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Bio 97 > Midterm 1 > Flashcards

Midterm 1 Flashcards

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1
Q

photograph 51

A

an x-ray crystallography exposure taken in 1952

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2
Q

why was photograph 51 so important

A

it was a key piece of data supporting the model that DNA was a helix

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3
Q

Who took photograph 51?

A

Dr. Rosalind Franklin but she didnt receive appropriate credt from Watson and Crick

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4
Q

famous quote from Watson and Crick

A

it has not escaped our notice that the specific base-pairing was have proposed immediately suggests a possible coping mechanism for the genetic material

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5
Q

what happens if we start with a souble stranded molecule and make a complement of each strand

A

we end up wth 2 double helical daughter molecules that are identical copies of their mother

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6
Q

Each DNA daughter strand contains …

A

one strand from mother and one newly synthesized strand

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7
Q

What happends to the mother DNA

A

she has been ripped in half and lives on only in her daughters

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8
Q

DNA replication is describes as what ( a specific word about the strand)

A

SEMICONSERVATIVE

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9
Q

what does the first cycle of semiconservative replication look like

A

two DNAs with each a new daughter strand and a new mother strand –> two combos old and new

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10
Q

what does the second cycle of semiconservative replication look like

A

two new DNAs with completely new dNA (daughter DNA) and two DNAs with combo DNA (mother and daughter half half )

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11
Q

How is the new DNA strand sythesized

A

new strand is synthesized one nucleotide at a time, and NTPs are used

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12
Q

why NTPS and not NMPs

A

NTPS are thermodynamically favorable

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13
Q

what is the direction of polyermization

A

5’ to 3’

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14
Q

nucleotides are added to which side of the strand

A

the 3’ OH of the growing strand

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15
Q

the 5’ end of the strand has what attached

A

a phosphate

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16
Q

what is the enzyme that synthesizes DNA

A

DNA polymerase

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17
Q

DNA polymerase needs what to start polymerization

A

a DNA or RNA primer is required

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18
Q

PCR benefits …

A

revolutionized medicine forensics, and experimental biology

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19
Q

what does PCR stand for

A

polymerase chain reaction

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20
Q

what is PCR

A

DNA replication in a test tube

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21
Q

what is interesting abt the number of copies in PCR

A

the number of molecules thats being replicated doubles each cycle/ chain reaction

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22
Q

what are some applications of PCR

A
  • pre implantation genetic diagnosis as an appplication of PCR
  • Forensics
  • Screening blood products for diseases
  • viral infections in wild monkeys by collecting feces
  • test for presence of SARS-CoV-2 (virus that causes COVID-19)
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23
Q

what does PCR require

A

requires a sequence specific primers
special polymerase

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24
Q

IN PCR what is the primer made of

A

primer made of DNA not RNA

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25
Q

Three steps of PCR

A
  1. denaturation
  2. Annealing
  3. Extension
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26
Q

What is denaturation

A

All the DNA duplexes melt into single strands

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27
Q

what is the temp of denaturation

A

95 degrees celcius

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28
Q

what happens in annealing

A

the primers anneal (bind) to complementary sequence on the template strands

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29
Q

what is the temp of annealing

A

50 degrees celcius

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30
Q

what is extension

A

the polymerase does its thing

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31
Q

what is the temp of extension

A

72 degrees celcius

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32
Q

Why do we need PCR

A

because we need more DNA
because we want to measure the size of a piece of target DNA

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33
Q

Chain terminating bases are the key

A

to Dideoxy DNA sequencing

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34
Q

Dideocy nucleotide is what

A

a nucleotide without the Oh attached to the 3’ carbon

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35
Q

sequencing reactions utilize

A

florescent chain terminating nucleotires

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36
Q

In Cells what is used as the primer

A

RNA

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37
Q

in cells enzymes do what to the DNA duplex

A

they unwind the DNA duplex

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38
Q

replication origins

A

sites where DNA synthesis initiates in cells

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39
Q

eukaryotic chromosomes have what when it comes to replication origins

A

have multiple replication orgins

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40
Q

the human genome contains more than _______ origins , ________ base pairs apart from each other

A

10,000, 50,000`

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41
Q

DNA is generally replicated in which direction

A

BOTH directions at once

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42
Q

what are the SIMILARITIES between DNA replication in cells vs PCR/DIDeocy sequencing

A

in cells and PCR : need template primers, DNA polymerase and nucleotides

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43
Q

CONTRAST DNA replication in cells and in PCR

A

in cells: RNA primer is used, enzymes unwind the DNA duples, rpelication origins, replication forks, leading strand, lagging strand, multiple enzymes and other proteins are involves

in pcr: DNA primers are used, heat is used to unwind the DNA, no rep origins or forks, no leading strann/lagging strand, only one enzyme needed

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44
Q

The central dogma explains

A

how DNA genotype becomes a phenotype

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45
Q

central dogma

A

DNA –> RNA –> protein

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46
Q

proteins give us our …

A

phenotype

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47
Q

DNA controls our ….

A

phenotype by encoding proteins

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48
Q

what other than DNA can CONTROL our phenotype

A

non coding RNAs such as TRNAs, rRNA…

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49
Q

GENE EXPRESSION IS …

A

the conversion of a gene into its product( generally a protein bis an RNA intermediate)

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50
Q

when we say a gene is being expressed we mean…

A

its being transcribes and translated into protein

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51
Q

many genes are not….

A

expressed all the time

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52
Q

many genes are only expressed some of the time… in

A

response to external or interal conditions or signals

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53
Q

many genes are not…

A

expressed in ALL cells

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54
Q

each cell of a multicellular organism contains

A

the same DNA = same genes

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55
Q

different cells

A

express different genes

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56
Q

genes that are expressed virtually in all cells

A

housekeeping genes

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57
Q

cell-type specific genes

A

expressed genes in only certain cells ex neurons, muscle cells, blood cells

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58
Q

regulated gene expression

A

only a subset of genes are expressed in any given cell type

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59
Q

transcription refers to

A

the process of RNA being synthesized from a DNA template

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60
Q

where does translation take place in the central dogma

A

from DNA to RNA

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61
Q

RNA is synthesized by

A

RNA POLYMERASE USING DNA AS A TEMPLATE

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62
Q

RNA strands are synthesized in which direction

A

in the 5’ to 3’ direction just like DNA strands are

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63
Q

DNA is composed of

A

dNMPS

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64
Q

RNA is composed of

A

NMPs

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65
Q

DNA is synthesized from

A

dNTPS

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66
Q

RNA is synthesized from

A

NTPs

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67
Q

DNA is copied into

A

nto messenger RNA before it becomes protein

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68
Q

coding strand is the

A

nontemplate strand

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69
Q

The DNA coding and the mRNA transcript

A

have the same polarity and sequence substituting U in mRNA for T in DNA

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70
Q

RNA polymerase binds to the …

A

promoter sequences in DNA to initiate transcription

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71
Q

the promoter consists

A

of two short sequences

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72
Q

what are the two sequences in a promoter sequence

A

the -10 and -35 sequence

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73
Q

RNA polymerase binds to what sequence

A

the -35 and -10 sequence of the promoter

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74
Q

Are the sequence of -10 and -35 boxes the same in different genes

A

the boxed are different in each gene

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75
Q

How can we find a consensus sequence for each box

A

by aligning the promoter regions of multiple genes

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76
Q

the level of gene expression can be affected by

A

how similar the 10 and -35 sequences are to the consensus sequence

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77
Q

what can regulate gene expression in eukaryotes

A

enhancers and silencers

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78
Q

silencers and enhancers are found where

A

they can be found close to the promoter or far upstream or downstream

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79
Q

enhancer ans silencers have binding sites ….

A

for specialized proteins called transcription factors

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80
Q

the promoter determines

A

where transcription starts and the direction in which it proceeds

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81
Q

RNA polymerase do not require

A

a primer to initiate transcription

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82
Q

termination sequences determine

A

where an mRNA ends

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83
Q

each eukaryotic mRNA encodes a

A

SINGLE protein

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84
Q

each prokaryotic mRNA can be

A

polysictronic (codes for multiple proteins)

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85
Q

polycistronic

A

codes for multiple proteins

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86
Q

the primary transcript is processed

A

into mRNA in eukaryotes

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87
Q

what is added to the primary transcript to become mRNA

A

5’cap and polyA tail

88
Q

mRNA splicing occurs where

A

at the the sites determined by consensus sequences & IN NUCLEUS

89
Q

mRNA requires many

A

proteins

90
Q

what happens to spliced out introns ..

A

degraded and the nucleotides are recycled

91
Q

splicing patterns can…

A

very under different conditions

92
Q

Alternative splicing of the same transcript

A

can give ride to different proteins

93
Q

introns are usually much larges than

A

exons

94
Q

alternative splicing can produce

A

forms of protein that have different functions

95
Q

splicing links up exons from within

A

given gene, not exons from different genes

96
Q

alternative splicing results in the inclusion of an exon OR exclusion of an exon BUT

A

but it doesnt change their order

97
Q

alternative splicing does’nt result in

A

the duplication of an exon in the mature mRNA

98
Q

Replication GOALs

A

to copy a cells genome so that the two copies can be partitioned to the two daughter cells during cell division/mitosis

99
Q

transcription GOAL

A

to copy the instructuon that are present in genes into an intermediate messenger molecule , mRNA

100
Q

TRANSLATION GOAL

A

to take the instruction s in mRNA and use them to build proteins

101
Q

building blocks for replication

A

DNA nucleotides are the nuilding blocks of new DNA strands

102
Q

TRANSCRIPTION BUILDING BLOCKS

A

RNA nucleotides are the building blocks of mRNAs

103
Q

TRANSLATION BUILDING BLOCKS

A

amino acids are the building blocks of proteins

104
Q

proteins are composed of

A

amino acids

105
Q

what are the three parts of an amino acid

A

amino group Nh2
carboxyl group
a side chain/ R group

106
Q

how many amino acids are there

A

20 amino acids

107
Q

what makes each amino acid unique

A

the side chain/ r group

108
Q

proteins=

A

amino acids linked in a chain by peptide bonds

109
Q

a typical protein is how many amino acids long

A

450 amino acids long

110
Q

although proteins are linear chains of AA’s…

A

they fold into complicated 3D structures

111
Q

in proteins what are the amino acids linked by

A

peptide bonds

112
Q

like the phophodiester bond formation, the peptide bind formation is

A

a dehydration synthesis reaction

113
Q

the peptide bond ties the

A

carboxy terminus (carbon) and the amino (nitrogen)

114
Q

the new amino acid is added to which terminus

A

the carboxyl terminus

115
Q

how is protein sequence encoded inn DNA/RNA

A

the protein coding region of mRNA is made up of non-overlapping nucleotide triplets (codons) each of which corresponds to an amino acid

116
Q

codon

A

nucleotide triplets

117
Q

with some minor expections, all living organisms on earth

A

use this same genetic code

118
Q

ATG/AUG =

A

signals the start of protein synthesis with M=Met= methionine

119
Q

Methionine other than start codon can also be

A

used internally in proteins

120
Q

how many stop codons are ther

A

3 stop codons

121
Q

what are some key players in translation

A

ribosomes, tRNAs, aminoacyl tRNA synthetases

122
Q

ribosomes

A

machine compoesed of 3-4 rRNAs and over 50 proteins

123
Q

what are the two parts of ribosomes

A

large and small subunits

124
Q

Ribosomes have channels that hold

A

the RNA and nascent polypeptide

125
Q

what are the three key functions of the ribosome

A
  1. bind mRNA and identify the start codon for translation
  2. help bring about complenetary pairing between mRNA codons and tRNA anti-codons
  3. catalyze peptide bond formation between amino acids
126
Q

transfer RNAs (tRNAs) pair codons with

A

with amino acids

127
Q

aminoacyl tRNA synthetases are enzymes that

A

recognize both the anticodon and the cognate (correct amino acid) and then attach this amino acid to the tRNA

128
Q

what is the cognate

A

the correct amino acid

129
Q

what is a charged tRNA

A

a tRNA attached to an amino acid

130
Q

translations 3 steps

A

initiation
elongation
termination

131
Q

the initiation complex binds to

A

5’ cap on mRNA

132
Q

the initiation complex scans along the

A

mRNA 5’ to 3’ until it finds an AUG

133
Q

peptidyl - p site

A

holds the tRNA to which the growing polypeptide chain is attached

134
Q

A site (acceptor)

A

binds tRNA carrying the next amino acid to be added

135
Q

E (exit) site

A

empty tRNAs leave from here after their amino acid has been added

136
Q

Elongation steps in translation

A

new tRNA enters the A site
peptide bond is formed between amino acids in the P and A site
Ribosomes moves down onw codon
tRNA in E site exits
next tRNA enters the A site; repeat

137
Q

when the ribosome moves down one codon the tRNA in P site moves to

A

E site

138
Q

when the ribosome moves down one codon the tRNA in A site moves to

A

P site

139
Q

termination steps in translation

A

release factors are recruited when a stop codon occurs at the A site , eRF fills the A site, triggering the release of the polypeptide by hyddrolysis of GTO, ribosome dissociation and mRNA release

140
Q

what is the portion of the mRNA after the stop codon

A

3’ UTR

141
Q

there is no tRNA for a stop codon, instead

A

instead release factors bind

142
Q

the anticodon is a apart of the

A

tRNA

143
Q

in eukaryotes where are proteins translated

A

mRNA is processed in the nucleaus then exported to the cytoplasm where it is translated

144
Q

where are proteins translated in prokaryotes

A

in prokaryotes, transcription and translation are coupled and occur in cytoplasm

145
Q

what are polysomes

A

many ribosomes simultaneously on a single mRNA

146
Q

researchers can isolate polysomes from cells and

A

figure out which mRNAs are being actively translated

147
Q

RNA polymerase reads template DNA strand in which direction

A

3’ to 5’ direction

148
Q

DNA polymerase reads a template DNA stran in which direction

A

3’ to 5’

149
Q

DNA polymerase builds a new DNA strand in which direction

A

5’ to 3 direction

150
Q

RNA polymerase builds new RNA strand in which direction

A

5’ to 3’

151
Q

The ribosome reads the codons in mRNA in which direction

A

5’ to 3’

152
Q

the ribosome builds a new protein in which direction

A

NH2 to COOH

153
Q

what does the aa-tRNA synthetases do?

A

it pairs the amino acid with the tRNA to create a chareged tRNA

154
Q

In DNA replication the genome is copied …

A

exactly once per cell

154
Q

Ribosomes choose _____ ____ that have _______ to form complementrary base pairs to the codons in the mRNA

A

charged tRNAs, anticodons

155
Q

many mRNA molecules are typically produced from each

A

actively transcribed gene

156
Q

mRNA time per gene and hour in eurkayotes

A

2mRNAs/gene/hour

157
Q

How many proteins are typically produced from each mRNA

A

MANY MANY

158
Q

chromosomes are …

A

single very long DNA molecules

159
Q

how many base pairs are on a chromosome

A

150 million base pairs

160
Q

chromatin is

A

DNA + protein

161
Q

humans have how many chromosomes and what types

A

46 total
22 pairs of autosomes
1 pair of sex chromosome
DIPLOID

162
Q

karyotype

A

image of stained metaphase chromosomes

163
Q

the two arms of the chromosomes are seperated by a

A

centromere

164
Q

what is the p and q in a chromosome

A

p= short arm
q= long arm

165
Q

in a pair of chromosme which comes from dad and mom

A

1 from dad and one from mom

166
Q

ideogram

A

shows a chromosomes relative size and banding pattern

167
Q

banding pattern=

A

the characteristic pattern of dark and light bands that appear when a chromosome is stained with a chemical solution then viewed under a microscope

168
Q

describe E. coli

A

a bacterium
a prokaryote
2um Long
has compacted DNA in the nuceleod

169
Q

the E coli genome is ———– than E coli

A

the e coli genome is 1000 x longer than e coli

170
Q

Bacterial chromosmes are what shape

A

circular

171
Q

Bacterial DNA is densely packed toform a region called

A

nucleoid

172
Q

what are two features that allow bacterial DNA compaction

A
  1. proteins help organize the DNA into a series of tight loops
  2. the circular DNA undergoes supercoiling
173
Q

The human genome is how many base pairs long

A

3 billion base pairs

174
Q

human DNA is about ____ more tightly packed than in E coli

A

10 x

175
Q

unwound DNA in a single cell would stretch to

A

6 feet

176
Q

chromatin is the material of which —— are composed of

A

chromosomes

177
Q

when is chromatin visible

A

only visible by light microscpy during mitosis when the NA is at its most compacted ( condensed)

178
Q

what doesnt play a major role in compaction in eukaryotes

A

supercoiling

179
Q

Each chromosome is half …

A

DNA and half protein

180
Q

types and ratio of proteins in chromosomes

A

half histone and half non histone proteins

181
Q

histones are …

A

small basic proteins that tightly bind DNA

182
Q

what are the 5 major types of histones in eukaryotes

A

H1, H2A H2B, H3, and H4

183
Q

lysine and arginine are important in what and why

A

20-30 % of the amino acids in histones are lysine and arginine which are positively charged amino acids

184
Q

what charge does DNA have

A

negative charge

185
Q

what is the nucelosome

A

146 bp of DNA wrapped around an octamer of histones

186
Q

when do chromosomes condense

A

during mitosis and meiosis

187
Q

euchromatin

A

areas of active expression, not tightly compacted

188
Q

where are most euchromtin genes found

A

in the middle of the chromosme arms

189
Q

heterochromatin

A

a few active genes, tightly compacted

190
Q

what are the two typed of heterochromatin and what do they mean

A

facultative (mostly condensed )
constitutive (always condensed)

191
Q

the centromere consists of several

A

types of repeated DNA sequences

192
Q

centromeres are what type of chromatin

A

heterochromatin

193
Q

telomeres are the

A

end of linear chromosomes

194
Q

telomeres are what type of chromatin

A

heterochromatin

195
Q

telomere replication requires what

A

a specialized polymerase called telomerase

196
Q

without telomerase, every chromosome would get ….

A

SHORTEr

197
Q

somatic cells

A

cells of the body

198
Q

what type of cells are somatic cells

A

diploid

199
Q

gametes

A

haploid cells used in reproduction

200
Q

what type of cells are gametes

A

haploid cells

201
Q

germ cells

A

gametes plus the germline stem cells that differentiate into gamestes

202
Q

sex linked genes/loci

A

are genes that are on one of the sex chromosomes

203
Q

where are autosomal genes/loci

A

on the other, non-sex chromosome (1-22)

204
Q

heterozygous genotype means what phenotype

A

dominant phenotype

205
Q

what is selfing in plants

A

plants have female parts (ovule) and male parts (pollen) thus they can fertilize themselves = selfing

206
Q

what is a true Breed

A

when two Homozygous dominate mate together or when two Homozygous recessive mate together

207
Q

Mendelian Genetics

A

the theory of knowedege that allows us to use approches such as Punnet squares to predict the genotypic and phenotypic outcome of crossed

208
Q

what did mendel want to answer

A

How are the traits inherited?
How are the traits of parents transmitted to their offspring?

209
Q

blend theory of inheritence

A

it viewed the traits in offspring as a mixture of the parental traits

210
Q

what were the 5 experimental design of Medels experiments

A
  1. traits with clearly distinguisgable phenotypes
  2. controlled crosses between plants
  3. Pure breeding stains
  4. Quantification of results
  5. replicate, reciprocal and Test cross analysis
211
Q

explain a little bit about controlled crosses between plant?

A

plants have female parts and male parts, this allows for both self–fertilization and cross fertilization

212
Q

are pure breeding strains homozygous or heterozygous

A

homozygous

213
Q

F1 is

A

called a hybrid

214
Q

hybrid=

A

progeny of a cross between 2 pure-breeding strains

215
Q

mono hybrid

A

a hybrid of only one gene

216
Q
A

Bio 97 (4 decks)

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