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Biology 12 > Unit 3 > Flashcards

Unit 3 Flashcards

1
Q

Friedrich Miescher

A

investigated chemical composition of DNA using pus cells
discovered DNA but called it nuclein
found it to be slightly acidic and composed of large amounts of phosphorus and nitrogen
caused debate of if protein or nuclein is hereditary material

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2
Q

Hammerling experiment

A

removed caps of algae and they regrew, removed feet of algae (included nucleus) and they did not regrow
concluded hereditary info is found in the nucleus

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3
Q

Griffith

A

discovered transforming principle in experiments with lethal/non-lethal strains of pneumonia

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4
Q

Hershey & Chase

A

confirmation of DNA

infected bacteria with 2 different kinds of radioactive viruses (S and P)

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5
Q

Chargaff’s rule

A

In DNA, percent composition of adenine is the same as thymine, and percent composition of cytosine is the same as guanine

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6
Q

DNA structure

A

a polymer of nucleotides
each of the four types of nucleotides contain a phosphate group, a deoxyribose sugar, and one of four possible nitrogen-containinng bases (adenine, guanine, cytosine, and thymine)

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7
Q

Linus Pauling

A

discovered many proteins have helix-shaped structures

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8
Q

Rosalind Franklin

A

used X-ray diffraction to analyze structure, patterns in pictures suggested a double helix shape
based on reactions with water, concluded that nitrogenous bases were located on the inside of the helix and sugar-phosphate backbone was located on the outside

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9
Q

Watson and Crick

A

deduced structure of DNA using other’s works

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10
Q

what is DNA

A

deoxyribonucleic acid
what chromosomes and genes are made of
made up of repeating nucleotide subunits

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11
Q

types of nitrogenous bases

A

adenine and guanine are purines (two rings of nitrogen atoms)
cytosine and thymine are pyrimidines (one ring of nitrogen atoms)

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12
Q

bonds in nucleotides

A

nitrogenous base is attached to the 1’C of the sugar by a GLYCOSYL bond
phosphate group is attached to a 5’C by a PHOSPHODIESTER BOND

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13
Q

DNA consists of 2 antiparallel strands of nucleotides. what does this mean

A

parallel, but running in opposite directions; the 5’end of one strand of DNA aligns with the 3’ end of the other strand in a double helix

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14
Q

hydrogen bonds in DNA

A

2 hydrogen bonds between A and T

3 hydrogen bonds between G and C

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15
Q

when does DNA replication occur

A

S stage of interphase

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16
Q

semi-conservative model

A

two parent strands are separated and a new complementary replacement strand is built for each
new DNA molecules would consist of one parent strand and one new strand

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17
Q

meselson & stahl experiment

A

concluded DNA replication is semi-conservative

used nitrogen isotopes and bacteria

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18
Q

three basic phases of DNA replication

A

initiation - portion of DNA is unzipped to exposes bases for new base pairing
elongation - two new strands of DNA are assembled using parent DNA as a template and then re-formed into double helices
termination - replication is done, two new DNA molecules separate, replication machinery is dismantled

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19
Q

when does replication begin

A

proteins bind at the replication origin

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20
Q

difference in replication origin in prokaryotes and eukaryotes

A

prokaryotes - one replication origin

eukaryotes - several

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21
Q

enzymes for strand separation

A

DNA helicase - the enzyme that unwinds double-helical DNA by disrupting the H bonds between the nitrogenous base pairs

Single-stranded binding proteins (SSBs) - a protein that prevents exposed strands from re-attaching together by blocking hydrogen bonding

topoisomerase (gyrase) - relieves the stress and kinks in the strands caused by separated by breaking and resealing the DNA strand

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22
Q

a new DNA strand is only made in the ________ direction

A

5’ to 3’

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23
Q

leading strand vs lagging strand

A

leading strand - copies continuously towards the replication fork
lagging strand - copies discontinuously, opposite the replication fork

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24
Q

RNA primase and RNA primers

A

RNA primase enzymes begin the replication process by building a small complementary RNA segment (RNA primer) on the strand at the beginning of the replication fork
RNA primer serves as a starting point for replication
RNA primer only needs to be added once for the leading strand

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25
Q

DNA polymerase III

A

attaches to 3’ end of each primer and begins assembling new DNA strands

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26
Q

okazaki fragments

A

series of short segments synthesized in the 5’ to 3’ direction copied discontinuously
each fragment is initiated by an RNA primer
fragment will eventually run into RNA primer

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27
Q

DNA polymerase I

A

removes RNA primers from both leading and lagging strands, appropriate DNA nucleotides replace them

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28
Q

DNA ligase

A

links together Okazaki fragments through creation of phosphodiester bonds

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29
Q

errors in DNA replication

A

mispairing nucleotide bases

strand slippage that causes additions or omissions of nucleotides

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30
Q

correcting errors

A

DNA polymerase II - proofreads newly synthesized DNA. incorrect base is removed and replaced

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31
Q

telomeres and telomerase

A

telomeres - repeating, non-coding sequences at the end of chromosomes, protective cap
telomerase - extends telomeres, can add DNA bases at 5’ end

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32
Q

difference between RNA and DNA

A

AUCG
ribose sugar
single stranded

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33
Q

how is RNA involved in protein synthesis

A

mRNA - template for translations

tRNA and rRNA - involved in translation of mRNA

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34
Q

Archibald Garrod

A

studies on alcaptonuria showed that having the black urine phenotype was due to what Mendel called a recessive inheritance factor. having this defective factor resulted in the production of a defective enzyme

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35
Q

Beadle and Tatum

A

bread mold experiments showed that a single gene produces one enzyme

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36
Q

Jacob and Monod

A

hypothesized existence of messenger RNA (mRNA)

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37
Q

mRNA

A

RNA that contains the genetic info of a gene and carries it to the protein synthesis machinery
provides the info that determines the amino acid sequence of a protein
base sequence is complementary to gene DNA sequence

38
Q

Jacob, Brenner, Meselson

A

confirmed the messenger RNA hypothesis with experiments with bacteria and viruses

when bacteria were infected by a virus, virus-specific RNA molecule was synthesized and became associated with bacterial ribosomes. RNA molecule had complementary base to DNA and carried genetic info to make viral protein. viral RNA molecule was synthesized and was not a permanent part of the bacterial ribosomes

39
Q

genetic code

A

a set of rules for determining how genetic info in the form of a nucleotide sequence is converted to an amino acid sequence of a protein

40
Q

triplet hypothesis

A

a proposal that the genetic code is read three nucleotide bases at a time
each triplet is called a codon

41
Q

genetic code is always interpreted in terms of the ______ codon rather than the nucleotide sequence of the _______

A

mRNA, DNA

42
Q

three important characteristics of the genetic code

A

genetic code is redundant - more than one codon can code for the same amino acid
3 codons that do not code for amino acids but for stop signals to end protein synthesis

genetic code is continuous - reads as a series of 3-letter codons without spaces, punctuation or overlap
shift of one or two nucleotides in either direction can alter codon groupings and result in an incorrect amino acid sequence

genetic code is nearly universal - almost all organisms build proteins with this genetic code
important implications for genetic techniques, such as cloning

43
Q

the central dogma of genetics describes the

A

transfer of genetic info from DNA, to RNA, and finally to proteins

44
Q

gene expression

A

synthesis of a protein based on the DNA sequence of a gene

45
Q

steps in gene expression

A

transcription - mRNA is synthesized based on the DNA template of a gene
translation - protein is synthesized with an amino acid sequence that is based on the nucleotide sequence of the mRNA

46
Q

antisense vs sense strand

A

template/transcribed DNA strand vs coding/untranscribed DNA strand

47
Q

three phases of transcription

A

initiation - transcriptional machinery is assembled on the sense strand. RNA polymerase binds to the promoter region of the sense strand, DNA is unwound

elongation - RNA polymerase synthesizes a strand of mRNA that is complementary to the sense strand of DNA

termination - RNA polymerase detaches from the DNA strand when it reaches a stop signal. the mRNA strand is released and the DNA double helix reforms

48
Q

mRNA modifications

A

modifications covert precursor mRNA to mature mRNA before it is transported across the nuclear membrane in the cytoplasm for protection
done through capping and tailing, and splicing

49
Q

capping

A

5’ cap consisting of 7-methyl guanosine units is added

protects the mRNA from digestion from nucleases and phophatases

50
Q

tailing

A

a poly-A tail is added to the 3’ end
consists of approximately 200-300 adenine ribonucleotides added by poly-A polymerase
protection from degradation, facilitates attachment to ribosomal complex

51
Q

exons, introns, spliceosomes, SnRNPS

A

exons - coding regions
introns - non-coding regions interspersed on exons
spliceosomes - cut out introns and rejoin exons
small nuclear ribonucleoproteins - play a key role in RNA splicing

52
Q

true or false: prokaryotic DNA does not contain any introns

A

TRUE

53
Q

removal of non-coding regions

A

mRNA splicing removes introns from pre-mRNA and joins exons together
snRNPS recognize and bind to regions where exons and introns meet

54
Q

major components of translation

A

mRNA
tRNA
ribosomes
translation factors

55
Q

tRNA

A

each tRNA has 2 functional regions:
anticodon loop - sequence of 3 nucleotides that is complementary to a specific mRNA codon
acceptor stem - at 3’ single-stranded region where amino acid is attached

tRNA links condons on mRNA to corresponding amino acid for protein synthesis

aminoacyl-tRNA synthetase - enzyme responsible for attaching amino acid to tRNA

56
Q

ribosomes in translation

A
  • cell structure in cytoplasm composed of proteins and ribsomal RNAs (rRNAs)
  • site of protein synthesis
  • each ribosome has a large and small sub-unit composed of different proteins and rRNA molecules
  • has a binding site for mRNA and 3 binding sites for tRNA
57
Q

initiation in translation

A

initiation - proteins called initiation factors assemble the small ribosomal sub-unit, mRNA, initiator tRNA and large ribosomal sub-unit for start of protein synthesis
mRNA is sandwiched between the two ribosome subunits
ribosome reads downstream until it reaches start codon - AUG. the corresponding tRNA carrying methionine binds to the P (peptide site)

58
Q

three binding sites for tRNA

A

P (peptide) site - contains tRNA with growing polypeptide attached to it; at initiation, initiator tRNA carrying methionine binds to the P site
A (amino acid) site - contains tRNA with next amino acid to be added to polypeptide chain
E (exit) site - uncharged tRNA that has lost amino acid is ejected at the E site

59
Q

elongation in translation

A

cycle of 4 steps is rapidly repeated. tRNA with attached polypeptide is in P site, tRNA carrying next amino acid enters A site. polypeptide chain is transferred to amino acid of tRNA in A site which makes the chain one amino acid longer. mRNA moves forward by one codon and tRNA with polypeptide is now at P site. empty tRNA exits from E site

60
Q

termination in translation

A

termination begins when a stop codon on mRNA is reached.
a protein called a release factor cleaves polypeptide from last tRNA
ribosome splits into its subunits
ribosome and mRNA are recycled

61
Q

mutation

A

permanent change in nucleotide sequence of a cell’s DNA

can arise spontaneously (DNA replication error) or be induced by a mutagen (ex. chemicals and radiation)

62
Q

point mutation, types

A

single base change

silent mutation - no amino acid change, redundancy in code
missense - change amino acid
nonsense - premature stop codon

63
Q

frameshift mutation

A

shift in the reading frame, changes everything “downstream”

insertion or deletion of bases

64
Q

chrosome mutations

A

involves large segments of DNA (chromosomes)

deletion
duplication
inversions
translocations

65
Q

why regulate genes

A

maintain homeostasis

multicellular organisms have specialized cells

66
Q

gene regulation

A

blocks transcription of genes to save energy by not wasting it on unnecessary protein synthesis

67
Q

regulation of gene expression in prokaryotes

A

in prokaryotes, many genes are clustered together in a region under the control of a single promoter - region is called an operon

all genes in the operon are transcribed together into one continuous mRNA strand - polycistronic mRNA

individual proteins are then synthesized from mRNA

68
Q

operons

A

found in prokaryotic genomes
group of genes that are transcribed together
consists of a coding region and a regulatory region

69
Q

parts of an operon

A

Promoter - sequence of DNA where RNA polymerase binds and begins transcription
Repressor - proteins that binds to an operator site, preventing transcription of genes in operon
Operator - regulatory DNA sequence to which a repressor protein binds - inhibits transcription initiation
Genes

70
Q

repressible operons vs inducible operons

A

repressible operons are on and can be turned off ex. trp operon

inducible operons are off and can be turned on ex. lac operon

71
Q

gene regulation for eukaryotes

A

methods for regulating eukaryotic gene expression are complex and require large number of steps

do not use operon systems

control mechanisms fall into four general categories:

  1. transcriptional (as mRNA is being synthesized)
  2. post-transcriptional (as mRNA is being processed)
  3. translational (as protein is being synthesized)
  4. post-translational (after protein has been synthesized)
72
Q

transcriptional control

A

each gene has its own promoter
transcriptional control regulates which genes are transcribed and/or rate of transcription
access to promoters is provided by loosening DNA molecules from histones

73
Q

post-transcriptional control

A

controls availability of mRNA molecules to ribosomes

masking proteins bind to mRNA and inhibit further processing

74
Q

translational control

A

controls how often and how rapidly mRNA transcripts will be translated into proteins
variation of the length of the poly (A) tail on mRNA is related to rate of translation
initiation of translation stage can be blocked

75
Q

post-translational control

A

controls when proteins become fully functional, how long they are functional, and when they are degraded
ubiquitin-tagged proteins are degraded (DEATH TAG)

76
Q

recombinant DNA

A

cutting DNA fragments from different sources and recombining them together

purpose - to investigate genetic disorders, production of drugs (ex. insulin)

77
Q

restriction endonucleases / restriction enzymes

A
  • molecular scissors
  • recognize a specific DNA sequence and cuts the strands at a particular position or “recognition site”
  • isolated and purified only from bacteria
78
Q

how do restriction enzymes work

A
  • scans DNA and binds to its specific recognition sequence.
  • disrupts the phosphodiester and hydrogen bonds
  • results in 2 DNA fragments
79
Q

different DNA fragment ends produced after digestion by different restriction enzymes

A

sticky ends: DNA fragment ends with short single-stranded overhangs
blunt ends: DNA fragment ends are fully base paired

80
Q

restriction endonucleases: recognition sites

A

each restriction endonuclease recognizes its own specific recognition site (specific DNA sequence)
usually 4-8 base pairs long, characterized by a complementary palindromic sequence

81
Q

DNA ligase role with restriction endonucleases

A

DNA ligase rejoins cut strands of DNA together by reforming a phosphodiester bond
DNA ligase joins sticky ends and also blunt ends

82
Q

gel electrophoresis

A

technique used to separate charged molecules based on their size

restriction enzymes digest DNA into smaller fragments of diff lengths; diff DNA samples are loaded into wells of gel; negatively charged electrode at the end where wells are located with positively charged electrode at opposite end. negatively charged DNA migrate towards positive end due to attraction; smaller DNA fragments migrate faster

83
Q

plasmids

A

small, circular double-stranded DNA that can enter and exit bacterial cells
lack a protein coat
independent of bacterial chromosome
can be used to introduce foreign DNA into the bacteria to have the desired gene transcribed and translated

84
Q

plasmid mapping & restriction maps

A

diagrams that show restriction enzyme recognition sites and distances, measured in base pairs between the sites
allows scientists to determine which plasmids might be most suitable for a particular recombinant DNA procedure
used to determine which restriction enzyme should be used to cut the plasmid

85
Q

genetic engineering pioneers

A 
Stanley Cohen (plasmids) and Herbert Boyer (restriction enzymes)
experiments for selecting, recombining and transforming new genes into bacteria
ex. producing hormones like somatotropin and insulin with genetic engineering
86
Q

polymerase chain reaction

A

small sample of DNA can be amplified to make multiple copies of a desired DNA fragment, exponential growth using repeated cycles

one cycle:

  1. double stranded DNA is denatured with heat to separate strands by breaking H bonds (no DNA helicase or gyrase)
  2. DNA primers anneal to complementary template DNA that bracket the desired DNA sequence
  3. Taq polymerase add complementary nucleotides to synthesize new DNA strand

repeat cycle

87
Q

restriction fragment length polymorphism (RFLP)

A

polymorphism - any difference in DNA sequence (coding or non-coding) that can be detected between individuals
restriction fragment length polymorphism analysis - technique that compares different lengths of DNA fragments produced by restriction endonucleases to determine genetic differences between individuals by using complementary radioactive probes

88
Q

RFLP analysis

A
  1. digest DNA using restriction enzymes
  2. run digested DNA on gel using gel electrophoresis
  3. expose gel to a chemical to denature double-stranded DNA to become single-stranded
  4. southern blotting
89
Q

DNA sequencing

A

determine sequence of base pairs for genes

sanger dideoxy method

90
Q

sanger dideoxy method

A

dideoxy nucleotides lack an OH group
reaction stops when a dideoxynucletoide becomes incorporated (DNA polymerase cannot add next complementary base)
chain termination results in different DNA fragment lengths
separate different DNA lengths by gel electrophoresis, sequence can be read from gel in ascending order

Biology 12 (5 decks)

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