

Trypsin cleaves on the ____ side of residues arginine and lysine

A

carboxyl
Trypsin cleaves carboxyl

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16
Q

Chymotrypsin cleaves adjacent to hydrophobic residues like ____

A

phenylalanine
Chymotrypsin is a hydrophobe who likes phenylalanine

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17
Q

Cysteine is an amino acid with a _____ that can react with another____ of cyestine to make a _____

A

reactive thiol (sulfhydryl SH group)
another thiol of cysteine
disulfide bond

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18
Q

What does cysteine do?

A

Plays a key role in stabilizing tertiary protein structure (protein folding).

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19
Q

Cysteine x Cysteine =

A

Cystine

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20
Q

What is denaturation?

A

disruption of a protein’s shape without breaking peptide bonds

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21
Q

What can cause proteins to denature?

A

urea (disrupts hydrogen bonding interactions), extreme pH and temperature, and changes in salt concentration (tonicity).

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22
Q

Describe the primary structure 1

A

The linear ordering of amino acid residues bonded by peptide bonds.

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23
Q

Describe the secondary structure 2

A

Initial folding of a polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups. Certain motifs of a secondary structure are found in most proteins: Alpha Helix and Beta pleated sheets are the two most common.

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24
Q

What are parallel beta pleated sheets?

A

Adjacent polypeptide strands running in the same direction?

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25
What are antiparallel beta-pleated sheets?
polypeptide strands run in the opposite direction.
26
If a single polypeptide folds once and forms a Beta pleated sheet with itself, would this be a parallel or antiparallel Beta pleated sheet?
It would be antiparallel because one participant in the Beta pleated sheet would have a C to N direction, while the other would be running N to C.
27
Describe tertiary structure 3
Deals with hydrophobic/hydrophilic interactions between amino acid residues located ore distantly from one another in the polypeptide chain. Secondary structures (like alpha helices) fold into higher order tertiary structures due to R group interactions with each other and with the solvent (water). Hydrophobic R groups fold into the interior of the protein, away from the solvent, and hydrophilic R groups tend to be exposed to water on the surface of the protein.
28
Which of the following may be considered an example of a tertiary protein structure? I. van der Waals interactions between two Phe R-groups located far apart on a polypeptide. II. Hydrogen bonds between backbone amino and carboxyl groups. III. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide.
Item I is true this is a good example of a 3 structure. Item II is false; this describes 2 not 3. Item III describes the disulfide bridge which is tertiary. For Item III more info: Disulfide bonds make proteins less susceptible to unfolding; typically, they will link -sheets, -helices, and loops, which means that they primarily maintain tertiary structure, not secondary, which refers to local conformations, and is maintained largely by hydrogen bonds.
29
Describe quaternary 4 structure
Highest level of protein structure Describes interactions between polypeptide subunits which are part of a large complex containing many subunits (multisubunit complex). Forces stabilizing quaternary structures are generally the same as the tertiary structures. This includes non-covalent interactions, van der Waals forces, hydrogen bonds, disulfide bonds, and electrostatic interactions. Exception: No peptide bond involvement in quaternary structure because it defines 1 structure.
30
What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?
Quaternary disulfide bonds that form chains aren’t linked by peptide bonds. Tertiary disulfides are bonds that form between residues in the same polypeptide.
31
What is oxidation?
it is the breakdown of carbohydrates into CO2 aka burning/combustion. the principle source of energy in metabolism
32
What is a monosaccharide?
A simple carbohydrate molecule aka simple sugar. CnH2nOn
33
What is a disaccharide?
The carbohydrate formed when two monosaccharides are bound by a glycosidic linkage.
34
What is a polysaccharide?
The carbohydrate formed when more than two monosaccharides are bound by a glycosidic linkage.
35
What is glycosidic linkage?
A covalent bond that joins a carbohydrate group to another molecule. (bond between two sugar molecules)
36
What are some common disaccharides?
Sucrose, lactose, maltose, cellobiose.
37
Super Glowing Frogs Leave Gardens Glowing
Sucrose =Glucose + Fructose Lactose= Galactose + Glucose
38
Describe glycogen
serves as an energy storage carb in animals and is made of thousands of glucose units.
39
Describe starch
same as glycogen except branching is different and serves the same role in plants.
40
Describe cellulose
polymer of cellobiose doesn't exist freely in nature but rather in a polymerized cellulose form.
41
What three physiological roles do lipids play?
1) In adipose tissue, triglycerides (fats) store energy 2) In cell membranes phospholipids constitute a barrier between intracellular and extracellular environments. 3) Cholesterol is a special lipid that serves as the building block for hte hydrophobic steroid.
42
Hydrophobic
water fearing do not dissolve well in water C-C and C-H bonds are nonpolar
43
Hydrophillic
water-loving water is polar so polar substances dissolve well in water
44
Substances with only ___ and ___ will not dissolve well in water
only carbon and hydrogen
45
What is a synonym for hydrophobic
lipophilic (lipid loving)
46
What is a synonym for hydrophillic
lipophobic (lipid phobic)
47
What are fatty acids made of?
long unsubstituted alkanes that end in carboxylic acid. The chain is 14-18 carbons long
48
Why are only even-numbered fatty acids made in human cells?
Because two carbons at a time from acetate are syntheized
49
What does saturated mean?
a fatty acid with no C-C double bond and is saturated with hydrogen (every C bound to max number of H)
50
What does unsaturated mean?
fatty acids have one or more double bonds in the tail and they are almost always Z or cis.
51
How does the shape of an unsaturated fatty acid differ from that of a saturated fatty acid
An unsaturated fatty acid is bent or "kinked" at the cis double bond.
52
If fatty acids are mixed into water, how are they likely to associate with each other?
the long hydrophobic chains will interact with each other to minimize contact with water, exposing the charged carboxyl group to the aqueous environment.
53
What is triacylglycerol?
storage form of fatty acid Composed of three fatty acids esterified to a glycerol molecule
54
What are lipases?
Enzymes that hydrolyze fats (ase = enzyme)
55
Why are fats more efficient storage molecules than carbs?
Packing: Hydrophobicity allows fats to pack more closely together than carbs. Carbs carry a lot of water of solvation (water molecules hydrogen bonded to hydroxyl groups. Energy content: Fat molecules store more energy than carbs
56
Would a saturated or an unsaturated fatty acid have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?
the bent shape of an unsaturated fatty acid means it doesn't fit in as well and has less contact with neighboring groups to form van der Waals interactions. ] Phospholipids made of saturated fatty acids make the membrane more solid.
57
Double bonds (unsaturation) in phospholipid fatty acids ____
tend to increase membrane fluidity.
58
What does the steroid cholesterol do?
Keeps fluidity at optimum level.
59
What are the structural determinants of membrane fluidity?
degree of saturation, tail length, and amount of cholesterol.
60
Describe terpenes
member of a broad class of compounds built from isoprene units C5H8. The general formula is (C5H8)n
61
What are the different types of terpenes?
May be linear or cyclic Classified by number of isoprene units they contain. Monoterpene = two isoprene units Sesquiterpenes = three isoprene units Diterpenes = four isoprene units
62
What is squalene?
It is a triterpene (made of six isoprene units) that is biosynthetically utilized in the making of steroids.
63
What are terpenoids?
Natural and synthetically derived species built from an isoprene skeleton and functionalized with other elements. Ex: Vitamin A
64
What is the importance of steroids in the lipid bilayer?
Obtained from diet and synthesized in the liver. Carried in the blood packaged with fats and proteins into lipoproteins one of which has been attributed to the cause of cholesterol plaques inside blood vessels. . atherosclerotic vascular disease.
65
Describe phosphoric acid
Inorganic (no carbon) w/ potential to donate 3 protons.
66
What is pyrophosphate?
Two orthophosphates (phosphates) bound together via anhydride linkage form pyrophosphates
67
What is an example of a high-energy phosphate bond?
The P-O-P bond in pyrophosphate. Name derived from hydrolysis of pyrophosphates which is extremely favorable.
68
Why can phosphate anhydride bonds store so much energy?
1) When phosphates are linked together, their negative charges repel each other strongly. 2) Orthophosphate has more resonance forms and lower free energy than linked phosphates. 3) Orthophosphates have a more favorable interaction with the biological solvent (water) than linked phosphates
69
Key point about phosphates
Linked phosphates act like compressed strings that can provide energy for an enzyme to catalyze a reaction.
70
What are nucleotides and what are they composed of?
building blocks of nucleic acids (RNA and DNA) Each molecule contains a ribose (deoxyribose) sugar, a purine or pyrimidine base, and 2-3 phosphate units
71
Chapter 3 Summary
-Amino acids consist of a tetrahedral alpha carbon connected to an amino group, a carboxyl group, and a variable R group, which determines the AA's properties. - Proteins consist of amino acids linked by peptide bonds (very stable). The primary structure of proteins = amino acid sequence - Secondary structure of proteins = alpha helices and beta sheets formed through hydrogen bonding interactions between atoms in the backbone of the molecule. - Most stable tertiary protein structure puts polar AAs in the exterior and nonpolar AAs in the interior of the protein. (Minimizes interactions between nonpolar AAs and water while optimizing interactions between side chains and water). -Proteins act as enzymes, structural roles, hormones, receptors, channels, antibodies, transporters etc. -Monosaccharide: CnH2nOn examples are glucose, fructose, galactose, ribose, and deoxyribose - Disaccharide: Two monosaccharides joined by glycosidic linkage Examples include maltose, sucrose, and lactose. Mammals can digest alpha glycosidic linkages but not beta. -Polysaccharides are many monosaccharides linked together. Glycogen (animals) and starch (plants) are storage units for glucose and can be broken down for energy. Cellulose is also a glucose polymer but beta linkage prevents digestion (forms wood and cotton). -Lipids are found i several forms in the body including triglycerides, phospholipids, cholesterol and steroids, and terpenes. Triglycerides and phospholipids are linear while cholesterol and steroids have a ring structure. -Lipids are hydrophobic. Triglycerides are used for energy storage, phospholipids form membranes, and cholesterol is the precursor to steroid hormones. -The building blocks of nucleic acids (DNA and RNA) are nucleotides which are comprised of a pentose sugar, a purine or pyrimidine base and 2-3 phosphate units.
72
Which amino acids are basic?
histidine, arginine, lysine
73
Which amino acids are acidic?
glutamate and aspartate
74
Which amino acids are neutral?
glycine
75
What are the essential amino acids?
PVT TIM HALL Phenylalanine Valine Tryptophan Threonine Isoleucine Methionine Histidine Arginine Lysine Leucine
76

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