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Biochem > Final Review > Flashcards

Final Review Flashcards

1
Q

Fatty acid

A

Could be incorporated into a lipid membrane

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2
Q

Sugar

A

Could be incorporated into a polysaccride

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3
Q

Nucleotide

A

Could be incorporated into RNA

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4
Q

Amino acid

A

Could be incorporated into proteins

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5
Q

Amide bonds

A

Proteins

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6
Q

Phosphodiester bonds

A

Polynucleotides

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7
Q

Glycosidic bonds

A

Polysaccharide

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8
Q

Lewis acid

A

Acceptor
Electophile

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9
Q

Lewis base

A

Electron do not
Nucleophile

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10
Q

Smooth ER

A

Synthesizes complex lipids

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11
Q

Plasma membrane

A

Forms cellular boundary

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12
Q

Mitochondria

A

Harvest of energy through oxidative respiration

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13
Q

Nucleus

A

Storage of genetic information

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14
Q

Cytoplasm

A

Sea that fills the cell
Site of many biological pathways

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15
Q

Rough ER and Golgi

A

Site of protein synthesis and modification

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16
Q

Lysosome

A

Degrades and recycles cellular components

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17
Q

Peroxisome

A

Oxidizes very long chain fatty acids through peroxide metabolism

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18
Q

DNA replication

A

DNA to DNA

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19
Q

Reverse transcription

A

RNA to DNA

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20
Q

Transcription

A

DNA to RNA

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21
Q

Translation

A

RNA to protein

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22
Q

What makes ATP good molecule for reaction coupling

A

Product exhibits resonance stabilization
Products are ionized, which aids in solvation
When phosphates are removed, negative charge repulsion is reduced, making the products more stable

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23
Q

Flippases and floppases

A

Use energy to move lipids against their concentration gradient

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24
Q

Scramblases

A

Facilitate the movement of lipids downhill spontaneously

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25
Q

Decrease in temp would

A

Make membrane less fluid

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26
Q

An increase in temp

A

Make membrane more fluid

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27
Q

Uses of nucleotides

A

DNA/RNA
Energy currency
Phosphate group donor
Coenzyme
Second messenger
Bioconjuction

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28
Q

Monocistronic

A

One RNA that codes for one protein

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29
Q

Polycistronic

A

Has one RNA that codes for multiple proteins

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30
Q

DNA polymerase

A

Chain elongation

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31
Q

Coding strand

A

DNA strand that would match the sequence of new copy

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32
Q

HTS detector

A

Detect light emitted by fluorescent label

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33
Q

HTS primer

A

Allow enzyme to dock an begin elongation

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34
Q

Template strand

A

DNA used to generate the new copy strand

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35
Q

HTS capillary gel

A

Separate new strands by length, with shorter chains emerging first

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36
Q

HTS laser

A

Excite the fluorescent label

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37
Q

HTS dNTP

A

Allow for chain elongation

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38
Q

HTS ddNTP’s

A

Terminate chain elongation

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39
Q

DNA microarray

A

Used for transcriptome analysis

40
Q

Molecular cloning

A

Used to transfer a gene of interest into plasmid for expression of DNA and protein

41
Q

PCR with DNA polymerase

A

Used to replicate DNA to generate millions of identical copies

42
Q

HTS

A

Used to generate millions of different length copies to determine the sequence of a gene

43
Q

RT-PCR

A

Used to convert mRNA into millions of DNA copies

44
Q

Primary structure

A

Amino acids linked by peptide bonds
Linear amino acid sequence

45
Q

Secondary structure

A

Beta turns
Backbone hydrogen bonding
Beta strands
Alpha helices

46
Q

Tertiary structure

A

Supported by intracranial R group interactions
3D shape of protein
Supported by intracranial disulfide bonds

47
Q

Quaternary structure

A

Supported b inter chain disulfide bonds
Supported by interchain hydrophobic interactions
Multiple proteins chains interacting together
Supported by interchain R group interactions

48
Q

Silk fibroid

A

Majority hydrophobic beta-strand secondary structure
No covalent structural support between subunits
EX: spider webs

49
Q

Collagen

A

majority random coil secondary structure
Primary proline and hydroxyproline residues
Crosslinked lysine residues between subunits
EX: cartilage

50
Q

Keratin

A

Majority hydrophobic alpha-helical secondary structure
Disulfide bonds connecting numerous subunits
EX: hair

51
Q

Immunoglobulins

A

Disulfide bonds connecting 4 subunits
Majority amphipathic beta-strand secondary structure
Globular (soluble) protein
EX: antibodies

52
Q

Purification steps

A

Choose source, obtain large supply
Lose cells, centrifuge to obtain fractions
Salting out
Dialysis
Chromatography
Analyze purity and activity

53
Q

ESI mass spectrometry

A

Based on mass and acceleration through chamber ending in detector
Sample becomes ionized due to high voltage
Ionization evaporates the solvent, leaving the peptide in gas phase travels through separating mass spectrometer
High voltage can be used to fragment the sample
Uses a mass to charge ratio to determine molecular mass
Can be used for proteins that have been treated with proteases like trypsin

54
Q

MALDI

A

Based on mass and acceleration through chamber ending in detector
Uses a mass to charge ratio to determine molecular mass
Can be used for proteins that have been treated with proteases like trypsin
Peptides become fragmented and charged due to laser exposure
Proteins or peptides are mixed in a solid matrix rather than a solution
Laser will be absorbed by peptide containing material releasing the peptide into gas phase

55
Q

Collision chamber

A

Divide peptide fragment into smaller sub fragments

56
Q

Second mass spectrometer

A

Determine the masses the peptide sub fragments

57
Q

First mass spec

A

Determine the masses of protease digestion fragments and allow selection of fragments to further study

58
Q

NMR

A

Limited to less than 30 kD
Low resolution
Dynamic
Real time tracking of ligand binding
Require large concentration

59
Q

X-ray crystallography

A

High resolution
Static
No limit
Require large concentration

60
Q

Cryo-‘em

A

High resolution
Static
No upper limit
Require only small sample

61
Q

Monoclonal ab

A

Recognizes epitope
Very expensive
Yields unlimited supply
Ab harvested from hybrids as
Produced in mice

62
Q

Polyclonal ab

A

Recognizes epitopes
Relatively inexpensive to produce
Limited supply
Ab harvested from blood
Produced in rabbits

63
Q

Western blot steps

A

Separate proteins b SDS-PAGE
Transfer proteins to thin membrane
Block nonspecific binding using milk
Incubate with primary ab
Incubate with second ab - enzyme conjugate
Detect the antigen-ab complex

64
Q

Western blot

A

Detects whether a protein of interest present in a sample

65
Q

ELISA

A

Quantifies an ag or ab in sample

66
Q

Immunoprecipitation

A

Uses SDS-PAGE and MS to identify unknown proteins

67
Q

Immunofluorescence

A

Detects location of a protein of interest within a cell

68
Q

Genomic caretakers

A

Maintain and repair hereditary material
DNA ligaments

69
Q

Transport proteins

A

Move molecules or ions
Hemoglobin

70
Q

Metabolic enzymes

A

Hexokinase
Carry out catalytic reactions in catabolic and anabolic pathways

71
Q

Structural proteins

A

Help maintain cell shape
Collagen

72
Q

Signaling proteins

A

Convey messages between and within cells

73
Q

M domain

A

Contains the substrate binding sites, allowing for transport from one side of the membrane to the other

74
Q

N domain

A

Binds ATP and positions it for attack

75
Q

A domain

A

Communicates the movement between the P and M domains

76
Q

P domain

A

Accepts the phosphate from ATP during catalytic mechanism

77
Q

Muscle contraction mechanism

A

Calcium binds to troponin, uncovering myosin binding sites on actin thin filaments
Inorganic phosphate is released, triggering power stroke
ADP released from myosin head group
ATP docks onto myosin head group
Myosin head group is triggered to dissociate from actin
ATP hydrolysis induces the recovery conformation

78
Q

Holoenzyme

A

Enzyme with its cofactor or coenzyme bound

79
Q

Apoenzyme

A

Enzyme without its cofactor or coenzyme

80
Q

PKA activation steps

A

Adenylate cyclase converts ATP to cAMP
cAMP binds to regulatory subunits of PKA
Regulatory subunits of PKA dissociate from catabolic subunits
Catalytic subunits are now active and able to phosphorylase target proteins
cAMP phosphodiesterase converts cAMP to AMP
Regulatory subunits of PKA, no free of cAMP, associate with catabolic subunits
Calaytic subunits now deactivated and unable to phosphorylate target proteins

81
Q

Decreases beta-2 adreergic receptor signaling

A

Increased activity of cAMP phosphodiesterase
Increased GAP activity
Dephosphorylation of PKA substrate
Decreased activity of Adenylate cyclase
Decreased activity of PKA
Decreased GEF activity
Epinephrine dissociates from receptor

82
Q

Investment phases of glycolysis

A

Hexokinase
PFK1

83
Q

Harvest steps of glycolysis

A

GAPDH
PK
PGK

84
Q

Glycolysis regguulated and irreversible reactions

A

PFK1
PK
HK

85
Q

Inhibitors of PDH complex

A

NADH
ATP
Acetyl-CoA

86
Q

Citrate cycle steps that yield NADH

A

Isocitrate dehydrogenase
Malate dehydrogenase
Alpha-ketogluterate dehydrogenase

87
Q

Citrate cycle steps that yield FADH2

A

Succinate dehydrogenase

88
Q

Citrate cycle steps that yield GTP

A

Succinyl-CoA synthetase

89
Q

Chemiosmosis

A

Protons move downhill through ATP synthase
Proton gradient generated by ETC
Movement of proteins through ATP synthase coupled to ATP synthesis
Proton gradient represents both chemical and voltage difference across the inner mitochondrial membrane
Protons moved uphill by ETC

90
Q

Source of energy movement for movement of proteins by ETC

A

Spontaneous transfer of electrons from carrier with lower reduction potential to one with higher reduction potential

91
Q

Activators of oxidative phosphorylation

A

Pi
AMP
ADP
NAD+

92
Q

Cellulose

A

Main chain linked through B1->4 bonds
Glucose polymer with fibrous backbone
Major component of plant cell wall
Polymer of glucose resides

93
Q

Starch

A

Polymer of glucose residues
Main chain linked through a1->4 bonds
Major storage form of glucose in plants
Helical backbone shape
Branches a1->6 bonds

94
Q

Glycogen

A

Major storage form of glucose in animals
Polymer of glucose residues
Main chain linked through a1->4 bonds
Helical backbone shape
Branches linked through a1->6 bonds

95
Q

Raffinose

A

Galactose polymer
Main chain linked through a1->6 bonds

96
Q

Chitin

A

Major component of insect exoskeletons
Main chain linked through b1->4 bonds
Is GlcNAc polymer with fibrous backbone shape

97
Q

Uses of NADPH

A

Donates electrons to radicals to prevent cell damage
Used in bio synthetic and detoxification pathways

Biochem (10 decks)

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