Chapter 6 Molecular Information Flow and Protein Processing Flashcards
The 4 classes of Macromolecules:
- nucleic acids (DNA,RNA)
- Proteins
- Carbs
- Lipids
Nitrogenous bases -Nucleotides
C,T,A,G attached at the 1’ carbon of deoxyribose
DEOXY-ribose (ribose)
refers to the 2’ carbon
Pyrimidine bases
Cytosine, Thymine, Uracil
Purine Bases
Adenine, Guanine
Sugar phosphate backbone attaches to _____
3’ carbon on deoxyribose and 5’ carbon on adjacent deoxyribose
Differences btwn DNA and RNA
- 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
What is ATP
adenosine triphosphate
dNTP
deoxyribose nucleotide triphosphate- building block for DNA
- Adenine
-Triphosphate
-Deoxyribose
rNTP
ribose nucleotide triphosphate
- Adenine
- Ribose (2’ -OH)
- Triphosphate
DNA strands connect through __________ bonds
hydrogen
Double-stranded DNA is a helix of two __________ strands of DNA
antiparallel
What happens to the DNA bonds in order to make a copy of the sequence of nucleotides in DNA?
The double helix must break the h-bonds
What process starts with a one double stranded DNA and becomes a two complementary (anti parellel) DNA strands?
Melting Denaturation
Does it take more energy to melt AT (2H bonds) pair or GC par (3H bonds)
Gc pair
Order of the Central Dogma
- DNA strand
- Transcription
- mRNA
- translation
- protein
gene
segment of the chromosome that encodes 1 protein
Escherichia coli (e.coli)
- 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
Visual difference between human chromosome and E.coli chromosome
E.coil chromosome is round/ circular
Bacterial genomes
-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)
Chromsome
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
How does all the DNA fit in a teeny cell?
- architectural proteins
- negative supercoiling
oriC
origin of Chromosome replication
DNA Gyrase
Adds negative supercoils to DNA
- important to relieve mechanical stress on DNA, as the double stranded DNA is opened for replication
- Topoisomerase
Topoisomerase
an enzyme that breaks dsDNA and either add or remove supercoils in DNA
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
DNA polymerase
responsible for the process of DNA replication
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
DnaA
Many copies of this protein cooperatively bind to TTATCCACA (DnaA box) in oriC region => breaks hydrogen bonds between bases (uses energy from ATP)
DNA helicase
Unwinds the DNA at the replication fork so DNA polymerase can access ssDNA (uses ATP)
SSB
Single-strand binding protein, coats ssDNA
Primase
Makes a complementary, short RNA used by Pol III to start DNA synthesis
DNA polymerase III (complex)
Synthesizes new, complementary strand of DNA
DNA pol I
Replaces all RNA primers with DNA
DNA ligase
Repairs breaks in backbone (lagging strand)
Topoisomerase IV
Unlinks interlocked circles
Gyrase
Relieves mechanical stress on DNA
What is the name of the enzyme that synthesizes a new strand of DNA?
*DNA polymerase
*Gyrase
*Topoisomerase IV
*Helicase
*Primase
DNA polymerase
Which enzyme unwinds DNA to expose
a single strand for replication?
* DNA polymerase
* Gyrase
* Topoisomerase IV
* Helicase
* Primase
Helicase
Which enzyme counter unwinds DNA to relieve pressure created by unwinding?
* DNA polymerase
* Gyrase
* Topoisomerase IV
* Helicase
* Primase
Gyrase
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
Bacterial chromosomes are often but not always _______ double-stranded DNA circles
closed
DNA polymerase needs a _________ to know where to start synthesis
primer
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
The first site of the RNAP binding is to the __________
promoter
RNAP will travel down the DNA and transcribe until it reaches the _____________
terminator
If the RNA produced is an mRNA it will have an _____________ which is the part that codes for a protein
open reading frame
RNAP transcribes what?
mRNA
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
Operator
– DNA sequences recognized by either repressor proteins or activator proteins that modulate gene expression
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
Terminator
–RNA polymerase stops transcribing and is released from the DNA
Bacterial RNAP is made up of ___ subunits (4 unique proteins)
5
_______ and ______ RNAP are more similar to each other and more complex (>10 subunits)
Archaea and Eukarya
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)
The RNA produced has the exact same code (expect with U’s) as the ________ DNA strand
coding
“Core” polymerase
made of 5 polypeptides responsible for RNA synthesis
Holoenzyme
Core plus a sigma factor
- scans DNA “looking” for the promoter
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
Promoter sequences are recognized by ______
sigma 70 (sigma factor)
What are the “stable” RNAs?
rRNA and tRNA
What are the “short lived” RNAs?
mRNA
Does capping, polydenylation, or splicing of mRNA occur in bacteria and archaea?
No
RNases
Ribonucleases- enzymes that cut or degrade RNA (break the sugar phosphate backbone)
- recycling, regulation
rRNA operon
multiple RNAs made in a single transcript
Primary RNA structures
Just the single strand
Secondary RNA strucue
higher order interactions, hydrogen bonds, Double strand
What does a tRNA secondary structure look like?
a 3D T shape
Two ways to stop making RNA…..
- 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 - 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
RNA building blocked are _______
rNTPs
Products of transcription include ______, ______ ,and _________
mRNA, rRNA, tRNA
What are the parts used in Translation?
ribosome, tRNA, tRNA synthetase
Ribosome binding site
RNA sequence upstream of the start codon
Start codon
Three nucleotide sequence that codes for the amino acid N-formyl-Methionine
Stop codon
Three nucleotide sequence that codes for no amino acid and signals the ribosome to halt translation
Promotor
Site of RNA polymerase binding
RBS
ribosome binding site where ribosome will bind on the mRNA
Open reading frame
the coding region that will be translated into protein
Terminator
the region that kick RNA polymerase off the DNA
RNAP binds to the DNA at the _________ and terminates transcription at the ______________
promotor
terminator
Ribosome binds to the mRNA at the ______________ and leaves the reading frame at the ___________
ribosome binding site
stop codon
RBS
aka Shine Dalgarno sequence
- 9 bases upstream of start codon
-purine rich
Open Reading Frame
gene-sized stretch of codons from the start codon to the stop codon
4^3 RNA triplet codons = ____ different codons
64
Whats a codon?
made up of 3 nucleic acid pairs
Protease
an enzyme that breaks down proteins and peptides
Amino acid structure
-amino group
-R group
-carboxylic acid group
Amino acids are connected by _________
peptide bonds
Peptide chain growth proceeds in an _________ terminus to __________ terminus direction
amino (N)
carboxyl (C)
What determines the protein’s function?
The structure of the amino acid “R” groups
Primary protein structure
sequence of a chain of amino acids
Secondary protein structure
hydrogen bonding in the peptide backbone causes the amino acids to fold into a repeating pattern
Teritiary protein structure
three- demential folding pattern of a protein due to side chain interactions
Quaternary protein structure
protein consisting of more than one amino acid chain
The _______ of the amino acids determines the structure of the protein
order
The _________ of the protein determines its function
The role of the tRNA synthetase….
recognizes the anticodon and then attaches the correct amino acid tot hat particular tRNA
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
Polypeptide elongation process
- codon recognition
- peptide bond formation
- translocation
- cycle continues three times
STOP codon has no corresponding _________ to recognize it. Instead it is recognized by a release factor called ________
tRNA
RF1
Role of RF1
Hydrolyzes (breaks the bond) between the polypeptide and the tRNA in the p-site
What is needed for other RF’s to unlock the 30S and 50S subunits from mRNA?
GTP hydrolysis
Transcription and translation are coupled in _____________
Bacteria
Ribosomes can start translating an ___________ before _________ has finished transcribing the message
mRNA
RNA polymerase
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
In bacteria, translation may start even _________ a transcript is released from RNA polymerase
before
