LESSON 6 DNA & RNA STRUCTURE Flashcards by Arriane Cyrel (MTI)

FUNCTION
Long term storage of genetic information

DNA

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FUNCTION
Used to transfer genetic information in organisms

RNA

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COMPOSITION
Adenine, guanine, cytosine, thymine bases

DNA

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COMPOSITION
Adenine, guanine, cytosine, uracil bases

RNA

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PROPAGATION
selfreplicating

DNA

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PROPAGATION
It is synthesized from DNA on an asneeded basis

RNA

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LOCATION
Nucleus
Mitochondria (circular)
Bacteria, Viruses

DNA

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LOCATION
Cytoplasm
Ribosomes
Nucleolus
Bacteria, Viruses

RNA

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STRUCTURE
Double stranded

DNA

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STRUCTURE
Linear or circular

DNA

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STRUCTURE
Single stranded

RNA

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STRUCTURE
Branched

RNA

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SUGAR
2’-Deoxyribose

DNA

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SUGAR
Ribose

RNA

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PYRIMIDINE
Cytosine
Thymine

DNA

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PYRIMIDINE
Cytosine
Uracil

RNA

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PURINE
Adenine
Guanine

DNA

RNA

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PHOSPHATE/ PHOSPHORIC ACID PRESENT

DNA

RNA

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from phosphoruc acid

PHOSPHORIC ACID

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gives the acidity to the nucleic acids

PHOSPHORIC ACID

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one of the unique structures found in the nucleic acid

PHOSPHORIC ACID

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: concentrated in the nucleus, and condensed during mitosis in the Ch

Prokaryotes

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2 cpt carrying genetic info in bacteria:

Ch and plasmids

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: has DNA; resistant to antibiotics and metals

Plasmid

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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

1. Sugar (Pentose) 2. Phosphate from Phosphoric acid 3. 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? 1. Organize [?] 2. Structure that helps in taking the instructions from the mRNA and use these to organize the tRNA carrying amino acids to assemble the [?] 3. 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

1. Subunit: small (40s) and large subunits (60s) 2. 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

1. Process of unwinding and unzipping 2. Single strand binding proteins 3. Primase 4. DNA polymerase 5. RNA primase 6. DNA Ligase

- uses helicase enzyme to unwind and unzip the DNA structure

1. Process of unwinding and unzipping

- bind to DNA strands to prevent reannealing of single strands

2. Single strand binding proteins

- creates RNA primers on both strands

3. Primase

- primers will give the DNA polymerase a point to start

3. Primase

- responsible for adding nucleotide bases

4. DNA polymerase

- only works on a 5' to 3' process

4. DNA polymerase

- will make extra primers down the lagging strand

5. RNA primase

- contains fragments of DNA known as "okazaki fragments"

- lagging strand

- will take care or connect the gaps on the "okazaki fragment"

6. 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'

LESSON 6 DNA & RNA STRUCTURE Flashcards

(211 cards)