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Bioinformatics 523 > Week 2 > Flashcards

Week 2 Flashcards

1
Q

chromosomes

A

carriers of genetic information

contain both proteins and nucleic acids

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2
Q

Griffith and Avery experiments

A

S bacteria: fatal to mouse, infectivity killed by heat
R bacteria: not fatal

smooth (S) bacteria contain something not destroyed by heat, can be passed on to R bacteria so that they kill and pass on

conclusion: molecule that carries heritable information is dna

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3
Q

Hershey and Chase

A

virus: consists of both dna and proteins

labeled dna with 32P, proteins with 35S

infected bacteria contain 32P but not 35S

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4
Q

Chargaff’s rules

A

dna, not proteins, is heritable material

A:T and G:C ratio always 1

A/T:G/C ratio variable from species to species

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5
Q

Franklin and Wilkens, Watson and Crick

A

showed dna is double helix (X-ray crystallography)

built model of structure of dna

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6
Q

nucleus of cell

A

the design and management center of the cell

stores dna

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7
Q

cytoplasm

A

production site of the cell, makes proteins

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8
Q

mRNA

A

messenger rna, used to transmit information from the nucleus to the cytoplasm

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9
Q

tRNA

A

transfer dna, adaptors from 4 base dna code to 20 amino acid protein code

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10
Q

ribosomes

A

make proteins using mRNA as template, amino acids as building blocks

large, complex molecules consisting of both proteins and rRNA

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11
Q

central dogma

A

Francis Crick, 1958

dna, rna, and proteins are linear, sequential polymers

each position in sequence is drawn from fixed alphabet (nucleotides for dna, rna—4, and amino acids for proteins—20)

flow of primary sequence information: conversion between alphabets (translation)

no way to convert protein alphabet back to nucleic acid

transcription from dna to rna, then translation from rna to protein

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12
Q

gene expression

A

regulation of this determines if cell is liver, muscle, nerve

levels vary from cell to cell in same organism, at times in development, and with outside signals

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13
Q

RNA polymerases

A

enzymes that carry out transcription

synthesis of rna from 5’ to 3’

signals on dna that tell rna polymerases where to start/stop (subject to regulation)

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14
Q

promoter

A

defines where transcription should begin

rna poly. binding site

then coding region

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15
Q

prokaryotes

A

have no nucleus

single cellular (but may join together)

can live in diverse temps

can grow and evolve quickly

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16
Q

eukaryotes

A

have nucleus

are multicellular

have other intracellular organelles (some of which are thought to have evolved from invading bacteria—mitochondria, chloroplasts)

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17
Q

prokaryotic genes

A

minimal gene

promoter—binding site for rna polymerase

ribosome binding site (initiate protein synthesis in mRNA)

coding sequence—encodes protein synthesis

transcriptional terminator—stop mRNA synthesis

often multiple protein coding regions controlled by single promoter (operon)
-polycistronic: more than one protein encoded in single mRNA molecule

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18
Q

polycistronic mRNA

A

more than one protein encoded on single mRNA molecule

common in prokaryotes

19
Q

eukaryotic genes

A

5’ caps and 3’ poly-A- tails

require general transcription factors

most have introns (noncoding regions) that are spliced

can be simple of very large

20
Q

introns and exons

A

noncoding and coding regions in the dna

21
Q

splicing

A

requires intronic signal sequences

lariat formed from introns

22
Q

alternative splicing

A

can be differentially regulated

enables a mRNA to direct synthesis of different protein variants

23
Q

translation

A

once mRNA is out of nucleus, it is translated into proteins—different alphabet

genetic code

24
Q

genetic code

A

directional: 5’ to 3’ mRNA

no doves to indicate start or stop of words

6 different reading frames from dna to proteins

25
Q

Kozak sequence

A

all proteins start with amino acid methionine

A/GccAUGG/A

26
Q

stop signal

A

TGA, TAA, TAC (UGA, UAA, UAC)

27
Q

tRNA synthetases

A

charge tRNA with amino acids

28
Q

tRNA anticodons

A

base pair with the correct codon on mRNA (after tRNA synthetases charge)

29
Q

rRNA

A

ribosomal rna, most abundant rna in most cells

form the core of the ribosome and catalyze protein synthesis

30
Q

ribosome sites for tRNA

A

A—admission of codon if mRNA, checking and decoding

P—peptide synthesis, consolidation, elongation, transfer of peptide chain to site A

E—preparation of now uncharged tRNA for exit

31
Q

electrophoresis

A

separation of charged biomolecules in a gel matrix in which an electric field has been established

separates proteins, rna, dna

32
Q

phosphate moieties of dna/rna

A

provide nucleic acid molecules with constant, negative charge to mass ratio

charge of protein depends on primary structure and ph of the solution

33
Q

equipment for gel electrophoresis

A

power source, electrophoresis tank, anode (+) and cathode cable, support, comb

34
Q

bands on electrophoresis gel

A

population of identical molecules that are not exactly identical in migration behavior -> distribution

variables affecting: molecular, thermal, gel heterogeneity, observation error

35
Q

the southern blot

A

dna separated on gel and dna as the probe

36
Q

the northern blot

A

rna separated on gel and dna as the probe

37
Q

charge/mass ratio

A

constant for dna and rna (so just separate by size)

unique for every protein

38
Q

two solutions for unique charge:mass ratio in proteins

A

treat proteins to give them uniform charge

take advantage of this property to separate proteins

39
Q

SDS (sodium dodecyl sulfate)

A

strongly denaturing detergent (disrupts 2o-4o structures)

binds and confers negative charge to proteins (charge ~ mass)

40
Q

denaturing protein gel electrophoresis

A

proteins unfolded by loss of disulfide and hydrogen bonds

SDS coating -> uniform charge/mass ratio

mobility is inverse of mass

proteins of known mass used as standards to calibrate gel

41
Q

isoelectric focusing

A

not denatured, ph gradient within gel

protein migrated from well to ph where is has no net charge (isoelectric pt, pi)

42
Q

2d gel

A

electrophoresis in 1st rim by isoelectric point (native)

electrophoresis in 2nd din by size (reduced/SDS)

43
Q

antibodies

A

proteins that bind strongly with specific 3D structure (specific protein)

produced naturally by immune system to help in detection of foreign antigens

used to identify proteins in bio samples

44
Q

Western blot

A

detection of specific protein structure using antibody

Bioinformatics 523 (6 decks)

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