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MCAT Quicksheets > Biochemistry > Flashcards

Biochemistry Flashcards

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1
Q

Glycine

A

Gly, G
pKa: neutral
Group: small
Properties: not chiral; found in structural loops

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2
Q

Alanine

A

Ala, A
pKa: neutral
Group: polar

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3
Q

Serine

A

Ser, S
pKa: neutral
Group: polar
Properties: can form H-bonds; can be phosphorylated to introduce a negative charge

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4
Q

Threonine

A

Thr, T
pKa: neutral
Group: polar
Properties: can form H-bonds; can be phosphorylated to introduce a negative charge

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5
Q

Cysteine

A

Cys, C
pKa: slightly basic
Group: polar
Properties: forms disulfide bridges, important for 3 and 4 structure

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6
Q

Valine

A

Val, V
pKa: neutral
Group: nonpolar

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7
Q

Leucine

A

Leu, L
pKa: neutral
Group: nonpolar

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8
Q

Isoleucine

A

Ile, I
pKa: neutral
Group: nonpolar

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9
Q

Methionine

A

Met, M
pKa: neutral
Group: nonpolar
Properties: “start” amino acid (can also be found at other positions)

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10
Q

Proline

A

Pro, P
pKa: neutral
Group: nonpolar
Properties: the only cis-amino acid; side chain part of peptide bond; introduces kinks in α-helices; found in loops and turns

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11
Q

Phenylalanine

A

Phe, F
pKa: neutral
Group: nonpolar
Properties: aromatic

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12
Q

Tyrosine

A

Tyr, Y
pKa: neutral
Group: nonpolar
Properties: aromatic; can be phosphorylated to introduce a negative charge

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13
Q

Tryptophan

A

Trp, W
pKa: neutral
Group: nonpolar
Properties: aromatic

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14
Q

Aspartate

A

Asp, D
pKa: acidic
Group: negatively charged at physiological pH
Properties: side chain can form salt bridge

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15
Q

Glutamate

A

Glu, E
pKa: acidic
Group: negatively charged at physiological pH
Properties: side chain can form salt bridge

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16
Q

Asparagine

A

Asn, N
pKa: neutral
Group: polar
Properties: side chain can form H-bonds

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17
Q

Glutamine

A

Gln, Q
pKa: neutral
Group: polar
Properties: side chain can form H-bonds

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18
Q

Histidine

A

His, H
pKa: slightly acidic
Group: polar
Properties: aromatic; can be positively charged at acidic pH

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19
Q

Lysine

A

Lys, K
pKa: basic
Group: positively charged at physiological pH
Properties: side chain can form salt bridge; can be acetylated to mask the positive charge (important in DNA-protein interaction)

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20
Q

Arginine

A

Arg, R
pKa: basic
Group: positively charged
Properties: side chain can form salt bridge

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21
Q

Acid-base chemistry of AA

A
  • At low (acidic) pH: full protonated
  • When pH = pI: zwitterion
  • At high (basic) pH: full deprotonated
  • pI is determined by averaging the pKa values that refer to protonation and deprotonation of the zwitterion
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22
Q

Peptide bonds

A

Formation is a condensation (dehydration) rxn with a nucleophilic amino group attacking an electrophilic carbonyl; peptide bonds are broken by hydrolysis

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23
Q

Tertiary structure

A

3D structure stabilized by hydrophobic interactions, acid-base interactions (salt-bridges), H-bonding, and disulfide bonds

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24
Q

Quaternary structure

A

Interactions between subunits; heat and solutes can cause denaturation

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25
Q

Polyacrylamide gel electrophoresis (PAGE)

A

Proteins migrate through porous matrix according to size and charge; (1) native PAGE is used to analyze the protein in folded state (2) SDS-PAGE uses detergent to break all noncovalent interactions and analyzes the unfolded state

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26
Q

Reducing reagents

A

Can be used to break covalent disulfide bonds

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27
Q

Structural proteins

A

Generally fibrous; include collagen, elastin, keratin, actin, and tubulin

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28
Q

Motor proteins

A

Capable of force generation through a conformation change; include myosin, kinesin, and dynein

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29
Q

Cell adhesion molecules (CAM)

A

Bind cells to other cells or surfaces; include cadherins, integrins, and selectins

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30
Q

Enzyme-linked receptors

A

Participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades

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31
Q

G protein-coupled receptors

A

Have a membrane-bound protein associated with a trimeric G protein; they also initiate second messenger systems

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32
Q

Binding site, impact on Km, impact on Vmax

A

Competitive: active site, increases, no change
Noncompetitive: allosteric site, no change, decreases
Mixed: allosteric site, increases/decreases, decreases
Uncompetitive: enzyme-substrate complex, decreases, decreases

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33
Q

Saturation kinetics

A

As substrate concentration increases, the reaction rate also increases until a maximum value is reached
v = vmax [S] / km + [S]
- At one-half Vmax, [S] = Km

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34
Q

Lineweaver-Burk

A

kcat = vmax / [enzyme]
Catalytic efficiency = kcat / Km

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35
Q

Ligases

A

Responsible for joining two large biomolecules, often of the same type

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36
Q

Isomerases

A

Catalyze the interconversion of isomers, including both constitutional and stereoisomers

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37
Q

Lyases

A

Catalyze cleavage without the addition of water and without the transfer of electrons; the reverse reaction (synthesis) is usually more biologically important

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38
Q

Hydrolases

A

Catalyze cleavage with the addition of water

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39
Q

Oxidoreductases

A

Catalyze oxidation-reduction reactions that involve the transfer of electrons

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40
Q

Transferases

A

Move a functional group from one molecule to another

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41
Q

Michaelis-Menten

A

Cooperative enzymes show a sigmoidal curve

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42
Q

Enzymes

A

Like all catalysts, lower the activation energy necessary for rxns; they do not alter the free energy or enthalpy change that accompanies the rxn nor the final equilibrium position; rather, they change the kinetics (rate) at which equilibrium is reached

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43
Q

Aldoses

A

Sugars with aldehydes as their most oxidized group

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44
Q

Ketoses

A

Sugars with ketones as their most oxidized group

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45
Q

D vs. L sugars

A

Sugars with the highest-numbered chiral carbon with the -Oh group on the right are D-sugars; those with the -OH on the left are L-sugar; D- and L-forms of the same sugar are enantiomers

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46
Q

Diastereomers

A

Differ at least one - but not all - chiral carbons
Also include: (1) epimers differ at exactly one chiral carbon (2) anomers are a subtype of epimers that differ at the anomeric carbon

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47
Q

Anomeric carbon

A

The new chiral center formed in ring closure; it was the carbon-containing the carbonyl in the straight-chain form
- α-anomers have the -OH on the anomeric carbon trans to the free -CH2OH group
- β-anomers have the -OH on the anomeric carbon cis to the free -CH2OH group

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48
Q

Mutarotation

A

One anomeric form shifts to another, with the straight-chain form as an intermediate

49
Q

Monosaccharides

A

Single carbohydrate units and can undergo three main reactions: oxidation-reduction, esterification, and glycoside formation (the basis for building complex carbs and requires the anomeric carbon to link to another sugar)
- Sugars with an -H replacing an -Oh are termed deoxy sugars

50
Q

Disaccharides

A

Sucrose (glucose-α-1,2-fructose), lactose (galactose-β-1,4-glucose), and maltose (glucose-α-1,4-glucose)

51
Q

Cellulose

A

Main structural component of plant cell walls; main source of fiber in the human diet

52
Q

Starches

A

Amylose and amylopectin; main energy storage forms for plants

53
Q

Glycogen

A

A major energy storage form for animals

54
Q

Reducing sugars

A

Any sugar with an anomeric carbon not bound in a glycosidic bond will react with reagents like Tollens’ and Benedict’s

55
Q

Nucleotide vs nucleosides

A

Nucleosides contain a five-carbon sugar bonded to a nitrogenous base; nucleotides are nucleosides with one to three phosphate groups added; ATP is a high-energy nucleotide with an adenosine nucleoside

56
Q

Watson-Crick Model

A
  • DNA backbone is composed of alternating sugar and phosphate groups, and is always read 5’ to 3’
  • There are two strands with antiparallel polarity, wound into a double helix
  • A-T and A-U with two H-bonds
  • C-G with three H-bonds
57
Q

Chargaff’s rules

A

Purines and pyrimidines are equal in number in a DNA molecule; the amount of A equals T and vise versa

58
Q

Euk. chromosome organization

A

In euk, DNA is wound around histone proteins to form nucleosomes, which may be stabilized by another histone protein
- DNA and its associated histones make up chromatin in the nucleus

59
Q

Heterochromatin

A

Dense, transcriptionally silent DNA

60
Q

Euchromatin

A

Less dense, transcriptionally active DNA

61
Q

Telomeres

A

Are the ends of chromosomes; they contain high GC-content to prevent DNA unraveling

62
Q

Centromeres

A

Hold sister chromatids together until they are separated during anaphase in mitosis; they also contain a high GC-content

63
Q

Recombinant DNA

A

DNA composed of nucleotides from two different sources

64
Q

DNA cloning

A

Introduces a fragment of DNA into a vector plasmid; a restriction enzyme (restriction endonuclease) cuts both the plasmid and the fragment, leaving them with sticky ends, which can bind
- Restriction enzyme sites are often palindromic

65
Q

DNA replication

A

Is semiconservative: one old parent strand and one new daughter strand is incorporated into each of the two new DNA molecules

66
Q

DNA polymerase

A

Synthesizes new DNA strands, reading the template DNA 3’ to 5’ and synthesizing the new strand 5’ to 3’
- The leading strand requires only one primer and can then be synthesized continuously
- The lagging strand requires many primers and is synthesized is discrete sections called Okazaki fragments

67
Q

Origin of replication

A

Pro: one per chromosome
Euk: multiple per chromosome

68
Q

Unwinding of DNA double helix

A

Pro: helicase
Euk: helicase

69
Q

Stabilization of unwound template strands

A

Pro: single-stranded DNA-binding protein
Euk: single-stranded DNA-binding protein

70
Q

Synthesis of RNA primers

A

Pro: primase
Euk: primase

71
Q

Synthesis of DNA

A

Pro: DNA polymerase III
Euk: DNA polymerase α, δ, ε

72
Q

Removal of primers

A

Pro: DNA polymerase I (5’ - 3’ exonuclease)
Euk: RNase H (5’ - 3’ exonuclease)

73
Q

Replacement of RNA with DNA

A

Pro: DNA polymerase I
Euk: DNA polymerase δ

74
Q

Joining of Okazaki fragments

A

Pro: DNA ligase
Euk: DNA ligase

75
Q

Removal of positive supercoils ahead of advancing replication forks

A

Pro: DNA topoisomerases (DNA gyrase)
Euk: DNA topoisomerases

76
Q

Synthesis of telomeres

A

Pro: N/A
Euk: Telomerase

77
Q

Genomic libraries

A

Contain large fragments of DNA, including both coding and noncoding regions of the genome; they cannot be used to make recombinant proteins or for gene therapy

78
Q

cDNA libraries (expression libraries)

A

Are generated by reverse transcribing mRNA of sample tissue. The resulting DNA library only includes exons of expressed genes; they can be used to make recombinant proteins or for gene therapy

79
Q

PCR

A

An automated process by which millions of copies of a DNA sequence can be created from a very small sample by hybridization (the joining of complementary base pair sequences)

80
Q

SNOW DROP

A

Southern - DNA
Northern - RNA
Western - proteins

81
Q

Deoxyribonucleotides

A

Terminate the DNA chain because they lack a 3’ - OH group

82
Q

Central dogma

A

DNA –> RNA –> proteins

83
Q

Initiation and termination

A

Initiation: AUG (methionine)
Termination: UAA, UGA, UAG
- Redundancy and wobble (third base in the codon) allow mutations to occur without affecting the protein

84
Q

Point mutations

A

Silent: no effect on protein synthesis
Nonsense (truncation): produce a premature stop codon
Missense: produce a codon that codes for a different AA
Frameshift: result from nucleotide addition or deletion and change the reading frame of subsequent codons

85
Q

RNA is structurally similar to DNA except:

A
  • Substitution of a ribose sugar for deoxyribose
  • Substitution of uracil for thymine
  • Single-stranded instead of double
86
Q

Major types of RNA

A

mRNA: carries the message from DNA in the nucleus via transcription of the gene; travels into the cytoplasm to be translated
tRNA: brings in AA; recognizes the codon on the mRNA using its anticodon
rRNA: makes up much of the ribosome; enzymatically active

87
Q

Transcription steps

A
  • Helicase and topoisomerase unwind DNA double helix
  • RNA polymerase II binds to TATA box within promoter region of gene
  • hnRNA synthesized from DNA template (antisense) strand
88
Q

Posttranscriptional modifcations

A
  • 7-methylguanylate triphosphate cap added to 5’ end
  • Polyadenosyl (poly-A) tail added to 3’ end
  • Splicing done by spliceosome; introns removed and exons ligated together. Alternative splicing combines different exons to acquire different gene products
89
Q

Translation steps

A
  • Initiation, elongation, termination
  • Posttranslational modifications: (1) folding of chaperones (2) formation of quaternary structure (3) cleavage of proteins or signal sequences (4) covalent addition of other biomolecules
90
Q

Transcription factors

A
  • Promoters are within 25 base pairs of the transcription start site
  • Enhancers are more than 25 base pairs away from the transcription start site
91
Q

Operons (Jacon-Monod model)

A

Are inducible or repressible clusters of genes transcribed as a single mRNA

92
Q

Osmotic pressure

A

A colligative property, is the pressure applied to a pure solvent to prevent osmosis and is related to the concentration of the solution
∏ = iMRT

93
Q

Passive transport

A

Simple diffusion: does not require a transporter; small, nonpolar molecules passively move from an area of high concentration to an area of low concentration until equilibrium is achieved
Osmosis: diffusion of water across a selectively permeable membrane
Facilitated diffusion: uses transport proteins to move impermeable solutes across the cell membrane

94
Q

Active transport

A

Requires energy in the form of ATP (primary) or an existing favorable ion gradient (secondary); secondary active transport can be further classified as symport or antiport

95
Q

Endocytosis and exocytosis

A

Methods of engulfing material into cells or releasing material to the exterior of cells; both via the cell membrane

96
Q

Pinocytosis

A

Ingestion of liquid into the cell from vesicles formed from the cell membrane

97
Q

Phagocytosis

A

Ingestion of solid material

98
Q

Glucokinase

A

Present in liver and pancreatic β cells, responsive to insulin; phosphorylates glucose

99
Q

Hexokinase

A

Present in all tissue; phosphorylates glucose to trap it in cells

100
Q

Phosphofructokinase-1 (PFK-1)

A

Rate-limiting step

101
Q

Phosphofructokinase-2 (PFK-2)

A

Produces F2-6-BP, which activates PFK-1

102
Q

Glyceraldehyde-3-phosphate dehydrogenase

A

Produces NADH

103
Q

3-phosphoglycerate kinase and pyruvate kinase

A

Perform substrate-level phosphorylation

104
Q

The NADH produced in glycolysis:

A

Is oxidized aerobically by the mitochondrial electron transport chain and anaerobically by cytoplasmic lactate dehydrogenase

105
Q

Glycolysis

A

Occurs in the cytoplasm of all cells, and does not require O2; yields 2 ATP per glucose

106
Q

Pyruvate dehydrogenase

A

Converts pyruvate to acetyl-CoA; stimulated by insulin and inhibited by acetyl-CoA

107
Q

ETC

A
  • Takes place on the matrix-facing surface of the inner mitochondrial membrane
  • NADH donates e to the chain, which are passed from one complex to the next; reduction potentials increase down the chain, until the electrons end up on O2, which has the highest reduction potential
  • NADH cannot cross the inner membrane, so must use one of two shuttle mechanisms to transfer its e to energy carriers in the mitochondrial matrix: glycerol 3-phosphate shuttle or the malate-aspartate shuttle
108
Q

Oxidative phosphorylation

A

The proton-motive force is the electrochemical gradient generated by the ETC across the inner mitochondrial membrane; the intermembrane space has a higher concen. of protons than the matrix; this gradient stores energy, which can be used to form ATP via chemiosmotic coupling

109
Q

Summary of energy yield of carbohydrate metabolism processes:

A

Glycolysis: 2 NADH and 2 ATP
Pyruvate dehydrogenase: 1 NADH (2 NADH per molecule of glucose because each glucose forms two molecules of pyruvate)
CAC: 3 NADH, 1 FADH2, and 1 GTP (6 NADH, 2 FADH2, and 2 GTP per molecule of glucose)
- Each NADH: 2.5 ATP; 10 NADH form 25 ATP
- Each FADH2: 1.5 ATP
- GTP converted to ATP
= 32 ATP per molecule of glucose; 30-32 per molecule is the commonly accepted range

110
Q

ATP synthase

A

Enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi)

111
Q

Glycogenesis (glycogen synthesis)

A

The building of glycogen uses two main enzymes:
- Glycogen synthase, which creates α-1,4 glycosidic links between glucose molecules; it is activated by insulin in the liver and muscles
- Branching enzyme, which moves a block of oligoglucose from one chain and connects it as a branch using an α-1,6 glycosidic link

112
Q

Glycogenolysis

A

Breakdown of glycogen using two main enzymes:
- Glycogen phosphorylase, removes single glucose 1-phosphate molecules by breaking α-1,4 glycosidic links. In the liver, it is activated by glucagon to prevent low blood sugar. In exercising skeletal muscle, it is activated by epinephrine and AMP to provide glucose for the muscle itself
- Debranching enzyme, moves a block of oligoglucose from one branch and connects it to the chain using an α-1,4 glycosidic link

113
Q

Gluconeogenesis

A

Occurs in both the cytoplasm and mito; predominantly in the liver.
- Most is just reverse of glycolysis, using same enzymes

114
Q

Three irreversible steps of glycolysis must be bypassed by different enzymes:

A
  • Pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase
  • Fructose-1,6-bisphosphatase bypasses phosphofructokinase-1
  • Glucose-6-phosphatase bypasses hexokinase/glucokinase
115
Q

Pentose phosphate pathway

A

Occurs in the cytoplasm of most cells, generating NADPH and sugars for biosynthesis; rate-limiting enzyme is glucose-6-phosphate dehydrogenase, which is activated by NADP+ and insulin and inhibited by NADPH

116
Q

Metabolic states

A
  • Postprandial/well-fed (absorptive): insulin secretion is high and anabolic metabolism prevails
  • Postabsoptive (fasting): insulin secretion decreases while glucagon and catecholamine secretion increases
  • Prolonged fasting (starvation): dramatically increases glucagon and catecholamine secretion; most tissues rely on FAs
117
Q

Tissue-specific metabolism

A
  • Liver: maintains blood glucose through glycogenolysis and gluconeogenesis; processes lipids, cholesterol, bile, urea, and toxins
  • Adipose: stores and releases lipids
  • Resting muscle: conserves carbohydrates as glycogen and uses free FAs for fuel
  • Active muscle: may use anaerobic metabolism, oxidative phosphorylation, direct phosphorylation (creatine phosphate), or FA oxidation
  • Cardiac muscle: uses FA oxidation
  • Brain: uses glucose except in prolonged starvation, when it can use ketolysis
118
Q

Lipid transport

A

Via chylomicrons, VLDL, IDL, LDL, and HDL

119
Q

Cholesterol metabolism

A
  • Cholesterol may be obtained through dietary sources or through synthesis in the liver
  • The key enzyme in cholesterol biosynthesis is HMG-CoA
  • Palmitic acid, only FA that humans can synthesize
  • Fatty acid oxidation occurs in the mito. following transport by the carnitine shuttle, via β-oxidation
  • Ketone bodies form (ketogenesis) during a prolonged starvation state due to excess acetyl-CoA in the liver; ketolysis regenerates acetyl-CoA for use as an energy source in peripheral tissues

MCAT Quicksheets (6 decks)

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