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AP Biology > Ch. 9: Molecular Biology > Flashcards

Ch. 9: Molecular Biology Flashcards

1
Q

Central dogma

A

DNA –> RNA –> protein –> trait

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2
Q

Griffith’s experiment

A

genetic info. can be transferred from dead bacteria to living bacteria (bacteria can uptake genetic info. from environment)
nonvirulent strain of pneumonia transformed into virulent strain when mixed w/ heat killed virulent strain

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3
Q

Transformation

A

ability of bacteria to absorb and express genetic information (DNA) obtained from their surroundings

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4
Q

Avery’s experiment

A

identified DNA as the heredity information of a cell

after removing protein coats from dead virulent bacteria stuff that was left was still able to transform bacteria (DNA)

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5
Q

Hershey and Chase experiment

A

est. that DNA was genetic material of phages
used simple structured phages (viruses that infect bacteria) injected w/ radioactive sulfur in proteins and radioactive phosphorus in DNA to show that DNA went into bacteria and it was DNA and not protein

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6
Q

Franklin, Watson, and Crick experiments

A

determine structure of DNA

x-ray diffraction photographs by Franklin helped Watson and Crick’s double helix twisted ladder model

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7
Q

One-gene-one-enzyme (polypeptide)-hypothesis

A

gene is defined as the segment of DNA that codes for a particular enzyme/ polypeptide

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8
Q

DNA replication (theory)

A

during interphase, a second chromatid copy of DNA is assembled
DNA molecule is unzipped, each strand serves as template to new, complementary strand. result is two identical double-stranded molecules of DNA

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9
Q

Semiconservative model

A

each new double-stranded molecule of DNA consists of template strand (old strand) and complementary strand (new, replicated DNA)

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10
Q

Helicase/ Replication fork

A

unwinds DNA helix during replication, forming Y-shaped replication fork

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11
Q

Single-stranded binding proteins

A

attach to each strand of uncoiled DNA during DNA replication to keep them separate

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12
Q

Topoisomerase

A

removes twists and knots that form in the double-stranded template as a result of the unwinding induced by helicase

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13
Q

DNA polymerase

A

enzyme that assembles the new DNA strand

moves in the 3’–>5’ so complement (new) strand is made in antiparallel, 5’–3’ direction

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14
Q

Leading strand

A

for the 3’–>5’ template strand, replication occurs continuously as DNA polymerase follows the replication fork, assembling a 5’–>3’ complementary strand

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15
Q

Lagging strand/ Okazaki fragments

A

DNA polymerase moves away from replication fork bc can only add nucleotides to the 3’ end
as DNA is uncoiled, DNA polymerase creates Okazaki fragments, requiring more time

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16
Q

DNA ligase

A

connects Okazaki fragments to produce a single complementary strand

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17
Q

Primase/ RNA primer

A

begins replication by forming RNA primer
leading strand and every Okazaki fragment on lagging strand must begin w/ RNA primer
DNA polymerase attaches to primer and makes DNA nucleotides

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18
Q

DNA replication (steps)

A
  1. Helicase unwinds, SSBPs and Topoisomerase keep apart
  2. Primase makes RNA primer to start
  3. DNA polymerase begins elongation
  4. Leading complementary strand assembled continuously
  5. Lagging strand assembled in Okazaki fragments
  6. Okazaki fragments joined by DNA ligase
  7. RNA primers replaced w/ DNA nucleotides
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19
Q

Prokaryotic vs. eukaryotic DNA replication

A
  1. Chromosome structure: prokaryotes have circular chromosome while eukaryotic chromosomes is linear w/ telomere ends
  2. Origins of replication: prokaryotic chromosome has one unique origin of replication while eukaryotes have multiple bc much larger chromosomes
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20
Q

Proofreading (DNA repair)

A

DNA polymerase checks if each newly added nucleotide correctly base-pairs with the template strand, if not the correct one is put in

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21
Q

Mismatch repair proteins (DNA repair)

A

repair errors that escape the proofreading ability of DNA polymerase

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22
Q

Excision repair proteins (DNA repair)

A

identify and remove damaged nucleotides caused by environmental factors like toxins or radiation
polymerase then uses the undamaged complementary strand as a template to repair damage

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23
Q

Excision repair proteins (DNA repair)

A

identify and remove damaged nucleotides caused by environmental factors like toxins or radiation
polymerase then uses the undamaged complementary strand as a template to repair damage

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24
Q

Protein synthesis steps

A
  1. Transcription: RNA molecules created by using one strand of DNA as template
  2. RNA processing: RNA is modified w/ deletions and additions
  3. Translation: processed RNA molecules used to assemble amino acids into a polypeptide
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25
Q

Replication of telomeres

A

during lagging strand replication RNA primer is removed and replaced w/ DNA nucleotides by DNA polymerase
problems that can occur when replication reaches end of DNA: not enough template strand remains for primase to attach/ at last primase no next Okazaki fragment for DNA polymerase to attach to so empty space is left
solution: enzyme telomerase attaches to end of template strand and extends template strand by adding repeat nucleotides… lagging strand will not lose DNA

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26
Q

Telomerase (aging)

A

telomerase active in young cells, but activity declines as cells age, eventually stopping; once telomerase stops, chromosome becomes shorter w/ each replication and DNA is slowly lost, resulting in non-viable daughter cells and aging affects seen

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27
Q

Kinds of RNA needed for protein synthesis (produced during transcription)

A

Messenger RNA (mRNA), Transfer RNA (tRNA), Ribosomal RNA (rRNA)

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28
Q

Messenger RNA (mRNA)

A

single strand of RNA that provides template (codons, 64 possible) for making amino acids into polypeptide

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29
Q

Transfer RNA (rRNA)/ Anticodon

A

short RNA molecule used for transporting amino acids to their proper place on the mRNA
nucleotides within tRNA interact/ pair and it folds into 3D molecule; one end of tRNA attaches to an amino acid, other end has the anticodon which binds w/ the codon on the mRNA during translation

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30
Q

Wobble pairing

A

exact base pairing between third nucleotide of the tRNA anticodon and the nucleotide of the rRNA codon often not required
allows the anticodon of some tRNAs to base pair w/ more than on kind of codon

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31
Q

Ribosomal RNA (rRNA)

A

combine w/ various proteins to form ribosomes
rRNA molecules are transcribed in the nucleolus and assembled w/ proteins imported from the cytoplasm to form a large and a small ribosome subunit… in cytoplasm these two subunits join to form ribosome (coordinates mRNA and tRNA during translation)

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32
Q

Transcription (steps)

A
  1. Initiation
  2. Elongation
  3. Termination
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33
Q

Initiation (transcription)

A

RNA polymerase attaches to promoter region (TATA box) and begins to unzip the DNA into two strands

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34
Q

Elongation (transcription)

A

occurs as RNA polymerase unzips DNA and assembles RNA nucleotides using one strand of the DNA as a template
5’ –> 3’
in contrast to DNA replication new nucleotides are RNA nucleotides and not DNA, only one DNA strand is transcribed and primers are not required

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35
Q

Termination (transcription)

A

RNA polymerase reaches special sequence of nucleotides that serve as termination point

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36
Q

5’ cap (mRNA processing)

A

guanine nucleotide w/ 2 additional phosphate groups, forming GTP
added to 5’ end of mRNA
provides stability to mRNA and point of attachment for small subunit of ribosome

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37
Q

Poly-A-tail (mRNA processing)

A

attached to 3’ end of mRNA
200 adenine nucleotides
provides stability to mRNA and controls movement of mRNA across nuclear envelope

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38
Q

RNA splicing (mRNA processing)

A

small nuclear ribonucleoproteins (snRNPs) delete introns (intervening non coding sequences) and splice exons (express polypeptide code)

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39
Q

Alternative splicing (mRNA processing)

A

selectively removing different parts of an RNA allows different mRNAs to be generated from the same RNA transcript

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40
Q

Where does translation occur?

A

cytoplasm

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41
Q

Translation (steps)

A
  1. mRNA attaches to ribosome
  2. sequence of codons on mRNA determines the sequence of amino acids in the polypeptide to be synthesized
  3. One by one, tRNA brings an amino acid to the ribosome such that the anticodon of the tRNA base-pairs w/ the codon of the mRNA
  4. newly arrived amino acid is attached w/ a peptide bond to the other amino acids already present
  5. tRNA released from ribosome
  6. process is repeated until “stop” codon on mRNA reached and full polypeptide made
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42
Q

Where does energy from translation come from?

A

GTP

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43
Q

Ribosome binding sites?

A

A, P and E

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44
Q

A site

A

for Amino acid/ Acceptor
in the first position, accepts an incoming tRNA carrying an amino acid to be then passed on to the tRNA in the second position

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45
Q

P site

A

for Polypeptide

in the second position, holds the tRNA w/ a growing chain of amino acids

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46
Q

E site

A

for Exit

in the third position, holds the tRNA after it gives up its amino acid

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47
Q

Initiation (translation)

A
  1. begins when small ribosomal subunit attaches near the end of the mRNA
  2. tRNA w/ anticodon UAC carrying methionine attaches to the mRNA at start codon AUG
  3. large ribosomal subunit attaches to the mRNA w/ the tRNA (that has methionine), occupying the P site (middle)
    ribosome is now completely assembled w/ the mRNA and one tRNA
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48
Q

Elongation (translation)

A
  1. occurs as additional tRNAs arrive w/ their amino acids; newly arrived tRNA attaches to A site w/ anticodon of the mRNA codon
  2. amino acid on tRNA in P site is transferred to the amino acid on the newly arrived tRNA in the A site
  3. translocation occurs as the ribosome moves over one binding site, A site open for new tRNA; meanwhile, tRNA in E site is released, free to bind w/ its specific amino acid and provide another delivery to the mRNA
  4. Elongation as tRNA continues to bring amino acids, polypeptide growing one amino acid at a time
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49
Q

Termination (translation)

A

occurs when the ribosome encounters one of three STOP codons
completed polypeptide, last tRNA, and two ribosomal subunits are released… they can now attach to same/ another mRNA and repeat the process

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50
Q

Mutation

A

any sequence of nucleotides in a DNA molecules that does not exactly match the original DNA from which it was copied
occur as result of replication error or mutagens

51
Q

Mutagen

A

radiation or chemicals that cause mutations

carcinogens activate uncontrolled cell growth (cancer)

52
Q

When are mutations passed down?

A

when it occurs in a sex cell to introduce new allelic variation into the pop. and potential for evolutionary change

53
Q

Point mutation

A

single nucleotide error

Ex. substitution, deletion, insertion, frameshift

54
Q

Substitution (point mutation)

A

occurs when the DNA sequence contains an incorrect nucleotide in place of the correct nucleotide

55
Q

Deletion (point mutation)

A

occurs when a nucleotide is omitted from the nucleotide sequence

56
Q

Insertion (point mutation)

A

occurs when a nucleotide is added to the nucleotide sequence

57
Q

Frameshift

A

occurs as a result of a nucleotide deletion/ insertion –> cause all subsequent nucleotides to be displaced one position
if occurs in DNA segment whose transcription produces mRNA, all codons following transcribed mutation will change

58
Q

Mutations that result if mRNA is produced from a DNA w/ point mutation

A

silent mutation, missense mutation, nonsense mutation

59
Q

Silent mutation

A

new codon still codes for same amino acid by code redundancy/ wobble pairing (relaxed requirement for nucleotide in third position)

60
Q

Missense mutation

A

new codon codes for a new amino acid
effect can be minor, or can produce a protein unable to fold into its proper 3D shape and therefor unable to function
Ex. hemoglobin protein that causes sickle-cell disease

61
Q

Nonsense mutation

A

new codon codes for STOP codon

Ex. hemoglobin protein that causes some forms of thalassemia

62
Q

Chromosomal aberrations

A

changes in the chromosome structure/ makeup of genome

Ex. deletions, duplication (globin genes, antifreeze genes), inversions, translocations, transposons)

63
Q

Deletions (chromosomal abberation)

A

occur when segments of chromosomes are lost

fatal is significant loss of important DNA

64
Q

Duplications (chromosomal abberation)

A

occur when segments of chromosome are repeated; if occur within gene segment likely to cause frameshift mutation w/ harmful consequences
can be beneficial: provides additional gene products for processes that are in high demand/ provide opportunity for subsequent mutations to create novel gene variation w/out disrupting original gene activity
Ex. globin genes, antifreeze genes

65
Q

Globin genes (duplication)

A

similarities among various globin chains of hemoglobin suggest that they each evolved from a common gene
in humans, multiple variations of the gene occur on two separate chromosomes

66
Q

Antifreeze genes (duplication)

A

shows how novel genes can originate from gene duplication of genes originally used for a totally different purpose
glycoproteins in blood of certain arctic fish provide resistance to freezing
appear to be result of many duplications and divergence of gene that codes for trypsinogen (digests proteins in small intestine)

67
Q

Inversions (chromosomal abberation)

A

occur when DNA segment is reversed

depending on where chromosome breaks happen, mutation may not have significant effect

68
Q

Translocations (chromosomal abberation)

A

occur when segments of chromosome are deleted and inserted elsewhere, within same chromosome of another
Ex. form of Down syndrome happens when piece of 21 translocated to 14

69
Q

Transposons (chromosomal abberation)

A

naturally occurring mutations; are DNA segments that insert themselves throughout the genome after copying/ deleting themselves from another area
Ex. in corn transposons responsible for mutants w/ weird pigment; human genome has as much as 50% of DNA from transposons, although most in introns

70
Q

Virus mechanism

A

virus penetrates cell, takes over its metabolic machinery, assembles hundreds of new viruses that are copies of itself, then leaves the cell to infect other cells, host cell usually destroyed

71
Q

Bacteriophage

A

viruses that only attack bacteria

72
Q

Virus structure

A

nucleic acid: RNA/ DNA not both to house hereditary info
capsid/ protein coat: encloses nucleic acid
envelope: surrounds capsid of some viruses, incorporates phospholipids and proteins obtained from cell membrane of host cell

73
Q

Lytic cycle

A

follow virus mechanism, and host cell destroyed
in most DNA viruses, DNA –> new viral DNA –> viral mRNA –> viral proteins to make more viruses
for some RNA viruses, RNA serves as mRNA or as template to make mRNA to be then translated to make proteins

74
Q

Lysogenic cycle

A

viral DNA temporarily incorporated into the DNA of the host cell where it remains inactive until some trigger causes the virus to begin cycle

75
Q

Provirus

A

virus in dormant state

76
Q

Retrovirus

A

ssRNA viruses that use reverse transcriptase to make a DNA complement of their RNA. DNA complement either transcribed to mRNA (lytic) or begins lysogenic so incorporates into host DNA
no specificity to where it inserts into host genome so special kind of transposon
Ex. HIV

77
Q

RNA viruses

A

have much higher rates of replication errors bc RNA replication lacks the repair that happens in DNA replication so mutations in RNA viruses more frequent
Ex. HIV, flu, common cold

78
Q

How do viruses intensify in their pathogenicity?

A

high rates of mutation bc no correction; host populations don’t evolve immune systems as fast as viruses so stay v virulent, esp. RNA

79
Q

Binary fission

A

reproduction of a prokaryotic cell
chromosome replicates and the cell divides into two identical cells, each w/ one chromosome; there is no nucleus to divide so spindle/ microtubules not needed

80
Q

Plasmid

A

short, circular dsDNA molecules outside the chromosome
carry genes beneficial but not normally essential to the survival of a prokaryote
replicate independently of the chromosome

81
Q

R Plasmid

A

provide bacteria w/ resistance to antibiotics

82
Q

Episome

A

plasmid that can become incorporated into the prokaryotic chromosome

83
Q

Prokaryotic vs. Eukaryotic DNA replication

A

prokaryotic DNA is circular so replication begins at a single unique origin then progresses in both directions until they meet; eukaryotes have larger chromosomes so need multiple origin sites
prokaryotes also don’t have the telomere problem bc circular

84
Q

Transcription/ translation in prokaryotes

A

transcription similar but prokaryotes don’t have introns

translation and transcription happen simultaneously in the cytoplasm bc no nucleus

85
Q

Horizontal gene transfer

A

how genetic variation is introduced into prokaryotes

Ex. conjugation, transduction, transformation

86
Q

Conjugation

A

DNA exchange (chromosomal/ plasmid DNA) between bacteria through donor pilus attaching to recipient

87
Q

F plasmid

A

contains genes enabling bacteria to produce pili; when received, recipient can too become a donor cell

88
Q

Transduction

A

new DNA is introduced into the genome of a bacterium by a virus

89
Q

Transformation

A

bacteria absorb DNA from their surroundings and incorporate it into their genome facilitated by specialized proteins on some cell membrane of some bacteria

90
Q

Operon

A

unit of DNA that contains multiple genes whose products work together to direct a single metabolic pathway
structure: PROG
Ex. trp operon, lac operon

91
Q

Promoter region (operon)

A

sequence of DNA to which RNA polymerase attaches to begin transcription

92
Q

Operator region (operon)

A

engaged by a regulatory protein to either block/ promote action of RNA polymerase (turn operon on/ off)

93
Q

Structural gene (operon)

A

contain coding DNA to direct the production of some particular end product

94
Q

Regulatory gene/ protein (operon)

A

outside operon region, produces regulatory protein that engages the operator region and governs whether RNA polymerase can bind to the promoter region
are allosteric –> become active/ inactive only when they bind to specific substrate
Ex. repressor (blocks attachment), activator (promotes attachment)

95
Q

Trp operon

A

repressible operon that produces enzymes for the synthesis of tryptophan in E. coli
when there is not a lot of tryptophan, regulatory gene produces inactive repressor that DOES NOT bind to operator so RNA polymerase activates, then when there is enough tryp., the tryp. acts as corepressor and makes repressor active so it binds to the operator and prevents RNA polymerase from doin its thing
negative regulation

96
Q

Lac operon

A

inducible operon that controls the breakdown of lactose in E. coli
regulatory gene produces active repressor that binds to operator which disables RNA polymerase… when lots lactose, repressor becomes inactive and RNA polymerase can act
negative regulation

97
Q

Glucose repression

A

second regulatory process that influences lac operon
when glucose and lactose both present, glucose is preferred for energy. but when only lactose, this process enhances the breakdown of lactose
activator regulatory protein CAP is activated by cAMP when glucose is absent so CAP binds and promotes RNA polymerase to transcribe
positive regulation

98
Q

Negative feedback mechanism

A

turn on in response to change in environment and turn off when suitable conditions return

99
Q

Why is gene regulation more complicated in eukaryotes than prokaryotes?

A
  1. Multicellularity: different gene regulation programs for different cells
  2. Chromosome complexity: chromosomes more complex bc bigger and proteins involved, some metabolic process require activation of more than one gene on dif. chromosomes so coordinated expression requires complicated regulation
  3. Uncoupling of transcription and translation: transcription occurs isolated from translation so more mechanisms needed to control gene expression
100
Q

Gene regulation in eukaryotes

A

DNA methylation, histone modification, X inactivation, Transcription initiation, RNA processing, RNA interference (RNAi), mRNA degradation, Protein degradation

101
Q

DNA methylation

A

methyl groups (CH3) attach to DNA bases to make it more difficult for transcription factors to bind, essentially DNA inactivation

102
Q

Histone modification

A

change in org. of histone proteins within DNA
Acetylation: acetyl group (-COOH3) attaches to histone to loosen their grip on DNA molecule –> activate transcription
Methylation: (-CH3) methyl group attached to histones to repress transcription

103
Q

X inactivation

A

few days after fertilization, one of two X sex chromosomes of female embryo gets randomly inactivated; descendants of each cell maintain same inactivated X
purpose: equalize gene dosage that both males (only one X) and females express

104
Q

Transcription initiation/ Transcription complex

A

transcription complex: proteins associated w/ RNA polymerase activity regulate transcription
components: general transcription factors, specific transcription factors, coactivators, mediators

105
Q

General transcription factors

A

proteins needed by transcription events to successfully initiate transcription by RNA polymerase
attach w/ RNA pol. to promoter region upstream and adjacent to gene to be transcribed
some target TATA box

106
Q

Specific transcription factors

A

additional proteins regulate specific transcription activities, specific to cell type, gene, or timing
2 kinds: activators and repressors
attach to enhancers: DNA binding site that can be far away from gene; bc distance, DNA w/ enhancer, and so specific transcription factor, folds so that it can join the general transcription factors and RNA pol. on promoter

107
Q

RNA processing

A

can produce different mRNAs by slicing the primary RNA transcript in different ways
allows single gene to encode proteins specific to cell type/ stage

108
Q

RNA interference (RNAi)

A

gene silencing by short RNA molecules (mRNAs and siRNAs)
3 ways:
- bind to complementary sequences of mRNAs in cytoplasm and block their transcription
- bind to, cleave, and degrade complementary sequences of mRNA
- bind to chromatin in nucleus and prevent gene transcription

109
Q

MicroRNAs (mRNAs)

A

ssRNAs that originate from mRNAs that have been transcribed from regulatory genes –> these mRNAs are truncated in cytoplasm to form miRNAs

110
Q

Short interfering RNAs (siRNAs)

A

ssRNAs that originate from dsRNAs that have formed in cytoplasm from ss/ds RNAs introduced into cell experimentally –> dsRNAs truncated in cytoplasm to form siRNAs

111
Q

mRNA degradation

A

occurs bc of RNAi and bc mRNA are unstable

as mRNA ages degrading enzymes target poly-A tail and 5’ cap

112
Q

Protein degradation

A

final life stage for proteins

as proteins age, their 3D shape changes and they lose function to be destroyed by ubiquitin

113
Q

Stem cells

A

cells in early stages of embryonic development, have potential to become any kind of fetal/ adult cell
as cells divide, transcription factors activate some genes and repress others, so causing cell specialization and cell determination

114
Q

Reproductive cloning

A

process of making an individual w/ the same nuclear DNA as another animal
nucleus of fully differentiated cell swapped in for nucleus of stem cell where transcription factors absent (Dolly the sheep)

115
Q

Recombinant DNA

A

contains DNA segments/ genes from different sources
Ex. DNA from one part of molecule to another, chromosome to chromosome, one organism to another
can occur by: viral transduction, bacterial conjugation, transposons, crossing over, biotechnology

116
Q

Restriction enzymes/ Restriction site/ Sticky end

A

cut DNA at restriction sites in recombinant DNA technology
cut across dsDNA in staggered way, producing one strand of DNA extending beyond complementary strand (sticky end)
obtained from bacteria that make these enzymes to combat viruses

117
Q

DNA cloning (steps)

A
  1. Use restriction enzymes to cut up foreign DNA that contains a gene to be copied
  2. Use same restriction enzyme to cut up DNA of cloning vector (transfers DNA; ex. plasmid)
    - use plasmid that has: ampR, GFP, lacZ genes
  3. Mix cut foreign DNA w/ cut plasmids
  4. Apply DNA ligase to stabilize attachments
  5. Mix plasmids w/ bacteria to allow transformation
  6. Grow the transformed bacteria in presence of ampicillin and X-gal (to see which has desired gene expressed)
118
Q

Genomic library

A

collection of bacteria, each of which contain a fragment of the genome of the foreign DNA but together contain the entire genome of the foreign DNA
end product of DNA cloning

119
Q

Complementary DNA (cDNA)

A

to avoid intron prevention transcription of foreign genes, reverse transcriptase is used to obtain the DNA fragment w/ desired gene directly form the mRNA that codes for the desired polypeptide

120
Q

Polymerase chain reaction (PCR) (steps)

A

technique used to make large numbers of DNA copies faster than DNA cloning… often to amplify v small gene

  1. DNA is heated to denature H bonds in dsDNA
  2. DNA is cooled and ssDNA primers added
  3. Special heat tolerant DNA polymerase added
  4. Repeat above steps (2^n each time)
121
Q

Gel electrophoresis

A

procedure that separates restriction fragments
DNA fragments of different lengths are separated as they diffuse through electric gel, bc DNA is (-) bc of phosphate groups, it moves towards (+) anode so shorter move farther
often used to compare DNA of close species

122
Q

Restriction fragment length polymorphisms (RFLPs)

A

fragments that differ in length bc of polymorphisms: slight differences in DNA sequencing
in DNA fingerprinting, RFLPs produced from DNA left at scene compared to RFLPs of suspects

123
Q

Short tandem repeats (STRs)

A

polymorphism where short sequences of nucleotides (2-5 bp) repeat multiple times, w/ the # of repeats varying a lot between ppl

124
Q

Issues that biotechnology presents

A

w/ new tech., always ethical questions arrise
Pharmaceuticals: Insulin and HGH
Human disease profiles: side effects
Transgenic organisms: GMOs, GMAs and effects on food chain
Reproductive cloning: selective breeding that often fails

AP Biology (15 decks)

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