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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
Q

define heterochromatin

A
  • tightly packed
  • genetically inactive
  • found in outer nucleus
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26
Q

describe the genes of a humans smallest chromosome

A
  • chromosome 21
  • contains 48 million base pairs
  • measure 1.5 inches (40mm) long
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27
Q

describe the genome of E. coli

A
  • 4 million base pairs
  • measures 1mm
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28
Q

describe the total human genome

A
  • 3 billion base pairs
  • measures 6 feet
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29
Q

what bonds are between nucleotides

A

hydrogen bonds

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30
Q

how many hydrogen bonds are between adenine and thymine

A

2

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31
Q

how many hydrogen bonds are between guanine and cytosine

A

3

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32
Q

what are the 3 parts of nucleotides

A
  • deoxyribose (5 C sugar)
  • phosphate group
  • nitrogenous base
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33
Q

way to remember which nucleotides are purines

A
  • pure as gold
  • adenine
  • guanine
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34
Q

way to remember which nucleotides are pyrimidines

A
  • cut the pie (py)
  • cytosine
  • thymine
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35
Q

describe the direction of antiparallel strand of DNA in the double-helix

A
  • 5’ to 3’
  • 5’: where phosphate is
  • 3’: where sugar is
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36
Q

define the semi-conservative model of DNA replication

A
  • 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
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37
Q

define origin of replication

A
  • where DNA begins to unwind
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38
Q

describe the number of origins of replication in prokaryotes vs eukaryotes

A
  • prokaryotes: one origin
  • eukaryotes: several origins
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39
Q

describe the chromosome structure in prokaryotes vs eukaryotes

A
  • prokaryotes: one circular
  • eukaryotes: several linear
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40
Q

describe the rate of replication in prokaryotes vs eukaryotes

A
  • prokaryotes: 1000 nucleotides/sec
  • eukaryotes: 50 to 100 nucleotides/sec
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41
Q

which cells have telomeres: prokaryotes or eukaryotes

A
  • eukaryotes
  • ends of linear chromosomes
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42
Q

is DNA replication exergonic/catabolic or endergonic/anabolic

A
  • endergonic/anabolic
  • takes a lot of energy to build DNA
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43
Q

where does energy come from for DNA replication

A
  • ATP, GTP, TTP, CTP
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44
Q

how does the replication machinery know where to begin

A
  • origin of replication
  • identified by specific nucleotide sequences
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45
Q

how is the DNA unwound

A

helicase enzyme

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46
Q

how many replication forks are formed and which direction does the replication proceed

A
  • 2 replication forks
  • goes in both directions
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47
Q

is DNA replication conservative or semiconservative

A
  • semiconservative
  • parent double helix unwinds and each strand become template
  • two DNA molecules are created from one
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48
Q

what are the limitations of DNA polymerase and how are those limitations overcome

A
  • cannot intiate DNA synthesis
  • solved with RNA primer
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49
Q

how does DNA polymerase add the first nucleotide

A
  • where the RNA primer is
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50
Q

how is over-winding of the DNA polymerase prevented

A

topoisomerase

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51
Q

how many primers are needed on the leading and lagging strands

A
  • leading: 1
  • lagging: multiple
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52
Q

summarize the process of DNA replication

A
  • 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
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53
Q

what direction is DNA read during replication

A
  • read up
  • from 3’ to 5’ end of parental strand
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54
Q

what direction is the new DNA strand written during replication

A
  • write down
  • from 5’ to 3’ end of new strand
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55
Q

which end of a DNA strand are nucleotides added to

A

3’ end of growing strand

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56
Q

define leading strand

A
  • 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
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57
Q

define lagging strand

A
  • 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
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58
Q

define helicase and it’s involvement in DNA replication

A
  • unwinds DNA double helix at replication fork
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59
Q

define single-stranded binding proteins and their involvement in DNA replication

A
  • prevent DNA from refolding into double helix
  • stabilizes DNA strands
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60
Q

define topoisomerase and it’s involvement in DNA replication

A
  • prevents DNA from overwinding on the ends
  • ahead of replication fork
  • breaking, swiveling, and rejoingin DNA strands
61
Q

define primase and it’s involvement in DNA replication

A
  • make RNA primers
  • at 5’ end of leading strand
  • at 5’ end of each okazaki fragment in lagging strand
62
Q

define DNA polymerase 3 and it’s involvement in DNA replication

A
  • read template strand and synthesizes new strand
  • adds nucleotides to RNA primer or pre-existing DNA strand
63
Q

define DNA polymerase 1 and it’s involvement in DNA replication

A
  • replaces RNA bases from RNA primers with DNA bases
64
Q

define DNA ligase and it’s involvement in DNA replication

A
  • 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
Q

define RNA primers and their involvement in DNA replication

A
  • RNA nucleotides put down to help DNA polymerase know where to start
  • short sequence of RNA bases
  • made by enzyme primase
66
Q

define okazaki fragments

A
  • fragments made on lagging strand of DNA
67
Q

what is a problem in eukaryotic DNA replication; explain the effects on the leading strand and the lagging strand

A
  • 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
Q

how do cells overcome the problem of DNA replication in the lagging strand leaving a portion unpaired

A
  • 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
Q

what is the sequence in telomeres in humans and how many times is it repeated

A
  • TTAGGG
  • repeated 100 to 1000 times in each chromosome
70
Q

what does the small loss in sequences of telomeres potentially cause

A
  • aging
71
Q

describe the process of telomere replication

A
  • 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
Q

define DNA proofreading

A
  • 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
Q

define mismatch repair

A
  • mismatch repairs enzymes recognize incorrect bases AFTER replication
  • excises incorrect base and replaces it
74
Q

define nucleotide excision repair

A
  • 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
Q

define thymine dimers

A
  • two thymines forming a bond on the same strand of DNA
  • usually caused by UV light
  • fixed by nucleotide excision repair
76
Q

define the central dogma

A
  • 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
Q

define transcription

A
  • synthesis of RNA under direction of DNA
  • produces mRNA: template for translation
78
Q

define translation

A
  • synthesis of a polypeptide occurring under the direction of mRNA
  • occurs in ribosomes
79
Q

define gene expression

A
  • process by which DNA directs protein synthesis
  • includes transcription and translation
80
Q

does all DNA and all genes code for a product

A
  • no
81
Q

where does DNA transcription take place

A
  • nucleus
82
Q

where does mRNA translation take place

A
  • ribosomes in the cytoplasm
83
Q

are proteins functional right after being made

A
  • no
  • must be folded in endoplasmic reticulum and packaged in golgi apparatus
84
Q

define non-protein coding genes and give an example

A
  • genes that don’t code for a protein
  • functional RNAs: tRNA that carries amino acids
85
Q

are non-protein coding genes like functional RNAs transcribed, translated, or both

A
  • transcribed but not translated
86
Q

what is special about transcription and translation in prokaryotic cells

A
  • have no nucleus so both take place in the cytoplasm
  • transcription and translation can happen at the same time
87
Q

define operons

A
  • 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
Q

define the lac operon

A
  • set of genes that makes all proteins needed to take in and break down lactose
89
Q

define the one gene-one enzyme hypothesis

A
  • original thought behind transcription and translation
  • each gene codes for one enzyme
90
Q

what four things disprove the one gene-one enzyme hypothesis

A
  • 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
Q

describe the smallest gene in the human genome

A
  • SRY gene
  • determines male characteristics: on Y chromosome
  • has 828 nucleotides and makes 204 amino acids
92
Q

define transcription factors

A
  • 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
Q

define promoter

A
  • region of DNA where transcription is initiated
94
Q

define RNA polymerase

A
  • enzyme that transcribes DNA into mRNA
  • catalyzes process of transcription
  • synthesizes RNA in a 5’ to 3’ direction (read up, write down)
95
Q

define non-template DNA

A
  • coding strand
  • DNA strand that is not being transcribed
  • will have similar sequence to the new RNA strand
96
Q

define template DNA

A
  • strand of DNA being transcribed
  • strand that mRNA is based off of in transcription
  • will have opposite bases as mRNA
97
Q

define RNA transcript

A
  • mRNA that is made from transcription
98
Q

define transcription initiation

A
  • 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
Q

define transcription elongation

A
  • 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
Q

define transcription termination

A
  • 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
Q

define polyadenylation sequence

A
  • termination sequence in eukaryotic cells
  • AAUAAA
102
Q

define post-transcriptional pre-mRNA processing

A
  • modifications to mRNA before it can be translated in eukaryotic cells
  • modifications: 5’ capping, poly A tail addition, RNA splicing
103
Q

describe the difference between DNA polymerase and RNA polymerase

A
  • DNA polymerase: makes DNA during DNA replication
  • RNA polymerase: make RNA during transcription
104
Q

why does transcription not require ssb proteins to prevent rewinding of the DNA

A
  • RNA polymerase only unwinds 10 to 20 bases at a time
  • small section has little chance of rewinding
105
Q

what are the RNA complementary bases to DNA bases (formatted DNA-RNA)

A
  • A-U
  • T-A
  • G-C
  • C-G
106
Q

how is transcription termination different in prokaryotes and eukaryotes

A
  • 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
Q

what are 2 unique features of prokaryotic gene expression

A
  • happens solely in the cytoplasm
  • RNA transcript does not need modification
108
Q

how do the unique features of prokaryotic transcription affect gene expression

A
  • multiple RNA polymerases can transcribe a single gene at the same time
  • multiple ribosomes can simultaneously translate mRNA transcripts
109
Q

where and when does post-transcriptional pre-mRNA processing take place

A
  • in the nucleus
  • after transcription, before translation
110
Q

define exons and introns

A
  • only in eukaryotic cells
  • exons: coding sequences
  • introns: non-coding sequences
111
Q

what is removed in RNA splicing

A
  • introns
  • sometimes exons: creates different proteins from the same gene
112
Q

what is the 5’ and 3’ end of the RNA transcript capped with during modification

A
  • 5’: guanine nucleotide
  • 3’: multiple adenine nucleotides
113
Q

explain the relationship between the amount of genes and proteins a person has

A
  • more proteins than genes
  • multiple proteins can be made from one gene due to RNA splicing modification
114
Q

what is the size of the human genome

A
  • 3000 genes
115
Q

define mRNAs (messenger RNAs)

A
  • directs recruitment of tRNA molecules and production of the polypeptide
  • determines sequences of amino acids in polypeptide
  • binds to the small ribosomal subunit
116
Q

define tRNAs (transfer RNAs): what 4 things do they all have

A
  • 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
Q

define anticodon

A
  • 3 complementary nucleotides on tRNA
118
Q

define aminoacyl-tRNA synthetase

A
  • enzyme on tRNA that attaches a specific amino acid
119
Q

define ribosome (in translation)

A
  • reads mRNA and produces corresponding polypeptide
  • made of proteins and rRNA
  • has 2 subunits
  • has 3 binding sites for tRNAs
120
Q

define a site (aminoacyl-tRNA binding site)

A
  • on large ribosomal subunit
  • where all tRNA after 1st enter and bind to codon of mRNA
121
Q

define p site (peptidyl-tRNA binding site)

A
  • on large ribosomal subunit
  • where 1st tRNA enters
  • forms peptide bond between amino acid in p site and a site
122
Q

define e site (exit site)

A
  • on large ribosomal subunit
  • where tRNA goes after adding amino acid to polypeptide chain
  • where tRNA exits ribosome
123
Q

define genetic code and why it’s known as conserved and redundant

A
  • 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
Q

what are the 4 components of translation

A
  • ribosome
  • transfer RNA
  • messenger RNA
  • polypeptide
125
Q

what is the breakdown of what ribosomes are made of

A
  • 1/3 protein
  • 2/3 rRNA
126
Q

what are the 2 subunits of a ribosome and what are their purposes

A
  • small subunit: decodes genetic message (mRNA)
  • large subunit: catalyzes peptide bond formation
127
Q

what are the 3 tRNA binding sites on ribosomes

A
  • E
  • P
  • A
128
Q

which binding site on ribosomes do tRNA enter

A
  • a site
  • first tRNA enters at p site
129
Q

describe how mRNA is read during translation, including the start codon

A
  • 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
Q

what is the product of translation

A
  • polypeptide
131
Q

how are polypeptides produced in translation

A
  • amino acids bonded together through interaction of tRNA on p site and tRNA on a site
132
Q

what type of bonds are formed during translation

A
  • peptide bonds
  • covalent
133
Q

how are transcription and translation different in regards to how strands are read

A
  • transcription: read 3’ to 5’
  • translation: read 5’ to 3’
134
Q

how is the genetic code decoded

A
  • translation
  • nucleotides decoded/translated into amino acids
135
Q

what are the 3 stop codons

A
  • UAA (u are annoying)
  • UGA (u go away)
  • UAG (u are gone)
136
Q

what animo acid does the start codon (AUG) code for

A
  • methionine
137
Q

does the stop codon code for an amino acid

A
  • no
138
Q

what is the reading frame

A
  • determined by the first codon (AUG on mRNA)
  • sequence of 3 bases read at a time
139
Q

describe translation initiation

A
  • 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
Q

describe translation elongation

A
  • 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
Q

describe translation termination

A
  • 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
Q

what happens to the polypeptide chain after translation

A
  • goes to endoplasmic reticulum to be folded
  • taken to golgi apparatus to be processed and transported
143
Q

define gene expression

A
  • process of “turning on” a gene to produce RNA and proteins
  • done through stopping transcription or translation
144
Q

why are genes regulated

A
  • to control timing, location, and amount of gene expression
145
Q

do all cells need to express all genes

A
  • no
146
Q

how are genes regulated in prokaryotes

A
  • almost entirely through transcription
  • because transcription and translation can happen simultaneously, transcription must be stopped so gene isn’t automatically translated
147
Q

how are genes regulated in eukaryotes

A
  • multiple levels:
  • epigenetic
  • transcriptional
  • post-transcriptional
  • translational
  • post-translational
148
Q

define epigenetic

A
  • one gene affects regulation of another gene

BIOL 107 (18 decks)

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