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Biochemistry Flashcards

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1
Q

Stereochemistry of Amino Acids

A

All L in eukaryotes, All chiral are S, except cysteine is R and all amino acids have chiral center except glycine

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2
Q

Amphoteric

A

Amino acids can act as a base or an acid

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3
Q

Formation of Peptide Bonds

A

Forming a peptide bond is a dehydration reaction. The nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid.

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4
Q

How is a 3 Protein Structure stabilized?

A

With hydrophobic interactions; it pushes hydrophobic R groups to the interior or a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free
energy.

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5
Q

Prosthetic Group

A

The attached molecule in a conjugated protein. Can
be a metal ion, vitamin, lipid, carbohydrate, or
nucleic acid

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6
Q

6 Types of Enzymes

A
  • Oxidoreductases: REDOX reactions that involve the transfer of e-
  • Transferases: Move a functional group from one molecule to another.
  • Hydrolases: Catalyze cleavage with the addition of H2O.
  • Lyases: Catalyze cleavage without the addition of H2O andwithout the transfer of e-
  • Isomerases: Catalyze to create an isomer
  • Ligases: Join two large biomolecules, often of the same type.
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7
Q

Lipases

A

Catalyze the hydrolysis of fats. Dietary fats are broken down into fatty acids and glycerol or other alcohols.

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8
Q

Kinases

A

ADD a phosphate group. A type of transferase

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9
Q

Phosphatases

A

REMOVE a phosphate group. A type of transferase

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10
Q

Phosphorylases

A

Introduces a phosphate group into an organic molecule, notably glucose

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11
Q

Cooperative Enzymes

A

Display a sigmoidal curve because of the change in activity with substrate binding.

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12
Q

Cofactors

A

Metal cation that is required by some enzymes.

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13
Q

Coenzyme

A

Organic molecule that is required by some enzymes.

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14
Q

Feedback Inhibition

A

An enzyme is inhibited by high levels of a product from later in the same pathway.

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15
Q

Reversible Inhibition

A

The ability to replace the inhibitor with a compound of greater affinity or to remove it using mild laboratory treatment.

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16
Q

Competitive Inhibition

A

When the inhibitor is similar to the substrate and binds at the active site, blocking the substrate from binding. Can be overcome by adding more substrate.
Vmax is unchanged, Km increases.

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17
Q

Uncompetitive Inhibition

A

When the inhibitor binds only with the enzyme-

substrate complex. Vmax and Km both decrease.

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18
Q

Noncompetitive Inhibition

A

When the inhibitor binds with equal affinity to the

enzyme and the enzyme-substrate complex. Vmax decreases, Km is unchanged.

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19
Q

Mixed Inhibition

A

When the inhibitor binds with unequal affinity to the enzyme and the enzyme-complex. Vmax decreases, Km is increased or decreased depending on if the
inhibitor has a higher affinity for the enzyme or
enzyme-substrate complex.

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20
Q

Irreversible Inhibition

A

Alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently.

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21
Q

Suicide Inhibitor

A

A substrate analogue that binds IRREVSERIBLY to the

active site via a covalent bond.

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22
Q

Allosteric Effector

A

Binds at the allosteric site and induces a change in the conformation of the enzyme so the substrate can no longer bind to the active site. Displays cooperativity, so it does not obey Michaelis-Menten kinetics.

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23
Q

Homotropic Effector

A

An allosteric regulator that IS ALSO the substrate. Ex: O2 is a homotropic allosteric regulator of hemoglobin.

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24
Q

Heterotropic Effector

A

An allosteric regulator molecule that is DIFFERENT from the substrate.

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25
Phosphorylation
Covalent modification with phosphate. Catabolism: Phosphorylated = active Anabolism: Phosphorylated = inactive
26
Glycosylation
Covalent modification with carbohydrate.
27
Zymogens
Precursor to an enzyme. Secreted in an inactive form and are activated by cleavage.
28
Structural Proteins
The most common | structural proteins are collagen, elastin, keratin, actin, and tubulin. They are generally fibrous in nature.
29
Motor Proteins
myosin, kinesin, and dynein
30
Electrophoresis
Uses a gel matrix to observe the migration of proteins in responses to an electric field
31
Native PAGE
Maintains the protein’s shape, but results are difficult to compare because the mass / charge ratio differs for each protein.
32
SDS-PAGE
Denatures the proteins and masks the native charge so that comparison of size is more accurate, but functional protein cannot be recaptured from the gel.
33
Isoelectric Focusing
Separates proteins by their isoelectric point (pI); the protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein.
34
Chromatography
Separates protein mixtures on the basis of their affinity for a stationary phase or a mobile phase.
35
Column Chromatography
Uses beads of a polar compound (stationary phase) with a nonpolar solvent (mobile phase).
36
Ion-Exchange Chromatography
Uses a charged column and a variably saline eluent.
37
Size-Exclusion Chromatography
Relies on porous beads. Larger molecules elute first because they are not trapped in the small pores.
38
Affinity Chromatography
Uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest.
39
Carbohydrates have what configuration?
D- Configuration
40
Types of Diasteromers
- Epimers: Subtype of diastereomers that differ at exactly one chiral carbon. - Anomers: A subtype of epimers that differ at the anomeric carbon.
41
Monosaccharides can go through what kind of reactions? | Glucose, fructose and galactose
Can undergo | oxidation/reduction, esterification, and glycoside formation
42
Deoxy Sugars
-H replaces –OH
43
Glycoside Formation
The basis for building complex carbohydrates and requires the anomeric carbon to link to another sugar
44
Disaccharides
Form as a result of glycosidic bonding between two monosaccharide subunits. Common examples: sucrose (glucose + fructose), lactose (galactose + glucose with beta) , maltose (glucose + glucose with alpha) .
45
Starches
Amylose: Unbranched Amylopectin: Branched
46
Amphipathic
having both hydrophilic and hydrophobic pa
47
Phospholipids have what kind of attachment to the head?
phosphodiester linkage
48
Waxes
Contain long-chain fatty acids esterified to long- | chain alcohols. Used as protection against evaporation and parasites in plants and animals.
49
Steroids
Contain 3 cyclohexane rings and 1 cyclopentane; Have high-affinity receptors, work at low concentrations, and affect gene expression and metabolism.
50
Prostaglandins
Are autocrine and paracrine signaling molecules that | regulate cAMP levels. Affect smooth muscle contraction, body temp, sleep-wake cycle, fever, pain.
51
Fat Soluble Vitamins
Vitamin A: Carotene, vision. Vitamin D: Cholecalciferol, bone formation. Vitamin E: Tocopherols, antioxidants. Vitamin K: Phylloquinone & menaquinones. Forms prothrombin, a clotting factor.
52
Triacylglycerols
Storage form of fatty acids. Contain 1 glycerol attached to 3 fatty acids by ester bonds. Very hydrophobic so do not carry additional water weight
53
Adipocytes
Animal cells used specifically for storage of large | triacylglycerol deposits
54
Free Fatty Acids
Unesterified fatty acids that travel in the bloodstream. Salts of free fatty acids are soaps.
55
Saponification
The ester hydrolysis of triacylglycerols using a strong base like sodium or KOH.
56
Micelle
Can dissolve a lipid-soluble molecule in its fatty acid core, and washes away with water because of its shell of carboxylate head groups.
57
RNA 2° structure has 4 basic elements
Loops, helices, bulges, | and junctions.
58
Nucleoside
5-carbon sugar + nitrogenous base. NO PHOSPHATE groups.
59
Nitrogenous Bases
- Purines: Adenine and Guanine. Made of two rings. | - Pyrimidines: Cytosine, Thymine, Uracil. Made of one ring.
60
B-DNA vs Z-DNA
Most DNA is B-DNA, forming a right-handed helix. Low concentrations of Z-DNA, with a zigzag shape, may be seen with high GC-content or high salt concentration
61
DNA Replication
- Topoisomerase: Unwinds the DNA double helix. - Helicase: Breaks the hydrogen bonds between the nitrogenous bases in order to separate the DNA strands. - Single Strand Binding Protein: (SSB). Binds to ssDNA and prevents annealing of ssDNA into double-stranded DNA. - DNA Primase: Catalyzes the synthesis of the RNA primer. - RNA Primers: Short RNA nucleotide sequences that are complementary to the ssDNA. They allow DNA replication to start. - DNA Polymerase: Adds nucleotides to the growing strand. It reads the template 3’ ® 5’ and synthesize the new strand 5’ ® 3’. DNA Polymerase also removes the RNA primer at the end of the strand. There are many varieties of DNA polymerase. - Okazaki Fragment: Short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication. - DNA Ligase: Joins DNA strands together by catalyzing the formation of phosphodiester bonds.
62
Proofreading
DNA Polymerase proofreads its work and excises | incorrectly matched bases. The daughter strand is identified by its lack of methylation and corrected accordingly.
63
Mismatch Repair
Occurs during G2 phase using the genes MSH2 and MLH1.
64
Chromatin
- Heterochromatin: Dark, dense, and silent - Euchromatin: Light, uncondensed, and expressed (HAT) - DNA is wound around histone proteins to form nucleosomes, which may be stabilized by another histone protein. As a whole, DNA and its associated histones make up chromatin in the nucleus.
65
Acrocentric Chromosome
When the centromere is located near one end of the | chromosome and not in the middle.
66
Hybridization
The joining of complementary base pair sequences
67
Degenerate Code
Allows for multiple codons to encode for the same amino acid.
68
Start / Stop Codons
Initiation (start): AUG | Termination (stop): UAA, UGA, UAG
69
Wobble
3rd base in the codon. Allows for mutations to occur without effects in the protein. Wobble base pairings are less stable.
70
Exons vs Introns (Transcription)
Exons: Exit the nucleus and form mRNA. Introns: Spliced out so they stay in nucleus. Introns also enable alternative splicing.
71
Cholesterol
Is present in large amounts and contributes to membrane fluidity and stability low temp = INCREASE fluidity high ­temp = DECREASE fluidity
72
Desmosomes & Hemidesmosomes
Desmosomes bind adjacent cells by anchoring to their cytoskeletons. Hemidesmosomes are similar, but their main function is to attach epithelial cells to underlying structures
73
Secondary Active Transport
“Coupled transport”. Harnesses the energy released by one particle going down its electrochemical gradient to drive a different particle up its gradient. Symport: Both particles flow the same direction Antiport: The particles flow in opposite directions
74
GLUT-2
Found in liver (for glucose storage) and pancreatic b-islet | cells (as part of the glucose sensor). Has ­increased Km
75
GLUT- 4
Found in adipose tissue and muscle. Stimulated by insulin. | Has decrease Km
76
Glucogenic Amino Acids
Can be converted into glucose through gluconeogenesis. All but leucine and lysine.
77
Ketogenic Amino Acids
Can be converted into acetyl-CoA and ketone bodies. Leucine and lysine are the only amino acids that are solely ketogenic.
78
Fatty Acid Oxidation
Oxidation occurs in the mitochondria following transport by the carnitine shuttle. b-oxidation uses cycles of oxidation, hydration, oxidation, and thiolysis cleavage. The fatty acid chain is shortened by two carbon atoms. FADH2, NADH, and acetyl CoA are generated.

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