Module 4: Deoxyribonucleic Acid Flashcards
1
Q
DNA has…
A
- a common structure across all organisms
- structure of dna is linked to it’s function
- stores genetic information
- copy itself to transmit info from one generation to the next
2
Q
How do we know DNA is the genetic material?
A
- Experiments conducted by F. Griffith in 1928 demonstrated that DNA is the genetic material
- know mice
3
Q
What was key evidence that DNA is the genetic material?
A
- research conducted by Avery, MacLeod & McCarty in 1944 identified the molecule that transformed the non-virulent to virulent bacteria
4
Q
DNA is a linear polymer of four different subunits called
A
nucleotides
5
Q
Nucleotides consist of three parts:
A
- A five-carbon sugar
- A base, attached to the 1’ carbon
- One or more phosphate groups
6
Q
The sugar in DNA is deoxyribose…
A
“minus oxygen” at the 2’ carbon
7
Q
The phosphate group has two __ charges on its __ atoms, due to the __ of the __ groups attached to the __ atom at cellular pH (~7)
A
negative
oxygen
ionization
hydroxyl
phosphorus
8
Q
A sugar and a base
A
nucleoside
9
Q
nucleoside with one or more phosphate groups
A
nucleotide
10
Q
One end of a DNA strand differs from the other due to
A
polarity
11
Q
Free ____ at top of strand
Free ____ at bottom
A
5’ phosphate group
3’ hydroxyl group
12
Q
Bases can only be added to the __ on the sugar
DNA grows in the __ direction
A
3’-OH
5’-3’ (we read it that way too)
13
Q
Phosphodiester bond
A
C-O-P-O-C
- bond between phosphate group and next sugar
14
Q
3-D Structure of DNA
A
- two strands of DNA are wrapped around each other to form a helix, coiled right
- sugar-phosphate backbone wind around outside of molecule
- bases point inward
- two strands run in opposite direction, antiparallel
- outside contours from an uneven pair of grooves called the major (big space before next turn) and minor (little space before turns against) grooves
15
Q
Bases A&T and G&C are known as
A
- complementary
16
Q
Why is there specificity of base pairing?
A
- Specificity arises due to hydrogen bonds that form between A and T and G and C
- H-bonds form when an electronegative atom (O or N) in one base shared a proton with another electronegative atom
17
Q
What are the two factors that contribute to the stability of DNA?
A
- Hydrogen bonds
- Weak bonds, when there are many they contribute to the stability of the DNA double helix
- A&T are held together by two H-bonds
- G&C are held together by 3 H-bonds - Base stacking
- Interactions between bases on the same strand
18
Q
The sequences of bases of a DNA molecule carries information about its…
A
genetic makeup
19
Q
DNA can be copied in a process known as…
A
replication
20
Q
The complimentary base pairing ensures…
A
fidelity (accuracy, how precise can we be?) of DNA replication
21
Q
DNA Replication
A
- two strands of original DNA double helix are known as parental strands
- each parental strand serves as a template for synthesis of a complementary strand knows as a daughter strand
22
Q
Central Dogma
A
DNA is transcribed into RNA, which is then translated into protein
23
Q
The term transcription is used…
A
for the generation of RNA from DNA
- DNA is the template
- Emphasizes that DNA and RNA use the same “language” of nucleic acids
24
Q
Protein synthesis is dependent on…
A
the “code” carried on a molecule of messenger RNA (mRNA)
- the term translation is used since this indicates a change in the language used, from nuclei acids to amino acids
25
What are the exceptions to the general DNA to RNA to protein flow?
- reverse transcription from RNA to DNA
-- uses an RNA template for synthesis of DNA
-- Enzyme reverse transcriptase catalyzes this reaction
-- ex; HIV converts its RNA into DNA
26
What is a gene?
The unit of heredity affecting one or more traits of an organism; the DNA sequence that corresponds to a specific protein
27
What is gene expression?
The production of a functional gene product, such as protein
- gene expression is regulated
- genes can be expressed, "turned on" or not expressed, "turned off"
28
Where does transcription occur?
Prokaryote: transcription and translation occur in cytoplasm
Eukaryotes: transcription occurs in nucleus and translation occurs in cytoplasm
29
Difference in RNA and DNA
| (5)
- sugar
(DNA: deoxyribose
RNA: ribose)
- nitrogenous base
(DNA: thymine
RNA: uracil)
[A pairs with U in RNA]
- 5' end
(DNA: monophosphate
RNA: triphosphate)
- size
(DNA: very large
RNA: smaller)
- strands
(DNA: double
RNA: single)
30
What is needed for transcription to occur?
| (4)
1. a DNA template
2. RNA polymerase is the enzyme needed for transcription
3. polymerase moves in a 3' to 5' direction along template DNA strand
- RNA grows in a 5' to 3' direction
4. uses ribonucleotide triphosphates (ATP,CTP, GTP,UTP)
- provides energy to drive the anabolic/synthetic reaction
31
How does transcription take place?
A region of DNA unwinds and one strand will be used as a template for the RNA transcript
- only difference is that T's are replaced with U's
- new RNA strands grow in the 5' to 3' direction
-- the template DNA strand is read in the 3' to 5' direction by RNA polymerase
- transcription takes place in 3 stages, (initiation, elongation, termination)
32
Initiation of Transcription
- transcription is initiated at a specific region of DNA, the promoter
- this is a double stranded DNA sequence that proteins known as transcription factors and RNA polymerase bind
-- promoter sequences are conserved DNA sequences
-- one very common base pair sequence is in eukaryotes 5'-TATAAA-3', called the TATA box
33
Where is the 1st nucleotide to be transcribed found?
~25 base pairs away from the TATA box
34
Transcription proceeds until RNA polymerase gets to a ...
terminator
35
In bacteria, promoter recognition is mediated by a...
protein, sigma factor
- this protein associates with RNA polymerase (RNA Pol) and RNA Pol's binding to specific promoters
36
In eukaryotes at least...
six proteins must work together to initiate transcription
37
General transcription factors:
- they bind to promoter region
- transcriptional activator proteins will bind to enhance sequences on the DNA
- this recruits RNA polymerase complex II (RNA Pol II)
- the mediator complex associates with the general transcription factors and RNA Pol II
- he looping of the DNA brings activator proteins into contact with the proteins bound at the promoter region, this initiates transcription (there is a loop that must happen)
- this forms a "bubble" that is about 14 base pairs in length
-- the RNA-DNA duplex in the bubble is about 8 pairs in length
38
Transcription Elongation
- RNA Pol (prokaryotes) and RNA Pol II (eukaryotes) allows for unwinding of the DNA
- this allows complementary nucleotides to be added to the growing messenger RNA (mRNA) transcript
- RNA nucleotide triphosphates can enter via channels
- there are also channels for:
-- the DNA double helix to enter/exit
-- an exit of growing mRNA
-- the release of the mRNA when transcription is terminated
39
Steps of polymerization reaction:
1. RNA polymerase detects incoming ribonucleic triphosphate and if it base pairs appropriately, joins it to the expanding transcript
2. RNA Pol orients with oxygen in hydroxyl group at the 3' end of the growing strand into a position from which it can attack the innermost phosphate of the triphosphate, which provides the energy for the reaction
3. a pyrophosphate group, P-P, is then released
4. this creates a permanent attachment of the ribonucleotide and allows the next nucleotide to be linked
(1. orient correctly, 2. take off phosphate and create some energy)
40
Transcription and translation...
are coupled, they are connected in space and time
41
Prokaryotic Transcription
- RNA transcript that comes off the template DNA strand is known as the primary transcript
- it contains the information of the gene using an RNA code
- for genes that code for a protein, the primary transcript (mRNA) has the information to direct the ribosome to translate the protein
- primary transcript = mRNA
- when primary transcripts contain information for more then one gene the the mRNA is called, polycistronic mRNA
42
What makes there an added layer of complexity for T&T in eukaryotes?
the nuclear membrane
- primary transcript needs to be modified so the message can move from nucleus to cytoplasm
43
Chemical modifications that are done to the primary transcript...
RNA processing
- addition of a 5' cap
- removal of introns
addition of the poly A tail (AAAAA)
44
5' cap
- 7-methylgluanosine to the 5' end of the primary transcript
- this is a unique 5'-5' bond, helps protect mRNA from exonucleases & provides stability
- addition of 5' cap is needed since the ribosome would not recognize the mRNA, thus translation could not occur
45
Poly (A) tail
- addition of about 250 consecutive adenines to the 3' end of the mRNA
- this process is known as polyadenylation
- serves important role in transcription termination, export of mRNA to cytoplasm and protection form degradation by exonucleases
46
Introns
- primary transcript undergoes the excision of certain sequences (introns)
- this leaves intact exons
- this process is known as RNA splicing
47
Alternative splicing
- some genes primary transcripts can b spliced in different ways
- a single gene may produce different but related protein products in different cells, splicing results in different mRNAs
