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chapter 1 Flashcards

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1
Q

what is polarity?

A
  • describes the distribution of charge within a molecule as mediated by electrons
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2
Q

what are nonpolar molecules?

A
  • in nonpolar molecules, electrons are distributed fairly evenly, although transient and induced dipoles may be present
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3
Q

what are polar molecules?

A
  • In polar molecules, one or more electronegative atoms attract electrons creating areas of higher electron density or low electron density
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4
Q

what are charged molecules?

A
  • charged molecules have one or more full positive or negative charges
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5
Q

what is the concept “functional group”?

A
  • a useful way to explain the reactivity and chemical/physical properties of classes of molecules
    • it’s a specific group of atoms that contribute in a predictable way to the behaviour of a molecule
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6
Q

functional groups on a spectrum of polarity from least to most polar:

A
  • hydrocarbons
  • aldehydes and ketones
  • amines (primary and secondary)
  • alcohols
  • carboxylic acids
  • charged molecules
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7
Q

What happens if a molecules has more than one functional group?

A
  • look at if the non polar aspects of the molecule outweigh the polar aspects
    • ex. steroids
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8
Q

what are amphipathic molecules?

A
  • they exhibit significant polar and nonpolar properties localized to different parts of the molecules
    • ex. fatty acids which have a polar head and a nonpolar tail
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9
Q

what determining whether a molecule is polar or nonpolar, what should be taken into account?

A
  • its molecular geometry
    • look for dipoles cancelling each other out!
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10
Q

polarity is also often discussed in terms of what?

A
  • solubility
    • like dissolves like
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11
Q

how can polar molecules be described?

A
  • water-soluble
  • hydrophilic
  • lipophobic
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12
Q

how can non-polar molecules be described?

A
  • non-water soluble
  • hydrophobic
  • lipophilic
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13
Q

what are proteins?

A
  • the building blocks of life which are composed of amino acids
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14
Q

what is the structure of an amino acid?

A

the central carbon has 4 substituents

  • has an amine functional group
  • a carboxylic acid functional group
  • an H group
  • an R group unique to each amino acid (side chain)
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15
Q

structure and description of glycine?

A
  • non polar
  • achiral
  • Gly
  • G
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16
Q

structure and description of alanine

A
  • nonpolar
  • Ala
  • A
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17
Q

structure and description of Valine?

A
  • Val
  • V
  • nonpolar
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18
Q

structure and description of isoleucine?

A
  • Ile
  • I
  • nonpolar
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19
Q

structure and description of methionine?

A
  • Met
  • M
  • nonpolar
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20
Q

structure and description of proline?

A
  • Pro
  • P
  • “proline kink”
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21
Q

structure and description of phenylalanine?

A
  • Phe
  • F
  • nonpolar
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22
Q

structure and description of tyrosine?

A
  • Tyr
  • Y
  • Pka of 10
  • nonpolar
  • aromatic
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23
Q

structure and description of tryptophan?

A
  • Trp
  • W
  • nonpolar
  • aromatic
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24
Q

structure and description of serine

A
  • Ser
  • S
  • polar uncharged
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25
Q

structure and description of threonine?

A
  • Thr
  • T
  • polar uncharged
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26
Q

structure and description of asparagine?

A
  • Asp
  • N
  • polar uncharged
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27
Q

structure and description of glutamine?

A
  • Gln
  • Q
  • polar uncharged
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28
Q

structure and description of arginine?

A
  • Arg
  • R
  • Pka of 12
  • basic/positively charged
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29
Q

structure and description of Histidine?

A
  • His
  • H
  • basic/postively charged
  • pKa of 6
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30
Q

structure and description of Lysine?

A
  • Lys
  • K
  • basic/positively charged
  • pKa of 10.5
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31
Q

structure and description of aspartic acid (aspartate)?

A
  • Asp
  • D
  • negatively charged/acidic
  • pKa of 4
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32
Q

structure and description of glutamic acid (glutamate)

A
  • Glu
  • E
  • negatively charged/acidic
  • pKa of 4
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33
Q

pKa of N terminus?

A

9

34
Q

pKa of C terminus?

A
  • 2
35
Q

what are the aromatic amino acids?

A
  • Phe
  • Tyr
  • Trp
36
Q

what are the sulfur containing amino acids?

A
  • Met
  • Cys
37
Q

what amino acid breaks up secondary structure?

A
  • Proline
38
Q

Cysteine residues form what?

A
  • Disulfide bridhes resulting in cystine and form a crucial part of tertiary structure
39
Q

which amino acid can serve as a buffer at pH levels slightly more acidic than physiological pH but the deprotonated, non-charged form is prevalent at physiological pH?

A
  • Histidine
40
Q

Amino acids are joined together through what kind of bonds?

A
  • peptide bonds in which the COOH group of one amino acid binds with the NH2 group of another, releasing water
41
Q

Notes about pKa and pI of proteins

A

For most carboxyl groups (COOH), the pKa range is between 1-3. For most amino groups (NH3), the pKa range is between 9-11. Since every amino acid has a carboxy terminus and an amino terminus, the pI will be the average of their pKa’s + the pKa of any ionizable group on its side chain.

Of the basic amino acids, Lysine and Arginine have side chains with high pKas of 10-12, which brings their total isoelectric points to about 9-10. Histidine is the exception here, with a side chain pKa of 6 which brings the overall pI of His to ~7.5.

Of the acidic amino acids, both Asp and Glu have ionizable side chains with pKas around 3-4 (since they are carboxyl groups), which brings their overall pI to about 2-3.

All the other amino acids (uncharged) will have pI values in the range of 5-6 because their pKa is the average of their C-terminus pKa (1-2) and their N-terminus pKa (~8-10).

42
Q

what is protein primary structure?

A
  • defined as the sequence of amino acids itself
43
Q

what is protein secondary structure?

A
  • formed by H-bonding interactions between the carboxyl and amine components of the amino acid backbone (not the side chains)
    • alpha helices
    • beta sheets
44
Q

what is protein tertiary structure?

A
  • is defined by side chain interactions including”
    • Hydrophobic interactions between side chains
    • salt bridges formed by interactions between charged side chains
    • disulfide bonding between Cysteine residues
45
Q

What is protein quaternary structure?

A
  • formed by interactions between polypeptide chains
46
Q

All proteins have?

A
  • primary, secondary and tertiary structures but not all proteins have quaternary structure
47
Q

what is the driving force that determines how proteins interact with their surroundings?

A
  • Polarity
48
Q

In aqueous solution, non polar a.a. tend to be part of the?

A
  • internal core of the 3D structure, while polar and charged a.a. tend to be on the outside
49
Q

how many domains do transmembrane proteins have and what are they?

A
  • 3 domains
    • an extracellular domain (hydrophilic)
    • an intracellular domain (hydrophilic)
    • a transmembrane domain that spans the membrane (hydrophobic)
50
Q

proteins interact with other molecules at specialized areas known as?

A
  • binding sites
51
Q

what are lipids?

A
  • hydrophobic
  • have a diverse range of structural functions in the body
    • contributing to energy, storage, structure, and signaling
52
Q

what are the four main classes of lipids?

A
  • fatty acids and derivatives
  • cholesterol and derivatives
  • eicosanoids including prostaglandins
  • terpenes and terpenoids
53
Q

What are fatty acids?

A
  • relatively long chain carboxylic acids (13-21 C)
54
Q

what are triacylglycerols?

A
  • have 3 fatty acid chains (R-COOH) attahced to a glycerol backbone
55
Q

what is the process of saponification?

A
  • the esters formed between the (-COOH) groups of fatty acids and the (-OH) gorups of the glycerol can be broken down under basic conditions known as saponification
56
Q

what are phospholipids?

A
  • replacing one of the fatty acid chaine with a polar phosphate group, which itself can also be modified
  • most well known for being the major components of the lipid bilayer of the plasma membrane in eukaryotic cells
57
Q

what are sphingolipids?

A
  • based on a molecule known as sphingosine and all have a fatty acid residue bonded to the amine group of sphingosine
    • the simplest shingolipids are known as ceramides
58
Q

what are waxes?

A
  • complicated naturally occuring mixtures of lipids that include fatty acid, long-chain alcohold, aromatic compounds, and other functional groups
  • secreted by plants and animals and are solid at room temperature
59
Q

what is the characteristic structure of cholesterol and its derivatives?

A
  • four-ring structure
60
Q

what is the function of cholesterol?

A
  • plays a role in the formation of atherosclerotic plaques, it is also an essential component of lige, as it contributes to the fluidity of the plasma membrane and serves as the precurosr for steroid hormones and other biologically essential molecules such as vitamin D
61
Q

what are eicosanoids?

A
  • a very broad family of signalling molecules, the most imortant subclass of which are prostaglandins
62
Q

what are prostaglandins?

A
  • are syntehsized from arachidonic acid and have 20 carbons and a five-carbon ring
  • they have many effects like the regulation of inflammation
    • some are pro-inflammatory and some are anti-inflammatory
63
Q

what are terpenes and terpenoids?

A
  • terpenes are hydrocarbons composed of repeating isoprene units (C5H8) and terpenoids are terpenes that are modified with other organic subtituents
    • terpenes are produced by many plants and have many functions
  • vitamin A is a terpene derivative
  • squalene is a precursor of cholesterol, steroid hormones and vitamin D
64
Q

what other vitamins are lipids as well other than vitamin A and D?

A
  • E and K
65
Q

What are carbohydrates?

A
  • a major source of energy and have a general formula of Cx(H2O)y
66
Q

In eukaryotes, carbohydrates occur in their?

A

D-isomers

67
Q

What is glucose?

A
  • type: alsohexose
  • main source of fuel for the organism
68
Q

what is fructose?

A
  • type- ketohexose
  • produced by many plants/fruits, commonly used as a sweetner
69
Q

what is galactose?

A
  • aldohexose
  • found in dairy products and sugar beets; cen be rapidly converted to glucose
70
Q

what is sucrose?

A
  • a disaccharide
  • glucose + fructose
  • table sugar
71
Q

what is lactose?

A
  • disaccharide
  • glucose + galactose
  • lactose intolerance depends on continued expression of lactase
72
Q

what is maltose?

A
  • disaccharide
  • glucose + glucose
  • found in beer, cereal, pasta, etc. produced by the breakdown of starch
73
Q

what is amylose?

A
  • a polysaccharide
  • linear chains of glucose linked by alpha(1-4) glycosidic bonds
  • a major component of starch (20-30%) but less easily digested than amylopectin
74
Q

what is amylopectin?

A
  • polysaccharide
  • linear chains of glucose linked by alpha(1-4) glycosidic bonds + branching due to alpha(1-6) glycosidic bonds every 24-30 units
  • comprises approximately 70-80% of starch; broken down more easily than amylose
75
Q

what is glycogen?

A
  • polysaccharide
  • linear chains of glucose linked by alpha(1-4) glycosidic bonds + branching due to due to alpha(1-6) glycosidic bonds every 8-12 units)
  • synthesized in liver and stored there or in muscle cells
76
Q

what is starch?

A
  • amylose and amylopectin
77
Q

what is cellulose?

A
  • linear chain of glucose units linked by bets(1-4) bonds
  • produced by many plants
  • not digestable by humans “fiber”
78
Q

What are nucleic acids?

A
  • involved in the storage and transmission of biological information
    • made up of nucleotides which have 3 components: a nitrogenous base, a 5 carbon sugar, and a phosphate group
    • “nucleoside” which have 2 components: a nitrogenous base, a 5 carbon sugar
79
Q

what are the nitrogenous bases?

A
  • adenine- purine
  • cytosine- pyrimidine
  • guanine- purine
  • thymine- pyrimidine
  • uracil- pyrimidine
80
Q

Nucleic acids are chained together by?

A
  • a sugar-phosphate backbone, connected by phosphodiester linkages

MCAT biology (12 decks)

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