BioChem Flashcards

1
Q

What amino acids are chiral/optically active/rotate plane polarized light?

A

All EXCEPT Glycine (Gly, G)

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2
Q

What amino acids are (S) configuration?

A

All EXCEPT Cysteine (Cys, C)

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3
Q

K38A means what?

A

Lysine (Lys, K) at position 38 is mutated to Alanine (Ala, A)

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4
Q

What is the average weight on an amino acid?

A

110 Da

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5
Q

Amino acids are ampho..?

A

Amphoteric: react as both acid and base, can gain protons under acidic conditions and lose protons under basic conditions

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6
Q

When pH < pKa…?

A

Protonated

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7
Q

When pH > pKa…?

A

Deprotonated

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8
Q

What is the pKa of carboxyl group?

A

~2

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9
Q

What is the pKa of amino group?

A

~9-10

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10
Q

What is a zwitterion?

A

A neutrally charged molecule by way of (+) and (-) charges offsetting each other

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11
Q

What is the pH and pKa relationship in a buffer?

A

pH approximately equals pKa +/- 1

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12
Q

What is a peptide bond and how is it formed/broken?

A

Peptide bond is an amide/covalent bond b/w a carboxyl and amino group that has partial double bond character through resonance (also means less rotation)

It is formed by dehydration/condensation (removing H2O) and broken by hydrolysis (adding H2O)

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13
Q

What is primary protein structure?

A

Amino acid sequence that runs from N-terminus to C-terminus

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14
Q

What is secondary protein structure?

A

The alpha-helices or beta-pleated-sheets that are formed by hydrogen bonding b/w amide protons and carbonyl oxygen

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15
Q

What is the role of Proline (Pro, P) in protein structure?

A

It destabilizes alpha-helices but is found in beta-pleated-sheet turns (which are rigid loops)

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16
Q

What is tertiary protein structure?

A

The 3D shape of a protein determined by hydrophobic groups sequestered inside and hydrophilic groups on the surface (that folding is b/c of increased entropy)

Formed by disulfide bonds b/w Cysteine (Cys, C) residues, formed by oxidation, broken by reduction

Also formed by salt bridges and hydrogen bonds

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17
Q

What is protein quaternary structure?

A

Found only in proteins w/ multiple subunits/chains like hemoglobin

Usually exhibit cooperative/allosteric effects

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18
Q

What is denaturation?

A

The unfolding of a protein’s 3D structure which results in inactivation of the protein

By: temperature, pH, and salinity (increase salt can disrupt bonds)

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19
Q

What are features of enzymes?

A
  • lower Ea with no change in deltaG (increase rate without affecting equilibrium)
  • specificity to substrate
  • not consumed by reaction
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20
Q

Ligase function?

A

In synthesis reactions

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21
Q

Isomerase function?

A

In bond rearragement

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22
Q

Lyase function?

A

In single molecular cleavage into two products

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23
Q

Hydrolase function?

A

Cleavage by hydrolysis or addition of H2O

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24
Q

Protease function?

A

Protein cleavage by hydrolysis

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25
Oxidoreductase function?
In redox reactions
26
Transferase function?
Movement of a functional from one molecule to another
27
How do enzymes work?
1) create favorable microenvironment in charge/pH 2) stabilize transition state 3) bring reactants in close position in active site
28
What is the induced fit model?
Enzyme active site adjusts shape to conform to substrate transition state (stabilizing it) NOT active site is lock and substrate is key that fit together
29
What is a cofactor/coenzyme?
Nonprotein molecules that aid in catalysis (for example vitamins)
30
What is the Michaelis-Menten equation? constant? Vmax equation? Catalytic efficiency equation? Shape of curve?
Vo = Vmax[S] / Km + [S] Km = [S] at half maximal velocity Vmax = [E]Kcat Kcat = turnover number and is directly proportional to Vmax Efficiency = Kcat / Km ABOUT INTIAL STATE HYPERBOLIC SHAPED CURVE
31
What is cooperativity? Hill coefficient? Shape of curve?
When there are multiple subunits/active sites and the binding of one increases the affinity for future bindings Hill coefficient = 1, no cooperativity (hyperbolic) <1, negative cooperativity (hyperbolic) >1, positive cooperativity (sigmoidal)
32
What is Lineweaver-Burk plot?
Double reciprocal Y-axis: 1/V Down shift means increase in Vmax X-axis: 1/[S] Right shift means increase in Km Y-intercept: 1/Vmax X-intercept: -1/Km Slope: Km/Vmax
33
``` What is reversible inhibition? Competitive? Non-competitive? Uncompetitive? Mixed? ```
Non-covalent binding and faster inhibition Competitive: Inhibitor competes for active site resulting in no change in Vmax, increase in Km, lines intersect on y-axis Non-competitive: Inhibitor binds to an allosteric site resulting in decrease in Vmax, no change in Km, lines intersect on x-axis Uncompetitive: Inhibitor binds to ES complex only resulting in decrease in Vmax and Km, lines are parallel each other Mixed: Inhibitor binds to allosteric site of ES complex
34
What is irreversible inhibition?
Covalent binding of inhibitor to enzyme and results in slower inhibition because covalent bonds take longer to form
35
GPCR functionality?
Gs: activation of AC increases cAMP Gi: activation of AC inhibits cAMP Gq: activation of PLC increases PIP2 which increases DAG +IP3 which increases Ca GTP: active GDP: inactive GTP is hydrolyzed to GDP GDP exchange results in GTP
36
What is gel electrophoresis/PAGE?
Separates proteins based on size and electrical charge Anode (is +) and attracts negative charges Cathode (is -) and attracts positives charges Smaller particles travel faster and larger particles travel slower
37
What is SDS PAGE?
Separates proteins on mass alone b/c SDS breaks all non-covalent bonds and (-) charges all chains DOES NOT BREAK DISULFIDE (COVALENT) BONDS, DTT DOES THAT
38
What is isoelectric focusing?
Separates proteins by pI using a pH gradient so once a protein reaches a pH=pI then it is no longer charged so stops moving increased pI = basic decreased pI = acidic
39
What is X-ray crystalloghraphy?
Measures electron density, 3D structure
40
What is a non-reducing sugar?
Sucrose
41
How are carbohydrates bonded together?
By glycosidic linkages (covalent bond) between OH groups
42
What are the different glycosidic linkages?
alpha-1,4: in human starch, non-branching (main glycogen synthase line creates this) alpha-1,6: highly branched (glycogen) beta-1,4: plant cellulose, indigestible by humans, non-branching beta-1,6: highly branched Branching = more soluble, more storage/energy efficient
43
What are lipids soluble in?
Non-polar organic solvents, NOT soluble in water
44
What are the structural lipids? Impact on fluidity?
Phospholipid: An amphipathic structural lipid with a polar head group (alcohol + phosphate) and a fatty acid tail (hydrophobic hydrocarbon chain) Sphingolipid: long saturated fatty acid tails that decrease fluidity (versus short unsaturated fatty acid tails increase fluidity as it prevents phospholipids from clustering)
45
Saturated vs. unsaturated fatty acid?
Saturated: all single bonds, stable, solid at room temp. Unsaturated: at least one double bond which can be cis or trans (cis = kinks), not solid at room temp.
46
What are the signaling lipids?
Terpenes, steroids, prostaglandins, fat-soluble vitamins Steroids: four ringed cholesterol derivative - cholesterol has chicken wire structure - cholesterol maintains membrane fluidity Prostaglandins: arachidonic acid derivative, inflammatory response ``` Fat-Soluble Vitamins: A: vision, growth/development, immune functions D: calcium and phosphorus E: anti-oxidant K: clotting factor ```
47
What are the energy storage lipids?
TAG/Triacylglycerides, three fatty tails bonded to glycerol by ester linkages, nonpolar/hydrophobic
48
How does saponification work?
Emulsifiers (soap, bile) are amphipathic so have hydrophobic and hydrophilic functionalities that form fatty acids into micelles so hydrophilic is exposed and dissolvable Surfactants: lower surface tension
49
What does fatty acid synthesis need?
CoA and NADPH
50
Nucleoside vs. nucleotide?
Nucleoside: pentose bonded to a nitrogenous base Nucleotide: phosphate group + nucleoside (this is building block of DNA)
51
How is DNA held together? What influences stability?
Sugar-phosphate backbone: phosphodiester bonds between 3' carbon and 5' sugar linked by phosphate group Length: longer more stable pH: extremes can disrupt h-bonding Salinity: more salt more stable
52
Purines vs. pyrimidines?
Purines: PUAG -- two ringed - Adenine: no C=O bond - Guanine: has C=O bond (2 donors, 1 acceptor for h-bonds) Pyrimidines: CUT -- single ringed - Cytosine: no NH group (1 donor, 2 acceptor) - Uracil - Thymine: has NH group Both are aromatic: cyclic, planar, conjugated (double bonds), 4n+2 pi electrons
53
What is the structure of DNA/Watson-Crick?
Two anti-parallel linear DNA chains wound together in a helix with nitrogenous bases inside and sugar-phosphate backbone outside AT: two h-bonds GC: three h-bonds
54
How many human chromosomes are there?
46 total
55
How is DNA organized?
Histones: DNA wraps (-) around histones (+) Heterochromatin vs. Euchromatin - hetero: tight/compact, less transcribed, repetitive sequence GC -eu: more open and actively transcribed Telomeres: repeating sequence at end of DNA (prevents unraveling) that shortens during every round of replication, telomerase re-adds telomeres Centromere: the center DNA of a chromosome
56
How is DNA replicated?
It is semi-conservative: one parent strand in each daughter strand (gen 0: all parental, gen 1: both contain a parental, gen 2: 50% contain a parental, gen 3: 12.5%) 1) strand separation - helicase unwinds DNA - SSBP's bind to unwounded ends to prevent re- annealing and degradation - topoisomerase prevents supercoiling 2) synthesis of daughter strands - DNA polymerase reads 3'-5' and synthesizes new strand 5'-3' (needs primer) - leading strand is synthesized continuously, but lagging strand is by okazaki fragments that DNA ligase connects
57
Oncogene vs. proto-oncogene?
Oncogene: cancerous Proto-oncogene: normal tumor suppressor: p53, Rb - need accumulated mutations to result in loss of tumor suppression
58
What is hybridization?
Complementary base pairing - only in anti-parallel strands In parallel strands the base pairs are the same ( A and A instead of A and T)
59
What is PCR?
Amplifies DNA regions between known primers (high in GC content) using temp. resistant Taq polymerase in a series of heating (denature), replication, and cooling (re-anneal) steps
60
What is western blot? southern blot? northern blot?
Western = protein Southern: DNA Northern: RNA
61
What is the central dogma?
DNA-->RNA-->Protein 1) Transcription 2) Translation
62
What is mRNA? Location? Role? Euks vs. Proks?
Transcribed in the nucleus from DNA then exported out to the cytoplasm and translated to proteins in ribosomes Euks: one mRNA = one protein
63
What is tRNA?
Carries amino acid that matches mRNA codon for translation
64
What is a codon? Features? Start? Stop?
Three letter sequence that corresponds to an amino acid Codons are unambiguous: every codon codes for a specific amino acid, and degenerate: multiple codons can code for the same amino acid b/c of third base wobble Start: AUG (methionine) Stop: UAA, UGA, UAG (also called amber codon) ORF: b/w the start and stop codons
65
What is transcription? Mechanism? PTM's?
DNA --> mRNA that happens in the nucleus 1) helicase unwinds DNA strand 2) topoisomerase stabilizes ends 3) RNA polymerase locates the promoter region (TATA box) and binds with help of transcription factors, no need for primer 4) reads DNA 3'-5' to synthesize mRNA 5'-3' Thymine --> Uracil PTM's: 1) excision of introns (non-coding regions) and ligation of exons (coding regions) 2) alternative splicing of exons can happen so one gene can code for multiple proteins 3) 5' cap and 3' poly-A tail that help stabilize mRNA and prevent degradation
66
What is translation? Mechanism? PTM's?
mRNA --> protein that happens in ribosomes Ribosome structure: A, P, E site and euk ribosomes are bigger than prok ribosomes 1) initiation: tRNA binds AUG in P-site, IF's help bind ribosome together, euks: 5' cap, proks: shine-dalgarno sequence 2) elongation: A-site: holds tRNA/amino acid, P-site: peptide bond formation, E-site: tRNA exits 3) termination: stop codon in A site recruits RF's, polypeptide is released from P-site, ribosome dissociates PTM's: chaperone proteins help polypeptide fold into protein or cleavage into final protein, phosphorylation/glycosylation--cell signalling and recognition etc. (happens in endomembrane system)
67
How is gene expression controlled in proks? Examples?
Operons: a cluster of genes on a single mRNA w/ one promoter (so multiple things controlled by one) Inducible: lac operon, positive control, inducer binds repressor so it falls off Repressible: trp operon, negative control, corepressor binds repressor to activate it
68
How is gene expression controlled in euks? Chromatin structure?
Transcription factors, enhancers that upregulate/amplify expression Chromatin structure can be regulated by acetylation: promotes euchromatin, weakens (+) charge on histones so DNA wrap less around it and more open, methylation: promotes heterochromatin, closed and silenced genes
69
What is the structure of the plasma membrane? Function? What can cross?
A phospholipid bi-layer with: - lipid rafts: high cholesterol, receptors, proteins For compartmentalization, separate interior and exterior environment Fat-soluble, nonpolar can cross Water-soluble, polar, cannot cross
70
What are the different type of membrane bound proteins?
Transmembrane: cross through membrane completely (associated with hydrophobic residues), so are on both sides Embedded: inside phospholipid bi-layer (channel proteins) Peripheral: bound to other proteins Integral: anything associated with the inside of the membrane (transmembrane and embedded)
71
What are the different cell-cell junctions?
Gap junctions: direct cell-cell communication (cardiac tissue) Tight junctions: physical link b/w cells so prevents leaking Desmosomes: anchors cytoskeletons
72
What is passive transport? Types?
No use of ATP and uses concentration gradient instead Simple: just moves down concentration gradient and diffuses through membrane Facilitated: requires a channel/carrier for molecules impermeable to membrane Osmosis: special type for water
73
What is active transport? Types?
Uses ATP to go against concentration gradient Primary: pumps Secondary: coupled transport using the gradient created to move something (antiport: opposite direction, symport: same direction) Endocytosis: big group of stuff into cell by engulfing membrane Exocytosis: release stuff to outside
74
What is glycolysis? Where? What enzymes? Regulation?
Glucose --> 2 pyruvate (3 carbon) + net 2 ATP and NADH happens in the cytoplasm Gluco/hexokinase: glucose --> G6P, irreversible (gluco: in liver) PFK-1: F6P --> F 1,6BP, RDS and irreversible PKF-2: F6P --> F 2,6BP G3P Dehydrogenase: G3P --> 1,3 BPG and NAD+ --> NADH 3PG Kinase: 1,3 BPG --> 3PG, generates ATP Pyruvate Kinase: PEP --> pyruvate, generates ATP, irreversible Upregulated: ADP, insulin, F 2,6BP Downregulated: ATP, glucagon, citrate
75
What is fermentation? When? Where?
Pyruvate--> lactate and NADH--> NAD+ RDS: Lactate dehydrogenase Happens in the absence of oxygen and mostly in muscles
76
What is gluconeogenesis? Where? What enzymes? Regulation? Cori Cycle? Starting material?
Opposite of glycolysis, forms glucose in the cytoplasm Starting material: lactate, pyruvate, oxaloacetate, glycerol, amino acids Irreversible steps in glycolysis are bypassed by using different enzymes Cori Cycle: connects glycolysis in the muscle and gluconeogenesis in the liver (through lactate) Regulation is just the opposite of glycolysis with the addition of epi/norepi, cortisol upregulating gluconeogenesis
77
What is pentose phosphate pathway?
Responsible for biosynthesis of NADPH and ribose in the cytoplasm from G6P Phosphogluconate
78
What are the different ways Acetyl-CoA is formed? How many C's?
Pyruvate dehydrogenase: pyruvate --> acetyl-CoA - connects glycolysis to TCA cycle in mitochondria - lipoic acid is a co-factor FA beta-oxidation: breaks down FA's to acetyl-CoA in mitochondria, RDS: CPT-1 (acylcarnitine) VERSUS FA synthesis in the cytosol Amino acid catabolism: ketone bodies --> acetyl-CoA Alcohol dehydrogenase: forms acetyl-CoA but also build up NADH so TCA doesn't happen, instead FA synthesis does 2C in Acetyl-CoA
79
What is the TCA cycle? Where? What steps? Regulation?
Acetyl-CoA generates GTP, NADH, FADH2 in the mitochondria citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate (+): ADP, NAD+ (-): ATP, NADH The reducing equivalents generated are used in the ETC
80
What is the ETC? Where? What complexes? Role of O?
Series of electron transfers increasing in reduction potential to O while also pumping protons from matrix to intermembrane space to create a gradient that is coupled to ATP synthesis Complex I: uses NADH to reduce Q (uniquinone)--> QH2 (ubiquinol) and pump protons out Complex II: coupled to succinate --> fumarate in TCA cycle where the FADH2 is used to reduce Q--> QH2 Complex III: the QH2's from I and II reduce cytochrome c in two steps (cyt-c can only carry 1 electron while Q can carry two) and pump protons out Complex IV: cyt-c reduces O to H2O and pump protons out ETC requires O (final electron acceptor) to function, if no O then reducing equivalents will buildup and inhibit TCA cycle
81
What is oxidative phosphorylation?
ADP + Pi --> ATP by ATP synthase The energy is taken from the proton motive force/electrochemical gradient formed, when protons move back down concentration gradient it spins ATP synthase F0: interacts with H+ gradient F1: turbine Generates heat as well, thermogenesis
82
How are lipids transported?
TAGS and cholesterol are transported as lipoproteins - HDL - LDL: delivery to cells - IDL - LDL - VLDL - Chylomicrons Named by their density %protein so VLDL/Chylomicron have little protein and transport a lot of TAG/cholesterol whereas HDL has a lot of protein and recovers excess cholesterol
83
What reactions are protein catabolism associated with?
Transaminations
84
What is ubiquitination?
Signals protein degradation by the proteasome
85
What are ketone bodies? When are they used?
Formed from acetyl-CoA They are used as energy sources in starvation
86
What are the hydrolyzable lipids? Non-hydrolyzable lipids?
Hydrolyzable: - TAGs - phospholipids - sphingolipids - waxes Non-hydrolyzable: signaling - steroids - prostaglandins - vitamins All lipids are emuslified
87
What are proenzymes/zymogens?
They inactive enzymes that require cleavage (proteolysis) as a post-translational modification to be active
88
Glycogen synthesis vs. glycogen lysis
Synthesis: glycogen synthase Lysis: glycogen phosporylase
89
What is galactose?
A C-4 epimer of glucose, six carbon aldose
90
What is a ternary complex?
An enzyme + two substrate bound
91
Is the unfolding of proteins cooperative?
Yes
92
What is a homodimer?
A dimer (two subunits) where both subunits are the same MW So one band would appear in electrophoresis/