Weeks 0-6 Flashcards
1
Q
Are covalent bonds stronger or weaker than non-covalent bonds?
A
Covalent bonds»_space;> non covalent bonds
2
Q
What are ionic bonds?
A
They involve the complete transfer (either gain or loss) of electrons between two opposite charged ions
3
Q
Why do hydrogen bonds occur?
A
Due to the attraction of positively charged H atoms to negatively charged atoms
4
Q
What happens to H bonds when mixed with water?
A
H bonds are weakened by water as water competes for H bond interactions
5
Q
Define Van der waals forces?
A
They are weak electrostatic interactions (either attraction or repulsion) between atoms due to polarity
6
Q
How do hydrophobic forces occur?
A
Due to the attraction between non polar molecules and the exclusion of water
7
Q
What are the weakest chemical bonds?
A
Van der Waal forces
8
Q
Which type of bond requires the most energy to break?
A
Covalent bonds
9
Q
What are the subunits and macromolecule of carbohydrates?
A
Subunit = Monosaccharide
Macromolecule = Polysaccharide
10
Q
What is the bond between each unit of a carbohydate?
A
Glycosidic bond
11
Q
What are the subunits and macromolecule of protein?
A
Subunit = Amino acid
Macromolecule = Polypeptide
12
Q
What is the bond between each unit of a protein?
A
Peptide (covalent) bond
13
Q
What are the subunits and macromolecule of nucleic acid?
A
Subunit = nucleotide
Macromolecule = nucleic acid
14
Q
What is the bond between each unit of a nucleic acid?
A
Phosphodiester bond
15
Q
What are the subunits and macromolecule of fats?
A
Subunit = Fatty acid
Macromolecule = Triglyceride, cholesterol
16
Q
What is the bond between each unit of a fats?
A
Ester bond
17
Q
What are these structures?
A
18
Q
What are these structures?
A
Amino acid
19
Q
What are these structures?
A
Nucleic acid
*Phosphate group + sugar + nitrogenous base
20
Q
What are these structures?
A
21
Q
List the functions of carbohydrates?
A
SACS
- Storage in the form of glycogen
- Metabolism to produce energy (ATP) by glycolysis
- Conversion to fatty acids and triglycerides for long-term storage
- Synthesis of other cellular components, such as the cell membrane
22
Q
List the functions of proteins?
A
SCRAP
- Providing structure and support (e.g. actin and tubulin)
- Catalysing metabolic reactions (e.g. enzymes)
- Regulating cell signalling and transmitting signals (e.g. hormones)
- Acting as transport or storage molecules (e.g. albumin)
- Providing protection and defence (e.g. antibodies)
23
Q
What can amino acids exist as and where are they common?
A
Amino acids can exist as 2 isomers:
L isomers are common in proteins found in humans
D isomers are common in the cell wall of microbes
24
Q
What are the main classes of nucleic acids?
A
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
25
List the functions of fats?
My Kitchen Rules (MKR)
1. Major form of energy storage
2. Key components of cell membranes
3. Roles in cell signaling
26
What is this reaction and identify the subunits?
Condensation reaction:
Glycerol + 3 fatty acids = triglyceride
27
You discover that you have a deficiency in the amino acid triptophan. At the pharmacy you find both L-tryptophan and D-tryptophan supplements. Which should you purchase?
L-Tryptophan
28
A nucleotide can vary in...
The sugar and the base
29
What is the relationship with melting point and carbon chain length?
As the carbon chain increases, the melting point increases regardless of the bonds present
30
Identify what type of fat compound A and B are?
A = trans unsaturated fatty acid
B = cis unsaturated fatty acid
31
What is special about phospholipids?
They are amphipathic
32
What does it mean if a substance is amphipathic?
They consist of a hydrophobic fatty acid chain tail and hydrophilic phosphate head
33
What does the cell theory state?
States that all organisms are composed of similar units of organisation, called cells
34
What do cells use to grow?
Adenosine triphosphate (ATP) as their energy currency
35
What are mammalian cells enclosed by?
A plasma membrane
36
What do cell membranes typically contain?
Pumps, carriers and channels
All of these allow molecules (e.g. nutrients) to pass into the cell and release waste out of the cell
37
How is genetic information normally stored?
In the form of nucleic acids (usually DNA)
38
What is the function of proteins in cells?
1. To catalyse chemical reactions
2. Synthesise proteins on ribosomes
3. Derive energy by breaking down simple sugars and lipids
39
What is special about cells?
Cells are dynamic
This means cells respond to a variety of stimuli including chemical, electrical and hormonal signals
40
What are prokaryotes?
Unicellular organisms that lack a nucleus and other membrane-bound structures (organelles)
41
What are examples of prokaryote cells?
Bacteria
Archaea
42
What is a simplistic explanation of the structure of prokaryotes?
Tend to be small and simple
43
How do prokaryote cells divide and reproduce?
By binary fission
44
What are the main structure found in prokaryotic cells?
Plasma membrane
Nucleoid
Ribosomes
Cytoskeleton
Cytoplasm
Pili
Flagella
45
What is a nucleoid?
A central region of the cell containing the genetic material (DNA bundled together)
46
What is a pili?
Rod-shaped structure on the cell membrane involved in attachment and DNA transfer
47
What is a flagella?
Tail-like structures on the cell membrane that assist in movement
48
What is special about prokaryotic cells (in particular bacteria)?
They contain both a cell wall and plasma membrane
49
What are eukaryotes?
Multicellular organisms that contain a nucleus and other membrane-bound structures (organelles)
50
What are examples of eukaryotes cells?
Plant and animal cells
51
What is a simplistic explanation of the structure of eukaryotes?
Large and complex
52
How do eukaryote cells divide and reproduce?
Mitosis/Meiosis
53
What is an acronym for distinguishing between prokaryotes and eukaryotes?
Prokaryotic cell = ‘Pro’ rhymes with ‘no’ (no membrane-bound organelles)
Eukaryotic cell = ‘Eu’ rhymes with ‘do’ (do contain membrane-bound organelles)
54
What is the structure of the plasma membrane?
A lipid bilayer (a thin doubled-layered film of lipids where each layer is one phospholipid thick)
55
What do phospholipids contain?
A hydrophilic head and a hydrophobic tail (tail faces towards each other to exclude water)
56
What is the function of the plasma membrane?
Acts as the interface of the cell and its extracellular environment
57
What is the function of transmembrane receptors in the plasma membrane in eukaryotic cells?
Convert the binding of extracellular signaling molecules into signals that influence processes within the cell
58
What is the function of adhesion complexes in the plasma membrane of eukaryotic cells?
Allows cells to bind to each other, or to the extracellular matrix
59
What is the nucleus often referred to as?
The brain of the cell
60
What is the structure of the nuclear envelope?
Consists of two nuclear membranes (inner and outer membranes) that separate the nucleus from the cytoplasm
61
What is the outer membrane of the nuclear envelope continuous with?
The membrane of the rough endoplasmic reticulum
62
What controls the entry and exit of molecules and compound in and out of the nucleus?
Nuclear pores
63
What is the nuclear lamina, and what is its function?
A network for intermediate filaments that form a thick mesh just underneath the inner nuclear membrane (to support the nuclear membrane)
64
What is chromatin?
Small uncoiled strands consisting of DNA with proteins to form chromosomes (all housed within the nucleus)
65
What is the nucleolus?
An area within the nucleus where ribosomes are assembled
66
What is the function of ribosomes?
Aid in the synthesis of protein, using messenger RNA as a template
67
What occurs in the cytoplasm?
The main site of protein synthesis and degradation, and is where some stages of metabolism occur
68
What is the function of the cytoskeleton?
Gives a cell its shape and structure and provides a framework for movement within the cell
69
What are the main components of the cytoskeleton?
Actin (microfilaments) filaments
Intermediate filaments
Microtubules
70
Identify the function of the components of the cytoskeleton?
Actin (microfilaments) filaments = transport organelles through the cytoplasm and provide tracks for protein that allow for cellular movements
Intermediate filaments = transport organelles through the cytoplasm and provide tracks for protein that allow for cellular movements
Microtubules = important in cell division
71
What are centrosomes and centrioles mainly composed of?
Tubulin (a type of protein)
72
What is the function of centrosomes and centrioles?
Regulate cell division by forming the microtubule organising centre (MTOC) from the microtubule spindle apparatus (the structure that separates chromosomes during mitosis and meiosis)
73
Why is the mitochondria referred to as the powerhouse of the cell?
Because it generates most of the energy (i.e. ATP) the cell uses to drive chemical reactions
74
What does the mitochondria contain?
Two lipid bilayer-protein membranes (an outer and inner membrane)
75
Define cristae?
It is a fold in the inner membrane of mitochondria
76
What is the function of cristae?
To maximise the surface area available for cellular energy production
77
What is the wall structure of the endoplasmic reticulum?
Composed of a single lipid bilayer membrane
78
What is the function of the smooth and rough ER?
Smooth ER = do not contain ribosomes = phospholipid synthesis
Rough ER = does contain ribosomes = protein synthesis
79
Describe what happens in the rough ER?
1. Protein synthesis and folding occur, which are then stored in the cisternal space (lumen)
2. When enough proteins are present, they collect and are pinched off in vesicles
80
Why is the golgi apparatus referred to as the traffic director?
Because they receive lipids and proteins from the ER, and modifies them before sending them on
81
Describe what happens in the golgi apparatus?
1. As the proteins move through the golgi membrane, enzymes within the Golgi attach sugar side chains to these proteins (a process called glycosylation).
2. Processed proteins are then segregated into different vesicles destined for lysosomes or the plasma membrane
82
Describe the function of lysosomes?
Lysosomes contain enzymes which can degrade old organelle and microorganisms
83
What is a characteristic of the lumen of a lysosome?
It has a pH of 4.5-5.0 (acidic range)
84
Explain how a lysosome deal with intracellular and extracellular materials?
Intracellular = digested through autophagy within the lysosome
Extracellular = delivered to the lysosome in endosomes, via endocytosis, and degraded
85
Describe the endosome system?
A transport network which deliver materials from the Golgi to lysosomes or from the Golgi to the plasma membrane
86
How are materials transported via the endosome system?
Content is transported via vesicles/endosomes which are lipid membrane structures that form during protein secretion (exocytosis) or uptake of extracellular content (endocytosis)
87
Where are vacuoles found?
In plants and fungi
88
What is the function of vacuoles?
Used for storage
89
What do peroxisomes contain?
1. Enzymes needed for the oxidation of organic compounds (fatty acids)
2. Enzymes (e.g. catalase) that breakdown hydrogen peroxide, a toxic by-product of oxidation
90
What is another function of peroxisomes apart from the functions of its enzymes?
Are also involved in the synthesis of lipids (e.g. cholesterol, and bile acids)
91
Which organelles have two lipid bilayer?
Mitochondria
Nucleus
92
What is the function of chloroplast?
Conduct photosynthesis in plants and algae?
93
Differentiate between the nucleus, nucleoid and nucleolus?
Nucleus = houses DNA in eukaryotic cells
Nucleoid = where DNA is located in prokaryotic cells, but is not membrane-bound
Nucleolus = structure within the nucleus responsible for ribosome production
94
Differentiate between heterochromatin and euchromatin?
Hetero = tightly packed form of DNA and is transcriptionally inactive
Eu = loosely packed form of DNA and is transcriptionally active
95
Differentiate between the cell membrane and cell wall?
Cell membrane = semi-permeable membrane that encloses the cell's cytoplasm
Cell wall = rigid layer outside the cell membrane, found in plants, fungi and bacteria
96
97
List the phases of the mitotic cell cycle?
Interphase = G1, S, G2 phases
Mitosis (M) phase = Prophase, Metaphase, Anaphase, Telophase
98
What happens in the G1 (GAP 1) phase?
1. Cell duplicates organelles
2. Cell synthesises proteins and different enzymes to help aid in the DNA process
3. protein mass doubles
99
What happens in the G1/S checkpoint?
1. Cell senses if nutrients are present and DNA is intact.
* If conditions are not suitable, the cell has mechanisms to pause progress to the next phase at this checkpoint
* In order to pass this restriction point, mitogens (a specific growth signal in mammalian cells that trigger cell cycle entry) must be present
100
What happens in the S (synthesis) phase?
1. DNA replication occurs in this phase.
2. Each of the 46 chromosomes is duplicated in the cell, to produce sister chromatids (duplicated chromosomes)
101
Describe the function of centromeres and cohesion complexes?
Hold the sister chromatids together so they aren’t floating randomly around the cell
102
What happens in the G2 (GAP 2) checkpoint?
A period of general cellular growth (the cytoplasm grows in size here).
103
Why is the G2 (GAP 2) phase important?
This phase separates the S phase (DNA replication) and the M phase (chromosome separation) to allow the cell time to completely replicate before chromosome segregation
104
What happens in the G2/M checkpoint?
Cells can activate this checkpoint (i.e. to pause the cycle) allowing the cells time to fix any DNA that may be damaged
105
What occurs in phase 1 of the prophase?
1. The nuclear envelope starts to break down so the sister chromatids can begin to be segregated
2. The mitotic spindle starts to form from 2 organelles:
Centrosomes move to opposite poles.
Centrioles build long polymers of tubulin
106
What occurs in phase 2 of the prophase?
1. Chromosomes condense (makes it easier for them to separate into 2 identical daughter cells)
2. Kinetochores bind to the long polymer chains of tubulin, which connect to the microtubule organisation centre that is beginning to form
107
Describe the function of kinetochores?
Are protein complexes that are in direct contact with the chromatids) and attach to the long polymers of tubulin, allowing these string-like pieces to split the 2 chromatids
108
Where do the microtubules attach to during prophase?
The microtubule organisation centre
109
Describe the function of the mitotic spindle?
Ensures that chromosomes in the parent cell are split equally and identically for the daughter cell
110
What occurs in the metaphase?
1. The nuclear envelope disintegrates during metaphase to allow the spindle fibers to attach to the kinetochores of the chromosomes.
2. The microtubule organisation centre (MTC) go to each poles, allowing the microtubules from each pole to attach to the kinetochore which hooks the sister chromatids to separate them both.
3. The chromosomes them align on the spindle equator (the metaphase plate)
4.kinetochores push and pull until they are in line and each sister chromatids are facing opposite pole
111
What is the function of the metaphase-anaphase checkpoint?
Checks if the kinetochores are correctly attached to the sister chromatids
checks for DNA damage
also called spindle checkpoint
112
What occurs in the anaphase?
The poles continue to exert force on the kinetochores hooking onto the sister chromatids. Eventually, the cohesin (the protein binding both sister chromatids together) breaks causing the sister chromatids to separate from one another
113
Explain the process of the sister chromatids separating in the anaphase?
1. Astral microtubules attach to cell membranes and pull spindle poles apart.
2. Motor proteins play a role in pushing and pulling – kinesins (+) and dyneins (-)
3. kinetochore microtubules shorten pulling sister chromatids apart
114
What are motor proteins?
They literally form the motor/engine of the force (i.e. they pull anything behind them with them in the direction they want to go)
In this case, they go from the centre to the cell membrane to assist in splitting the sister chromatids apart
115
Explain what happens in the telophase?
1. The mitotic spindle breaks down to allow the nuclear envelope to form around both separate sister chromatids.
2. chromosomes de-condense
116
Explain how cytokinesis occurs?
the contractile ring forms and pull the centre of the plasma membrane inward until the cell separates into 2 IDENTICAL daughter cells
117
What happens once cytokinesis is complete?
Some cells go back to G0 phase to rest, while other cells go straight back to the G1 phase to undergo mitosis again
118
Define the cell cycle control system?
A system which integrates internal and external signals to activate or inhibit cell division
119
What are checkpoints regulated by?
Cyclin activated protein kinases
120
Describe the function of kinase?
An enzyme that causes the ADDITION of a phosphate group
121
Describe the function of phosphatase?
An enzyme that causes the REMOVAL of a phosphate group
122
Why is cyclin important to the checkpoints?
If cyclin (specific to each checkpoint) is present, this activates the kinase to phosphorylate proteins allowing the cell cycle to exit each checkpoint and continue the cell cycle
123
What happens if there is no checkpoint-specific cyclin?
No checkpoint specific cyclin = these kinases will remain inactive, preventing the cell cycle from continuing
124
Identify the cyclins used at each checkpoint?
G1-S checkpoint = cyclin D
S-G2 checkpoint = cyclin A
G2-M checkpoint = cyclin B
125
What is the function of mitogens?
Stimulate production of the first cyclin for cell cycle entry
126
Why is cyclin destruction important?
It ensures the cycle does not go backward
127
Name 2 important ubiquitin ligase complexes?
SCF
APC/C
128
Why are SCF and APC/C ubiquitin ligase complexes important?
They contribute to cyclin destruction = ensuring the cell cycle progresses forward, and to promote cell cycle exit
129
What are the 2 functions of the anaphase promoting complex/cyclosome (APC/C ligase)?
1. Initiates anaphase by targeting securin
2. Assists in moving from mitosis to the G1 phase of the cell cycle
130
How does the APC/C ligase initiate anaphase?
By targeting securin to break it down, the degradation of securin releases separase, which then breaks the cohesin complexes holding the sister chromatids together
131
How does the APC/C ligase assist in moving from mitosis to the G1 phase of the cell cycle?
By targeting mitotic cyclins (e.g. cyclin B), the breakdown of these cyclins leads to its complementary kinase becoming inactive, which is necessary for the transition from mitosis to the G1 phase of the cell cycle
132
What happens if the cell cycle is controlled?
Controlled cell cycle = genomic stability and tissue homeostasis
133
What happens if the cell cycle is out of control?
Uncontrolled cell cycle = mutation, aneuploidy (cell death, cancer, dysfunction)
***Review the content about aneuploidy
134
135
136
List the process of DNA replication?
1. Initiation of DNA replication (DNA unwinding)
2. Priming
3. Elongation
4. Termination
137
What are the different forms of DNA?
Stringy DNA
Condense DNA chromosomes
Double stranded DNA helix
138
Where does DNA replication occur in the cell cycle?
In the S (synthesis) phase
139
How long does DNA replication typically last for?
Approximately 8 hours
140
What does it mean that DNA replication is a semi-conservative process?
Every new DNA double helix consists of an original and new strand joined together
141
In which direction does DNA replication occur?
DNA replication occurs bi-directionally
142
Describe the structure of DNA?
--> 3 components in DNA: Sugar, phosphate group, bases
--> Sugar-phosphate chains form the DNA backbone and are on the outside
--> Two strands are antiparallel (one runs 5’→3’ and the other 3’→5’.
--> Bases are on the inside, stacked perpendicular (A-T, G-C)
143
Describe the structure of a chromosome?
--> The short arm of the chromosome is labelled the ‘p arm’
--> The long arm of the chromosome is labelled the ‘q arm’
--> The centromere (in the centre of the chromosome) divides the long and short arm.
144
What is the longest chromosome in the human body?
Chromosome 1
145
Describe the BMOL1001 aspect of DNA replication? (1)
--> Phosphodiester bonds between 3’C of one nucleotide with the 5’C of another nucleotide
--> Glycosidic bond between base and sugar
146
Describe the BMOL1001 aspect of DNA replication? (2)
--> Nucleotides contain a base and a sugar WITH a phosphate group
--> Nucleosides contain a base and a sugar WITHOUT a phosphate group
147
What is the first step of initiating DNA replication?
To locate the origin of replication
148
Where is the origin of replication located?
In A-T rich areas because it is easier to break 2 hydrogen bonds between A-T (therefore less energy) and harder to break 3 hydrogen bonds between G-C
149
How many origins of replications are there?
Multiple in eukaryotic cells
150
Explain the events that happen at the origin of replication?
(Note: ORC falls under the general group pre-replication protein complex)
1. Origin recognition complex (ORC): Attaches to adenine and thymine (A-T) to break the hydrogen bonds and forms a replication bubble
2. ORC recruits ‘cell division cycle 6’ (CDC6) which facilitates the loading of the MCM2-7-Cdt1 complex which consists of helicase proteins that move along the leading strands of DNA at each replication fork unwinding the two DNA strands
151
What is the function of the replication fork?
Unwinds the unreplicated DNA ahead of it through a helicase enzyme complex
152
What is the function of helicase?
The protein complex that is recruited to help the replication fork unwind the unreplicated DNA (requires a lot of energy)
153
What is the function of the single-stranded binding protein?
Surrounds the single old DNA strand to prevent the parental strand from reannealing (collapsing back together) and protects the parental strands from nucleases
154
Define endonucleases?
155
Define exonucleases?
156
What is the function of the replication protein A?
Binds and coats the single stranded DNA to prevent DNA damage activation and prevent the parent DNA strands from rejoining
157
What is the function of topoisomerase?
Prevents the over-winding of the DNA double helix ahead of the replication fork by making a transient single ‘nick’ in the DNA backbone to unwind the supercoil and then reseals the ‘nick’ to prevent the DNA from continuously unwinding
158
What are the functions of the 2 domains on the topoisomerase?
Nuclease domain = Makes the ‘nick’ to unwind the backbone
Ligase domain = Reseals the ‘nick’ to prevent continuous unwinding
159
When does DNA priming (step 2) occur?
Once the DNA strands are separated
160
What is the point of DNA priming?
To produce DNA primers that will be elongated by DNA polymerase a
161
What is the function of DNA primase (an RNA polymerase) in DNA priming?
To synthesise short DNA primers (~12 nucleotides) that are complementary to unwound DNA strands
162
What is the action of DNA priming?
Reads 3' to 5'
Synthesises 5' to 3'
DNA primase reads the parent backbone from 3’ to 5’ and then synthesises from 5’ to 3’ in the new DNA strand
163
When does DNA elongation occur?
Once the DNA primers have synthesised the primers in the 5’ to 3’ direction
164
What occurs once primase creates the RNA primer?
DNA polymerase alpha starts to elongate the primer (from the 3’-OH end) with ~20 nucleotidesD
165
Define leading strand?
One of two daughter DNA strands formed by continuous synthesis (i.e. contains 1 strand of RNA primer and 1 continuous DNA strain)
166
Define lagging strand?
One of two daughter DNA strands synthesised in the opposite direction to fork movement, in short stretches called Okazaki fragments (i.e. multiple RNA primers and multiple elongated DNA strands)
167
When does termination of DNA replication occur?
Once both the leading and lagging strands have finished elongating the new DNA strands bonded to the RNA primers
168
Explain the enzymes used during the termination phase of DNA replication?
1. DNA polymerase type 1: Removes RNA primers and replaces them with DNA chain growth.
2. DNA ligase: Joins the adjacent fragments by catalysing the formation of phosphodiester bond between 3’ OH and 5’-phosphate groups of adjacent nucleotides
169
What are the 2 ways that DNA polymerase type 1 removes DNA primers?
1. FEN1 endonuclease = Dominant pathway to remove RNA primers, by cleaving single stranded FLAP.
2. RNAse H endonuclease = Also contributes by removing the RNA portion of the RNA:DNA hybrid.
170
Explain the function and characteristics of DNA polymerase alpha?
→ Extends the RNA primer
→ Has a high error rate because it is very fast and doesn’t have endonuclease and exonuclease
→ Detaches very often, because the sliding clamp doesn’t prevent it from falling off
171
Explain the function and characteristics of DNA polymerase delta?
→ Extends the DNA strand on the lagging strand (i.e. lagging strand DNA synthesis)
→ DNA strand displacement activity: Breaks the hydrogen bonds between the DNA and RNA and the endonucleases and exonucleases eat the primers away
→ Doesn’t detach very often, because the sliding clamp prevents it from falling off
172
Explain the function and characteristics of DNA polymerase epsilon?
→ Extends the DNA strand on the leading strand (i.e. leading strand DNA synthesis)
→ Doesn’t detach very often, because the sliding clamp prevents it from falling off
173
174
What does PCNA stand for when talking about the PCNA sliding clamp?
Proliferating cell nuclear antigen (PCNA) sliding clamp
175
What is the function of the DNA sliding clamp?
PCNA sliding clamp prevents polymerase delta and polymerase epsilon from falling off
176
How does the PCNA ensure DNA polymerases delta and epsilon don't fall off the DNA strand?
1. Forms a large ring around DNA
2. Binds to DNA polymerases
3. Slides along DNA as polymerase moves along DNA
177
When are the polymerases released on the lagging strand?
The polymerase is released each time it reaches the 5’ end of the preceding Okazaki fragment on the DNA lagging strand
178
Why is it important that DNA replication is linked to the cell cycle?
This ensures that DNA is only replicated once during the cell cycle
179
180
What is the primary function of DNA polymerase?
They have catalytic activity to drive nucleotide addition to growing chains
181
What are most DNA polymerases also capable of doing?
Inbuilt nuclease activity to autocorrect as they go, if they insert an incorrect mismatched base
182
What is the issue with the double helix unwinding to give 2 single-stranded DNA (ssDNA)?
Since many viruses contain ssDNA, nucleases have evolved to see ssDNA as foreign cells and attack them to breakdown the phosphodiester bonds
183
What protein is important to protect ssDNA from nuclease attack?
Single-stranded binding protein
184
What happens if the ssDNA is exposed?
Nuclease attack
Re-annealing of the double strand
Self-annealing of the double strand
185
What is the consequence of self-annealing and re-annealing?
Prevent replication progression
186
Describe self-annealing of the single-stranded DNA?
The ability of ssDNA to base pair with itself on the same strand causing a hairpin loop
187
What can also pause the replication fork extension?
Upstream supercoiling
188
What are Okazaki fragments?
Short sequences of DNA nucleotides which are synthesized discontinuously
189
What is strand displacement?
DNA strand displacement occurs when a single nucleic acid strand invades and replaces another nearly identical strand in a duplex
190
What is the whole point of DNA transcription?
To convert DNA to RNA
191
Describe the primary structure of DNA?
--> 5’ C bound to phosphate group
--> 3’ C bound to hydroxyl group - the next nucleotide is added here
--> Phosphodiester linkages connect the 3’ C of one sugar with the 5’ C of another sugar
--> Glycosidic bond between base and sugar
192
What is the structure of RNA?
RNA is single stranded
RNA has a same base pairing to DNA (adenine to uracil and cytosine to guanine)
193
What is the central dogma?
The flow of genetic information from DNA to RNA to proteins
194
In which phase of the cell cycle does DNA transcription occur?
Primarily occurs after cell division in the G1 phase
195
196
Why is the transcription start site important?
Because this is where the messenger copy of the RNA begins (i.e. this is where transcription starts)
197
Why is the transcription start site associated with being '+1'?
Because the transcription starts here
Anything toward the 5’ side is a negative number and anything to the 3’ side is a positive number.
198
What are some reasons why the promoter region is important?
This protein allows transcription to begin specifically at the TSS
Promoters are a nucleotide sequence that allow proteins (e.g. RNA polymerases) to bind to the DNA and move along the DNA to make RNA
199
What happens at the transcription termination sequence?
RNA polymerases fall off at this point to stop transcription
200
What is the untranslated region?
The part of exons that remain untranslated from DNA to mRNA
201
Why is the untranslated region on exons important?
Important for stability and protein synthesis
202
Compare the length of introns and exons?
Intron length >>> exon length
203
What makes introns different from exons?
Introns are non-coding (i.e. they do not code for protein) and are removed from the mature mRNA
204
What are some functions of codons in DNA transcription?
1. Instruct the cell to start creating a protein chain
2. To add a specific amino acid to the growing chain
3. To end the protein chain
205
When is protein synthesis completed?
Protein synthesis is terminated when the ribosomes reach a termination codon (since there are no transfer RNA molecules that can recognise these codons, ribosomes recognise that translation is complete and fall off)
206
What do general transcription factors bind together?
The promoter and RNA polymeraseq
207
