unit two and three Flashcards
(89 cards)
1
Q
what is the general structure of a nucleotide?
A
- a phosphate group attached to a 5 carbon ring
2
Q
what carbon is the new nucleotide added to?
A
3’ carbon
3
Q
what is the polymer of nucleotides?
A
nucleic acids
4
Q
what are the two types of bases?
A
purines and pyramidines
5
Q
what is the difference between a purine and a pyramidine?
A
purines are double ring, pyramidine are single ring
6
Q
what are the purine bases?
A
adenine and guanine
7
Q
what are the pyramidine bases?
A
thymine, uracil, and cytosine
8
Q
what holds the base pairs together?
A
hydrogen bonds
9
Q
what is base-stacking?
A
base stacking (ID-ID) between non-polar surfaces contribute to the bases packing together
10
Q
why do purines bind with pyramidines?
A
because it allows for a uniform structure
- same distance between bases in the two strands
- same regular hydrogen bonding interaction
- same stacking interactions between bases above and below
11
Q
what is a phosphodiester bond?
A
two ester linkages form a phosphodiester bond - links the two nucleotides together
12
Q
what is the directionality of a nucleic acid? (ie. DNA/ RNA)
A
5’ to 3’
13
Q
what are the levels of structures of DNA?
A
primary: 1 strand of DNA
secondary: double helix
tertiary: chromatin
14
Q
describe the double helix structure of DNA
A
- 2 strands of DNA wound together
- major and minor groove - where proteins bind
- DNA sequences on both strands are complementary to each other
- each strand is anti-parallel
15
Q
what are the differences between DNA and RNA?
A
- ribose has OH on 2’ carbon, deoxyribose has H on 2’ carbon
- DNA has deoxyribose sugar, RNA has ribose sugar
- Bases: RNA uses uracil instead of thymine
- RNA is single-stranded, DNA is double-stranded
- DNA is larger than RNA
- DNA has a monophosphate on the 5’ end, RNA has a triphosphate on the 5’ end
16
Q
what is the central dogma?
A
DNA - RNA - Protein
17
Q
what is called when DNA goes to RNA?
A
transcription
18
Q
what is called when RNA goes to protein?
A
translation
19
Q
what are the types of RNA?
A
- rRNA
- tRNA
- mRNA
20
Q
what is rRNA?
A
ribosomal RNA, it is not translated, and is integrated with ribosomal proteins, stable
21
Q
what is tRNA?
A
transfer RNA, not translated, folded into secondary structure so it can contribute to translation, stable
22
Q
what is mRNA?
A
messenger RNA, translated into a protein, unstable, and easily degraded
23
Q
what way is the DNA template read?
A
3’ to 5’
24
Q
what way does RNA polymerase move?
A
3’ to 5’
25
what way does RNA grow?
5' to 3'
26
what is the template strand?
the strand read to code for the new strand
27
what is the coding strand?
the strand opposite to the template stand (it is the exact same as mRNA, but replace U and T)
28
describe the general differences between bacterial gene structure and eukaryotic gene structure?
LOOK AT DIAGRAM
29
what is the bacterial promoter? (structure + proteins)
-35, -10, sigma factors which recruits RNA polymerase, creating the holoenzyme
30
what is the eukaryotic promoter?
TATA box, with general transcription factors, and TATA binding protein, creating the basal complex
31
what is the location of T and T in bacteria?
both in the cytoplasm
32
what is the location of T and T in eukaryotes?
transcription: nucleus; translation: cytoplasm
33
what is RNA polymerase?
a very large protein (quatrenary structure) that is made up of several protein subunits that separates the DNA strands and threads the newly synthesized DNA through a channel. does not bind directly to the promoter, the proteins recruit it
34
what is the general transcription process?
1) RNA pol binds to the promoter (initiation)
2) transcription starts at +1 site/ transcription start site (elongation)
3) transcription stops after the RNA pol passes through the terminator (termination)
35
transcription summary in bacteria.
1. initiation of transcription happens at the promoter sequence
2. sigma factor protein binds to the promoter which helps recruit RNA pol to bind and promote the start of transcription
3. RNA pol bound to the DNA is oriented such that the catalytic site (catalyzes the phosphodiester bond) is about 10 bases from the -10 box
4. the first base that serves as the template to transcribe into RNA is called the +1 site
5. transcription continues until termination sequence is encountered and RNA pol transcribes through a termination sequence. a hairpin loop forms on the mRNA causes the RNA pol to dissociate from the gene (DNA)
36
transcription summary in eukaryotes.
1. initiation of transcription happens at promoter sequence (TATA box)
2. TBP and general transcription factors assemble at the promoter which helps RNA pol to bind and promote transcription. this creates the Basal complex
3. regulatory transcription factors bind to DNA sequences and regulate transcription
4. transcription start site is usually 25 base pairs from the TATA box
5. transcription continues until termination sequence is encountered which is transcribed as well.
37
what is the DNA binding protein?
- DNA binding proteins recognize specific sequences of base pairs
- R groups interacting with molecular groups on a GC base pair will be different than AT base pair
- bind in the major and minor groove
- bind by H bonds and other non-covalent interactions
38
how is transcription controlled?
1. how often RNA pol binds to the promoter
2. how tightly RNA pol binds to the promoter
39
RNA processing in eukaryotes?
- 5' cap added
- poly A tail on 3' end
- splicing done by spliceosomes (remove introns and keep extrons)
40
what is alternative splicing?
different splicing pattern creates different proteins
41
what are aminoacyl tRNA synthetases?
- translator for the code: matches codon to amino acid
- binds the amino acid to the correct tRNA molecule
- there is only one tRNA synthetase for each amino acid
42
Ribosomal subunits
- ribosomes have 2 subunits: large and small (small one binds first)
- ribosomes contain rRNA sequences, which catalyze the peptide bond
- within the large subunit, there is the E P and A site
43
what are initiation factors (translation)?
they recruit the small ribosomal subunit and tRNA (Met) and scan the mRNA for an AUG codon
44
what is the reading frame?
how to read each codon (3 bases) - first codon determines the rest of the reading frame
45
what does it mean by redundancy in the genetic code?
there are 20 amino acids but 64 codons - more than 1 codon for 1 amino acid
the code is not ambiguous though,
- only 1 amino acid for 1 codon
46
what is the wobble effect?
the third base in a codon does not typically affect the amino acid that is coded
47
what is the general process of translation?
1) initiation: AUG recognized and Met established as first amino acid
2) elongation: amino acids are added to the peptide
3) termination: stop codon is reached, no new amino acids are added, and the polypeptide is released from the ribosome
48
what is an electron micrograph?
photo taken using an electron microscope that captures protein synthesis in cytoplasm
49
how do you read an electron micrograph?
- longer chain = 5', shorter chain = 3'
- away from main line = 5' and N terminus, at main line = 3' and C terminus
50
what is gene regulation?
- a cell does not express all of its genes all of the time. they are selective about genes they express.
- how strongly they are expressed
- where they are expressed
- when they are expressed
51
when is a gene expressed
when the gene product is actively being synthesized and used in a cell
52
what are the three types of gene expression?
- environmentally-regulated gene
- developmentally-regulated gene
- constitutively-regulated gene
53
what is an environmentally regulated gene?
a gene whose expression level is linked to a condition in the environment (ex. nutrient availability)
- ex. mal and lac operon
54
what is a developmentally-regulated gene?
a gene that is expressed only at specific developmental periods of an organism
55
what is a constitutively expressed gene?
a gene that is expressed all the time because the gene product is always needed
56
what are the control mechanisms of constitutively expressed gene products?
- promoter strength
- mRNA half-life
57
how does promoter strength work in context of constitutively expressed gene products?
- how effectively RNA pol and transcription factors bind to the promoter
- determines how frequently transcription is initiated
- determines how many RNA molecules are made
58
how does mRNA half-life work in context of constitutively expressed gene products?
- how quickly mRNA is degraded after it is made
- the longer the mRNA lasts, the more protein copies can be translated per unit time
- only applies to protein encoding genes
59
why is gene regulation important?
cells are limited by their environment, hence regulation of gene expression is critical to the efficient use of resources and thus survival
60
what are the three levels of expression?
1) transcription control
2) translational control
3) post-translational control
61
what is transcription control in expression?
- how often we can produce RNA
- promoter strength: how strongly RNA pol + transcriptional factors bind to the promoter
- operons: regulatory proteins binding to a regulatory region "operator"
62
when do bacterial cells need to synthesize proteins in operons?
only if the sugars are present. ex. if maltose and lactose are present, the mal and lac operon will synthesized
63
are maltose and lactose considered inducers or repressors?
they are inducers - cause mal and lac operon to turn on and be active
64
what is an operon?
operons share a promoter and terminator sequence but have multiple coding regions. one mRNA is produced but multiple proteins are translated
65
what is the operator in an operon?
regulatory region can be found either upstream or downstream (and sometimes overlapping) the promoter. the regulatory protein binds here
66
what is positive regulation?
regulatory protein binds a region by the promoter (operator) and increases transcription. the regulatory protein is called an activator. (MalT)
67
what is negative regulation?
regulatory protein binds to a region by the promoter (operator) and decreases transcription. the regulatory protein is called a repressor. (LacI)
68
how are genes written?
no caps, italics/ underlined
69
how are proteins written?
caps, no italics, underlined
70
describe mal operon
- degrade maltose to glucose
- signal molecule: maltose
- operon: MalPQ
- regulatory protein: MalT
- MalT is a positive regulator of MalPQ
- promoter for MalPQ is weak and binds sigma / RNA pol weakly/
- there is always a little bit of MalT present in the cell to detect the presence of maltose in the cell
71
what happens in the absence of maltose?
- do not need to make enzymes MalP and MalQ
- RNA pol does not bind to promoter strongly, so no transcription
72
what happens in the presence of maltose?
-MalT binds to maltose and changes the conformation of MalT which allows this to bind near the promoter at the operator and helps RNA pol to bind and remain on the promoter
- causes malpq promoter to bind strongly and therefore transcription increases and lots of MalP and MalQ is created
73
describe the lac operon
- degrade lactose to glucose
- signal molecule: lactose
- operon: LacZYA
- regulatory protein: L
- MalT is a positive regulator of MalPQ
- promoter for MalPQ is weak and binds sigma / RNA pol weakly/
- there is always a little bit of MalT present in the cell to detect the presence of maltose in the cell
74
describe the lac operon
- degrade lactose to glucose
- signal molecule: lactose
- operon: LacZYA
- regulatory protein: LacI
- LacI is a negative regulator
- promoter for MalPQ is strong and binds sigma / RNA pol strongly
- operator is found downstream, but overlapping the promoter
- LacI is found upstream of the lac operon and is constitutively expressed
75
what does the LacZ protein do?
cleaves lactose into glucose and galactose
76
what does LacY protein do?
- transporter protein that transport lactose into the cell
- always a little bit present in the cell
77
what happens in the presence of lactose?
LacI protein binds with lactose, this form cannot bind to the operator and therefore no repression and RNA pol can bind (lots of transcription)
78
what happens in the absence of lactose?
- LacI does not bind with lactose
- can bind to the operator which presents RNA pol from binding so there is no transcription
79
what is a catabolic operon?
produce proteins that are involved in the catabolism (breakdown) of the signal molecule
80
what is a signal molecule?
presence determines whether the operons are expressed at high levels
81
what is an inducer?
when present, the lac and mal operons are expressed at high levels
82
what is a co-repressor?
when a signal molecule results in low levels of operon expression
83
what is an anabolic operon?
produce proteins that are involved in the synthesis (anabolism) of the signal molecule
ex. arginine
84
what is a point mutation?
mutation that changes a single base in the DNA
85
what are the three types of point mutations?
- silent mutation
- missense mutation
- nonsense mutation
86
what is a silent mutation?
a type of point mutation that changes the codon but not the amino acid
87
what is a missense mutation?
a type of point mutation that changes a codon and amino acid
88
what is a nonsense mutation?
a type of point mutation that creates a new stop codon
89
what is a deletion mutation?
sections of DNA removed and the remaining DNA joins together. (assume reading frame remains consistent)
