1
Q
Isoelectric focusing
A
Separates proteins by their isoelectric point; the protein migrated toward an electrode until it reaches the region where pH= pI of the protein
2
Q
Chromatography
A
Separates protein mixtures based on their affinity for a stationary phase or a mobile phase
3
Q
Column chromatography
A
Uses bead of a polar compound (stationary phase) with a nonpolar solvent (mobile phase)
4
Q
Ion-exchange chromatography
A
Uses a charged column and a variably saline eluent
5
Q
Size exclusion chromatography
A
Relies on porous beads. Large molecules elute first because they aren’t trapped in the small pores
6
Q
Affinity chromatography
A
Uses a bound receptor or ligand and an eluent with free ligand or receptor for the protein or interest
7
Q
What techniques allow for the anyalsis of protein structure
A
X ray crystallography
NMR
8
Q
What techniques are used for the determination of concentration of protein
A
UV spec
Bradford assay (brown green to blue)
BCA Assay
Lowry reagent assay
9
Q
Beer-Lambert Law
A
Absorbance = eCl
Extinction coeff
Concentration
Path length
10
Q
3 carbon carb
A
Triose
11
Q
4 carbon carb
A
Tetrose
12
Q
To determine L and D of carb
A
Look at the highest numbered chiral carbon if OH is on the right it is D if OH on left it is L
Most carbs are D
13
Q
Diasteromer
A
Any stereoisomer that is not an enantiomer
14
Q
Epimer
A
Subtype of diastereomer that differs at exactly one chiral carbon
15
Q
Anomer
A
A subtype of epimer that differ at the anomeric carbon
16
Q
Anomeric carbon
A
The new chiral center formed in ring closure. Carbon containing the carbonyl is straight form
17
Q
Alpha anomers
A
Have the OH trans to the free CH2OH
18
Q
B anomers
A
Have the OH group cis to the free CH2OH group
19
Q
Haworth projections
A
Represent 3D structure of monosaccharide
20
Q
Mutarotation
A
Spontaneous shift from one Anomeric form to another with the straight chain form as an intermediate
21
Q
Monosaccharides
A
Single carb units with glucose as most commonly observed monomer. Can undergo oxidation/reduction, esterification, and glycoside formation
22
Q
Aldoses
A
Oxidized to aldonic acids, reduced to alditols
23
Q
Esterification
A
Sugars react with carboxylic acids and their derivatives forming esters
24
Q
Phosphorylation
A
A phosphate ester is formed by transferring a phosphate group from ATP onto the sugar.
25
Glycoside formation
Basis for building complex carbohydrates and requires the Anomeric carbon to link to another sugar
26
Disaccharides
Form as a result of glycosidic bonding between two monosaccharide subunits. Common examples include sucrose, lactose, maltose
27
Polysaccharides
Formed by repeating monosaccharide or polysaccharide glycosidic bonding
28
Cellulose
Main structural component of plant cell walls. Main source of fiber in human diet
29
Starches
Main energy storage form for plants
Amylose: branched
Amylopectin: unbranched
30
Characteristics of lipids
Soluble in nonpolar organic solvents
Insoluble in water
31
Phospholipids
Amphipathic and form the bilayer of membranes. Contain a hydrophilic (polar) head and and hydrophobic (nonpolar) tail. Head is attached by phosphodiester linkage, and determines the function of the phospholipid
32
Saturation of fatty acid tails determines
Fluidity of membrane
Saturated fatty acid= less fluid
33
Glycerophospholipids
Phospholipids that contain glycerol backbone
34
Sphingolipids
Contain sphingosine backbone. Many sphingolipid are also phospholipids with a phosphodiester bond these are sphingophospholipids
35
Sphingomyelin
Major class of spingophospholipids and contain a phosphatidylcholine or phosphatidylethanoalamine head group. Part of myelin sheath
36
Gangliosides
Contain oligosaccharides with at least 1 terminal N-acetylneuraminic acid
37
Waxes
Long-chain fatty acids esterfied to long chain alcohols. Used as protection against evaporation and parasites in plants and animals
38
Cerebroside
A type of glycolipid. Any lipid linked to a sugar is a glycolipid
39
Terpenes
Odiferous steroid precursors made from isoprene. One terpene unit contains 2 isoprene units
40
Terpenoids
Derived from terpenes via oxygenation or backbone rearrangement. Odorous characteristics
41
Steroids
3 cyclohexane rings and 1 cyclopentane
42
Steroid hormones
Have high affinity receptors work at low concentrations and affect gene expression and metabolism
43
Cholesterol
A steroid important for membrane fluidity and stability. Serves as a precursor to many other molecules
44
Prostaglandins
Are autocrine and paracrine signaling molecules that regulate cAMP. Affect smooth muscle contraction, body temp, sleep wake cycle, fever, and pain
45
Fat soluble vitamins
a, d, e, and k
46
Vitamin A
Carotene
Vision
47
Vitamin D
Cholecalciferol
Bone formation
48
Vitamin e
Tocopherols
Antioxidants
49
Vitamin k
Phylloquinone
Menaquinone
Forms prothrombin
50
Triacyglycerol
Storage form of fatty acids
Contain one glycerol attached to 3 fatty acids by ester bonds
51
Adipocytes
Animal cells used for storage of large triaxylhlycerol deposits
52
Free fatty acids
Unesterifed fatty acids that travel in the bloodstream. Salts of free fatty acids and soaps
53
Saponification
The ester hydrolysis of triacylglycerol using a strong base like sodium or KOH
54
Micelle
Can dissolve a lipid soluble molecule in its fatty acid core and washes away with water bc of its shell of carboxylate head groups
55
Nucleic acid 1° structure
Linear sequence of nucleotides
56
Nucleic acid 2° structure
Interactions between bases within the same molecule. In DNA, the bases are held together by hydrogen bonds. Responsible for shape of nucleic acid
57
RNA 2° structure
4 basic elements: loops, helices, bulges, and junctions.
Loops include stem-loops, tetra loops, and psuedoknots
58
3° structure of nucleic acid
The location of the atoms in 3D space
59
4° structure of amino acids
Interactions of nuclei acids with other molecules. Example: chromatin interacting with histones
60
Nucleoside
5 carbon sugar and nitrogenous base
No phosphate groups
61
Nucleotide
A nucleoside with 1-3 phosphate groups added. Nucleotides contain deoxyribose. In RNA they contain ribose
62
Watson crick model
Backbone of alternating sugar/phosphate groups. Always read 5’ to 3’
Two strands w anti parallel polarity wound into double helix
63
Nitrogenous bases
Purines: adenine and guanine
Pyrimidines: cytosine, uracil, thymine
64
Chargaffs rule
Number of purines = number of pyrimidines
65
B-DNA vs Z-DNA
Most DNA is B DNA, forming a right handed helix. Low concentrations of Z-DNA with a zig zag shape may be seen with high GC content or high salt concentration
66
Oncogenes
Develop from mutations of proto-oncogenes and promote cell signaling. May lead to cancer
67
Tumor suppressor genes
Code for proteins that reduce cell cycling or promote dna repair
68
Mutated tumor suppressor gene
Is like cutting the breaks
69
Proofreading
DNA polymerase proofreads it’s work and excises incorrectly matched bases. The daughter strand is identified by its lack of methylation and corrected accordingly
70
Mismatch repair
Occurs during G2 phase using the genes MSH2 and MLH1
71
Nucleotide excision repair
Fixes helix-deforming lesions of DNA such as thymine dimers. A cut and patch process. Excision endonuclease
72
Base excision repair
Fixes nondeforming lesions of the DNA as cytosine deamination by removing the base, leaving the apurinic apyridimic site. AP Endonuclease then removes the damaged sequence which can be filled w the correct base
73
Chromatin
Dna and histones
74
Heterochromatin
Dark condensed
75
Euchromatin
Light
Uncondensed
Expressed
76
Telomeres
Ends of chromosomes. Contain high GC content to prevent unraveling of DNA. During replication, telomeres are shortened, but this can be partially reversed by telomerase
77
Centromeres
Middle of chromosomes and hold sister chromatids together until they are separated during anaphase in mitosis. High GC content to maintain a strong bond between chromatids
78
Acrocentric chromosome
When the centromere is located near one end of the chromosome and not the middle
79
Recombinant DNA
Dna composed of nucleotides from 2 different sources
80
Hybridization
The joining of complementary base pair sequences
81
Central dogma
States that DNA is transcribed to RNA which is translated to protein
82
Degenerate code
Allows for multiple codons to encode for same amino acid
83
Start codon
AUG
84
Stop codon
UAA, UGA, UAG
85
Wobble
3rd base in codon. Allows for mutations to occur without effects in protein. Wobble base pairing are less stable
86
Point mutations
Silent
Nonsense
Missense
87
Missense
Mutations that produce a codon that codes for diff amino acid
88
3 types of RNA
Messenger RNA
Transfer RNA
Ribosomal RNA
89
Helicase
Unwinds double helix
90
RNA polymerase II
Binds to TATA box within the promoter region of the gene
91
Exons
Exit the nucleus and form mRNA
92
Introns
Spliced out so they stay in the nucleus. Introns also enable alternative splicing
93
Alternative splicing
Usually Introns cut away. Exons remain. But alternative splicing may change that. A certain exon may be cut out or and intron may stay.
94
5’ cap and poly A tail
Added to mRNA. The cap and tail stabilize mRNA for translation
95
Operons
Inducible or repressive cluster of genes transcribed as a single mRNA
96
Promoters
Within 25 base pairs of transcription start site
97
Enhancers
Are more than 25 base pairs away from transcription start site
98
Histone acetlyation
Unravels DNA allows for transcription
99
Histone methylation
Decreased accessibility to dna
100
Flippases
Membrane proteins that maintain the bidirectional transport for lipids between layers of phospholipid membrane in cells
101
Primary component of membrane
Lipids
102
Triacyglycerols and fatty acids
Act as phospholipid precursors and are found in low levels in membrane
103
Cholesterol in membrane
At low temps increases fluidity
At high temps decreases fluidity
104
Carbohydrates in membrane
Can form a protective glycoprotein coat and function in cell recognition
105
Ligands
Extracellular ligands can bind to membrane receptors which function as channels or as enzymes in the second messenger pathways
106
Passive transport
Doesn’t require energy bc molecules is moving down concentration gradient
107
Simple diffusion
Form of passive transport. Small, nonpolar molecules passively move from an area of high concentration to an area of low concentration until equilibrium is reached
108
Osmosis
Diffusion of water across a semipermeable membrane
109
Facilitated diffusion
A form of passive transport, uses transport proteins to move impermeable solutes across the cell membrane
110
Active transport
Requires energy in the form of ATP or an existing favorable ion gradient
111
Primary active transport
Uses ATP or another energy molecule to directly lower the transport of molecules across a membrane
112
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
113
Symport
Both particles flow same direction
114
Antiport
The particles flow in opposite directions
115
Pinocytosis
Ingestion of liquids via vesicles
116
Membrane potential
Maintained by na/k pump and leaked channels. Resting potential of most cells is between -40 and -80 mv
117
The Nernst equation
Electrical potential created by one ion can be calculated using this
118
The Goldman Hodgkin Katz voltage equation
Resting potential of a membrane at a physiological temp can be calculated using this
119
GLUT-2
Found in liver for glucose storage and pancreatic B-islet cells as part of the glucose sensor. Has increased Km
120
GLUT-4
Found in adipose tissue and muscle. Stimulated by insulin. Has decreased Km
121
Glycogen synthase
Creates an alpha-1,4 glycosidic bond between gluxose
Biochemistry
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