Molecular Biology 1-7

put together by: Linda Fahlberg-Stojanovska

Disclaimer: I put these together for my kid for his smartphone. However, I found most images had very small type and increased the font size. I am posting it because another teacher might find this useful. The sources are given. If I have used anything illegally, write me and I will take it off.

Contents
Nucleic Acids RNA & DNA

RNA Types
RNA Synthesis = Transcription Protein Synthesis = Translation DNA Replication Chromosomes

Nucleic Acids and Nucleotides

Nucleic acids are macromolecules essential for life. Nucleic acids include
DNA (nucleotide is: deoxyribonucleic acid) and RNA (nucleotide is: ribonucleic acid).

Nucleic acids are linear polymers of nucleotides.

Each nucleotide consists of three components:
a purine or pyrimidine nucleobase (base), a pentose sugar and a phosphate group.

Nucleotides

Nucleic Acids, Nucleotides - Directionality

The sugars and phosphates alternate to form the sugar-phosphate backbone. They are connected with phosphodiester bonds at the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality.

Nucleic Acids: DNA vs. RNA

Nucleic acids differ in structure of the sugar in the nucleotides
DNA contains deoxyribose while RNA contains ribose The only difference is the hydroxyl group at 2 in DNA.

sugar of DNA

sugar of RNA

Nucleic Acids: DNA vs. RNA

Nucleosides
Nucleosides is a compound consisting of a nucleobase (base) bound to a ribose or deoxyribose sugar via a beta-glycosidic bond. Examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine. Nucleosides can be phosphorylated (phosphate group is added) by specific kinases in the cell on 5 of the sugar (it's primary alcohol group -CH2-OH), producing nucleotides.

Nucleobases: Purine vs Pyrimidine

Nucleic Acids: DNA

GC AT

Nucleic Acids: RNA

GC AU

Nucleic Acids Base Pairing

In molecular biology and genetics, the linking via hydrogen bonds between two nucleobases on opposite complementary DNA or certain types of RNA strands that are connected is called a base pair. DNA: adenine (A) thymine (T) guanine (G) cytosine (C) RNA: adenine (A) uracil (U)

guanine (G) cytosine (C)

Nucleic Acids Base Pairing

GC base pairing
Hydrogen bonds in red

http://en.wikipedia.org/wiki/Base_pair

Base Pairing in DNA

Nucleobases
in blue Hydrogen bonds in red

http://www.synapses.co.uk/genetics/dnastruc.html

Base Pairing in RNA

Nucleobases
in blue Hydrogen bonds in red

source not found

RNA Types
Basic purpose of RNA is to synthesize proteins
Step 1: Transcription RNAs are synthesized by DNA Step 2: Translation the RNAs synthesize the protein

RNA 3 main types with 3 functions

rRNA = ribosomal RNA

mRNA = messenger RNA

tRNA = transfer RNA

rRNA
rRNA = ribosomal RNA
rRNA is the RNA component of the ribosome (ribosome = the cellular unit where all protein synthesis occurs) 1. rRNA provides a mechanism for decoding the transcript on mRNA into the 3 letter codons for amino acids and 2. rRNA provides peptidyl transferase that forms the peptide bond between the amino acids that the tRNAs bring in during translation

In eukaryotic cells, rRNA is synthesized = transcribed by RNA Polymerase I (RNAP I).

mRNA
mRNA = messenger RNA mRNA serves serves as a messenger that tells the cell (ribosomes) what protein to synthesize.
mRNA is synthesized in the nucleus and then binds to ribosome to start protein synthesis = translation.

The information contained in mRNA is used to "translate" the protein with specific sequences (it tells the tRNA what amino acid to bring in next in the sequence).

In eukaryotic cells, mRNA is synthesized = transcribed by RNA Polymerase II (RNAP II)

tRNA
tRNA = transfer RNA
tRNA transfer amino acids to the ribosomes during protein synthesis = translation.
The tRNA are formed in the nucleus and migrate into the cytoplasm. The assignment of the correct amino acid to each form of tRNA is crucial to translation. There are 20 different enzymes called aminoacyl-tRNA synthetases (aaRS) for the 20 amino acids that are incorporated into proteins.

In eukaryotic cells, tRNA is synthesized = transcribed by RNA Polymerase III

Synthesis of RNA, DNA and Protein

RNA Synthesis = Transcription Protein Synthesis = Translation DNA Synthesis (Replication)

RNA Synthesis - Transcription

Transcription is the process of synthesizing RNA (mostly in order to synthesize proteins = translation). Transcription creates a complementary RNA copy of a sequence of DNA. RNA polymerase (RNAP) reads the DNA sequence to be copied and produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement and the nucleotides are composed of a ribose (5-carbon) sugar.and a single strand is made.

RNAP Types - Transcription

The type of RNAP (RNA polymerase) determines the type of the RNA produced in RNA synthesis = transcription. RNAP I: ribosomal RNA = rRNA RNAP II: messenger RNA = mRNA
and certain small nuclear RNAs

RNAP III: transfer RNA = tRNAs

and other small RNAs

RNA Synthesis - Transcription

Steps in RNA Transcription
pre-initiation (eukaryotes only)
7 factors for binding RNA Polymerase (RNAP) to the promoter rRNA, mRNA or tRNA depends on type of RNAP

initiation RNAP bound to promotor

promoter clearance getting over the promotor bump

elongation complementary strand is created termination RNA strand is disconnected

processing (eukaryotes only) the RNA is further processed
(addition of a 3' poly-A tail and a 5' cap) and exits through to the cytoplasm through the nuclear pore complex.

Promotor - Transcription
In genetics, a promoter is a region of DNA that initiates (promotes) the transcription of a particular gene Promoters are located near the genes they regulate
(on the same strand and typically upstream towards the 5' region of the sense strand or towards the 3' region of the anti-sense strand).

In bacteria: The promoter is recognized by RNA polymerase and an associated sigma factor and synthesis is initiated.

In eukaryotes: The process is more complicated with 7 factors for binding RNA polymerase to the promoter in the transcription step called pre-initiation.

RNA Synthesis - Transcription

initiation

elongation

termination

http://en.wikipedia.org/wiki/Transcription_%28genetics%29

Transcription elongation - Transcription

STEP: Transcription elongation appears as waves along the DNA.
RNAP (RNA Polymerase) moves the transcription bubble, a stretch of unpaired nucleotides, by breaking the hydrogen bonds between complementary nucleotides. RNAP adds matching RNA nucleotides that are paired with complementary DNA bases.

RNA sugar-phosphate backbone forms with help from RNAP.

Hydrogen bonds of the untwisted RNA+DNA helix break, freeing the newly synthesized RNA strand.

Protein Synthesis = Translation

A protein is required by the body (cell). 1. Transcription. 2. Translation. 1.DNA and RNA Polymerase transcribe RNA including gene (protein) specific mRNA.
This transcribed mRNA has the genetic code for the required protein.

2.The transcribed mRNA goes to a ribosome and together with rRNA and tRNA synthesize the protein by correctly organizing the amino acids, i.e. by translating the transcribed genetic code.

Protein Synthesis = Translation

DNA transcribes an mRNA for the required protein Translation initiation The mRNA travels through a nuclear pore to the cytoplasm of the cell and binds to the small ribosomal subunit.
the AUG codon on mRNA is the start translation codon Eukaryotes: A tRNA Met molecule (carrying the amino acid methionine) is called in. It has the anticodon UAC. The tRNA Met searches for and binds to the AUG start codon on the mRNA.

Translation starts

Protein Synthesis, Ribosomes and mRNA

How does mRNA bind with ribosome? Bacterial ribosome look for a specific sequence on the mRNA that has a Ribosome Binding Site (RBS) and start codon (AUG) in a specific pattern called Shine-Dalgarno sequence (the ribosome has the complementary sequence.)
In eukaryotes, the 5' end of the mRNA has a modified chemical structure ("cap") recognized by the ribosome. This ribosome binds the mRNA and moves along it ("scans") until it finds the first AUG codon in a specific pattern called the Kozak sequence and then calls in tRNA Met (does not require complementary pairing) .

Protein Synthesis and tRNA

tRNA = transfer RNA
Transfers amino acids to the ribosomes (translation). There are 2 parts of the tRNA: aminoacyl attachment site and anticodon
a specific amino acid is bound at the aminoacyl attachment site on the tRNA according to its anticodon. The 3 (mRNA) codons for which there is no matching tRNA (UAA, UGA, and UAG) serve as stop-translation signals, at which point the protein is done and detaches from ribosome.

Protein Synthesis Summary

mRNA arrives at and binds to ribosome
the mRNA has the transcription of the codons of the amino acids for the protein.

1. the rRNA in the ribosome reads the 3 letter codon on the mRNA of the next amino acid and calls in the tRNA with the corresponding anticodon. 2. the tRNA with this anticodon has the corresponding amino acid attached and links to the mRNA. 3. the rRNA binds this new amino acid with the previous amino acid thus forming the protein. 4. the empty tRNA unlinks from the mRNA (repeat from 1).

tRNA and Protein Synthesis

http://en.wikipedia.org/wiki/TRNA

RNA Synthesis and Protein Synthesis

RNA Synthesis and Protein Synthesis

DNA Synthesis - 1
Polymerization is always in the 5' to 3' direction with new nucleotides being added to the 3' end. Because of this directional demand of the polymerization, one of the DNA strands is easily replicated in a continuous fashion (leading strand). the other strand can only be replicated in short segmental pieces (lagging strand). Short segments of complementary DNA, called Okazaki fragments, are produced, and these are linked together later by the enzyme ligase. The lagging strand is considered the new strand.
http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nucacids.htm

DNA Synthesis - 2
Separation of a portion of the double helix takes place at a site called the replication fork. As replication of the separate strands occurs, the replication fork moves away and unwinds additional lengths of DNA (in diagram movement is to the left).

http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nucacids.htm

Topoisomerase Regulates Winding

Topoisomerase is the enzyme that regulates the overwinding or underwinding of DNA.

http://www.pdbj.org/eprots/index_en.cgi?PDB%3A3BEP

Heliacase - Unwind
Helicases are a class of enzymes. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating 2 annealed nucleic acid strands (DNA, RNA,) using energy derived from ATP hydrolysis.

DNA Synthesis - Enzymes

Once the double stranded DNA is exposed, a group of enzymes act to accomplish its replication. These are described briefly here:

Topoisomerase: regulates winding/unwinding of the double helix.

Helicase: cuts strands. Note that many hydrogen bonds must be broken if the strands are to be separated. SSB: A single-strand binding-protein stabilizes the separated strands, and prevents them from recombining, so that the polymerization chemistry can function on the individual strands. DNA Polymerase: This family of enzymes link together nucleotide triphosphate monomers as they hydrogen bond to complementary bases. These enzymes also check for errors (roughly ten per billion), and make corrections. Ligase: Small unattached DNA segments (Okazaki fragments) on a strand are united by this enzyme.

Restriction
A restriction enzyme (or restriction endonuclease) is an enzyme that cuts DNA at specific recognition nucleotide sequences (with Type II restriction enzymes cutting double-stranded DNA) known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses (bacteriophages).

Restriction

Chromosomes
The chromosomes of prokaryotes are circular and have one molecule DNA The chromosomes of eukaryotes are
long and linear packed in chromatin

Chromosomes - Eukaryotes

http://en.wikipedia.org/wiki/Chromosome

Chromatin
Chromatin is the combination of DNA and proteins that make up the nucleus of a cell. The primary functions of chromatin are to package DNA into a smaller volume to fit in the cell to strengthen the DNA to allow
mitosis and meiosis and prevent DNA damage, and

to control gene expression and DNA replication.

Chromosomes and DNA

The DNA of a cell is tightly packed into chromosomes. DNA is wrapped around small proteins called histones. The beady histones are then further organized and folded into chromatin aggregates that make up the chromosomes.
An overall packing efficiency of 7,000 or more is thus achieved.

http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nucacids.htm

Chromosomes and DNA Synthesis

Why does synthesis stop in some parts of DNA chains?
Because eukaryotes have linear chromosomes, DNA replication is unable to reach the very end of the chromosomes, but ends at the telomere close to the end.
This shortens the telomere of the daughter DNA strand. As a result, cells can only divide a certain number of times before the DNA loss prevents further division.