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Chapter Four: DNA, RNA, and the Flow of Genetic Information

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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The "Central Dogma"

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DNA RNA Protein

Replication

Transcription

Translation

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Polymers of nucleic acids serve as the repository of genetic information in living systems

Deoxyribonucleic acid (DNA): the genetic material in cells (dsDNA: 5’-ATGCCAT-3’);
Ribonucleic acid (RNA): functions to transcribe and translate this information into proteins (ssRNA: 5’-AUGCCAU-3’);
Some viruses use RNA as the genetic material.

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Nitrogenous Bases

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dsDNA

5’-AGCT-3’

3’-TCGA-5’

ssRNA

5’-AGCU-3’

Nitrogenous base

Nucleoside

Nucleotide

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Base

Nucleoside

Nucleotide

dsDNA

5’-AGCT-3’

3’-TCGA-5’

ssRNA

5’-AGCU-3’

Nucleoside

deoxyAdenosine

deoxyAdenosine 5’-monophosphatse

dAMP, dA, A

Nucleotide

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Base

Nucleoside

Nucleotide

dsDNA

5’-AGCT-3’

3’-TCGA-5’

ssRNA

5’-AGCU-3’

Nucleoside

deoxyGuanosine

deoxyGuanosine 5’-monophosphatse

dGMP, dG, G

Nucleotide

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Base

Nucleoside

Nucleotide

dsDNA

5’-AGCT-3’

3’-TCGA-5’

ssRNA

5’-AGCU-3’

Nucleoside

deoxyCytidine

deoxyCytidine 5’-monophosphate

dCMP, dC, C

Nucletide

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Nucleoside

Nucleotide

ssRNA

5’-AGCU-3’

Base

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Nucleotide

dUMP

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dsDNA

5’-AGCT-3’

3’-TCGA-5’

Nucleoside

Nucleotide

Base

Deoxythymidine

Deoxythymidine 5’-momophosphate

dTMP

dT

T

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Summary of Terms

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Base	Nucleoside	Nucleotide	Nucleotide RNA	Nucleotide DNA	Code
Adenine	(deoxy-) Adenosine	(deoxy-) Adenylic acid	Adenosine 5’-monoposphate (AMP)	dAMP	A
Guanine	(deoxy-) Guanosine	(deoxy-) Guanylic acid	Guanosine 5’-monophosphate (GMP)	dGMP	G
Cytosine	(deoxy-) Cytidine	(deoxy-) Cytidylic acid	Cytidine 5’-monphosphate (CMP)	dCMP	C
Thymine	Thymidine	Thymidylic acid		Deoxythymidine 5’-monphosphate (dTMP)	T
Uracil	Uridine	Uridylic acid	Uridine 5’-monophosphate (UMP)		U

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Nucleotides and Nucleic Acids

Nucleosides are compounds formed when a base is linked to a sugar. The sugars are pentoses;
Bases are almost water insoluble. Sugars make nucleosides more water-soluble than free bases. Nucleotides have higher solubility than nucleoside due to phosphate group;
D-ribose (in RNA);
2-deoxy-D-ribose (in DNA);
The difference - 2'-OH vs 2'-H;
This difference affects secondary structure and stability.

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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+

Phosphodiester bond

H₂O

H⁺

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3'-5' phosphodiester bridges link nucleotides together to form polynucleotide chains

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3'-5' phosphodiester bridges link nucleotides together to form polynucleotide chains

DNA

Thymidine

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Shorthand for Writing Oligonucleotide Sequences

GATTCATGCGATAG

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5’-GATTCATGCGATAG-3’

3’-GATTCATGCGATAG-5’

The orientation is assumed to be 5’ on the left and 3’ on the right.

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Cyclic Nucleotides

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Nucleoside monophosphates can have two ester bonds to the phosphoric acid, and these can be within the same molecule via an ester bond to both the 5' and 3' hydroxyl groups of the ribose sugar;
cAMP, and cGMP are important regulators of cell metabolism and are found in virtually all cells.

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Structures of the cyclic nucleotides cAMP and cGMP.

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Structure of ATP

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Large negative free energy change on hydrolysis is due to:

electrostatic repulsion in the reactant
stabilization of products by ionization and resonance
entropy increases

Large Negative Free Energy Change of ATP

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Feature of Double Helical Structures

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A double helix with two chains running in opposite directions;
[A]=[T] and [C]=[G];
The bases are directed towards the center (and stack on top of one another) and the sugar backbones face the outside of the helix;
A right-handed double helix;
34 Å per helical repeat;
10 base pairs per repeat (i.e. per turn of the helix).

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Consequences of the Model for Genetic Information

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G always paired with C, and T always paired with A;
The basis of the complementarity was hydrogen bonding;
G-C base pairs were stabilized by three hydrogen bonds, whereas A-T base pairs were stabilized by two. This meant that the G-C interaction was stronger than the A-T interaction;
The genetic information that DNA carried was within the unique base sequence of the DNA;
DNA helix would have major grooves and minor grooves.

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Major groove

Minor groove

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The antiparallel nature of the DNA double helix.

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The Watson–Crick base pairs A:T and G:C

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Hydrogen bonds between base pairs
Hydrogen bonds between polar sugar-phosphate backbone and water molecules
Electrostatic interactions between positive ions and phosphate groups
Base stacking together through π-π interaction (a type of hydrophobic interaction)

Stable Structure of Double DNA Helix

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Denaturation and Renaturation of DNA

Hyperchromic shift and Tm

What affect Tm?

Hypochromic shift

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Denaturation and Renaturation of DNA

Native DNA: double stranded, hydrogen binds between base pairs and right-handed helical shape

Denatured DNA: single stranded, no hydrogen bonds between base pairs

Denaturation: temperature increase

Renaturation: temperature decrease

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Denaturation and Renaturation of DNA

Hyperchromic shift and Tm

What affect Tm?

Hypochromic shift

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Hyperchromic Shift and T_m

When DNA is heated to >80 degrees Celsius, its UV absorbance at 260 nm increases by 30-40%. It is called hyperchromism or hyperchromic shift, which reflects the unwinding of the DNA double helix;
Hypochromism: stacked base pairs in native DNA absorb less light. When T is lowered, the absorbance drops, reflecting the re-establishment of stacking.

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Heat denaturation of DNA from various sources, so-called melting curves. The midpoint of the melting curve is defined as the melting temperature, T_m .

ssDNA

dsDNA

Half dsDNAs are separated.

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What factors affect T_m?

GC%: higher GC% a DNA fragment contains, higher Tm is.
Length: longer a DNA fragment is, higher Tm is.

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An example

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DNA fragment A: 400 bp and GC% = 40%

DNA fragment B: 600 bp and GC% = 60%

DNA fragment C: 600 bp and GC% = 40%

Rank DNA fragments based on T_m from low to high?

A < C < B

Why?

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Denaturation and Renaturation of DNA

Hyperchromic shift and Tm

What affect Tm?

Hypochromic shift

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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5’-GATTCATGCGATAG-3’

DNA Polymerase

3’-CTAAGTACGCTATC-5’

A primer

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DNA Polymerase

DNA polymerase: an enzyme that drives, or catalyzes, the synthesis of new DNA. It functions in DNA replication and DNA repair.
DNA nucleotides (dNTP: dATP, dGTP, dCTP, dTTP)
Template DNA: the DNA sequence
A primer: a single-stranded RNA or DNA
DNA polymerase has 3’ 🡪 5’ exonuclease activity.
DNA synthesis is from 5’ 🡪 3’.

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Overview of DNA Replication

DNA is the material of heredity. The transfer of information from a parental cell to two daughter cells requires exact duplication of DNA, a process known as DNA replication.
It reproduces with high fidelity so that no information is lost.
It resists the appearance of mutations, yet allows for evolution.
DNA replication is semiconservative, bidirectional and semidiscontinuous.
DNA replication is a coordinated process of several enzymes and proteins.
DNA synthesis is from 5’ 🡪 3’.

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E. coli RNA polymerase: synthesizes all major types of RNA (mRNA, tRNA, rRNA and small RNA)
RNA polymerase: is responsible for the function of initiation, elongation and termination in RNA synthesis

RNA Synthesis in E.coli

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5’-GATTCATGCGATAG-3’

RNA Polymerase

AGAACCCUAUC-5’

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RNA polymerase

DNA template
NTPs (ATP,CTP,GTP,UTP)
Mg²⁺
RNA polymerase does NOT require a primer.
RNA polymerase does not have 3’→5’ exonuclease activity.
RNA synthesis is from 5’ 🡪 3’.

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Reaction catalyzed by RNA polymerase

E.coli transcription rate: 30-85 nucleotides/sec
Error rate: 10⁶
RNA Polymerase has no exonuclease activity.

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Viruses and Bacterial, Plant and Animal Cells

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Plant and animal cells are highly structured and more complex. They are much greater in size than the bacterial cells.

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What Are Viruses?

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Viruses are not cells. They need host cell systems to replicate themselves.
Viruses are supramolecular complexes of nucleic acid encapsulated in a protein coat.
Viruses could be divided into two classes: DNA (double stranded or single stranded) viruses and RNA (double stranded or single stranded) viruses.
Mutation rate of virus is very high.
The complete virus life cycle includes: virus and host recognition, entry, replication, integration, transcription and translation, assembly, release.

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Human Immunodeficiency Virus (HIV)

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The virus causes Acquired Immunodeficiency Syndrome (AIDS). It was first exposed in 1981 in central Africa.

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Human CD4 T cells

CD4 receptor

Viral DNA

Nucleus

Genome

Viral RNA

Viral protein

Inactive

Active

Viral protein

Viral DNA

Viral RNA

Reverse transcriptase

Ribosome

RNA Pol

Protease

Integrase

HIV

gp120

ssRNA

CCR5

gp41

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Life Cycle of Human Immunodeficiency Virus (HIV)

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Viral Entry

(i) HIV binds to cell: gp120 interacts with host CD4 receptor mainly through electrostatic, but also van der Waals and hydrogen bond (Initial interaction between gp120 and CD4 receptor. And then conformational change in gp120 allows for secondary interaction with host CCR5).

(ii) Fuses with cell and injects its core: (The distal tips of gp41 are inserted into the cellular membrane. gp41 undergoes significant conformational change; folding in half and forming coiled-coils. This process pulls the viral and cellular membranes together, fusing them)

Viral Transfer

(i) Reverse transcriptase makes single-stranded DNA copy of viral RNA

(ii) DNA polymerase (reverse transcriptase has DNA polymerase activity) makes second DNA copy.

(iii) Integrates into cellular DNA (viral integrase)

(iv) Synthesize viral RNA using host RNA polymerase

(v) Translation of RNA into viral proteins

(vi) Viral protease cleaves viral enzymes/proteins

(vii) Proteins and RNA are assembled into new virions

Viral Exit

Viruses are released from cell surface

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Reverse Transcriptase

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Classes of Nucleic Acids

DNA and RNA
Several forms of RNA:

Messenger RNA (mRNA) and heterogeneous nuclear RNA (hnRNA);
Ribosomal RNA (rRNA): most abundant RNA;
Transfer RNA (tRNA);
Small nuclear RNA (snRNA): RNA splicing;
Small interfering RNAs (siRNAs): bind to mRNA, cause mRNA degradation and inhibit translation

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Ribosomal RNAs and Proteins

Ribosomes are complexes of RNAs and proteins
Ribosomes are about 2/3 RNA, 1/3 protein;
rRNA serves as a scaffold for ribosomal proteins;
23S rRNA in E. coli is the peptidyl transferase!

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The Organization and Composition of Prokaryotic and Eukaryotic Ribosomes

30S subunit: 16S RNA and 21 proteins

50S subunit: 5S & 23S RNA and 31 proteins

40S subunit: 18S RNA and 33 proteins

60S subunit: 5S & 28S RNA plus 5.8S RNA and 49 proteins

Prokaryotic

70S

Eukaryotic

80S

Ribosome

Sedimentation coefficient (S): depends on density, volume and frictional coefficient.

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Transfer RNA

Small polynucleotide chains: 73 to 94 nucleotides each;
Several bases usually methylated;
Each tRNA carries one amino acid. Each amino acid has at least one unique tRNA which carries the aa to the ribosome;
3'-terminal sequence is always CCA-amino acid;
Aminoacyl tRNA molecules are the substrates of protein synthesis.

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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mRNA

Single eukaryotic mRNA encodes one protein while single prokaryotic mRNA can encode one or more than one proteins;
Eukaryotic mRNAs typically contain a 5’-end cap of m⁷-GTP (occurs after first 20-30 nucleotides are transcribed. It protects RNA degradation from RNase) and poly A tails at 3’-end and while prokaryotic mRNAs do not;
Eukaryotic RNAs typically require splicing while prokaryotic RNAs do not;
Transcription and translation are two separated processes in eukaryotic cells while transcription and translation are coupled processes in prokaryotic cells.

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phosphohydrolase

guanylate base methyltransferase

ribose methyltransferase

guanylyl transferase

Step 1: phosphohydrolase

Step 2: guanylyltransferase

Step 3: guanylate base methyltransferase

Step 4: ribose methyltransferase

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CPSF-CstF-CFI-CFII complex cut pre-mRNA at 10-30 nt downstream of AAUAAA sequence.
poly A polymerase → poly A tail of < 250 As

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The polyadenylation signal–the sequence motif recognized by the RNA cleavage complex – varies between groups of eukaryotes. Most human polyadenylation sites contain the AAUAAA sequence, but this sequence is less common in plants and fungi. The RNA is typically cleaved before transcription termination, as CstF also binds to RNA polymerase II. Cleavage also involves the protein CFII, though it is unknown how the cleavage site associated with a polyadenylation signal can vary up to some 50 nucleotides.
When the RNA is cleaved, polyadenylation starts, catalyzed by polyadenylate polymerase.

The cleavage is catalyzed by the enzyme CPSF and occurs 10–30 nucleotides downstream of its binding site. This site often has the polyadenylation signal sequence AAUAAA on the RNA.
Two other proteins add specificity to the binding to an RNA: CstF and CFI. CstF binds to a GU-rich region further downstream of CPSF's site. CFI recognizes a third site on the RNA (a set of UGUAA sequences in mammals) and can recruit CPSF even if the AAUAAA sequence is missing.

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Triose Phosphate Isomerase Gene (Nine Exons and Eight Introns)

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Spliceosome

Splicing: removal of some internal pieces (introns) of the primary transcripts and rejoining of the remaining pieces (exons)
Splicing takes place on spliceosome complexes of 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6
snRNA associates with proteins
U3 is thought to guide site-specific cleavage of rRNA in nucleus

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Consensus Sequences at Splice Sites in Vertebrates

15-20 bp

Spliceosome assembly occurs at pyrimidine tract;
Spliceosome: 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Genome

RNA Polymerase

Promoter

+1

-1

Transcription

RNA

Ribosome

aa1-aa2-….

Translation

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Initiation of Transcription

σ subunit of RNA polymerase is responsible for specific initiation of transcription
σ recognizes promoter sequences
Strong promoters correspond to consensus sequence: once in 2 sec
Weak promoters have substitutions: ~ once in 10 minutes
σ70 recognizes promoters of house keeping genes
In eukaryotes, transcription factors are required for formation of transcription complex

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σ Subunit of E. coli

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Prokaryotc and Eukaryotic Gene Structures

Promoter: is the binding site of RNA polymerase. It determines transcription start site.

Each gene has a RNA polymerase binding site.

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Prokaryotc and Eukaryotic Gene Structures

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RNA hairpin based transcription termination
Rho dependent transcription termination

Transcription Termination in Prokaryotc Cells

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RNA hairpin based transcription termination

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Rho-dependent termination of transcription (E. coli)

NusA binds RNA polymerase and cause RNA polymerase stop, and it seems function in hairpin-dependent and also Rho-dependent termination.
Rho binds to new RNA, destabilizes RNA-DNA hybrid.
This binding of Rho to RNA is accompanied by ATP hydrolysis.

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Prokaryotc and Eukaryotic mRNA Structures

Shine-Dalgarno (SD) sequence

Stop codons:

UAA

UAG

UGA

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Orientation of A Gene

Mention +1 position of transcription

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Translation

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5’-AUGGCUAAUGAAUGCUAA-3’

Met

Ala

Asn

Glu

Cys

Add one amino acid each time by amino acid-attached tRNA

5’-ATGGCTAATGAATGCTAA-3’

3’-TACCGATTACTTACGATT-5’

Coding strand

Template strand

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The Genetic Code

Codon: A sequence of three ribonucleotides in the messenger RNA chain that codes for a specific amino acid; also a three-nucleotide sequence that is a stop codon and stops translation.
Genetic code: The sequence of nucleotides, coded in triplets (codons) in mRNA, that determines the sequence of amino acids in protein synthesis.
Of the 64 possible three-base combinations in RNA, 61 code for specific amino acids and 3 code for chain termination.
Start codon: AUG
Stop codons: UAA, UAG, and UGA

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Fundamental Secondary Structure: Stem-Loop

Intrastrand H-bonds between base pairs

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Secondary Structure of tRNA

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Anticodon loop

D loop

TΨC loop

Amino acid acceptor stem

variable loop

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3′ end

(acceptor

site)

5′ end

Double helix

Anticodon

Tertiary Structure of tRNA

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Transcription and translation

Nitrogenous bases, nucleosides and nucleotides

DNAs and RNAs

3’,5’-cAMP, 3’,5’-cGMP and ATP

General features of DNA double helical structure

Consequences of DNA double helical structure

Reversible melting process of DNA double helix

The secondary structure of RNA

DNA polymerase

Viruses

RNAs: mRNA, tRNA, rRNA, snRNA, siRNA

Translation process and the genetic code

Transcription start and termination sites (prokaryotic vs eukaryotic cells)

Translation start and termination sites (prokaryotic vs eukaryotic cells)

Background Information

Structures

DNA Double Helix

Forces to maintain double helical structure

Genetic Information Flow

RNA polymerase

DNAs

Type of Nucleic Acids

Transcription Translation

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Spliceosome assembly occurs at pyrimidine tract;
Spliceosome: 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6

1. What are two nucleotides at 5’ splicing site?

2. What are two nucleotides at 3’ splicing site?

3. What is the main function of pyrimidine tract?

15-20 bp

A pop quiz (2022):

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Thank you for your attention!

Have a good day!

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Suggestions for Thinking

Thoughtful questions help to stimulate thinking and learn course concepts.

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Suggestions for Thinking

Learning takes time, but enjoyable.

Learn one thing thoroughly at a time and move on to another one.

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Suggestions for Thinking

Be very patient when you are studying. You enjoy more and learn more if you spend more time!

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Suggestions for Thinking

“Good actions give strength to ourselves and inspire good actions in others”. - Plato