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

Chapter 3: Biologically Important Molecules Flashcards

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1
Q

Glycine

A

Gly (G) [Nonpolar]

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2
Q

Alanine

A

Ala (A) [Nonpolar]

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3
Q

Valine

A

Val (V) [Nonpolar]

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4
Q

Methionine

A

Met (M) [Nonpolar]

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5
Q

Leucine

A

Leu (L) [Nonpolar]

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6
Q

Isoleucine

A

Ile (I) [Nonpolar]

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7
Q

Proline

A

Pro (P) [Nonpolar]

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8
Q

Phenylanine

A

Phe (F) [Nonpolar]

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9
Q

Tryptophan

A

Trp (W) [Nonpolar]

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10
Q

Serine

A

Ser (S) [Polar]

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11
Q

Threonine

A

Thr (T) [Polar]

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12
Q

Asparagine

A

Asn (N) [Polar]

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13
Q

Glutamine

A

Gln (Q) [Polar]

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14
Q

Cysteine

A

Cys (C) [Polar]

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15
Q

Tyrosine

A

Tyr (Y) [Polar]

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16
Q

Aspartic Acid (Aspartate)

A

Asp (D) [electrically charged, NEGATIVELY charged at pH 7]

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17
Q

Glutamic Acid (Glutamate)

A

Glu (E) [electrically charged, NEGATIVELY charged at pH 7]

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18
Q

Histidine

A

His (H) [electrically charged, listed as positived charged at pH 7] BUT, technically Histidine can act as BASE and ACID.

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19
Q

Arginine

A

Arg (R) [electrically charged, POSITIVELY charged at pH 7]

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20
Q

Lysine

A

Lys (K) [electrically charged, POSITIVELY charged at pH 7]

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21
Q

What is special about the amino acid Proline?

A

It plays an important roles in turns . This is due to the fact proline is rigid and results in a kink in the peptide strand

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22
Q

2 common types of bonds between amino acids in proteins

A

1) the peptide bonds that link amino acids together into polypeptide chains
2) disulfide bridges between cysteine R groups

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23
Q

Polypeptides are formed by linking

A

amino acids together in peptide bonds

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24
Q

A peptide bond is formed between

A

the carboxyl group of one amino acid and the α amino group of another amino acids with the loss of water

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25
Q

Backbone of the polypeptide

A

In a polypeptide chain, the N-C-C-N-C-C pattern formed from the amino acids is known as the backbone of the polypeptide

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26
Q

Residue

A

An individual amino acids is termed a residue when it is part of a polypeptide chain

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27
Q

Thermodynamics states that ________ must decrease for a reaction to proceed spontaneously

A

free energy

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28
Q

proteolysis / proteolytic cleavage

A

hydrolysis of a protein by another protein

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29
Q

proteolytic enzyme (protease)

A

protein that does the cutting

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30
Q

The disulfide bond (Cysteine)

A

Cysteine is an amino acid that has a reactive thiol (SH) in its side chain. The thiol of one cysteine can react with the thiol of another cysteine to make a covalent sulfur-sulfur bond known as a disulfide bond. Cysteines can make this bond in same or different polypeptide chains. The disulfide bridge plays an important role in stabilizing tertiary protein structures. When cysteine is disulfide bonded to another cysteine residue it turns into cystine

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31
Q

Denaturation

A

disruption of the shape of a protein without breaking, this can result from urea (disrupts hydrogen bonding), by extremes of PH, extremes of temperature and by changes in salt concentration and etc.

32
Q

Do not expect a normally folded protein if

A

denaturation is still taking place

33
Q

Primary Structure

A
  • amino acid sequence
  • everything that is neccesary for proper protein folding is contained in the primary sequence
34
Q

Secondary Structure

A
  • held together by hydrogen bonding in the backbone

Alpha helix: H- bonding is parallel (polypeptide strands run in same direction) to principle axis

Beta sheet: H-bonding is perpendicular (polypeptide strands run in different direction) to principle axis

Turns: *proline is rigid and will result in a kink in the peptide strand and is often used in these turns (Proline will NEVER be used in alpha helix)

  • alpha helix is overall more favorable
35
Q

Tertiary Structure

A
  • orginization of secondary structures
  • In globular proteins, hydrophobic (water hating) areas will be inside while hydrophillic (water loving) areas will be on the outside
  • disulfide bridges between cysteine reside (covalent bonds)
  • ALL intermolecular forces are involved
36
Q

Quarternary Structure

A

-interaction of multiple subunits (SEPERATE peptide chains)

Example: Hemoglobin

  • EVERTHING involved in tertiary structure can be involved in quarternary structure
37
Q

Carbohydrates can be broken down into _______ in a process callled ___________

A

carbon dioxide in a process called oxidation (also know as burning or combustion) because this process releases large amounts of energy, carbohydrates generally serve as the principle energy source for celluar metabolism

38
Q

A single carbohydrate is called a _________ also known as simple sugar

A

monosachharide, they have the general foumula CnH2nOn

39
Q

Glycosidic Linkage

A

The bond between two sugar molecules is called a glycosidic linkage (a covalent bond, formed in a dehydration reaction that requires enzyme catalysis)

40
Q

hydrophobic

A

water fearing

41
Q

hydrophillic

A

water loving

42
Q

lipophillic

A

lipid loving

43
Q

lipophobic

A

lipid hating

44
Q

saturated

A

no double bonds

45
Q

unsaturated

A

has double bonds

46
Q

Micelle

A

when free fatty acids interact in an aqueous solution, it forms a structure called a micelle.

47
Q

What is the force that drives the tails into the center of the micelle?

A

It results from the fact that water molecules must form an orderly solvation shell around each hydrophobic substance. Water has a dipole that likes to share charges with other polar molecules. The solvation shell allows for most water to water interactions and least water lipid interactions. The problem is that forming a sovation shell is an increase in order and a decrease in entropy. which is unfavorable according to the second law of thermdynamics.

48
Q

triaglycerol

A

the technical name for fat is triaglycerol or tryglyceride, the triglyceride is composed of 3 fattty acids esterified to a glycerol molecule. Glycerol is a 3 carbon triol.

49
Q

The triaglycerol undergoes reactions typical of esters such as base catalyzed hydrolysis. _______ are the sodium salts of fatty acids. They are amphitatic which means they have both hydropillic and hydrophobic regions. Soap is economiclaly produced by base cataylyzed hydrolysis of trrigylcerides from animal fat into fatty acids (soaps). This rxn is called ________ .

A

The triaglycerol undergoes reactions typical of esters such as base catalyzed hydrolysis. Soaps are the sodium salts of fatty acids. They are amphitatic which means they have both hydropillic and hydrophobic regions. Soap is economiclaly produced by base cataylyzed hydrolysis of trrigylcerides from animal fat into fatty acids (soaps). This reaction is called saponification

50
Q

Lipases

A

are enzymes that hydrolyze fats

51
Q

Triaglycerols are stored in fat cells as an energy source. Fats are more efficient energy storage molecules than carbohydrates for what two reasons?

A

1) Packing: their hydrophobicity allows fats to pack together much more closely than carbohydrates

2) Energy: fat molecules store much more energy than carbohydrates

52
Q

Phospolipids are _________, substances that efficiently solubize oils while remaining highly water soluble

A

Phospolipids are detergents, substances that efficiently solubize oils while remaining highly water soluble. Detegents are like soaps, but stronger.

53
Q

Lipid Bilayer

A

phospholipids also minimize their interactions with water by forming an orderly structure, the lipid bilayer. Hydrophobic interactions drive formation of the bilayer and once formed is stabilized by van der walls forces between the long tails.

54
Q

What increases membrane fludity?

A

1) Unsaturation tends to increase membrane fludity. Unsaturation prevents membrane from solidifying by disrupting the orderly packing of the hydrophobic lipid tails.
2) Decreasing the length of fatty acid tails also increases fluidity
3) Cholesterol is a important concept for membrane fludity. At low temperature it increases fludity the same way as kinks in fatty acid tails (Remember cholesterol keeps fluidity at an optimum level)

55
Q

Terpenes

A
  • a member of a broad class of compound built from isoprene units (C5H8) with general formula (C5H8)n
  • may be linear or cyclic and are classified by # of isoprene units they contain
56
Q

Sqaulene

A

is a titerpene (made of 6 isoprene units) and its a particularly important compund as it is biosynthetically utilized in the manafacture of steroids

57
Q

Whereas a terpene is formally a simple hydrocarbon, there are a # of natural and synthetically derived species that are built from an isoprene skeleton and functionalized with other elements. These functionalized terpenes are known as ___________

A

terpenoids, Vitamin A is an example of a terpenoid

58
Q

All steroids have the basic ____________ based on the structure of cholesterol, a polycyclic amphipath

A

tetracyclic ring system

59
Q

Where does cholesterol come from?

A

It is both obtained from the diet and synthesized in the liver. It is carried in the blood packaged with fats and proteins into lipoproteins.

60
Q

Steroid hormones are made from

A

cholesterol, two examples are tesosterone ( androgen or male sex hormone) and estradiol ( estrogen or female sex hormone)

61
Q

Peptide hormones vs. steroid hormones

A

You must be aware of the contrast between peptide hormones such as insulin which exert their effects by binding to receptors at the cell surface, and steroid hormones such as estrogen which diffuse into cells to find their receptors

62
Q

Phosphoric acid

A

an inorganic acid with the potential to donate 3 protons.

63
Q

Phostphate is also known as ___________, 2 orthophosphates bound together via an anhydride linkage form pyrophosphate

A
  • orthophosphate, 2 of these are bound via an ahydride linkage. The POP bond in pyrophosphate is an example of a high energy phosphate bond.
    1) When phospates are linked together, their negative charges repel each other strongly
    2) Orthophosphate has more resonance forms and thus a lower energy than linked phosphates
    3) orthophosphates has a more favorable interaction with the biological solvent (water) than linked phosphates. What is essential is that you fix the image in your mind of linked phosphates acting like compressed sprngs just waiting to fly open and provide energy for an enzyme to catalyze a rxn
64
Q

Nucleotides

A

are the building blocks of nucleic acids (RNA and DNA. Each nucleotide contains a ribose or deoxyribose suagr group, a pyrine or pyrimidine base joined to carbon 1 of the ribose ring and 1, 2 or 3 phosphate units joined to carbon 5 of the ribose ring.

65
Q

What is the main function of ATP?

A

universal short term energy storage molecule

66
Q

Proteins consists of amino acid linked by what?

A

peptide bonds

67
Q

The most stable tertiary protein structure generally

A

places polar AA’s on the exterior and nonpolar AA’s on the interior of the protein. This minimizes interaction between nonpolar AA’s and water while optimizing interaction between side chains inside the protein

68
Q

Proteins have a ________ of functions in the body

A

variety

69
Q

The monomer for a carbohydrate is a

A
  • monosaccharide with the moecular formula CnH2nOn
  • Common monosaccharides a lucose, fructose, galactose, ribose and deoxyribose.
70
Q

2 monosaccharides joined with a glycosidic linkage form a _________

A

disaccharide, common disaccharides are maltose, sucrose, and lactose. Mammals can digest α glycosidic linkages but not β glycosidic linkages.

71
Q

Polysaccharides consist of many _________ linked together

A

monosaccharides. Glycogen (animals) and starch (plants) are storage units for glucose and can be broken down for energy. Celluose is a glucose polymer but the beta linkage prevents digestion. It forms wood and cotton.

72
Q

Lpids are found in several forms in the body, including tryglycerides, phospholipids, cholesterol, steroids, and terpenes.

How do tryglycerides and phospholipids differ from cholesterol and steroids in structure?

A

Tryglyerides and phospholipids are linear while cholesterol and steroids have a ring structure

73
Q

Lipids are ________. Tryglycerides are used for _____ _____. Phospholipids _______ _______ and cholesterol is the precursor to the _____ _____.

A

Lipids are hydrophilic. Tryglycerides are used for energy storage, phospholipids form mebranes and cholesterol is the precursor to the steroid hormones.

74
Q

The building blocks of nucleic acids are ___ and ___ which are composed of ___________

A

The building blocks of nucleic acids (DNA and RNA) are nucleotides, which are compromised of a pentose sugar, a purine or pyrimidine base, and 2 to 3 phosphate units.

75
Q

More about disulfide bonds

A

The formation of a disulfide bridge happens on the exterior of the cell, separation of thiol groups on the interior of the cell. This is because the interior of the cell has antioxidants which generate a reduced enviroment. Exterior has oxidizing enviroment.

MCAT Biology Review (4 decks)

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