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Genetics > Exam 2: Genomics contd and Proteomics > Flashcards

Exam 2: Genomics contd and Proteomics Flashcards

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Biology 101 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
Q

isoelectric focusing (IEF)

A

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)

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26
Q

IEF takes advantage of

A

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
Q

how a protein moves:
above pI
below pI
at pI

A
  • 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
Q

t/f: proteins are amphoteric

A

true; contain acidic and basic residues

29
Q

2D-PAGE is

A

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
Q

mass spectrometry (MS)

A

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
Q

types of samples for MS

A

solid, liquid, or gas

32
Q

how does MS work?

A

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
Q

_ can be used to separate complex mixtures prior to MS

A

liquid chromatography

34
Q

determination of cellular proteins in MS

A

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
Q

the 4 steps to Western blot

A
  1. extract proteins
  2. electrophorese
  3. transfer to membrane
  4. detect w/ protein specific antibodies
36
Q

protein microarrays can be used to study

A

protein - protein interactions (thousands of proteins at once) also protein antibody interaction system

37
Q

protein microarrays are primarily used for

A

diagnostics, protein expression profiling, protein functional analysis, antibody characterization, and treatment development

38
Q

protein microarray: use in diagnostics

A

involves detection of biomarkers: antigens and antibodies in blood samples; monitoring of disease states and response to therapy; monitoring of environment and food

39
Q

protein microarray: use in protein expression profiling

A

identifies variation in quantities of proteins in extracts from tissues or cells

40
Q

protein microarray: use in protein functional analysis

A

identification of protein-protein interactions (members of a protein complex), protein-phospholipid interactions, small molecule targets, enzymatic substrates (kinases) and receptor ligands

41
Q

protein microarray: use in antibody characterization

A

examines cross-reactivity, antibody specificity and antibody epitope mapping

42
Q

protein microarray: use in treatment development

A

involves the design of antigen-specific therapies for autoimmune disease, cancer and allergies; small molecule targets to be used as new drugs

43
Q

affinity capture

A

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
Q

yeast 2 hybrid system:

A

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
Q

the key to the 2 hybrid screen is that

A

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
Q

the protein fused to the BD (binding domain) may be referred to as the bait protein, and is typically a known protein that

A

new binding partners are to be identified; 2 hybrid screens can provide an important first hint for the identification of interaction partners

47
Q

interactome

A

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
Q

reactome

A

protein metabolism; metabolism of proteins covers the full life cycle of a protein from its synthesis to its post-translational modification and degradation

49
Q

post-translational modification

A

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
Q

proteopathies/protein folding disorders

A

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
Q

seeding/permissive templating describes:

A

some proteins can be induced to form abnormal assemblies by exposure to the same protein that has folded into a disease-causing conformation

52
Q

prions

A

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
Q

genetic prion diseases are caused by

A

autosomal-dominant mutations in the prion protein gene; genotype-phenotype association in the way it folds and how severe the disease is

54
Q

prion disease represents a group of conditions that affect the

A

nervous sys in humans and animals

55
Q

SIFT predicts

A

whether an aa substitution affects protein fcn, highly reliable in conclusions of aa change

56
Q

SIFT can be applied to naturally occuring

A

nonsynonymous polymorphisms or laboratory-induced missense mutations

57
Q

PolyPhen-2 is a tool which predicts

A

possible impact of an aa substitution on the same structure and fcn of a human protein using straightforward physical and comparative considerations

58
Q

what is the protein functional database called

A

Uniprot; provides scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information; various aa changes

59
Q

what is a the protein structural prediction tool called

A

Phyre; predict the 3D structure adopted by a user-supplied protein sequence

60
Q

the Phyre and Phyre2 servers predict

A

the 3D structure of a protein seq using the principles and techniques of homology modeling

61
Q

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 _

A

conserved; sequence alignment

62
Q

what is a con to protein microarray

A

cannot tell you information about an unknown protein, only those that you have an antibody for

63
Q

increase protein expression may affect

A

the severity of the disease

Genetics (37 decks)

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