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BIOL 107 > Chapter 9: Molecular Biology > Flashcards

Chapter 9: Molecular Biology Flashcards

1
Q

define photograph 51

A
  • x-ray crystallography picture of DNA
  • showed double-helix structure of DNA
  • taken by Rosalind Franklin
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2
Q

what did Rosalind Franklin and Maurice Wilkins do

A
  • used x-ray crystallography to study DNA structure
  • photograph 51
  • concluded DNA was composed on 2 antiparallel sugar-phosphate backbones with nitrogenous bases paired in the interior
  • determined that DNA has a uniform diameter from purine and pyrimidine
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3
Q

what did James Watson and Francis Crick do

A
  • developed double-helical model for DNA
  • concluded there are 2 polynucleotide strands in antiparallel orientation
  • determined the nitrogenous bases in the interior always paired with others; A paired with T; C paired with G
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4
Q

who won the nobel prize in 1962

A
  • Watson
  • Crick
  • Wilkins
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5
Q

why didn’t Rosalind Franklin win the nobel prize in 1962

A
  • she died before the prize was awarded
  • died from ovarian cancer probably from exposure to radiation from her experiments
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6
Q

what did scientists think were inheritable features before it was discovered that it was DNA

A
  • proteins
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7
Q

describe the timeline of the human genome project

A
  • began 1990
  • declared complete in 2003 with 92% of human genome
  • entire genome complete in january 2022
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8
Q

what was the goal of the human genome project

A
  • sequence all the nucleotides that make up human DNA
  • identify, map, and sequence all of the genes
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9
Q

define the nucleotide adenine

A
  • pairs with thymine
  • double ringed purine
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10
Q

define the nucleotide guanine

A
  • pairs with cytosine
  • double ringed purine
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11
Q

define the nucleotide cytosine

A
  • pairs with guanine
  • single ringed pyrimidine
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12
Q

define the nucleotide thymine

A
  • pairs with adenine
  • single ringed pyrimidine
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13
Q

define the nucleotide uracil

A
  • pairs with adenine in RNA
  • single ringed pyrimidine
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14
Q

define complementary base pairs

A
  • A pairs with T
  • G pairs with C
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15
Q

define double helix

A
  • two strands of DNA twist around each other
  • uniform diameter
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16
Q

define phosphodiester backbone

A
  • backbone of DNA
  • made from phosphate group of one nucleotide and sugar molecule of another nucleotide
  • covalently bonded
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17
Q

define histone

A
  • protein that DNA wraps around
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18
Q

define nucleosome

A
  • DNA wrapped around 8 histones
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19
Q

define chromatin

A
  • DNA and proteins
  • includes genes, regulatory elements
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20
Q

define chromosome

A
  • condensed chromatin
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21
Q

define chromatid (sister chromatid)

A
  • one half of a duplicated chromosome
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22
Q

define homologous chromosome

A
  • paired chromosomes that carry the same genes
  • one from each parent
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23
Q

define non-homologous/heterologous chromosome

A
  • not in a pair
  • do not have the same genes in the same place
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24
Q

define euchromatin

A
  • loosely packed
  • genetically active
  • rich in genes used for transcription process
  • found in inner nucleus
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25
define heterochromatin
- tightly packed - genetically inactive - found in outer nucleus
26
describe the genes of a humans smallest chromosome
- chromosome 21 - contains 48 million base pairs - measure 1.5 inches (40mm) long
27
describe the genome of E. coli
- 4 million base pairs - measures 1mm
28
describe the total human genome
- 3 billion base pairs - measures 6 feet
29
what bonds are between nucleotides
hydrogen bonds
30
how many hydrogen bonds are between adenine and thymine
2
31
how many hydrogen bonds are between guanine and cytosine
3
32
what are the 3 parts of nucleotides
- deoxyribose (5 C sugar) - phosphate group - nitrogenous base
33
way to remember which nucleotides are purines
- pure as gold - adenine - guanine
34
way to remember which nucleotides are pyrimidines
- cut the pie (py) - cytosine - thymine
35
describe the direction of antiparallel strand of DNA in the double-helix
- 5' to 3' - 5': where phosphate is - 3': where sugar is
36
define the semi-conservative model of DNA replication
- each of the two strands that make double helix serve as a template from which a new complementary strand is copied - one strand splits as two strands are made
37
define origin of replication
- where DNA begins to unwind
38
describe the number of origins of replication in prokaryotes vs eukaryotes
- prokaryotes: one origin - eukaryotes: several origins
39
describe the chromosome structure in prokaryotes vs eukaryotes
- prokaryotes: one circular - eukaryotes: several linear
40
describe the rate of replication in prokaryotes vs eukaryotes
- prokaryotes: 1000 nucleotides/sec - eukaryotes: 50 to 100 nucleotides/sec
41
which cells have telomeres: prokaryotes or eukaryotes
- eukaryotes - ends of linear chromosomes
42
is DNA replication exergonic/catabolic or endergonic/anabolic
- endergonic/anabolic - takes a lot of energy to build DNA
43
where does energy come from for DNA replication
- ATP, GTP, TTP, CTP
44
how does the replication machinery know where to begin
- origin of replication - identified by specific nucleotide sequences
45
how is the DNA unwound
helicase enzyme
46
how many replication forks are formed and which direction does the replication proceed
- 2 replication forks - goes in both directions
47
is DNA replication conservative or semiconservative
- semiconservative - parent double helix unwinds and each strand become template - two DNA molecules are created from one
48
what are the limitations of DNA polymerase and how are those limitations overcome
- cannot intiate DNA synthesis - solved with RNA primer
49
how does DNA polymerase add the first nucleotide
- where the RNA primer is
50
how is over-winding of the DNA polymerase prevented
topoisomerase
51
how many primers are needed on the leading and lagging strands
- leading: 1 - lagging: multiple
52
summarize the process of DNA replication
- DNA unwinds at the origin of replication - new bases are added to the complementary parental strands; one new strand is made continuously while the other is made in pieces - primers are removed and new DNA nucleotides are put in place - backbone is sealed by DNA ligase
53
what direction is DNA read during replication
- read up - from 3' to 5' end of parental strand
54
what direction is the new DNA strand written during replication
- write down - from 5' to 3' end of new strand
55
which end of a DNA strand are nucleotides added to
3' end of growing strand
56
define leading strand
- new strand being replicated that is continuously synthesized - doesn't need to stop because it reads form 3' to 5' - top left, bottom right of diagram
57
define lagging strand
- new strand being replicated that is discontinuously synthesized - stops and leap frogs; if not it would read in wrong direction from 5' to 3' - bottom left, top right on diagram
58
define helicase and it's involvement in DNA replication
- unwinds DNA double helix at replication fork
59
define single-stranded binding proteins and their involvement in DNA replication
- prevent DNA from refolding into double helix - stabilizes DNA strands
60
define topoisomerase and it's involvement in DNA replication
- prevents DNA from overwinding on the ends - ahead of replication fork - breaking, swiveling, and rejoingin DNA strands
61
define primase and it's involvement in DNA replication
- make RNA primers - at 5' end of leading strand - at 5' end of each okazaki fragment in lagging strand
62
define DNA polymerase 3 and it's involvement in DNA replication
- read template strand and synthesizes new strand - adds nucleotides to RNA primer or pre-existing DNA strand
63
define DNA polymerase 1 and it's involvement in DNA replication
- replaces RNA bases from RNA primers with DNA bases
64
define DNA ligase and it's involvement in DNA replication
- fixes gap in phosphodiester backbone - joins okazaki fragments of lagging strand - joins 3' end of leading stand that replaces primer to the rest of the leading strand
65
define RNA primers and their involvement in DNA replication
- RNA nucleotides put down to help DNA polymerase know where to start - short sequence of RNA bases - made by enzyme primase
66
define okazaki fragments
- fragments made on lagging strand of DNA
67
what is a problem in eukaryotic DNA replication; explain the effects on the leading strand and the lagging strand
- chromosomes are linear so DNA replication reaches an end - leading strand: synthesis continues until the end of the chromosome - lagging strand: no place for primer to be made for the end segment to be copied so the ends remain single-stranded (unpaired)
68
how do cells overcome the problem of DNA replication in the lagging strand leaving a portion unpaired
- telomeres at the ends of chromosomes - heterochromatin - repetitive sequence that doesn't code for a gene - there is small loss over time in the sequences as DNA continues to replicate
69
what is the sequence in telomeres in humans and how many times is it repeated
- TTAGGG - repeated 100 to 1000 times in each chromosome
70
what does the small loss in sequences of telomeres potentially cause
- aging
71
describe the process of telomere replication
- there is missing replication of DNA on the lagging strand - telomerase extends the unreplicated end - DNA polymerase can complete the replication of the lagging strand
72
define DNA proofreading
- DNA polymerase can make mistakes while adding nucleotides but it also proofreads every new base as it moves along - detects incorrect bases, removes them, and replaces them with the correct bases
73
define mismatch repair
- mismatch repairs enzymes recognize incorrect bases AFTER replication - excises incorrect base and replaces it
74
define nucleotide excision repair
- DNA double strand is unwound after replication - incorrect bases are removed by enzyme nuclease as well as a few others on each side of the mistake - DNA polymerase repairs the hole with the correct bases - DNA ligase forms final phosphodiester bond
75
define thymine dimers
- two thymines forming a bond on the same strand of DNA - usually caused by UV light - fixed by nucleotide excision repair
76
define the central dogma
- process from DNA to RNA to proteins - cellular chain of command that dictates the flow of genetic information - DNA transcribed to mRNA translated to proteins
77
define transcription
- synthesis of RNA under direction of DNA - produces mRNA: template for translation
78
define translation
- synthesis of a polypeptide occurring under the direction of mRNA - occurs in ribosomes
79
define gene expression
- process by which DNA directs protein synthesis - includes transcription and translation
80
does all DNA and all genes code for a product
- no
81
where does DNA transcription take place
- nucleus
82
where does mRNA translation take place
- ribosomes in the cytoplasm
83
are proteins functional right after being made
- no - must be folded in endoplasmic reticulum and packaged in golgi apparatus
84
define non-protein coding genes and give an example
- genes that don't code for a protein - functional RNAs: tRNA that carries amino acids
85
are non-protein coding genes like functional RNAs transcribed, translated, or both
- transcribed but not translated
86
what is special about transcription and translation in prokaryotic cells
- have no nucleus so both take place in the cytoplasm - transcription and translation can happen at the same time
87
define operons
- only in prokaryotes - transcribed regions that include more than one gene - cluster of genes with similar functions under the control of a single promoter
88
define the lac operon
- set of genes that makes all proteins needed to take in and break down lactose
89
define the one gene-one enzyme hypothesis
- original thought behind transcription and translation - each gene codes for one enzyme
90
what four things disprove the one gene-one enzyme hypothesis
- many genes encode for proteins other than enzymes: transport, signaling, structural proteins - some genes only encode for part of a protein - some genes encode for non-coding RNAs: rRNA, tRNA, etc - many genes have more than 1 exon and are processed differently to produce multiple products
91
describe the smallest gene in the human genome
- SRY gene - determines male characteristics: on Y chromosome - has 828 nucleotides and makes 204 amino acids
92
define transcription factors
- proteins that bind to the promoter region of the gene to be transcribed - recruit RNA polymerase and bind with it to form initiation complex
93
define promoter
- region of DNA where transcription is initiated
94
define RNA polymerase
- enzyme that transcribes DNA into mRNA - catalyzes process of transcription - synthesizes RNA in a 5' to 3' direction (read up, write down)
95
define non-template DNA
- coding strand - DNA strand that is not being transcribed - will have similar sequence to the new RNA strand
96
define template DNA
- strand of DNA being transcribed - strand that mRNA is based off of in transcription - will have opposite bases as mRNA
97
define RNA transcript
- mRNA that is made from transcription
98
define transcription initiation
- transcription factors bind to promoter region of the gene to be transcribed - transcription factors recruit RNA polymerase and bind with it to form initiation complex - RNA polymerase recognizes start sequence and begins synthesizing RNA transcript in 5' to 3' direction
99
define transcription elongation
- RNA polymerase unwinds the DNA (10 to 20 bases at a time) - RNA polymerase reads the DNA on the template strand and attaches the complementary RNA nucleotide - the RNA nucleotide is joined to the pervious one on the 3' end (of the RNA) via a phosphodiester bond along the backbone
100
define transcription termination
- RNA polymerase reaches and transcribes the termination sequence - the RNA transcript is released by RNA polymerase - RNA polymerase detaches from the DNA officially ending transcription
101
define polyadenylation sequence
- termination sequence in eukaryotic cells - AAUAAA
102
define post-transcriptional pre-mRNA processing
- modifications to mRNA before it can be translated in eukaryotic cells - modifications: 5' capping, poly A tail addition, RNA splicing
103
describe the difference between DNA polymerase and RNA polymerase
- DNA polymerase: makes DNA during DNA replication - RNA polymerase: make RNA during transcription
104
why does transcription not require ssb proteins to prevent rewinding of the DNA
- RNA polymerase only unwinds 10 to 20 bases at a time - small section has little chance of rewinding
105
what are the RNA complementary bases to DNA bases (formatted DNA-RNA)
- A-U - T-A - G-C - C-G
106
how is transcription termination different in prokaryotes and eukaryotes
- prokaryotes: RNA is immediately ready for translation or transcription and translation can happen at the same time - eukaryotes: RNA reads special termination sequence called polyadenylation sequence (AAUAAA); mRNA is bound by proteins and needs additional processes
107
what are 2 unique features of prokaryotic gene expression
- happens solely in the cytoplasm - RNA transcript does not need modification
108
how do the unique features of prokaryotic transcription affect gene expression
- multiple RNA polymerases can transcribe a single gene at the same time - multiple ribosomes can simultaneously translate mRNA transcripts
109
where and when does post-transcriptional pre-mRNA processing take place
- in the nucleus - after transcription, before translation
110
define exons and introns
- only in eukaryotic cells - exons: coding sequences - introns: non-coding sequences
111
what is removed in RNA splicing
- introns - sometimes exons: creates different proteins from the same gene
112
what is the 5' and 3' end of the RNA transcript capped with during modification
- 5': guanine nucleotide - 3': multiple adenine nucleotides
113
explain the relationship between the amount of genes and proteins a person has
- more proteins than genes - multiple proteins can be made from one gene due to RNA splicing modification
114
what is the size of the human genome
- 3000 genes
115
define mRNAs (messenger RNAs)
- directs recruitment of tRNA molecules and production of the polypeptide - determines sequences of amino acids in polypeptide - binds to the small ribosomal subunit
116
define tRNAs (transfer RNAs): what 4 things do they all have
- carry specific amino acid on one end - includes anticodon - single RNA strand about 80 nucleotides long that folds into classic tRNA shape - utilizes specific aminoacyl tRNA-synthetase to attach its amino acid
117
define anticodon
- 3 complementary nucleotides on tRNA
118
define aminoacyl-tRNA synthetase
- enzyme on tRNA that attaches a specific amino acid
119
define ribosome (in translation)
- reads mRNA and produces corresponding polypeptide - made of proteins and rRNA - has 2 subunits - has 3 binding sites for tRNAs
120
define a site (aminoacyl-tRNA binding site)
- on large ribosomal subunit - where all tRNA after 1st enter and bind to codon of mRNA
121
define p site (peptidyl-tRNA binding site)
- on large ribosomal subunit - where 1st tRNA enters - forms peptide bond between amino acid in p site and a site
122
define e site (exit site)
- on large ribosomal subunit - where tRNA goes after adding amino acid to polypeptide chain - where tRNA exits ribosome
123
define genetic code and why it's known as conserved and redundant
- nucleotide triplets; RNA codon table - conserved: bases make the same amino acids across all species - redundant: repetitive; multiple codons can code for the same amino acid
124
what are the 4 components of translation
- ribosome - transfer RNA - messenger RNA - polypeptide
125
what is the breakdown of what ribosomes are made of
- 1/3 protein - 2/3 rRNA
126
what are the 2 subunits of a ribosome and what are their purposes
- small subunit: decodes genetic message (mRNA) - large subunit: catalyzes peptide bond formation
127
what are the 3 tRNA binding sites on ribosomes
- E - P - A
128
which binding site on ribosomes do tRNA enter
- a site - first tRNA enters at p site
129
describe how mRNA is read during translation, including the start codon
- read in 3 base codon fashion - read 5' to 3' - each codon on mRNA interacts with anticodon on tRNA - start codon always AUG on mRNA
130
what is the product of translation
- polypeptide
131
how are polypeptides produced in translation
- amino acids bonded together through interaction of tRNA on p site and tRNA on a site
132
what type of bonds are formed during translation
- peptide bonds - covalent
133
how are transcription and translation different in regards to how strands are read
- transcription: read 3' to 5' - translation: read 5' to 3'
134
how is the genetic code decoded
- translation - nucleotides decoded/translated into amino acids
135
what are the 3 stop codons
- UAA (u are annoying) - UGA (u go away) - UAG (u are gone)
136
what animo acid does the start codon (AUG) code for
- methionine
137
does the stop codon code for an amino acid
- no
138
what is the reading frame
- determined by the first codon (AUG on mRNA) - sequence of 3 bases read at a time
139
describe translation initiation
- mRNA binds to small ribosomal subunit - start codon (AUG) is located - initiator tRNA binds to start codon at p site - energy is used to recruit and bind the large ribosomal subunit
140
describe translation elongation
- tRNA enters the a site and bonds to corresponding codon of mRNA - peptide bond formed between chain of amino acids at p site and new amino acid at a site - mRNA is shifted causing tRNAs to shift sites: tRNA at p site breaks its bond with mRNA and breaks away through e site; tRNA at a site shifted to p site and is attached to growing polypeptide chain
141
describe translation termination
- stop codon in mRNA is recognized (UAA, UGA, UAG) - release factor is recruited and binds to stop codon causing hydrolysis of polypeptide from tRNA - energy utilized to cause dissociation of translation components
142
what happens to the polypeptide chain after translation
- goes to endoplasmic reticulum to be folded - taken to golgi apparatus to be processed and transported
143
define gene expression
- process of "turning on" a gene to produce RNA and proteins - done through stopping transcription or translation
144
why are genes regulated
- to control timing, location, and amount of gene expression
145
do all cells need to express all genes
- no
146
how are genes regulated in prokaryotes
- almost entirely through transcription - because transcription and translation can happen simultaneously, transcription must be stopped so gene isn't automatically translated
147
how are genes regulated in eukaryotes
- multiple levels: - epigenetic - transcriptional - post-transcriptional - translational - post-translational
148
define epigenetic
- one gene affects regulation of another gene

BIOL 107 (18 decks)

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