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Genetics > Exam 2: Genomics contd and Proteomics > Flashcards

Exam 2: Genomics contd and Proteomics Flashcards

1
Q

define synthetic genomics

A

uses aspects of genetic modification on pre-existing life forms, or artificial gene synthesis to create new DNA/chromosomes or entire life forms

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2
Q

reporter genes can be used to examine

A

expression patterns of a gene

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3
Q

t/f: we are not yet capable of starting with nucleotides and a few additional chemicals to create a living, reproducing organism

A

true

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4
Q

metagenomics

A

study of genetic material recovered directly from environmental samples (aka: environmental genomics or community genomics)

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5
Q

human biome-metagenomics involves

A

understanding bacteria and fungi (microbiome) and their impact on human health (symbiosis is critical for maintaining good health)

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6
Q

the human microbiome project found that

A

the diversity and abundance of each habitat’s signature microbes vary widely even among healthy subjects; our genetics interact with genetics of microorganisms to created healthy microbiome

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7
Q

comparative genomics

A

is the science of comparison of genomic feats among organisms. bc all genomes presumably arose from a common ancestral genome, relationships btwn genomes help identify significance of those feats and help determine genotype-phenotype relationships

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8
Q

how might knowledge of the conservation of a nucleotide (or an aa) be useful in establishing the significance of a novel mutation in a diagnostic algorithm?

A

A highly conserved nucleotide or aa alludes to the fact that that nucleotide/aa is very important in the protein and therefore a change is more likely to impair the protein as a nucleotide/aa changed caused a clinical phenotype that may be casual to that mutation

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9
Q

paleogenomics

A

the study of past (evolutionary history) through the examination of preserved genetic material from the remains of ancient organisms (this is also comparative genomics)

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10
Q

Human Longevity Inc and J. Craig Ventor

A

understand how we age through genetic analysis (live longer and resist cancer); HLI combines genomic and phenotypic info to accelerate the understanding of human health

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11
Q

proteins are divided into 3 main classes which correlate with their typical tertiary structures:

A
  1. globular proteins (soluble, enzymes)
  2. fibrous proteins (structural ie collagen)
  3. membrane proteins (serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane)
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12
Q

what happens if there is a substitution of aa in a protein from the same class?

A

less damage to protein since they come from the same class of aas

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13
Q

what is a leader sequence

A

a sequence of NUCLEOTIDES at the 5’-END of MESSENGER RNA (and on DNA), UPSTREAM of the start CODON for TRANSLATION. This sequence contains the RIBOSOME BINDING SITE but is not normally translated into a part of the PROTEIN of the GENE (transcribed but not translated)

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14
Q

the primary structure is the

A

seq of aa that make up the polypeptide chain

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15
Q

the secondary structure takes the form of

A

takes the form of alpha-helix or beta-pleated sheet is maintained by hydrogen bonds btwn aas in different regions of the original polypeptide strand

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16
Q

tertiary structure occurs as a result of

A

further folding and bonding of secondary structure

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17
Q

quaternary structure occurs as a result

A

of interactions btwn 2 or more tertiary subunits ex is hemoglobin

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18
Q

t/f: 3D structure is very important for structure of a protein

A

true

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19
Q

determination of cellular proteins: 1D

A

western blot

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20
Q

determination of cellular proteins: 2D

A

polyacrylamide gel electrophoresis (2D-PAGE)

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21
Q

SDS-PAGE is an analytical method for

A

the separation of charged molecules in mixtures by their molecular masses in an electric field

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22
Q

SDS is

A

an anion surfactant (detergent) that binds to proteins and dentatures them; the negatively charged detergent provides all proteins with a similar net charge and thus a similar charge-to-mass ratio

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23
Q

denatured proteins are loaded onto a gel of polyacrylamide, which is placed in an electrophoresis buffer that when voltage is applied

A

causes a migration of negatively charged molecules through the gel in the direction of the anode (+ pole)

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24
Q

western blot separates protein by

A

size and charge

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25
isoelectric focusing (IEF)
technique for separating native (nondenatured) proteins by differences in their isoelectric point (pI, the pH at which a particular molecule carries no net electrical charge)
26
IEF takes advantage of
an electrophoretic separation that takes advantage of the fact that overall charge on the protein is a function of the pH of its surroundings
27
how a protein moves: above pI below pI at pI
- above pI = protein has overall neg charge and will migrate toward pos charged anode - below pI = protein has overall pos charge and will migrate toward neg charged cathode - at pI = protein does no move; focuses into a single band
28
t/f: proteins are amphoteric
true; contain acidic and basic residues
29
2D-PAGE is
1D is an IEF tube gel and 2D is when IEF gel is denatured and laid on top of an SDS-PAGE and electrophoresed again; mixture of proteins separated b charge in one dimension and by mass in second dimension, producing a series of spots on a gel
30
mass spectrometry (MS)
analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. A mass spectrum measures the masses within a sample
31
types of samples for MS
solid, liquid, or gas
32
how does MS work?
sample is ionized (bombarded w/ e-s) may cause some of the molecules in a sample to break into charged fragments; these ions are then separated according to mass-to-charge ratio by accelerating them and subjecting them to an electric/magnetic field
33
_ can be used to separate complex mixtures prior to MS
liquid chromatography
34
determination of cellular proteins in MS
expensive; take a crude protein mix, break them up, put a charge on them, and accelerate them through detector based on size (fragments create fingerprints that give proteins a unique signature) also detects aa changes in proteins (mutations) and sequence unknown proteins
35
the 4 steps to Western blot
1. extract proteins 2. electrophorese 3. transfer to membrane 4. detect w/ protein specific antibodies
36
protein microarrays can be used to study
protein - protein interactions (thousands of proteins at once) also protein antibody interaction system
37
protein microarrays are primarily used for
diagnostics, protein expression profiling, protein functional analysis, antibody characterization, and treatment development
38
protein microarray: use in diagnostics
involves detection of biomarkers: antigens and antibodies in blood samples; monitoring of disease states and response to therapy; monitoring of environment and food
39
protein microarray: use in protein expression profiling
identifies variation in quantities of proteins in extracts from tissues or cells
40
protein microarray: use in protein functional analysis
identification of protein-protein interactions (members of a protein complex), protein-phospholipid interactions, small molecule targets, enzymatic substrates (kinases) and receptor ligands
41
protein microarray: use in antibody characterization
examines cross-reactivity, antibody specificity and antibody epitope mapping
42
protein microarray: use in treatment development
involves the design of antigen-specific therapies for autoimmune disease, cancer and allergies; small molecule targets to be used as new drugs
43
affinity capture
purifying proteins to characterize; a method of separating biochemical mixtures based on a highly specific interaction such as that btwn antigen and antibody, enzyme and substrate, or receptor and ligand
44
yeast 2 hybrid system:
molecular technique used to discover protein-protein interactions and protein-DNA interactions by testing for physical interactions (binding) btwn 2 proteins or a single protein and a DNA molecule
45
the key to the 2 hybrid screen is that
transcription factors have a BD and AD that can be split and brought back together, you are trying to find proteins that interact with each other: finding the target protein and binding partner that will activate transcription
46
the protein fused to the BD (binding domain) may be referred to as the bait protein, and is typically a known protein that
new binding partners are to be identified; 2 hybrid screens can provide an important first hint for the identification of interaction partners
47
interactome
map (NIH) catalogs and curates known protein-protein interactions that lead to failing human health but can also describe sets of indirect interactions among genes (genetic interactions)
48
reactome
protein metabolism; metabolism of proteins covers the full life cycle of a protein from its synthesis to its post-translational modification and degradation
49
post-translational modification
adding atoms; refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. this increases protein diversity (controlling protein fcn and diversity through enzymatic chemistry)
50
proteopathies/protein folding disorders
a change in 3D folding (conformation) increases the tendency of a specific protein to bind to itself. the aggregated form of the protein is resistant to clearance and can interfere with organ fcn
51
seeding/permissive templating describes:
some proteins can be induced to form abnormal assemblies by exposure to the same protein that has folded into a disease-causing conformation
52
prions
infectious agents composed entirely of a protein material that can fold in multiple, structurally abstract ways, at least one of which is transmissible to other prion proteins, leading to disease in a manner that is epidemiologically comparable to the spread of viral infection
53
genetic prion diseases are caused by
autosomal-dominant mutations in the prion protein gene; genotype-phenotype association in the way it folds and how severe the disease is
54
prion disease represents a group of conditions that affect the
nervous sys in humans and animals
55
SIFT predicts
whether an aa substitution affects protein fcn, highly reliable in conclusions of aa change
56
SIFT can be applied to naturally occuring
nonsynonymous polymorphisms or laboratory-induced missense mutations
57
PolyPhen-2 is a tool which predicts
possible impact of an aa substitution on the same structure and fcn of a human protein using straightforward physical and comparative considerations
58
what is the protein functional database called
Uniprot; provides scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information; various aa changes
59
what is a the protein structural prediction tool called
Phyre; predict the 3D structure adopted by a user-supplied protein sequence
60
the Phyre and Phyre2 servers predict
the 3D structure of a protein seq using the principles and techniques of homology modeling
61
Phyre/Phyre2: bc the structure of a protein is more _ in evolution than its aa seq, a protein seq of interest (target) can be modeled with reasonable accuracy on a very distantly related seq of known structure (template) provided that the relationship btwn target and template can be discerned through _
conserved; sequence alignment
62
what is a con to protein microarray
cannot tell you information about an unknown protein, only those that you have an antibody for
63
increase protein expression may affect
the severity of the disease

Genetics (37 decks)

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