Chapter 6 Molecular Information Flow and Protein Processing Flashcards
(106 cards)
1
Q
The 4 classes of Macromolecules:
A
- nucleic acids (DNA,RNA)
- Proteins
- Carbs
- Lipids
2
Q
Nitrogenous bases -Nucleotides
A
C,T,A,G attached at the 1’ carbon of deoxyribose
3
Q
DEOXY-ribose (ribose)
A
refers to the 2’ carbon
4
Q
Pyrimidine bases
A
Cytosine, Thymine, Uracil
5
Q
Purine Bases
A
Adenine, Guanine
6
Q
Sugar phosphate backbone attaches to _____
A
3’ carbon on deoxyribose and 5’ carbon on adjacent deoxyribose
7
Q
Differences btwn DNA and RNA
A
- RNA is single stranded
- RNA uses uracil
- Uracil is not as expensive as thymine for the cell to make
- The backbone sugar of RNA is Ribose instead of Deoxyribose
8
Q
What is ATP
A
adenosine triphosphate
9
Q
dNTP
A
deoxyribose nucleotide triphosphate- building block for DNA
- Adenine
-Triphosphate
-Deoxyribose
10
Q
rNTP
A
ribose nucleotide triphosphate
- Adenine
- Ribose (2’ -OH)
- Triphosphate
11
Q
DNA strands connect through __________ bonds
A
hydrogen
12
Q
Double-stranded DNA is a helix of two __________ strands of DNA
A
antiparallel
13
Q
What happens to the DNA bonds in order to make a copy of the sequence of nucleotides in DNA?
A
The double helix must break the h-bonds
14
Q
What process starts with a one double stranded DNA and becomes a two complementary (anti parellel) DNA strands?
A
Melting Denaturation
15
Q
Does it take more energy to melt AT (2H bonds) pair or GC par (3H bonds)
A
Gc pair
16
Q
Order of the Central Dogma
A
- DNA strand
- Transcription
- mRNA
- translation
- protein
17
Q
gene
A
segment of the chromosome that encodes 1 protein
18
Q
Escherichia coli (e.coli)
A
- E.coli K-12 isolated from human feces in 1922
- Gammaproteobacterium (gram negative)
- Short generation time - divides once every 20 in in rich medium at 37 C with aeration
- Many tools have been developed to study the metabolism , biochem and genetics
19
Q
Visual difference between human chromosome and E.coli chromosome
A
E.coil chromosome is round/ circular
20
Q
Bacterial genomes
A
-Most are a single, covalently closed circular molecule of dsDNA
- ~0.14 to ~15 Mb in size
- May have non-essential genes on plasmids, may have viral genomes integrated into the chromosome
- Borrelia burgdorferi B31 (lyme diease spirochete)
21
Q
Chromsome
A
Harbors essential genes
- Most bacteria have a single covalently closed circular chromosome with a single site where DNA replication begins: oriC, origin of Chromosome replication
22
Q
How does all the DNA fit in a teeny cell?
A
- architectural proteins
- negative supercoiling
23
Q
oriC
A
origin of Chromosome replication
24
Q
DNA Gyrase
A
Adds negative supercoils to DNA
- important to relieve mechanical stress on DNA, as the double stranded DNA is opened for replication
- Topoisomerase
25
Topoisomerase
an enzyme that breaks dsDNA and either add or remove supercoils in DNA
26
Plasmids
Harbor non-essential genes (these genes may enhance survival)
- Size: ~1kb to >1mB
- Circular or linear DNA
-Single-copy or hundreds of copies
- Partitioned to offspring cells independent of chromosome
27
DNA polymerase
responsible for the process of DNA replication
28
DNA replication
- Genetic information flow to offspring
- DNA polymerase adds nucleotides to a free 3' -OH
- Chain growth from 5' to 3' dNTPs are the building blocks
29
DnaA
Many copies of this protein cooperatively bind to TTATCCACA (DnaA box) in oriC region => breaks hydrogen bonds between bases (uses energy from ATP)
30
DNA helicase
Unwinds the DNA at the replication fork so DNA polymerase can access ssDNA (uses ATP)
31
SSB
Single-strand binding protein, coats ssDNA
32
Primase
Makes a complementary, short RNA used by Pol III to start DNA synthesis
32
DNA polymerase III (complex)
Synthesizes new, complementary strand of DNA
33
DNA pol I
Replaces all RNA primers with DNA
34
DNA ligase
Repairs breaks in backbone (lagging strand)
35
Topoisomerase IV
Unlinks interlocked circles
36
Gyrase
Relieves mechanical stress on DNA
37
What is the name of the enzyme that synthesizes a new strand of DNA?
*DNA polymerase
*Gyrase
*Topoisomerase IV
*Helicase
*Primase
DNA polymerase
38
Which enzyme unwinds DNA to expose
a single strand for replication?
* DNA polymerase
* Gyrase
* Topoisomerase IV
* Helicase
* Primase
Helicase
39
Which enzyme counter unwinds DNA to relieve pressure created by unwinding?
* DNA polymerase
* Gyrase
* Topoisomerase IV
* Helicase
* Primase
Gyrase
40
What are the parts to cleaning up the lagging strand?
- Lagging strand has many, small complementary fragments (Okazaki fragments)
- DNA pol I removes the RNA, fills in missing DNA
- DNA ligase repairs the remaining gap in the backbone
41
Bacterial chromosomes are often but not always _______ double-stranded DNA circles
closed
42
DNA polymerase needs a _________ to know where to start synthesis
primer
43
During transcription, RNA polymerase interacts with the _________ strand and therefore produce an exact copy of the ____________ strand, expect with _____'s instead of T's
template
coding
U
44
The first site of the RNAP binding is to the __________
promoter
45
RNAP will travel down the DNA and transcribe until it reaches the _____________
terminator
46
If the RNA produced is an mRNA it will have an _____________ which is the part that codes for a protein
open reading frame
47
RNAP transcribes what?
mRNA
48
Promoter
– DNA sequences upstream of a gene, mark the site tostart making an RNA copy – Promoter sequence also determines when and how often a gene is transcribed
49
Operator
– DNA sequences recognized by either repressor proteins or activator proteins that modulate gene expression
50
Open reading frame (ORF)
– if the RNA is protein-coding mRNA,
the ORF is the portion of the gene that will be read by the ribosome to produce a protein
51
Terminator
–RNA polymerase stops transcribing and is released from the DNA
52
Bacterial RNAP is made up of ___ subunits (4 unique proteins)
5
53
_______ and ______ RNAP are more similar to each other and more complex (>10 subunits)
Archaea and Eukarya
54
Bacterial RNA polymerase
- no primer necessary
- RNAP binds to DNA at the promoter and then moves along the DNA until it reaches a terminator
- rNTPs are used to make the RNA polymer
- RNAP simply matches the incoming rNTPs to the DNA template (U with A and G with C)
55
The RNA produced has the exact same code (expect with U's) as the ________ DNA strand
coding
56
"Core" polymerase
made of 5 polypeptides responsible for RNA synthesis
57
Holoenzyme
Core plus a sigma factor
- scans DNA "looking" for the promoter
58
Sigma factor
- recognizes the promoter sequence
- Initiates seperation of the dsDNA
- Leaves once RNA synthesis begins
more sigma factors means more things looking for promoter sequences which increases transcription
59
Promoter sequences are recognized by ______
sigma 70 (sigma factor)
60
What are the "stable" RNAs?
rRNA and tRNA
61
What are the "short lived" RNAs?
mRNA
62
Does capping, polydenylation, or splicing of mRNA occur in bacteria and archaea?
No
63
RNases
Ribonucleases- enzymes that cut or degrade RNA (break the sugar phosphate backbone)
- recycling, regulation
64
rRNA operon
multiple RNAs made in a single transcript
65
Primary RNA structures
Just the single strand
66
Secondary RNA strucue
higher order interactions, hydrogen bonds, Double strand
67
What does a tRNA secondary structure look like?
a 3D T shape
68
Two ways to stop making RNA.....
1. Rho independent
- GC-rich stem loop structure interacts with RNAP, causing it to stall
- span of U's in the RNA interact weakly with the A's in the DNA
- the combination of the stalling and the weak RNA:DNA hybrid destabilizes the complex and RNAP will release the DNA
2. Rho dependent
- rho is a helicase (disrupts hydrogen bonds between nucleotides)
- rho binds C-rich region of the RNA
- RNAP pauses at a pause site in the DNA
- rho travels down the RNA towards the stalled RNAP
- rho uses its helicase activity to distrupt the RNA:DNA hybrid
69
RNA building blocked are _______
rNTPs
70
Products of transcription include ______, ______ ,and _________
mRNA, rRNA, tRNA
71
What are the parts used in Translation?
ribosome, tRNA, tRNA synthetase
72
Ribosome binding site
RNA sequence upstream of the start codon
73
Start codon
Three nucleotide sequence that codes for the amino acid N-formyl-Methionine
74
Stop codon
Three nucleotide sequence that codes for no amino acid and signals the ribosome to halt translation
75
Promotor
Site of RNA polymerase binding
76
RBS
ribosome binding site where ribosome will bind on the mRNA
77
Open reading frame
the coding region that will be translated into protein
78
Terminator
the region that kick RNA polymerase off the DNA
79
RNAP binds to the DNA at the _________ and terminates transcription at the ______________
promotor
terminator
80
Ribosome binds to the mRNA at the ______________ and leaves the reading frame at the ___________
ribosome binding site
stop codon
81
RBS
aka Shine Dalgarno sequence
- 9 bases upstream of start codon
-purine rich
82
Open Reading Frame
gene-sized stretch of codons from the start codon to the stop codon
83
4^3 RNA triplet codons = ____ different codons
64
84
Whats a codon?
made up of 3 nucleic acid pairs
85
Protease
an enzyme that breaks down proteins and peptides
86
Amino acid structure
-amino group
-R group
-carboxylic acid group
87
Amino acids are connected by _________
peptide bonds
88
Peptide chain growth proceeds in an _________ terminus to __________ terminus direction
amino (N)
carboxyl (C)
89
What determines the protein's function?
The structure of the amino acid "R" groups
90
Primary protein structure
sequence of a chain of amino acids
91
Secondary protein structure
hydrogen bonding in the peptide backbone causes the amino acids to fold into a repeating pattern
92
Teritiary protein structure
three- demential folding pattern of a protein due to side chain interactions
93
Quaternary protein structure
protein consisting of more than one amino acid chain
94
The _______ of the amino acids determines the structure of the protein
order
95
The _________ of the protein determines its function
96
The role of the tRNA synthetase....
recognizes the anticodon and then attaches the correct amino acid tot hat particular tRNA
97
Explain the process of how ribosome attaches to ________
30s ribosome subunit bind to mRNA at RBS
scans along mRNA to Start codon (AUG)
IF1, IF2, IF3 bind
50s ribosomal subunit clamps on to the initiation complex
98
Polypeptide elongation process
1. codon recognition
2. peptide bond formation
3. translocation
4. cycle continues three times
99
STOP codon has no corresponding _________ to recognize it. Instead it is recognized by a release factor called ________
tRNA
RF1
100
Role of RF1
Hydrolyzes (breaks the bond) between the polypeptide and the tRNA in the p-site
101
What is needed for other RF's to unlock the 30S and 50S subunits from mRNA?
GTP hydrolysis
102
Transcription and translation are coupled in _____________
Bacteria
103
Ribosomes can start translating an ___________ before _________ has finished transcribing the message
mRNA
RNA polymerase
104
Landmarks on the mRNA determine where a ribosome __________ and where it starts reading codons to make a protein, and later to ________ making a protein
binds
stop
105
In bacteria, translation may start even _________ a transcript is released from RNA polymerase
before
