LESSON 6 DNA & RNA STRUCTURE Flashcards
FUNCTION
Long term storage of genetic information
DNA
FUNCTION
Used to transfer genetic information in organisms
RNA
COMPOSITION
Adenine, guanine, cytosine, thymine bases
DNA
COMPOSITION
Adenine, guanine, cytosine, uracil bases
RNA
PROPAGATION
selfreplicating
DNA
PROPAGATION
It is synthesized from DNA on an asneeded basis
RNA
LOCATION
Nucleus
Mitochondria (circular)
Bacteria, Viruses
DNA
LOCATION
Cytoplasm
Ribosomes
Nucleolus
Bacteria, Viruses
RNA
STRUCTURE
Double stranded
DNA
STRUCTURE
Linear or circular
DNA
STRUCTURE
Single stranded
RNA
STRUCTURE
Branched
RNA
SUGAR
2’-Deoxyribose
DNA
SUGAR
Ribose
RNA
PYRIMIDINE
Cytosine
Thymine
DNA
PYRIMIDINE
Cytosine
Uracil
RNA
PURINE
Adenine
Guanine
DNA
RNA
PHOSPHATE/ PHOSPHORIC ACID PRESENT
DNA
RNA
from phosphoruc acid
PHOSPHORIC ACID
gives the acidity to the nucleic acids
PHOSPHORIC ACID
one of the unique structures found in the nucleic acid
PHOSPHORIC ACID
: concentrated in the nucleus, and condensed during mitosis in the Ch
Prokaryotes
2 cpt carrying genetic info in bacteria:
Ch and plasmids
: has DNA; resistant to antibiotics and metals
Plasmid
Only enclosed in the nucleus
DNA
Self-replicating so that the daughter cells would have the same DNA
DNA
Pivotal in transcription and translation
RNA
Can go out of the nucleus
RNA
Transitory molecules (messenger)
RNA
Made the copy of the genetic info from the nucleus
RNA
Transcription: serves as a scribe
RNA
Moves around the molecule from the nucleus to the cytoplasm to the ribosome
RNA
: pentose w/ 5 carbon sugar
Ribose
: takes the place of Thymine in DNA
Uracil
complementary base of adenine
Uracil
: makes up the ribosomes
rRNA
: initiates the creation of ribosomes
Nucleolus
dense portion inside the nucleus
Nucleolus
Can form complementary bases upon its folding
RNA
: backbone
Sugar and phosphate
Why does RNA has uracil?
1. Uracil uses [?] to produce than Thymine. Thymine needs more time to be produced
2. Uracil is [?] from the degradation of cytosine
3. Uracil is [?] to oxidation and photochemical mutations if it travels outside the nucleolus
less energy
easily produced
more resistant
: less energy to make and more stable
Transitory molecule
Requires less expenditure of ATP
Uracil
is a more convenient choice as a nitrogenous base
Uracil
is more hardy/tenacious from oxidative stress and mutation
Uracil
encounters enzymes, oxygen, etc. when it travels outside the nucleus, making it more resistant and more stable
RNA
is typically double stranded
DNA
is typically single stranded
RNA
Although it is single stranded, [?] can fold upon itself, with the folds stabilized by short areas of complementary base pairing within the molecule, forming a three-dimensional structure creating a hair-pin structure
RNA
A spiral ladder structure (helical)
Double helix
DNA
The 2 DNA strands are
antiparallel
DNA is composed of repeating units called
nucleotides
: side of ladder
Sugar-PO4
N bases are connected by
Hydrogen bonds
Nucleotide: [?]
Sugar + nitrogen base + P04
: [?] - fundamental sub-unit of Nucleic acid
Nucleotide
Yellow: [?]/alternate phosphate and sugar
sugar phosphate backbone
Sugar-PO4 Connected by
covalent bonding
in the process of replication are the construction workers who adds nucleotides to elongate the DNA
DNA polymerase
staircase:
nitrogenous bases
Directions: [?] - important in replication
3’ to 5’ and 5’ to 3’
Nucleic Acid Composition: Nucleotide
- Sugar (Pentose)
- Phosphate from Phosphoric acid
- Nitrogenous base
Adenine Guanine - bases with double ring structure
Purine
Cytosine Thymine (uracil in RNA) - bases with the singlering structure
Pyrimidine
phosphoric acid: red circle
pentose-shaped sugar
nitrogenous base
nulceotide
: adds nucleotide to the new daughter strand
DNA polymerase
: adds nucleotide to the mRNA
RNA polymerase
: gives the acidity of nucleic acids
PHOSPHATE GROUP
: purine (double ring structure)
NITROGENOUS BASE
- a weak bond in which two negatively charged atoms share a hydrogen atom
Hydrogen Bond
- holds the two bases from the different strands together
Hydrogen Bond
- holds the stacking of the base pairs on top of one another
Hydrogen Bond
- process of denaturation targets the
Hydrogen Bond
- adenine is paired w/ thymine (?); guanine pairs w/ cytosine (?) (Chargaff’s rule)
2 H bonds
3 H bonds
– negatively charged
DNA
= forms a base pair
1 nitrogenous base + 1 nitrogenous
Only [?] fit inside the double helix.
purine-pyrimidine pairs
- NOT ENOUGH SPACE
Purine-purine pair
- TOO MUCH SPACE
Pyrimidine-pyrimidine pair
- JUST RIGHT
Purine-pyrimidine pair
form between G-C pairs and A-T pairs
Hydrogen bonds
The rule that in DNA there is always equality in quantity between the bases A and T and between the bases G and C
Chargaff rule
If Guanine always pairs with Cytosine and Adenine always pairs with Thymine, they are always found in set amounts forming a total of 100%
Answer:
20% Guanines and 20% Cytosines
30% Adenines and 30% Thymines
Because of this complementary base pairing, the order of the bases in e strand determines the order of the bases in the other strand. This is the [?]
DNA’s secondary structure
The bases are arranged in triplets called
codons
AGG-CTC-AAG-TCC-TAG
TCC- GAG-TTC-AGG-ATC
: Held together by covalent bonds
Sides
(Sugar and phosphate)
: Held held together by hydrogen bonds
Middle
(Nitrogen bases)
consists of a sequence of nitrogen-containing bases.
Primary structure
results from complementary base pairing includes short regions of double helice: and structures called hairpins
Secondary structure
The bases of RNA typically form [?] with complementary bases on the same strand.
hydrogen bonds
RNA molecules can have
tertiary and quaternary structures
Not single stranded because it has already formed the secondary structure
RNA
Single-stranded: loop
Primary structure
Double-stranded: double helix
Secondary structure
Hairpins: where RNA structure is based
Secondary structure
: linear, single-stranded, primary structure
mRNA
: more complicated
rNA and tRNA
• make up an integral part of the ribosome
Ribosomal RNA (rRNA)
What is the purpose of ribosome?
- Organize [?]
- Structure that helps in taking the instructions from the mRNA and use these to organize the tRNA carrying amino acids to assemble the [?]
- Contains [?]
translation
protein sequence
proteins and rRNA
For protein synthesis
Ribosome
: act of decoding of mRNA by tRNA
translation
: factory
ribosome
: factory workers
characters/factors
: reads mRNA and carries designated amino acid based on the protein sequence
tRNA
: main factors
mRNA and tRNA
is a dynamic membrane-less structure whose primary function is ribosomal RNA (rRNA) synthesis and ribosome biogenesis
Nucleolus
contains the genetic information and instructions on making ribosomal RNA
Nucleolus
dense mass inside the nucleus
Nucleolus
important for rNA and ribosome synthesis
Nucleolus
Structure of ribosome
- Subunit: small (40s) and large subunits (60s)
- Binding sites
“S”:
sedimentation rate or Svedberg unit
– human
Eukaryotic
– bacteria
Prokaryotic
Antibiotics that prevents the process of protein synthesis attacks the
50s and 30s
: accepts the incoming aminoacylated tRNA
A site (amino-acyl)
landing site
A site (amino-acyl)
: holds the tRNA which is linked to the growing polypeptide chain
P site
: has A anticodon
tRNA
reads the code that matches the anticodon with a designated
tRNA
extends until protein synthesis is terminated
P site
: holds the tRNA before it leaves the ribosome
E site (exit)
• which acts as a template for protein synthesis and has the same sequence of bases as the DNA’strand that has the gene sequence
Messenger RNA (mRNA)
: mRNA product after transcription it is must be further processed for error, to prevent degradation and stability
• pre-mRNA transcripts
Created in transcription (first part of protein synthesis)
Messenger RNA (mRNA)
Copies the bases of the DNA strand
Messenger RNA (mRNA)
Transcription End product:
pre-mRNA
Addition of [?] increases the stability of mRNA
caps and tail
: protection of mRNA
5’ cap and poly a tail
Upon further processing, [?] are removed
non-coding regions (introns)
Left after further processing:
5’ cap, coding region (exon), Poly A tail
Important in translation
Transfer RBA (tRNA)
type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein
Transfer RBA (tRNA)
reads the mRNA from the 5’ to 3’ end
tRNA
has an anti-codon that binds to matching mRNA through base pairing
tRNA
on the opposite side has an amino acid covalently attached to it
tRNA
Has a secondary and tertiary structure
tRNA)
’: convenient and continuous; faster in replication
Always going to 3
: P site
Methionine
: A site
Phenylalanine
Phenylalanine switches to [?] to remove the previous tRNA
Methionine
: reads/decodes the codons of mRNA
Anticodons
tRNA:
anti-codons
mRNA:
codons
an amino acids corresponds to
anti-codons
very important in the growth process
REPLICATION
as the cells divide, each one would have the same genetic information
REPLICATION
happens in the S-phase (interphase)
REPLICATION
THREE THEORIES
Semi-conservative
Conservative
Dispersive
not founf to be biologically significant
Conservative
Dispersive
DNA divides into two, opens up, and one strand will be the template for the new strand. The other strand does the same.
Semi-conservative
Conservation of the original strand, to serve as a basis for the creation of the new strand.
Semi-conservative
Once DNA is replicated, it will make 2 distinct strands.
Conservative:
One strand from the parent strand, and one strand from the newly synthesized strand.
Conservative:
First part of one strand coming from the parent strand, following the second part coming from the newly synthesized strand.
Dispersive:
DNA must make an exact copy of itself to equally divide the genetic information during mitosis and meiosis
DNA REPLICATION
DNA REPLICATION Overview of the steps:
a. DNA molecule - [?]
b. [?] attached themselves in correct place of each strand
c. Each strand becomes a [?]
unzip
New bases
double helix
DNA replication is continuous in the
5’ to 3’ direction.
• Free nucleotides in
nucleoplasm
• are added one at a time to the growing end of a DNA strand in the 5’ to 3’ direction
nucleotides
Basic rules of replication
1. [?]
2. Starts at the [?]
3. Synthesis always in the [?]
4. Can be [?]
5. [?]
a. Leading strand
b. Lagging strand
6. [?] required
Semi-conservative
‘origin’
5-3’ direction
uni or bidirectional
Semi-discontinuous
RNA primers
will be the starting point for the DNA polymerase
Primers
once the double helix opens up, direction of replication form movement is from
5’ to 3’
leading strand; continuous; new strand created
5’ to 3’
where the template is added (antiparallel)
3’
slower (lagging strand); brand new strand
5’
removes helical twists by cutting a DNA strand and then resealing the cut
Topoisomerases
separates 2 strands (unwinds and opens the helix)
Helicases
RNA primer synthesis
Primase
protects the DNA strand from degradation, modulate the activity of proteins involved
Single strand binding protein (SSB)
synthesis of new strand
DNA polymerase
stabilises polymerase
Tethering protein
seals nick via phosphodiester linkage
DNA ligase
connects breakages between nucleotides
DNA ligase
construction workers; adds nucleotides
DNA polymerase
stabilizes the single strand of DNA
Single strand binding protein (SSB)
it attaches to the strands once separated, preventing other proteins from making a secondary structure/complementary bases
Single strand binding protein (SSB)
only limits the process to replication and no other extra activities
Single strand binding protein (SSB)
guides the DNA where to start
DNA primase
important in adding the primer, which will dictate the DNA polymerase where to start
RNA primer synthesis
stabilizes the twist; removes the stress
Helicases
slices the DNA strand to reduce the stress/torsion and straighten it
Topoisomerases
it could reseal the cut once done
Topoisomerases
relieves the stress from being helical
Topoisomerases
: made up of nucleotides; added portion by portion
Okazaki fragments
can only be found in the lagging strand; added by DNA polymerase
Okazaki fragments
The mechanism of DNA replication
Initiation
Elongation
Termination
Replication proteins bind to DNA and open up double helix by the helicase
Initiation
Prepare DNA for complementary base pairing
Initiation
Starting point
Initiation
: DNA polymerase adds the nucleotides to the 3’ end of the template where it is marked by a primer into a continuous new strand of DNA
• Leading strand
: The new stand is put together in short pieces called Okazaki fragments
• Lagging strand
• Proteins release the replication complex
Termination
Replication is already finished
Termination
Steps of DNA replication
- Process of unwinding and unzipping
- Single strand binding proteins
- Primase
- DNA polymerase
- RNA primase
- DNA Ligase
- uses helicase enzyme to unwind and unzip the DNA structure
- Process of unwinding and unzipping
- bind to DNA strands to prevent reannealing of single strands
- Single strand binding proteins
- creates RNA primers on both strands
- Primase
- primers will give the DNA polymerase a point to start
- Primase
- responsible for adding nucleotide bases
- DNA polymerase
- only works on a 5’ to 3’ process
- DNA polymerase
- will make extra primers down the lagging strand
- RNA primase
- contains fragments of DNA known as “okazaki fragments”
- lagging strand
- will take care or connect the gaps on the “okazaki fragment”
- DNA Ligase
By the helicase; stabilized by topoisomerase
Process of unwinding and unzipping
To prevent other proteins from attaching to the single stranded DNA once separated
Single strand binding proteins
To prevent from creating a secondary structure
Single strand binding proteins
replicated simultaneously
Anti parallel strands
• Leading strand synthesis continuously in
5’–3’
• Lagging strand synthesis in fragments in
3’-5’
