Extra resources Flashcards
(538 cards)
1
Q
What is DNA?
A
The molecule of inheritance in living organisms.
2
Q
Who created the modern discipline of geentics?
A
Gregor Mendel.
3
Q
What was Mendel’s experiment?
A
Breeding plants and animals.
4
Q
How did Mendel do his experiments?
A
With pea plants in his monastery garden.
5
Q
What was Mendel doing with peas in his experiment?
A
Observing several plants’ characteristics.
6
Q
What were some of the characteristics Mendel was observing in his experiments?
A
Seed colour, shape, flower location, colour, pod colour, shape, height.
7
Q
How was Mendel breeding the peas in his experiment?
A
Breeding standard generation twice –> 3 generations of peas.
8
Q
What did the standard deviation of Mendel’s experiment have?
A
One homozygous plant dominant.
One homozygous recessive.
9
Q
What did the first generation of Mendel’s experiment with peas have?
A
All peas heterozygous.
10
Q
What did the second generation of peas in Mendel’s experiment have?
A
- homozygous dominant.
- homozygous recessive.
3 & 4. heterozygous.
11
Q
What were the generalizations of Mendel’s experiment?
A
- Mendel’s Law of Segregation: every organism has 2 alleles of a gene.
- Mendel’s Law of Independent Assortment: alleles are passed on independently of each other.
12
Q
What did Mendel proposed?
A
Dominant traits mask recessive traits.
13
Q
Where else is Mendel’s experiment applied?
A
On individual genes.
14
Q
What experiments did August Weismann do?
A
With mice.
15
Q
What did mice experiments of Weismann show?
A
Traits inherited by organisms during lifetime did not pass on to offspring.
16
Q
What theory did Weismann proposed?
A
The germ plasm theory.
17
Q
What did the germ plasm theory state?
A
Hereditary information stored in egg and sperm cells of eukaryotic organisms.
18
Q
What were proteins responsible for?
A
Genetic inheritance.
19
Q
What did Johann Miescher do in 1869?
A
Isolated DNA from white blood cells.
20
Q
What did Albrecht Kossel do in 1878?
A
Isolated nucleic acids of DNA and RNA.
21
Q
What were the 3 choices presented for genetic inheritance?
A
- DNA.
- RNA.
- Proteins.
22
Q
What was Frederick Griffith investigating?
A
How organisms pass on genetic information to their offspring.
23
Q
With what was Griffith working?
A
Streptococcus pneumoniae bacteria.
24
Q
With which types of Streptococcus pneumoniae did Griffith work?
A
Rough.
Smooth.
25
What was the differences between rough and smooth Streptococcus pneumoniae bacteria that Griffith worked with?
Smooth: covered with saccharide layer, harder to detect for white blood cells.
Rough: easily killed.
26
Where did Griffith test bacteria?
On mice.
27
What did Griffith find about testing bacteria on mice?
Mice exposed to smooth bacteria --> died.
Mice exposed to rough bacteria --> survived.
28
What else did Griffith do with the bacteria?
Exposed them to heat.
29
What did Griffith with bacteria exposed to heat?
Exposed them to mice.
30
What did Griffith find when exposed heat bacteria to mice?
Heat stressed rough bacteria --> no negative effects on mice.
Heat stressed smooth bacteria --> died.
31
What did Oswald Aver, Colin MacLeod and Maclyn McCarty do experiments for?
To show if DNA, proteins, or RNA acted as the molecule of genetic transmission.
32
What did Avery's team do?
Isolated DNA, RNA, Proteins from cells of strep pneumoniae as Griffith --> treated with enzyme to break down one type of molecules --> solutions exposed to rough strains --> injected to mice --> not died.
33
What was the conclusion of Avery's team?
DNA is the molecule of genetic inheritance.
34
What experiments did Hershey and Chase do?
Experiments on bacteriophages, viruses that infected bacteria --> proliferate themselves --> exposing bacteriophages to radioactive isotopes of phosphorus and sulphur --> incorporated in virus' DNA or proteins --> sulphur found in one of each not in both --> phosphorus into DNA & sulphur into proteins --> check which bacteria inherited radioactive indicators --> bacteria with phosphorus became radioactive --> bacteria with sulphur did not.
35
What was the conclusion of Hershey and Chase experiment?
Virus molecule of inheritance is DNA.
36
What did Edward Tatum and George Beadle show in 1940?
DNA genes are directly responsible for creation of cellular proteins.
37
What did Tatum and Beadle use for experimental subject?
Neurospora crassa = bread mould.
38
How did Beadle and Tatum use Neurospora crassa?
Spores of Neurospora lighted --> mutate genes --> crossed mutated spores with normal ones --> mutant offspring.
39
What happened in Beadle and Tatum's experiment with Neurospora?
Normal spores grew on regular growth medium.
| Mutant offspring required addition of arginine to grow on medium.
40
Why did the mutant offspring require addition of arginine to grow on medium?
Mutated genes are coded for protein that produces arginine amino acid.
41
What did Levene identify in 1919?
Deoxyribose saccharide phosphate group.
Nucleic acids DNA is made up of.
42
What did Levene propose?
DNA consists of nucleotides linked by phosphorus groups.
DNA is very short.
43
What did Elsif propose?
DNA structure = 2 strands = template for reproduction.
44
What did Jean Brock show in 1933?
DNA is organised in chromosomes.
45
What did William Astbury provide in 1937?
X-ray diffraction images --> DNA regular structure.
46
What else did Chargaff use?
X-ray chromatography.
47
What did Chargaff find with X-ray chromatography?
Relative amount of each nucleic acid in DNA.
```
Cytosine = Guanine.
Adenine = Thymine.
```
48
What did James Watson and Francis Crick create in 1953?
Double helix model of Deoxyribonucleic acid.
49
What is important about Francis and Watson model?
Accepted DNA model today.
50
On what was Watson and Crick's model based?
On X-ray diffraction by Rosalind Franklin.
51
What did Watson and Crick find with Rosalind's model?
2 strands of DNA backbone = identical.
52
On what is molecular biology based?
Double helix model of DNA with nucleic acids in centre and phosphate + deoxyribose groups chains.
53
What did Matthew Mason and Franklin Stoll show in 1958?
DNA replicates semi-conservatively = DNA replicates --> half of new strand from parent strand + half newly made up.
54
What did Mason and Stoll do?
Bacterial DNA --> took light and heavy isotopes of Nitrogen --> centrifuged DNA after replication --> separating it by consistency.
55
How is DNA used?
Template --> transcription --> creates RNA --> template --> translation --> creates proteins.
56
What happens during transcription?
mRNA lives cell nucleus --> enters cytoplasm --> binds ribosome --> 3 nucleic acid of RNA interpreted as a codon --> correspond to an amino acid --> amino acids go to ribosome by tRNAs --> synthesized into primary protein structures --> fold in functioning proteins.
57
What can we find inside DNA?
Double-stranded DNA = 2 strands braid --> form double helix.
58
What is the most common form of a DNA double helix?
B-form DNA.
59
What is each strand of DNA?
A polynucleotide made up of many individual units, nucleotides.
60
What does a nucleotide have?
3 components:
1. 5-C sugar.
2. Phosphate.
3. One possible base (A, G, T, C).
61
Where is the nitrogenous base always attached?
At 1-C of sugar.
62
Where is the phosphate attached?
At 5-C of sugar on 1 nucleotide and 3-C sugar on previous nucleotide.
63
How is the sugar of DNA called?
Deoxyribose.
64
Why is the sugar called deoxyribose?
Missing a OH group at 2-C present in ribose.
65
How are nucleotides in DNA, called?
Deoxynucleotides.
66
How are nucleotides bind to each other in a DNA strand?
By phosphodiester bonds.
67
What do phosphate group + sugar make?
DNA backbone.
68
What is the direction of the DNA strands?
Top: 5'- 3'.
Bottom: 3'- 5'.
69
How can we see clearly the structure of DNA?
Unwinding.
| Flattening double helix.
70
How do the 2 DNA strands interact with each other?
Through non-covalent hydrogen bonds between bases..
71
What does each base of DNA structure form?
Hydrogen bonds with the complementary base on the opposite strand.
72
What is a base pair?
A unit of 2 bases connected with each other through hydrogen bonds.
73
How are bases connected?
```
A = T (2 H bonds)
G = C (3 H bonds)
```
74
How are thymine and cytosine called?
Pyrimidines = single ring structure.
75
How are adenine and guanine called?
Purines = double rings.
76
Is the geometry of bases in DNA the same no matter what base is?
Yes.
77
Why can not other bases form base pairs?
No geometry.
Not strong H bonds are formed.
Disturb helix.
78
How many base pairs occur in each turn of the DNA helix?
10.
79
What does the structure of bases and connection through H bonds forms?
Stable structure of DNA.
80
When are the pi-pi interactions formed?
When aromatic rings of bases stack next to each other --> share electron probabilities.
81
What else is it formed from the double helix structure of DNA?
2 spaces:
1. Major grooves.
2. Minor grooves.
82
How do grooves in DNA act?
Base pair recognition.
| Binding sites for proteins.
83
What does the major groove of DNA contain?
Base pair specific information.
84
What is the minor groove of DNA?
Base pair nonspecific.
85
Why are major and minor grooves of DNA different?
Due to different acceptors and donor which proteins can interact with.
86
In which ways can DNA be acted?
1. Sequence specific.
| 2. Non-sequence specific manner.
87
What is the cell?
The basic unit of all living tissue.
88
Where can nucleus be found and what does it contain?
In human cells.
| The genome.
89
Into what is the genome split in humans?
To 23 chromosome pairs.
90
What does each chromosome contain?
Long strand of DNA --> tightly packaged around proteins = histones.
91
What does occur within DNA?
Sectors = genes.
92
What do genes contain?
Instructions to make proteins.
93
What happens when a gene is switched on?
Enzyme RNA polymerase --> attaches gene's start.
94
What does RNA polymerase do?
Moves along DNA --> makes mRNA strand, in nucleus.
95
What does DNA do while RNA polymerase creates mRNA?
Codes bases of mRNA ON new strand.
96
Can the mRNA used as a template once it is transcribed from DNA?
No.
| It needs to be processed.
97
How is mRNA processed to used as a template?
Removing and adding RNA sections.
98
Where does mRNA go once it is processed?
Out of nucleus --> into cytoplasm.
99
What happens to mRNA once it enters cytoplasm?
Ribosomes bind to it --> read code on it --> produce amino acids chain.
100
How many different types of amino acid occur?
20.
101
What do tRNAs do?
Transfer amino acids to ribosome as each triplet on mRNA is read.
102
How is mRNA read?
3 bases at a time.
103
Where are amino acids from tRNA added?
To a growing chain of amino acids.
104
What happens once the last amino acid is added?
Chain falls to a 3D shape --> form protein.
105
What is transcription and translation?
Collective process where genetic code read by enzymes --> produces proteins in organism.
106
What is a chromosome?
A very long molecule.
107
Of what does a chromosome consist?
Millions of base pairs.
108
Are all of the parts of chromosome special?
No.
109
What parts of chromosomes are special?
Genes.
110
What do genes do?
Code for different things.
111
How long is a gene in humans?
10-50 thousand base pairs.
112
How long can the longest chromosome be?
2.5 million base pairs.
113
What happens when a gene is expressed?
A specific protein is produced?
114
What is transcription?
Process of enzymes use one of strands of DNA in gene as template --> produce mRNA.
115
How does transcription occur?
Enzyme RNA Polymerase + proteins transcription factors bind to specific sequence promoter --> 2 strands apart --> 1 strand = template/antisense strand --> used to generate mRNA --> other strand = nontemplate strand/sense strand.
116
Does RNA polymerase need a primer?
No.
117
What does RNA Polymerase do?
Moves along DNA --> elongation --> synthesizes mRNA as it goes.
Reading antisense strand from 3'- 5' --> generating mRNA 5' - 3'.
118
What is the difference between the newly synthesized mRNA and the template DNA strands?
DNA: deoxyribose sugar, A-C-G-T
RNA: ribose sugar, A-C-G-U
119
How many bases of DNA are exposed at a time?
10-20.
120
What happens to DNA strands after mRNA is synthesized?
Wraps back up.
121
What happens once RNA polymerase reaches the end of the gene?
Termination occurs =
| Enzyme detaches from gene --> DNA returns to original state --> mRNA produces.
122
Where does translation occur?
In ribosome.
123
What happens during translation?
mRNA acts as a code for a specific protein --> 3 codons on mRNA --> code for a specific anti-codon --> carried by tRNA --> covalently linked to amino acid.
124
What is the reading frame?
Nucleotides into codons on mRNA strand.
125
How many possible codons occur?
64 (3 on 4).
126
What is the strange thing in the universal genetic code?
Multiple codons code same amino acid.
127
To what does each codon correspond?
To a particular amino acid.
128
Which is the start codon?
AUG.
129
What does AUG codon do?
Initiates translation --> codes for Methionine.
130
Which are the stop codons?
UAA
UAG
UGA
131
What do stop codons do?
Terminate (finish) translation.
132
Where does the small ribosomal subunit bind?
To mRNA.
| To tRNA.
133
What does the large ribosomal subunit do?
Joins after first tRNA binds small ribosomal subunit --> completes translation initiation.
134
What happens after the large ribosomal subunit binds mRNA?
Second tRNA brings second anti-codon to mRNA (codon) --> second amino acid binds first amino acid --> first tRNA leaves --> process continues along mRNA sequence.
135
What happens in the end of translation process?
Polypeptide chain grows.
136
When does translation stop?
When a stop codon occur --> completed polypeptide flies away --> enters cell/organelle for modification.
137
How does DNA --> transcribed --> mRNA --> translated --> protein?
Obeying to base pairing in nucleic acids.
138
What do proteins do?
Make the most of us = tissues, organs, receptors, enzymes.
139
What does DNA do?
Carries genetic code for living organisms.
140
What is protein synthesis?
Process of making proteins.
141
Which steps include protein synthesis?
1. Transcription.
| 2. Translation.
142
What is transcritpion?
Copying a single DNA to mRNA.
143
What is Translation?
Taking mRNA strand --> use it --> produce a protein.
144
What does occur inside almost every cell?
Nucleus.
145
What occurs in nucleus?
All genetic material of each cell in DNA form.
146
Why do we save DNA?
1. Essential for life.
2. Controls what cells do.
3. Contains thousand genes.
147
What are genes?
Smaller DNA sections with specific sequences --> code for specific amino acids sequences --> combined --> form a protein.
148
How can we make a protein?
Specific sequence of gene --> read by ribosomes.
149
Where do ribosomes occur?
Outside nucleus.
150
Is DNA big?
Yes.
151
Why do we need to make a copy of a gene to use it?
Because DNA is so big --> cannot leave nucleus.
152
What do we actually copy?
A single gene.
| Not the whole DNA strand.
153
Can the copy of gene leave the nucleus?
Yes.
| Small enough.
154
Where does the copy of the gene go?
To the ribosome.
155
What is the copy of the gene?
mRNA = messenger RNA.
156
How is the structure of mRNA?
Mostly similar to DNA.
Differences:
Much shorter.
Only a single strand.
Uracil base not Thymine.
157
How do we see DNA normally in nucleus?
2 strands fold into a helix.
158
What is a simplified version of DNA?
Unwind.
159
How does Transcription process start?
With RNA Polymerase enzyme.
160
Where does RNA Polymerase bind?
To DNA right before the gene to be coded, starts.
161
Where do the 2 strands of DNA separate apat?
Just ahead of RNA Polymerase.
162
What happens when the 2 strands of DNA separate apart?
Bases are exposed.
163
What does RNA Polymerase do once the 2 strands separate?
Moves along DNA strand --> read bases one by one --> use them --> make mRNA.
164
What will always mRNA bases be?
Complementary to DNA bases.
165
With what will the DNA bases bind with an mRNA base?
| C, G, T, A?
```
C = G
G = C
T = A
A = U
```
166
With what are all of the thymine on DNA replaced on mRNA?
With Uracil.
167
What does the DNA strand do while RNA Polymerase is moving along the strand and synthesizing mRNA?
Opens up to the right and closes up from the left.
168
How much of the DNA is exposed at a time?
Only a small section of it at a time.
169
What do RNA Polymerase and DNA do once mRNA is fully synthesized?
RNA Pol: Detaches from DNA.
| DNA: closes back up.
170
Where does mRNA go at the end of transcription?
Leaves nucleus --> heads to ribosome.
171
How is the DNA strand where RNA Polymerase moved along, called?
Template Strand.
172
What is the template strand of DNA sued for?
To make mRNA.
173
Once mRNA moves to the ribosome what happens?
Undergoes translation --> produces protein.
174
How is each group of 3 bases for both DNA and RNA, called?
Codon/Triplet.
175
For what does triplet from DNA/RNA code?
A specific amino acid.
176
For which amino acid does the triplet 'AGU' code?
Serine.
177
'CCA'?
Proline.
178
How does the translation process start?
mRNA and ribosome bind together.
179
Where are amino acids bind?
At tRNA = transfer RNA.
180
What do tRNA molecules have?
Anti-codon on bottom.
| Amino acid on top.
181
What is an anti-codon?
3 bases complimentary to the 3 bases on mRNA.
182
What do the 3 bases on mRNA do?
Code for amino acid that tRNA carries.
183
To what is each type of tRNA specific?
To a particular triplet on mRNA.
184
Which anti-codon and amino acid does the codon 'AGU' code?
'UCA': anti-codon
| 'serine': amino acid.
185
What do linked amino acids build?
A chain of amino acids.
186
What does the ribosome do once the amino acids are linked together?
Moves along mRNA slightly, to the next codon.
187
What happens once ribosome moves to the next codon?
First tRNA is detached --> amino acid is left behind linked to the next amino acid.
188
What happens to the amino acid chain once is detached from the ribosome and mRNA?
Folds up itself --> forms a protein.
189
What does synthesis mean?
Make something.
190
Where are enzymes involved?
In transport.
Structure.
Enzymes to make materials.
Protecting the body.
191
Why is protein synthesis essential?
To live.
192
When does protein synthesis occur?
All the time.
193
Where is our DNA?
In nucleus.
194
What is RNA?
A nucleic acid like DNA, with few differences.
195
Which of the protein synthesis process comes first?
Transcription.
196
In what to transcribe DNA in transcription?
To a message.
197
Where does transcription occur?
In nucleus.
198
Of what does messenger RNA consist?
A message made from RNA based on the DNA.
199
What is the good thing about the mRNA in eukaryote organisms?
Gets out of nucleus.
In cytoplasm.
Attach ribosomes.
200
What do ribosomes make and where?
Proteins in translation.
201
Of what are ribosomes made?
rRNA = ribosomal RNA.
202
Where do we have tRNAs available?
In cytoplasm.
203
What are tRNAs?
Transfer RNAs.
204
What do tRNAs carry?
An amino acid.
205
What is an amino acid?
A monomer of a protein.
| A building block for a protein.
206
Why is mRNA important in translation process?
Directs which tRNAs come in --> which amino acids are transferred.
207
What are tRNAs looking for?
Complementary bases.
208
What do tRNAs do once they find their complementary base on mRNA?
Transfer their amino acid.
209
What do tRNAs read?
Bases on mRNAs as 3, in triplets = codon.
210
What do we use the codon chart for?
To find which amino acid each mRNA codon will code for.
211
Which is most of the times/normally the first amino acid in proteins?
Methionine = AUG.
212
How do tRNAs work in translation process?
Bring one amino acid --> link it --> leave --> bring another amino acid.
213
How are amino acids linked to build a protein (polypeptide)?
With a peptide bond.
214
What do stop codons do?
Indicate that protein building is finished.
215
Do stop codons code for an amino acid?
No.
216
What is the result of translation?
Build a chain of amino acids brought in based on mRNA coding, complementary to DNA.
217
Which molecule is the director of the entire protein building?
DNA.
218
Which molecules help in protein synthesis?
DNA
mRNA
rRNA
tRNA
219
What happens to the protein after it is detached from the mRNA?
Enters a cell/organelle --> folding --> modification --> transported: depends on protein structure & function.
220
Of what can proteins consist?
1 or more polypeptide chains.
221
What is the structure of DNA molecule?
Spiralling chain-like molecule.
222
How many different types of nucleotides does DNA have?
4: A, C, G, T.
223
What is a gene?
A specific sequence of DNA, of As, Cs, Ts, and Gs that codes for something.
224
What proteins do in our body?
Coded by genes --> interact with other proteins and molecule --> make living cells.
225
What do cells make?
Tissues.
226
What do tissues make?
Organs.
227
What do organs make?
Entire living creatures.
228
Why do individuals have different traits?
Due to mutations in their genetic code.
229
What do differences in humans' genetic code cause?
Changes in specific protein shape & its function.
230
What can mutations change?
When/how much of a particular protein can be produced.
231
What is a chromosome?
An entire chain of DNA + group of stabilizing proteins.
232
Of what do chromosomes consist?
Collection of histones wrapped with a string-like structure.
233
What are the histones wrapped with a string-like structure?
The chain of DNA.
234
How is the chain of DNA described?
Extremely long.
| With million nucleotides and hundred genes.
235
How are chromosomes packaged when cells are reproducing?
Tightly.
236
How do chromosomes exist for most of their lives?
Loose.
Noodle-like structure
With other chromosomes.
237
Where do chromosomes exist for most of their lives?
Inside nucleus/centre of each cell.
238
What is our genome?
The entire collection of genes that makes us who we are.
239
Of how many pairs of chromosomes does our genome consist?
23 pairs.
240
What does each cell of our, with few exception, contain?
Our body's full copy of chromosomes.
| Our entire genetic code.
241
What genes do our eye balls use?
Only eye ball cell genes.
| Rest are turned off.
242
What genes does each organ use?
Organ cells only.
| Rest is turned off.
243
From where does 1 member form each pair of chromosomes come?
1 from mother + 1 from father.
244
What can we say about 2 chromosome pairs if examined together?
They mostly have the exact same genes, at the exact same locations.
245
What would we find if we were testing the genetic code of 2 chromosome pairs?
Slight sequence variations between them.
246
Why do chromosome pairs have differences in genetic codes?
Due to mutations.
247
When do mutations happen?
Happened long ago --> passed down from parent to child : for many generations.
Or
Unique --> over development --> as we mature.
248
What mutations represent?
Brand new genetic information.
249
How many unique mutations does an average person have?
50-200.
250
Are all the mutation that happen to our genetic code bad?
No.
251
Why are not all the mutations bad?
Because they just make us different from each other.
252
What are the mutations?
Sequences of DNA we have never seen before in history.
253
What happens to chromosomes when it comes to reproduction?
Chromosomes --> copied --> condensed --> cell prepares for reproduction --> cells splits in 2.
254
Why is the DNA tightly packed up in our body?
To fit into the nucleus of every cell.
255
How does the process of packing tightly the DNA start?
A nucleosome is formed when eight separate histones attach DNA.
256
What is the nucleosome?
Combined tight loop of DNA + protein.
257
How are nucleosomes packed with DNA?
Multiple nucleosomes --> coiled together --> stack on top of each other.
258
What is the end result of packed nucleosomes all together?
A fibre of packed nucleosomes = chromatin.
259
How thick is the fibre of nucleosomes?
30nm.
260
What happens to the nucleosome fibre?
Nucleosome fibre --> looped --> further packaged with other proteins.
261
How much of DNA fits into the nucleus of each cell in our body?
6 feet.
262
How is nucleus described?
A really small object.
263
How many nuclei can fit on the tip of a needle?
10 thousand.
264
What is the end result of the DNA packaging process?
DNA --> tightly packed into chromosomes.
265
How can we see chromosomes?
Through a microscope.
266
Are chromosomes always present?
No.
267
When do chromosomes form?
Only when cells are dividing.
268
What happens at the end of cell division?
DNA --> less highly organized.
269
What does 'DNA Replication' mean?
Making more DNA.
270
Where does DNA Replication occur in eukarytic cells?
In nucleus.
271
Do all cells do DNA replication even if they are eukaryotic or prokaryotic?
Yes.
272
When does DNA replication occur?
Before cell division.
273
Why does DNA replication occur before cell division, in a cell?
So daughter cells can also get a copy of DNA.
274
When does DNA Replication happen, specifically in a eukaryotic cell?
Before mitosis/meiosis.
| In interphase.
275
What are many of the key players in DNA Replication?
Enzymes.
276
How can we recognise if something is an enzyme in biology?
If it ends with -ase.
277
What do enzymes do?
Speed up reactions.
Build up.
Break down items they act on.
278
How is 'helicase' characterised?
The unzipping enzyme.
279
What does helicase do?
Unzipping the 2 strands of DNA --> breaks through H bonds which hold DNA bases together.
280
How is 'DNA Polymerase' characterised?
The Builder.
281
What does DNA Polymerase do?
Replicates DNA molecules --> build new strand of DNA.
282
How is 'Primase' characterised?
The initializer.
283
Why do we need the primer?
Because DNA Polymerase can not figure out where to get started without it.
284
How can we get the primer?
Primase makes the primer.
285
Of what is the primer made?
RNA.
286
How is 'Ligase' characterised?
The gluer.
287
What does Ligase do?
Helps glue DNA fragments together.
288
Where does DNA replication start?
At a certain part called the origin.
289
How is the origin identified?
By certain DNA sequences.
290
What happens at the origin?
Helicase --> comes --> unwinds DNA.
291
Which proteins help the DNA strands to not zip back together once they unwind by helicase?
SSB Proteins.
292
What are the SSB Proteins?
Single stranded binding proteins.
293
What do SSB Proteins do?
Bind to the DNA strands --> keep them separated.
294
What does 'topoisomerase' do?
Keeps the DNA from supercoiling.
295
What is supercoiling?
Something that needs to be controlled during DNA replication.
296
What does supercoiling need to be controlled?
Because it can involve over-winding of DNA and we need separated strands for next steps.
297
What happens after 2 strands of DNA unwind?
Primase comes --> makes RNA primers on both strands.
298
What are the 2 DNA strands?
Antiparallel.
299
What does 'Antiparallel strands of DNA' mean?
They do not go in the same direction.
300
What is the sugar of DNA part of?
The DNA backbone.
301
What does the sugar of DNA have?
Carbons.
302
How are the carbons on the sugar numbered?
Right after the oxygen in a clockwise direction.
303
How are the 5 Carbons in the sugar placed?
4 carbons in the sugar and the 5th outside of the ring structure.
304
How do we count the carbons on the antiparallel sugar?
The same way, after the oxygen anticlockwise.
305
How do the DNA strands run?
One: 5' - 3' .
Other one: 3' - 5'.
Based on how the carbons are numbered.
306
How is the top original strand of DNA labelled?
3' - 5' .
307
How is the bottom original strand of the DNA labelled?
5' - 3' .
308
What happens after primase comes?
DNA Polymerase comes --> building the new strands on each original strand.
309
In what direction can DNA Polymerase build the new strand only?
5' - 3'.
310
Where does DNA Polymerase add new bases on the new strand?
On the 3' prime end.
311
How does DNA Polymerase keeps building the new strand?
As DNA unwinds.
312
Which is the Leading strand?
The new building strand with orientation 5' - 3'.
313
How is the new strand known?
As the Lagging strand with orientation 3' - 5'.
314
What must happen on the lagging strand?
Primers placed to help DNA Polymerase build the strand.
315
What occurs on the lagging strand?
Fragments.
316
How are the fragments on the lagging strand known?
'Okazaki Fragments'.
317
What do the primers do to the 'Okazaki Fragments' on the lagging strand?
Replace them with DNA bases.
318
What does happen after Okazaki fragments appear?
Ligase seals Okazaki fragments together.
319
What do we have at the end of DNA replication?
2 identical double helix DNA molecules from 1 original double helix DNA molecule.
320
How do we call the DNA replication?
'Semi-conservative'.
321
Why do we call DNA Replication 'Semi-conservative'?
The 2 copies contain 1 old original strand + 1 newly made strand.
322
What can happen if DNA Polymerase matches the wrong DNA bases?
We will get an incorrectly coded gene.
323
Where could an incorrectly coded gene end up?
In an incorrect protein/no protein.
324
What does DNA Polymerase have?
Proofreading ability.
325
What is the advantage of the proofreading ability of the DNA Polymerase?
It rarely makes a mistake.
326
Where did the understanding of DNA replication led?
To lifesaving medical treatments which can stop DNA replication in harmful cells of pathogenic bacteria/human cancer cells.
327
How are the 2 DNA strands characterised?
Complementary.
328
What does 'Complementary DNA strands' mean?
Where there is an A there is a T in the opposite strand, where there is a G there is a C in the opposite strand.
329
What does the direction of each DNA strand show?
How each strand is replicated.
330
What is the result of the helicase unzipping the DNA strands?
Forms replication fork.
331
What does each of the separated DNA strands provide?
A template for creating a new DNA strand.
332
What does the primase do?
Makes a small piece of RNA, the primer.
333
What does the primer do?
It marks the starting point for the construction of the new strand of DNA.
334
Where does DNA Polymerase bind?
To the primer.
335
How is the new leading strand of DNA made?
Continuously.
336
Can the other new lagging strand of DNA be made continuously?
No.
337
Why does the lagging strand not made continuously?
Because it runs in the opposite direction 3' - 5'.
338
How does the DNA Polymerase make the lagging strabd?
In a series of small chunks, Okazaki fragments.
339
How does each Okazaki fragment start?
With an RNA primer.
340
What happens after a primer comes to the lagging strabd?
DNA Polymerase adds DNA bases in 5'- 3' direction.
341
How often does a primer been added to the lagging strand?
On primer is added --> DNA polymerase adds a series of DNA bases --> another primer to a further point is added...
342
What happens once all the DNA strand is made?
Exonuclease removes --> RNA primer from both strand of DNA.
343
What happens once the primers are removed from DNA?
Another DNA Polymerase fills the gaps left behind with DNA.
344
What happens after DNA polymerase finishes filling the gaps with DNA?
DNA ligase --> seals up --> DNA fragments in both strands --> form continuous double strand (2).
345
How is the old strand of DNA called?
Conserved.
346
For what can gel electrophoresis used?
To separate molecules based on their size.
347
Where is gel electrophoresis sueful?
In DNA.
348
What can we find if we zoom in DNA?
A nucleotide.
349
What is the nucleotide?
A building block of DNA.
350
What are the phosphates in th enucleotides?
Negatively charged.
351
What does the negatively charged phosphate in the nucleotide, gives the whole DNA?
A negative charge.
352
Where does gel electrophoresis rely?
On the negatively charged DNA molecules.
353
What is the point of the gel electrophoresis machine?
To have an electrical charge running through a gel.
354
Of what is the gel in gel electrophoresis machine made?
Agarose.
355
What is agarose?
A polysaccharide polymer.
356
What are the polysaccharides?
Carbohydrates.
357
Where from does agarose come?
Seaweed.
358
What does the agarose gel do?
Lets DNA molecules travel in it.
359
What does the one end of the gel have?
Holes = wells.
360
What are the wells in gel electrophoresis?
Where DNA is placed into.
361
What is the area of the gel where the wells are?
Negatively charged.
362
What is the area of the other end of the gel?
Positively charged.
363
Towards where does DNA travel?
From negative area to positive area.
364
What do we use when we analyse DNA in electrophoresis?
Restriction enzymes.
365
Why do we use restriction enzymes to analyse DNA in electrophoresis?
To cut DNA up into tiny pieces.
366
What is the ability of restriction enzymes?
Cut up DNA in very specific areas, based on specific DNA bases.
367
How important are restriction enzymes in biotechnology?
Very useful.
368
How can we I compare DNA from a baby guppy and a mother gubby?
Use same restriction enzymes in both DNA samples.
369
Why should I use the same restriction enzyme to compare a baby DNA and a mother DNA?
To cut DNA at same identification points in DNA samples.
370
What is the result of adding restriction enzymes to DNA samples?
Pieces cut in samples --> have different size.
371
Why do the cut pieces of DNA have different sizes even if the same restriction enzymes have been used?
Because DNA of samples had differences in DNA bases sequence.
372
What happens after the samples of DNA are cut into pieces?
Samples --> loaded into --> gel.
373
What do we do after we load the samples in the gel?
Turn on the gel electrophoresis machine.
374
What happens once the machine is on?
DNA runs through gel towards positive side.
375
What will happen as DNA pieces move towards the positive side in the gel?
Some pieces move faster.
376
Which DNA pieces move faster in the gel?
Shorter pieces.
377
Why do longer DNA pieces move slower in the gel?
Because they have a higher molecular weight.
| They take more time to go across the gel.
378
What is the result image in the gel electrophoresis?
Fragments are spread out.
Longer pieces = closer to well.
Shorter pieces = closer to gel's opposite site.
379
How are the DNA pieces in the gel, called?
DNA bands.
380
How can we see the DNA bands in the gel?
Stain gel.
| View it under UV light.
381
If we test organisms that are not clones, will their DNA bands be identical?
No.
382
How can we compare the DNA bands?
Between each other.
Between babies and mothers.
With other mother.
See how similar they are.
383
What is a DNA Ladder?
A sample with known fragment sizes.
384
How can we use the DNA ladder?
Run it in gel --> find the known DNA bands --> use it as reference to compare the other fragments.
385
How can we make sure we are closer to the value of the DNA ladder bands?
We can use a 'Semi-Log Graph'.
386
Why do we use gel electrophoresis?
To show relatedness between different species --> classify organisms.
387
How else can we use gel electrophoresis?
Part of DNA fingerprinting.
388
What is DNA fingerprinting?
Identification of someone's DNA.
389
Where is DNA fingerprinting useful?
When solving a mystery in a crime scene.
390
How can we solve a mystery from a crime scene with DNA fingerprinting?
Sample from crime scene --> electrophoresis --> take results --> isolate genes of interest with southern blotting --> compare it to suspect DNA --> see likelihood of match
391
Where is gel electrophoresis useful?
In biotechnology.
392
What do we put in one of the lanes of gel electrophoresis?
A DNA ladder with DNA fragments of known sizes.
393
What do we put in another line of gel electrophoresis test?
A DNA sample with DNA fragment of unknown size.
394
What do we want to find in out gel electrophoresis test?
The size of the unknown band of our DNA sample.
395
What must we do once we image the gel?
Label it up.
396
How do we label our test in gel electrophoresis?
Put lane numbers on top.
| Label DNA ladder.
397
What do we do after labelling our test and DNA ladder?
Start collecting data from gel.
398
Why do we want to start collecting data from the gel?
To plot a calibration curve.
399
What do we know in our test?
The size of the DNA fragments in the DNA ladder.
400
Where do we put our known values?
Into a table.
401
How do we treat the data we know in the table?
Convert size numbers of DNA ladder to the log value.
402
Why do to convert the sizes to the log value?
Because when we plot the graph we will get a straight line.
403
What do we measure once we do our table and convert the values to the log?
The distances that the bands in DNA ladder moved.
404
How do we measure the bands of the DNA ladder?
From centre of well to the centre of band.
405
What else do we measure once we measure all the distances of all the bands in the DNA ladder?
The distances of unknown bands.
406
What do we do once we finish measuring the distances of the unknown bands?
Plot the graph.
407
Where do we plot the graph?
Using a graph paper.
408
What do we put on the x-axis of our graph?
The thing we know = log base pairs.
409
What do we put on y-axis of the graph?
The distance travelled in millimetres.
410
What is important to do on the graph?
Label the axis = Distance (mm), Log10 (Base Pairs).
411
Where do we always put the thing we know?
On the bottom of the graph.
412
What do we after we label the axis??
Plot the points.
413
What do we do after we plot the points on the graph?
Add line of best fit.
414
Why do we add a line of best fit with the points on the graph?
For the points to be equally balanced on either side.
415
What do we finally do?
Give a title to the graph = Graph of Distance (mm) against Log10 (Base Pairs).
416
How do we best write the title of the graph?
1st write thing we are measuring
| 2nd the thing we know (Log10 base).
417
Do we plot the unknown distance with the known distance point on the graph?
No.
418
How do we plot the unknown distance on the graph?
Find the point --> draw a line across until meets the straight line --> draw line down to log10 base pair axis --> read off the value on x-axis.
419
What do we find with drawing the line down to the x-axis, of the unknown value?
The Log10 base pairs.
420
What do we need to find about the unknown distance value?
The base-pair size.
421
How can we find the base-pair size of the unknown distance value, with having its Log10 value?
Anti-Log of the value --> get value of base-pairs.
422
What s the result of the gel electrophoresis testing?
Finding the size of the band on an agarose DNA gel.
423
What did diabetics have to inject in their bodies many years ago?
Coe/Pig insulin.
424
What insulin do humans inject nowadays?
Human insulin.
425
From what is the human insulin produced?
Microorganisms: E. coli bacterium,
| Certain yeast strains.
426
How do microorganisms produce human insulin?
With genetic engineering techniques.
427
What do scientists do in genetic engineering to turn microorganisms into human insulin for diabetics?
Turn certain microorganisms into --> mini factories --> make useful substances --> improve health, environment, economy.
428
What does organism's DNA make?
its genes --> code for all proteins organism needs --> survive .
429
For what does each gene code in microorganisms?
For a different protein/part of a protein.
430
What is genetic engineering?
Manipulation/changing of organism's DNA.
431
What does genetic engineering involve?
Removing a gene from one organism (donor) --> transferring to another organism (recipient).
432
What is the recipient?
The transgenic organism/genetically modified organism.
433
Which are the 2 basic purposes of genetic engineering?
1. Require large volumes of protein to be made --> use transgenic microorganisms --> produce large volumes of specific protein: insulin, growth hormone, vaccines.
2. Organism has gene from different organism introduced --> give advantage --> genetically modified organism/transgenic: gene manufactures toxic chemical in bacterium --> introduced in plant --> make --> toxic plant to insects: caterpillars.
434
How do we transfer genetic characteristics from one organism to another? (insulin)
Gene for human insulin is on chromosome 11 at position 15.5 --> insulin gene cut from chromosome 11 with restriction enzymes.
Bacteria have small circular strands of DNA (plasmids) in their cytoplasm.
--> Plasmid --> extracted from bacterium cell --> plasmid --> cut with same restriction enzymes cut insulin gene from human.
--> restriction enzymes --> leave sticky ends.
One of 2 DNA strands is longer than other.
Same restriction enzymes used = sticky ends on both DNA strands = complementary.
Sticky ends --> joined with complementary base pairing.
--> insulin gene --> joined to plasmid by sticky ends using ligase --> modified plasmid reinserted into bacterial cell.
435
How can we manufacture large amount of human insulin?
Insulin --> into bacterium --> large volumes of protein (insulin).
436
What is the modified bacterium?
Genetically modified/transgenic organism.
437
Why is the bacterium organism called modified/transgenic?
It contains some human DNA + own bacterial DNA.
438
How is the bacterial DNA called?
Recombinant DNA = bacterial DNA recombined with human DNA.
439
Where is the bacterial cell placed?
In a fermenter.
440
What does a fermenter allow?
Rapid asexual reproduction in ideal conditions.
441
Which are the ideal conditions in a fermenter for asexual reproduction?
Optimal temperature
pH
Lots of food
442
What happens to the offspring due to the asexual reproduction of bacteria in the fermenter?
Offspring = all clones of original transgenic bacterium.
443
What are the characteristics of the clones bacterium?
All have identical recombinant DNA.
444
How can the bacteria survive in the fermenter?
Make their own genes = normal bacterial proteins
| And human insulin gene --> make human insulin.
445
What has the fermenter become in genetics engineering?
A culture of mini factories --> producing human insulin.
446
What happens to the insulin once is produced?
Extracted --> purified --> packaged --> injected n diabetic humans.
447
What DNA do we digest?
Double stranded DNA.
448
What happens if we digest a circular plasmid with one restriction enzyme site?
We linearize.
| Get a single fragment.
449
Why do we get a linear fragment from one circular plasmid restriction enzyme?
No additional site, fragments are generated.
450
How does gel electrophoresis feel?
Small, jelly.
451
What does the word 'electrophoresis' mean?
Carried by electricity.
452
To what does 'electrophoresis' refer to in the lab?
Movement of molecules: DNA, RNA, protein --> mobilized by electric field through substance.
453
How many electrodes occur in electrophoresis?
2: negative, positive.
454
What doe happen when we turn the machine on?
Two electrodes create a difference in charge on the 2 sides of the gel --> electric field.
455
By what is electrophoresis separation of molecules affected?
Molecules' size, charge.
456
What does a charge cause to the molecule?
Move through the gel.
| Attracted to positively charged pole.
457
What is happening through the electrophoresis gel?
Positively charged electrodes --> towards negative pole and the opposite.
458
What do neutral molecules do?
Do not move at all.
459
What does DNA do?
Always negatively charged --> towards positive pole.
460
What does agarose gel have?
Irregular hole, pores.
| Like a sponge.
461
How does the situation of the agarose gel show the size of the DNA fragments?
Moving through a complex substance --> shows how quickly different sizes move through.
462
How will the longest DNA pieces move through the gel?
Will find more holes --> difficult to move on the complex substance of gel.
463
What do we need as a first step in gel electrophoresis?
Make the agarose gel.
464
How can we make the agarose gel?
Dissolve the sugar in a liquid --> boil it --> cool down --> thicken in a mould (like making a jelly)
= agarose --> electrophoresis buffer --> boil --> add to gel casting tray --> add DNA stain.
465
How does agarose come?
As a powder/pre-weighed tablet.
466
Why do we add a DNA stain to the agarose gel when making it?
Make samples visualization easier after.
467
How do we know where to place DNA samples on the gel?
Add comb at end.
468
When do we remove the comb from the gel?
Once the gel cools and hardens.
469
How do the wells look in the gel?
Little pockets.
470
Where do we place the gel once it cools down?
In a gel electrophoresis chamber.
471
With what do we cover the gel?
With running buffer.
472
Why do we cover the gel with running cover?
To guide electricity.
473
With what do we mix the DNA sample before we add it in the gel?
With a loading die.
474
Why do we mix the DNA sample with loading die?
For the gel to sit in.
For DNA to sink to bottom when added to the well with pipette.
Easily track movement of molecules through gel.
475
How do we know that the DNA samples have been added good in the wells?
From the colour of the dye.
476
What are the characteristics of the dye?
Negatively charged,
| Coloured.
477
What do we do once our samples are loaded?
Close lid.
| Turn on power of machine.
478
For how long does gel electrophoresis run?
20 mins.
479
How can we visualise the DNA?
Turn on the safe blue light on the blue gel machine.
Use a dark hood.
Take pictures with phone.
480
Why shall we use a dark hood?
To see the bands in bright room.
481
How does DNA bands move?
In straight line.
482
What can we say about the DNA samples?
They run through a single lane.
483
How can the DNA bands be realised?
They are bright lines in each sample lane.
484
How many fragments is each band?
Billion different fragments.
485
What is the characteristic of each band in the same lane?
Same length, identical.
486
What can the speed of each band tell us about each DNA band?
How big they are in comparison to one another.
487
Which band is smaller?
The band that travelled longer distance in the same time.
488
What do we want to find from gel electrophoresis?
The actual length of the fragments of DNA we are separating.
489
How can we better assess the size of the DNA bands?
Put DNA ladder.
490
How does the ladder act?
As a ruler on the left, we compare our samples to.
491
Which fragment will move the furthest through the gel?
The 100bp fragment.
492
What does gel electrophoresis allow us to see?
If a piece of DNA is present in the sample or not.
493
What can we find using a gel electorphoresis?
An infection.
| Individual identification by fingerprinting.
494
What process does gel electrophoresis do?
PCR.
495
What do we need to know before we make the agarose gel?
The % of the gel.
| The volume of gel (how much we need to make).
496
What buffers can we use to mix with agarose?
TBE Buffer = Tris/Borate/EDTA buffer.
497
Why should we not swirl the flask with agarose and buffer once we mix them?
Because agarose will stick to the flask --> will not dissolved.
498
What should we do once we put the flask with agarose + buffer in the microwave?
Loosen the cap of the flask.
499
Why should we loose the cap of the flask in the microwave?
To not explode.
500
For how long should we put the agarose + buffer mixture in the microwave?
45 seconds.
501
Where should we put the flask once removed from the microwave?
Room temperature --> cool down.
502
Where do we pour the agarose mixture once it cools down?
In the gel electrophoresis machine.
503
What else do we put once we put the agarose mixture in the machine?
A comb.
504
Where should we transfer the gel after it is still with the wells appeared?
In the gel tank where there is buffer.
505
How should we pour DNA samples in the agarose gel?
Put tip of pipette in well --> slowly pour sample in well.
506
How is the DNA sample chracterised?
Heavier than water.
507
What do the sample do?
Sinks down to the well.
508
What should we put once all the samples are loaded?
The lid.
509
On what does the voltage we use in the gel electrophoresis machine depend?
On how long the gel is.
510
On what does the time we run the DNA samples in the gel electrophoresis machine depend?
On the % of jell we have.
| On the voltage we run the gel at.
511
What is the relationship between voltage and time for DNA samples?
Higher voltage --> shorter time for DNA to run.
512
What is the relationship between % and time for DNA samples?
Lower % of gel --> shorter time for DNA to run.
513
What should we do once the samples stop running?
Unplug the machine.
| Take off lid.
514
How can we tell if the samples have finished running?
Look at dye migrated.
515
How do the samples run in gel electrophoresis?
Horizontally.
516
Why should we dilute buffers and dyes with DNA samples efficiently?
To control DNA samples in the wells.
517
Why is it important to know how much of DNA samples will be loaded in the wells?
To make sure the wells will hold the amounts.
518
What will happen if we load more DNA sample into the well?
Spill into the next well --> contamination --> false results.
519
What will bubbles at the tip of pipette cause?
Sample spreading --> sample loss.
520
What will happen if we do not load the sample into the well appropriately?
Sample will spilled out of the well.
521
What will happen if we do not remove the tip of the pipette once we put the DNA sample in the well?
Will remove some of the sample back in the pipette --> not quantitative --> false results.
522
What does Gel electrophoresis use?
Electricity.
523
Why does gel electrophoresis use electricity?
To separate DNA fragments by their length.
524
How are DNA ladders called?
Standards.
525
Where can standards prepared?
In the lab.
| Pre-made.
526
Why do we use standards in gel electrophoresis?
Better estimation of samples.
| See if samples contain DNA.
527
What do samples and standards contain?
Billion copies of same fragment --> form visible bands.
528
What do bands in the same position, in 2 different lanes, contain?
Fragments of same length.
529
Where do shorter fragments occur in the gel?
Lower (moved faster).
530
Do we need to run standards in each gel in electrophoresis?
Yes.
531
Why do we need to run standards at each gel in electrophoresis?
Because measurements change and we need to estimate the lengths of different bands.
532
Where can we build the table for our standard curve of the DNA samples we run in gel electrophoresis?
Excel.
533
How can we build our plot for gel electrophoresis in excel?
Scatterplot --> trend line.
534
How can we make the analysis of the plot of gel electrophoresis easier?
Convert DNA sized to Log10 base pairs.
535
Of which lane in gel electrophoresis samples do we build the plot for?
The DNA ladder (standard).
536
Why do we only plot the DNA ladder samples in gel electorphoresis?
To plot the line of best fit of estimation samples and compare the unknown values --> find them in the plot.
537
What do we always know about our DNA ladder?
The base pairs.
538
How can we sue the known values of base pairs we know for the DNA adder?
Base pair numbers --> Log10 base pairs --> plot a graph --> Log10 on x axis --> measure distance of each band on DNA ladder --> plot distance (mm) on y axis --> plot graph --> find unknown log base pair of known distance of DNA sample we run --> anti-log of value --> find value of unknown base pairs of DNA sample we run.
