Midterm 1 Flashcards
1
Q
photograph 51
A
an x-ray crystallography exposure taken in 1952
2
Q
why was photograph 51 so important
A
it was a key piece of data supporting the model that DNA was a helix
3
Q
Who took photograph 51?
A
Dr. Rosalind Franklin but she didnt receive appropriate credt from Watson and Crick
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
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
6
Q
Each DNA daughter strand contains …
A
one strand from mother and one newly synthesized strand
7
Q
What happends to the mother DNA
A
she has been ripped in half and lives on only in her daughters
8
Q
DNA replication is describes as what ( a specific word about the strand)
A
SEMICONSERVATIVE
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
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 )
11
Q
How is the new DNA strand sythesized
A
new strand is synthesized one nucleotide at a time, and NTPs are used
12
Q
why NTPS and not NMPs
A
NTPS are thermodynamically favorable
13
Q
what is the direction of polyermization
A
5’ to 3’
14
Q
nucleotides are added to which side of the strand
A
the 3’ OH of the growing strand
15
Q
the 5’ end of the strand has what attached
A
a phosphate
16
Q
what is the enzyme that synthesizes DNA
A
DNA polymerase
17
Q
DNA polymerase needs what to start polymerization
A
a DNA or RNA primer is required
18
Q
PCR benefits …
A
revolutionized medicine forensics, and experimental biology
19
Q
what does PCR stand for
A
polymerase chain reaction
20
Q
what is PCR
A
DNA replication in a test tube
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
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)
23
Q
what does PCR require
A
requires a sequence specific primers
special polymerase
24
Q
IN PCR what is the primer made of
A
primer made of DNA not RNA
25
Three steps of PCR
1. denaturation
2. Annealing
3. Extension
26
What is denaturation
All the DNA duplexes melt into single strands
27
what is the temp of denaturation
95 degrees celcius
28
what happens in annealing
the primers anneal (bind) to complementary sequence on the template strands
29
what is the temp of annealing
50 degrees celcius
30
what is extension
the polymerase does its thing
31
what is the temp of extension
72 degrees celcius
32
Why do we need PCR
because we need more DNA
because we want to measure the size of a piece of target DNA
33
Chain terminating bases are the key
to Dideoxy DNA sequencing
34
Dideocy nucleotide is what
a nucleotide without the Oh attached to the 3' carbon
35
sequencing reactions utilize
florescent chain terminating nucleotires
36
In Cells what is used as the primer
RNA
37
in cells enzymes do what to the DNA duplex
they unwind the DNA duplex
38
replication origins
sites where DNA synthesis initiates in cells
39
eukaryotic chromosomes have what when it comes to replication origins
have multiple replication orgins
40
the human genome contains more than _______ origins , ________ base pairs apart from each other
10,000, 50,000`
41
DNA is generally replicated in which direction
BOTH directions at once
42
what are the SIMILARITIES between DNA replication in cells vs PCR/DIDeocy sequencing
in cells and PCR : need template primers, DNA polymerase and nucleotides
43
CONTRAST DNA replication in cells and in PCR
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
44
The central dogma explains
how DNA genotype becomes a phenotype
45
central dogma
DNA --> RNA --> protein
46
proteins give us our ...
phenotype
47
DNA controls our ....
phenotype by encoding proteins
48
what other than DNA can CONTROL our phenotype
non coding RNAs such as TRNAs, rRNA...
49
GENE EXPRESSION IS ...
the conversion of a gene into its product( generally a protein bis an RNA intermediate)
50
when we say a gene is being expressed we mean...
its being transcribes and translated into protein
51
many genes are not....
expressed all the time
52
many genes are only expressed some of the time... in
response to external or interal conditions or signals
53
many genes are not...
expressed in ALL cells
54
each cell of a multicellular organism contains
the same DNA = same genes
55
different cells
express different genes
56
genes that are expressed virtually in all cells
housekeeping genes
57
cell-type specific genes
expressed genes in only certain cells ex neurons, muscle cells, blood cells
58
regulated gene expression
only a subset of genes are expressed in any given cell type
59
transcription refers to
the process of RNA being synthesized from a DNA template
60
where does translation take place in the central dogma
from DNA to RNA
61
RNA is synthesized by
RNA POLYMERASE USING DNA AS A TEMPLATE
62
RNA strands are synthesized in which direction
in the 5' to 3' direction just like DNA strands are
63
DNA is composed of
dNMPS
64
RNA is composed of
NMPs
65
DNA is synthesized from
dNTPS
66
RNA is synthesized from
NTPs
67
DNA is copied into
nto messenger RNA before it becomes protein
68
coding strand is the
nontemplate strand
69
The DNA coding and the mRNA transcript
have the same polarity and sequence substituting U in mRNA for T in DNA
70
RNA polymerase binds to the ...
promoter sequences in DNA to initiate transcription
71
the promoter consists
of two short sequences
72
what are the two sequences in a promoter sequence
the -10 and -35 sequence
73
RNA polymerase binds to what sequence
the -35 and -10 sequence of the promoter
74
Are the sequence of -10 and -35 boxes the same in different genes
the boxed are different in each gene
75
How can we find a consensus sequence for each box
by aligning the promoter regions of multiple genes
76
the level of gene expression can be affected by
how similar the 10 and -35 sequences are to the consensus sequence
77
what can regulate gene expression in eukaryotes
enhancers and silencers
78
silencers and enhancers are found where
they can be found close to the promoter or far upstream or downstream
79
enhancer ans silencers have binding sites ....
for specialized proteins called transcription factors
80
the promoter determines
where transcription starts and the direction in which it proceeds
81
RNA polymerase do not require
a primer to initiate transcription
82
termination sequences determine
where an mRNA ends
83
each eukaryotic mRNA encodes a
SINGLE protein
84
each prokaryotic mRNA can be
polysictronic (codes for multiple proteins)
85
polycistronic
codes for multiple proteins
86
the primary transcript is processed
into mRNA in eukaryotes
87
what is added to the primary transcript to become mRNA
5'cap and polyA tail
88
mRNA splicing occurs where
at the the sites determined by consensus sequences & IN NUCLEUS
89
mRNA requires many
proteins
90
what happens to spliced out introns ..
degraded and the nucleotides are recycled
91
splicing patterns can...
very under different conditions
92
Alternative splicing of the same transcript
can give ride to different proteins
93
introns are usually much larges than
exons
94
alternative splicing can produce
forms of protein that have different functions
95
splicing links up exons from within
given gene, not exons from different genes
96
alternative splicing results in the inclusion of an exon OR exclusion of an exon BUT
but it doesnt change their order
97
alternative splicing does'nt result in
the duplication of an exon in the mature mRNA
98
Replication GOALs
to copy a cells genome so that the two copies can be partitioned to the two daughter cells during cell division/mitosis
99
transcription GOAL
to copy the instructuon that are present in genes into an intermediate messenger molecule , mRNA
100
TRANSLATION GOAL
to take the instruction s in mRNA and use them to build proteins
101
building blocks for replication
DNA nucleotides are the nuilding blocks of new DNA strands
102
TRANSCRIPTION BUILDING BLOCKS
RNA nucleotides are the building blocks of mRNAs
103
TRANSLATION BUILDING BLOCKS
amino acids are the building blocks of proteins
104
proteins are composed of
amino acids
105
what are the three parts of an amino acid
amino group Nh2
carboxyl group
a side chain/ R group
106
how many amino acids are there
20 amino acids
107
what makes each amino acid unique
the side chain/ r group
108
proteins=
amino acids linked in a chain by peptide bonds
109
a typical protein is how many amino acids long
450 amino acids long
110
although proteins are linear chains of AA's...
they fold into complicated 3D structures
111
in proteins what are the amino acids linked by
peptide bonds
112
like the phophodiester bond formation, the peptide bind formation is
a dehydration synthesis reaction
113
the peptide bond ties the
carboxy terminus (carbon) and the amino (nitrogen)
114
the new amino acid is added to which terminus
the carboxyl terminus
115
how is protein sequence encoded inn DNA/RNA
the protein coding region of mRNA is made up of non-overlapping nucleotide triplets (codons) each of which corresponds to an amino acid
116
codon
nucleotide triplets
117
with some minor expections, all living organisms on earth
use this same genetic code
118
ATG/AUG =
signals the start of protein synthesis with M=Met= methionine
119
Methionine other than start codon can also be
used internally in proteins
120
how many stop codons are ther
3 stop codons
121
what are some key players in translation
ribosomes, tRNAs, aminoacyl tRNA synthetases
122
ribosomes
machine compoesed of 3-4 rRNAs and over 50 proteins
123
what are the two parts of ribosomes
large and small subunits
124
Ribosomes have channels that hold
the RNA and nascent polypeptide
125
what are the three key functions of the ribosome
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
transfer RNAs (tRNAs) pair codons with
with amino acids
127
aminoacyl tRNA synthetases are enzymes that
recognize both the anticodon and the cognate (correct amino acid) and then attach this amino acid to the tRNA
128
what is the cognate
the correct amino acid
129
what is a charged tRNA
a tRNA attached to an amino acid
130
translations 3 steps
initiation
elongation
termination
131
the initiation complex binds to
5' cap on mRNA
132
the initiation complex scans along the
mRNA 5' to 3' until it finds an AUG
133
peptidyl - p site
holds the tRNA to which the growing polypeptide chain is attached
134
A site (acceptor)
binds tRNA carrying the next amino acid to be added
135
E (exit) site
empty tRNAs leave from here after their amino acid has been added
136
Elongation steps in translation
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
when the ribosome moves down one codon the tRNA in P site moves to
E site
138
when the ribosome moves down one codon the tRNA in A site moves to
P site
139
termination steps in translation
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
what is the portion of the mRNA after the stop codon
3' UTR
141
there is no tRNA for a stop codon, instead
instead release factors bind
142
the anticodon is a apart of the
tRNA
143
in eukaryotes where are proteins translated
mRNA is processed in the nucleaus then exported to the cytoplasm where it is translated
144
where are proteins translated in prokaryotes
in prokaryotes, transcription and translation are coupled and occur in cytoplasm
145
what are polysomes
many ribosomes simultaneously on a single mRNA
146
researchers can isolate polysomes from cells and
figure out which mRNAs are being actively translated
147
RNA polymerase reads template DNA strand in which direction
3' to 5' direction
148
DNA polymerase reads a template DNA stran in which direction
3' to 5'
149
DNA polymerase builds a new DNA strand in which direction
5' to 3 direction
150
RNA polymerase builds new RNA strand in which direction
5' to 3'
151
The ribosome reads the codons in mRNA in which direction
5' to 3'
152
the ribosome builds a new protein in which direction
NH2 to COOH
153
what does the aa-tRNA synthetases do?
it pairs the amino acid with the tRNA to create a chareged tRNA
154
In DNA replication the genome is copied ...
exactly once per cell
154
Ribosomes choose _____ ____ that have _______ to form complementrary base pairs to the codons in the mRNA
charged tRNAs, anticodons
155
many mRNA molecules are typically produced from each
actively transcribed gene
156
mRNA time per gene and hour in eurkayotes
2mRNAs/gene/hour
157
How many proteins are typically produced from each mRNA
MANY MANY
158
chromosomes are ...
single very long DNA molecules
159
how many base pairs are on a chromosome
150 million base pairs
160
chromatin is
DNA + protein
161
humans have how many chromosomes and what types
46 total
22 pairs of autosomes
1 pair of sex chromosome
DIPLOID
162
karyotype
image of stained metaphase chromosomes
163
the two arms of the chromosomes are seperated by a
centromere
164
what is the p and q in a chromosome
p= short arm
q= long arm
165
in a pair of chromosme which comes from dad and mom
1 from dad and one from mom
166
ideogram
shows a chromosomes relative size and banding pattern
167
banding pattern=
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
describe E. coli
a bacterium
a prokaryote
2um Long
has compacted DNA in the nuceleod
169
the E coli genome is ----------- than E coli
the e coli genome is 1000 x longer than e coli
170
Bacterial chromosmes are what shape
circular
171
Bacterial DNA is densely packed toform a region called
nucleoid
172
what are two features that allow bacterial DNA compaction
1. proteins help organize the DNA into a series of tight loops
2. the circular DNA undergoes supercoiling
173
The human genome is how many base pairs long
3 billion base pairs
174
human DNA is about ____ more tightly packed than in E coli
10 x
175
unwound DNA in a single cell would stretch to
6 feet
176
chromatin is the material of which ------ are composed of
chromosomes
177
when is chromatin visible
only visible by light microscpy during mitosis when the NA is at its most compacted ( condensed)
178
what doesnt play a major role in compaction in eukaryotes
supercoiling
179
Each chromosome is half ...
DNA and half protein
180
types and ratio of proteins in chromosomes
half histone and half non histone proteins
181
histones are ...
small basic proteins that tightly bind DNA
182
what are the 5 major types of histones in eukaryotes
H1, H2A H2B, H3, and H4
183
lysine and arginine are important in what and why
20-30 % of the amino acids in histones are lysine and arginine which are positively charged amino acids
184
what charge does DNA have
negative charge
185
what is the nucelosome
146 bp of DNA wrapped around an octamer of histones
186
when do chromosomes condense
during mitosis and meiosis
187
euchromatin
areas of active expression, not tightly compacted
188
where are most euchromtin genes found
in the middle of the chromosme arms
189
heterochromatin
a few active genes, tightly compacted
190
what are the two typed of heterochromatin and what do they mean
facultative (mostly condensed )
constitutive (always condensed)
191
the centromere consists of several
types of repeated DNA sequences
192
centromeres are what type of chromatin
heterochromatin
193
telomeres are the
end of linear chromosomes
194
telomeres are what type of chromatin
heterochromatin
195
telomere replication requires what
a specialized polymerase called telomerase
196
without telomerase, every chromosome would get ....
SHORTEr
197
somatic cells
cells of the body
198
what type of cells are somatic cells
diploid
199
gametes
haploid cells used in reproduction
200
what type of cells are gametes
haploid cells
201
germ cells
gametes plus the germline stem cells that differentiate into gamestes
202
sex linked genes/loci
are genes that are on one of the sex chromosomes
203
where are autosomal genes/loci
on the other, non-sex chromosome (1-22)
204
heterozygous genotype means what phenotype
dominant phenotype
205
what is selfing in plants
plants have female parts (ovule) and male parts (pollen) thus they can fertilize themselves = selfing
206
what is a true Breed
when two Homozygous dominate mate together or when two Homozygous recessive mate together
207
Mendelian Genetics
the theory of knowedege that allows us to use approches such as Punnet squares to predict the genotypic and phenotypic outcome of crossed
208
what did mendel want to answer
How are the traits inherited?
How are the traits of parents transmitted to their offspring?
209
blend theory of inheritence
it viewed the traits in offspring as a mixture of the parental traits
210
what were the 5 experimental design of Medels experiments
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
explain a little bit about controlled crosses between plant?
plants have female parts and male parts, this allows for both self--fertilization and cross fertilization
212
are pure breeding strains homozygous or heterozygous
homozygous
213
F1 is
called a hybrid
214
hybrid=
progeny of a cross between 2 pure-breeding strains
215
mono hybrid
a hybrid of only one gene
216
