Biochemistry Flashcards

Question

Polyacrylamide gel electrophoresis (PAGE)

Answer 1

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

Answer 2

Can be used to break covalent disulfide bonds

Answer 3

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

Answer 4

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

Answer 5

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

Answer 6

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

Answer 7

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

Answer 8

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

Answer 9

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

Answer 10

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

Answer 11

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

Answer 12

Catalyze the interconversion of isomers, including both constitutional and stereoisomers

Answer 13

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

Answer 14

Catalyze cleavage with the addition of water

Answer 15

Catalyze oxidation-reduction reactions that involve the transfer of electrons

Answer 16

Move a functional group from one molecule to another

Answer 17

Cooperative enzymes show a sigmoidal curve

Answer 18

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

Answer 19

Sugars with aldehydes as their most oxidized group

Answer 20

Sugars with ketones as their most oxidized group

Answer 21

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

Answer 22

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

Answer 23

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

Answer 24

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

Answer 25

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

Answer 26

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

Answer 27

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

Answer 28

Amylose and amylopectin; main energy storage forms for plants

Answer 29

A major energy storage form for animals

Answer 30

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

Answer 31

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

Answer 32

- 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

Answer 33

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

Answer 34

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

Answer 35

Dense, transcriptionally silent DNA

Answer 36

Less dense, transcriptionally active DNA

Answer 37

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

Answer 38

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

Answer 39

DNA composed of nucleotides from two different sources

Answer 40

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

Answer 41

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

Answer 42

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

Answer 43

Pro: one per chromosome Euk: multiple per chromosome

Answer 44

Pro: helicase Euk: helicase

Answer 45

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

Answer 46

Pro: primase Euk: primase

Answer 47

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

Answer 48

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

Answer 49

Pro: DNA polymerase I Euk: DNA polymerase δ

Answer 50

Pro: DNA ligase Euk: DNA ligase

Answer 51

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

Answer 52

Pro: N/A Euk: Telomerase

Answer 53

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

Answer 54

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

Answer 55

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)

Answer 56

Southern - DNA Northern - RNA Western - proteins

Answer 57

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

Answer 58

DNA --> RNA --> proteins

Answer 59

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

Answer 60

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

Answer 61

- Substitution of a ribose sugar for deoxyribose - Substitution of uracil for thymine - Single-stranded instead of double

Answer 62

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

Answer 63

- 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

Answer 64

- 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

Answer 65

- 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

Answer 66

- Promoters are within 25 base pairs of the transcription start site - Enhancers are more than 25 base pairs away from the transcription start site

Answer 67

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

Answer 68

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

Answer 69

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

Answer 70

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

Answer 71

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

Answer 72

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

Answer 73

Ingestion of solid material

Answer 74

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

Answer 75

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

Answer 76

Rate-limiting step

Answer 77

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

Answer 78

Produces NADH

Answer 79

Perform substrate-level phosphorylation

Answer 80

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

Answer 81

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

Answer 82

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

Answer 83

- 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

Answer 84

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

Answer 85

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

Answer 86

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

Answer 87

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

Answer 88

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

Answer 89

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

Answer 90

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

Answer 91

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

Answer 92

- 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

Answer 93

- 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

Answer 94

Via chylomicrons, VLDL, IDL, LDL, and HDL

Answer 95

- 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