MOL BIO LAB L2 (Prelim- DNA & RNA) Flashcards
He discovered the DNA. The first person who identified “nuclein” inside the nuclei of our White Blood Cells (WBC)
Friedrich Miescher
He investigated the structure of DNA
Phoebus Levene
Created/Discovered the Chargaff’s rule
Erwin Chargaff
According to this, the total amount of purines which is the Adenine plus Guanine would equate or equal to the total amount of pyrimidines which are the Cytosine and Thymine
Chargaff’s rule
Responsible for the realization of the double helix structure of DNA
James Watson and Francis Crick
They are responsible for the X-ray Crystallography
Rosalind Franklin and
Maurice Wilkins
The Human Genome Project in 1987 was proposed by?
Dr. Alvin W. Trivelpiece
The human genome project was estimated to complete in ________ but it actually only took _______.
15 years; 13 years
What are the five macromolecules of the DNA?
- Carbon
- Nitrogen
- Oxygen
- Phosphorus/ Phosphate
- Hydrogen
DNA is found in the nucleus of the cell, but we also have what
we call _________
mitochondrial DNA
The information in the DNA storage system is based on the order or sequence of _________ in the nucleic acid polymer.
nucleotides
What are the three main components or three main structures of a DNA?
- Nitrogenous Base
- Pentose Sugar
- Phosphate Group
There are 4 Nitrogenous bases that make up the majority of DNA found in all organisms and these are:
- Adenine
- Guanine
- Cytosine
- Thymine
Nine-membered ring; double ring and is composed of 9 carbons.
Purine
Six-membered ring: single ring and is composed of 6 carbons.
Pyrimidine
What are the two groups based on the number of nitrogens in the structure:
Purine and Pyrimidine
These nitrogenous bases are a purine
Guanine & Adenine
These nitrogenous bases are a pyrimidine.
Cytosine, Uracil, and Thymine
In RNA, what is attached to the Carbon-2 position?
hydroxyl group (OH)
Nitrogenous base + Pentose sugar=
Nucleoside
In DNA, it does not contain a hydroxyl group but instead a __________?
Hydrogen atom
Nucleoside + phosphate group=
Nucleotide
When this attaches to a nucleoside through a phosphoester bond, the entire complex becomes a nucleotide (nucleic acid)
Phosphate group
Ends with Phosphate group
5’ end
Ends with Hydroxyl group
3’ end
Wherein the nitrogenous bases will form hydrogen bonds with its complementary pair.
Hybridization
What is the complementary pair of guanine?
Cytosine
What is the complementary pair of adenine?
thymine
How many hydrogen bonds does cytosine and guanine have?
three
How many hydrogen bonds does adenine and thymine have?
two
Th hydrogen bond between these two are much difficult to destroy or unwind
cytosine and guanine
Two long polynucleotide chains are coiled around a central axis, forming a right-handed double helix.
Chargaff’s rule
The two DNA strand are ______ to each other
antiparallel
These are 2 regions formed in the sugar phosphate backbone of the helix
- Major groove and Minor groove
What is the distance between the major grooves?
22A°
In minor groove, the distance between 2 DNA strands is only?
12A°
Each complete turn of helix is _____ long
34A° (angstrom)
The double helix has a diameter of ______ and the distance between the adjacent nuclear diet is _______
20A°; 3.32 or 3.4
TRUE OR FALSE: The percentage of (G+C) is
equal the percentage of (A+T)
FALSE. It is not necessarily equal
These are target areas of denaturing agents. If you want to destroy DNA these are the areas to target.
Major & Minor groove
What are the three proposed models of replication?
- Semi-conservative model
- Conservative model
- Dispersive model
In this model, base pairing allows each strand to serve as a template for a new strand. The new strand is 1/2 parent template & 1/2 new DNA
Semi-conservative model
Nucleotides in DNA backbone are bonded from phosphate to sugar between __________?
3’ & 5’ carbons
DNA molecule has “direction” complementary strand runs in ________ direction
opposite
In connecting nucleotides, 1 phosphate group connects to the ______ to form a nucleotide and it will then connect to the ________ of the next nucleotide
c5 or 5-carbon; c3 or
3-carbon
One strand of a DNA can end in a phosphate group or a hydroxyl group. Because of that, DNA is given what is called?
Polarity
What is the first step in DNA replication?
Unwinding of DNA
This unwinds the DNA
Helicase
Enzyme that prevents tangling upstream from the replication fork
DNA gyrase
Adds small section of RNA (RNA primer) to the 3’ end of template DNA
RNA Primase
This enzyme builds new DNA strand
DNA polymerase III
TRUE OR FALSE: DNA polymerase III can only add nucleotides to existing strands of DNA
TRUE
The main enzyme in all the replication. It cannot synthesize or cannot build new DNA strand but can only synthesize from an existing nucleotide
DNA polymerase
Replication cannot be initiated without an?
existing strand
What is the third step in DNA replication?
Building of daughter strand
What is the fourth step in DNA replication?
Replacement of RNA primer by DNA
Replacement of RNA primer by DNA is done by?
DNA Polymerase I
The direction of the replication fork is?
towards the left
What is the limit of DNA polymerase III?
can only build onto 3’ end of an existing DNA strand
These are the short lengths of DNA that are produced by the discontinuous replication of the lagging strand
Okazaki fragments
This join together fragments of newly synthesized DNA to form a seamless strand
Ligase
Continuously synthesized strand
leading strand
Synthesized discontinuously in DNA replication
Lagging strand
In DNA replication, the reading is done in what direction?
Read UP; read from 3’ to 5’
In DNA replication, adding of a complementary base is done in what direction?
Adding of complementary base is from 5’ to 3’
This initiates DNA synthesis
RNA Primer
Built by primase. It serves as starter sequence for DNA polymerase III, however, short segments called Okazaki fragments are made because it can only go in a 5’ –> 3’ direction
RNA Primer
Removes sections of RNA primer and replaces with DNA nucleotides
DNA polymerase I
Strands are glued together by?
DNA ligase
A complex compound of high molecular weight that functions in cellular protein synthesis and replaces DNA as a carrier of genetic codes in some viruses.
RNA
In DNA , in the Carbon 2 position you will find a?
hydrogen
In Ribose (RNA), in Carbon 2 you will find a?
hydroxyl group
Structural components of ribosome it composes 80% of RNA
Ribosomal RNA (rRNA)
Carries amino acids to the ribosome during translation. Accounts for up to 15% of the RNA
Transfer RNA (tRNA)
Carry genetic information from the DNA of the gene
Messenger RNA (mRNA)
Unlike ________ molecules; these RNAs (the________) are not subsequently translated to form proteins and they remain in RNA form.
mRNA; rRNA and tRNA
They remain in RNA form, and they only aid in the formation of proteins.
rRNA and tRNA
Considered the first step in gene expression
Transcription
The process by which the information is transferred from one strand of the DNA to RNA by the enzyme RNA polymerase
Transcription
Uses a single-stranded DNA template to synthesize a complementary strand of RNA.
RNA polymerase
RNA polymerase builds an RNA strand in the ________ direction, adding each new nucleotide to the 3’ end of the strand.
5’ to 3’
The strand that is used as template is called the?
template strand or antisense strand or the negative strand or non-coding strand (pilii nalang :P)
It directs the synthesis of RNA.
template strand
The coding strand is also called the?
positive strand or the sense strand
Its sequence is the same as the RNA sequence that is produced with the exception of uracil replacing thymine
Coding strand
The nucleotide at the 5-prime end of the chain retains its?
triphosphate group
It carries a copy of genetic information to the ribosome.
messenger RNA (mRNA)
The main enzyme that catalyzes replication and transcription.
RNA polymerase
It fills the RNA from the 5’ to 3’ direction by adding nucleotide to the 3-prime end of the strand.
RNA polymerase
The 3 Steps in RNA Transcription:
- Initiation
- Elongation
- Termination
In this step, there is what we call the promoter region of each gene. Each gene has its own promoter. Once found, the RNA polymerase will separate the DNA strands and provide the single stranded template needed for transcription
Initiation
In this step, the template strand acts as a template and it will be read one base at a time. Again, the chain grows from 5’ to 3’.
Elongation
In this step, there is what we call sequence terminators. They are signaled that the RNA transcript is complete and once they are transcribed, they cause the transcript to be released from the RNA polymerase.
Termination
Each genetic code consists of three ribonucleotide letters thus referred to as?
triplet code
Each group of three ribonucleotides is called?
codons
The genetic code can be defined as?
unambiguous, degenerate, and universal.
In _______, the mature mRNA molecules must leave the nucleus and travel to the cytoplasm where the ribosomes are located.
eukaryotes
In____________, ribosomes can attach to mRNA while still being transcribed
prokaryotic organisms
There are how many codons?
64 codons
Area of the near the 5-prime end of the molecule that is not translated.
Untranslated Region (UTR)
UTR is also called?
Leader sequence
This portion of mRNA is located between the first nucleotide that is transcribed and the start codon (AUG) of the coding region and it does not affect the sequence of amino acids in a protein.
Leader sequence or UTR
In bacteria, the ribosome binding site is known as?
Shine Delgarno
In vertebrates, the ribosome binding site is known as?
Kozak box
Why is UTR important?
it contains the ribosome binding site
In bacterial mRNA, the 5-prime UTR is usually short while in human mRNA the median length of the 5-prime UTR is about _________
170 nucleotides
Stages of Translation
- Chain initiation
- Chain elongation
- Chain termination
What are the first three initiation proteins?
IF1, IF2, IF3
Pre-initiation complex and a ________ will then bind to the mRNA near the AUG start codon forming what is called the ‘Initiation Complex’.
methionine carrier tRNA
TRUE OR FALSE: Although methionine is the first amino acid incorporated into any new protein, it is not always the first amino acid in mature proteins
TRUE
If methionine is followed by alanine, the methionine is?
Removed
The location at which the aminoacyl tRNA anticodon B pairs up with the mRNA codon
Amino Acid (A) site
If methionine is followed by lysine, the methionine is?
retained
The location at which the amino acid is transferred from its tRNA to the growing polypeptide chain
Polypeptide (P) site
The location at which the mt-tRNA sits before being released back to the cytoplasm to bind another amino acid.
Exit (E) site
In a ribosome, what are the three sites at which the tRNA molecules can bind?
- Amino Acid (A) site
- Polypeptide (P) site
- Exit (E) site
The initiator, _______ is the only aminoacyl tRNA that can bind in the P site of the ribosome
methionine tRNA
In elongation, the ribosome moves along the mRNA in a ______ direction. Which requires the _______, in a process called translocation.
5’ to 3’ ; elongation factor G
What is the energy source in the translocation process?
guanine triphosphate (GTP)
For many years, it was thought an enzyme catalyzed this step (elongation), but recent evidence indicates that the ____________ is the catalytic function of ribosomal RNA
transferase activity
When translocation is terminated what is must be released from the mRNA and the ribosome?
nascent protein
What are the three termination codons employed at the end of a protein sequence in an mRNA?
UAA, UAG, and UGA
mRNA are simultaneous and short-lived in?
Prokaryotes
mRNA are highly variable half-lives, subject to modifications, and must exit the nucleus to be translated. In what organism?
Eukaryotes
What are the release factors on the stop codons that will enter the vacant A site?
RF1 and RF2
Trigger the peptidyl transferase to cleave the now completed polypeptide from its tRNA, located in the P-site of the ribosome.
release factors
