Module 1- Central Dogma

DNA

Hereditary material present in most organisms and are the building blocks of life

Genes

Contain information to create proteins

• A nitrogenous base

• Deoxyribose

• Phosphate group

What does a DNA nucleotide have?

• Adenine and guanine (purines)

• Thymine and cytosine (pyrimidines)

What are the 4 nitrogenous bases in DNA?

By joining nucleotides in a phosphodiester bond

How are DNA strands formed?

• A & T

• C & G

What pairs of nitrogenous bases form hydrogen bonds?

DNA to RNA to Protein

What is the central dogma?

To create identical copies of a DNA strand

What is the purpose of replication?

Steps of replication

Initiation, elongation, leading and lagging strands, and termination

Helicase

Breaks hydrogen bonds between nitrogenous bases to “unwind” DNA

Single-stranded binding proteins

Prevent DNA from reforming double helix

Topoisomerase

Prevents DNA from becoming too tightly wound

Primase

Synthesizes an RNA primer, which provides a 3’ end for DNA polymerase to add to 

DNA Polymerase III

Synthesizes new DNA complementary to the template

Leading strands

• Reads in 3’ to 5’ direction

• DNA synthesis of this stand is continuous

Lagging strand

• Read in the 5’ to 3’ direction

• This strand is composed of okazaki fragments

Okazaki fragments

Short, newly synthesized DNA sequences that are formed on the lagging strand during DNA replication

DNA polymerase I

Replaces RNA primers with DNA

DNA Ligase

Joins okazaki fragments together to create one complete DNA strand

Purpose of transcription

To create a ribonucleic acid (RNA) copy of a specific gene

Steps of transcription

Initiation, elongation, and termination

Initiation in transcription 

• RNA polymerase binds to a promoter sequence on the DNA.

• In eukaryotes, transcription factors are often required to help the polymerase bind. 

Elongation in transcription

• RNA polymerase moves along the DNA, unwinding it and synthesizing a new RNA strand by adding complementary RNA nucleotides.

• It uses one strand of DNA as a template and builds the new RNA chain in the  5’ to 3’ direction

Termination in transcription

• RNA polymerase reaches a terminator sequence, signals the end of transcription, and detaches from the DNA.

• The newly formed mRNA strand separates from the DNA template and the DNA strands rejoin. 

Difference between DNA and RNA

DNA is a double-stranded helix with a deoxyribose sugar and uses the base thymine (T), while RNA is typically single-stranded with a ribose sugar and uses the base uracil (U) instead of thymine.

Purpose of translation

Converts mRNA to a polypeptide 

Codon

• Group of 3 nucleotides

• Has a specific sequence of nitrogenous bases 

64

How many codons are there?

61

How many codons code for amino acids?

3

How many stop codons are there to end translation?

Transfer RNA (tRNA)

Matches the correct amino acid to an mRNA codon

An mRNA codon contains…

• An anticodon that is complementary to the mRNA codon

• An amino acid that corresponds to the codon

Ribosomes

• Act as the site of translation in all living organisms

• Components:

  • Small ribosomal subunit 

  • Large ribosomal subunit

Small ribosomal subunit

Reads the mRNA

Large ribosomal subunit

Binds amino acids to forma polypeptide chain

Initiation in translation

• The small ribosomal subunit binds to the mRNA, and the first tRNA (carrying methionine) binds to the start codon (AUG).

• The large ribosomal subunit then joins to form the complete ribosome, and the first tRNA occupies the P site.

Elongation in translation

• The small ribosomal subunit binds to the mRNA, and the first tRNA (carrying methionine) binds to the start codon (AUG).

• The large ribosomal subunit then joins to form the complete ribosome, and the first tRNA occupies the P site.

Termination in translation

• When a stop codon is reached, a release factor protein binds to the A site instead of a tRNA. This causes the polypeptide to be released from the last tRNA.

• The ribosome subunits and the polypeptide are released from the mRNA, and the ribosome disassembles.

Proteins

• Consist of 1 or more polypeptides in a specific conformation 

• Examples of proteins include enzymes and receptors 

Primary, secondary, tertiary, and quaternary 

What are the levels of protein structure?

Primary structure

• What it is: The unique, linear sequence of amino acids in a polypeptide chain. 

• What determines it: The genetic code in DNA is transcribed and translated into this sequence. 

• Bonds involved: Peptide bonds hold the amino acids together

Secondary structure

• What it is: The local folding of the polypeptide chain into regular structures. 

• Key formations: Alpha-helices and beta-pleated sheets are the most common. 

• Bonds involved: Hydrogen bonds between the polypeptide backbone's amino and carboxyl groups stabilize these structures. 

Tertiary structure

• What it is: The overall three-dimensional shape of a single polypeptide chain. 

• What determines it: Interactions between the side chains of the amino acids, including hydrogen bonds, ionic bonds, van der Waals interactions, and disulfide bridges. 

• Importance: This folding is crucial for the protein's specific function.

Quaternary structure

• What it is: The arrangement of multiple polypeptide chains (subunits) into a single functional protein. 

• Key formations: This level is only present in proteins that consist of more than one subunit. 

• Bonds involved: Interactions between the side chains of different subunits, similar to those in the tertiary structure. 

• Example: Hemoglobin has a quaternary structure made of four subunits (two alpha and two beta). 

Eukaryote

Their cells’ genetic material is held within a distinct nucleus

Prokaryote

Their cells lack an envelope-enclosed nucleus

Virus

A microscopic parasite that requires a host to reproduce

DNA replication in eukaryotes

• Eukaryotes have linear, double-stranded DNA (dsDNA)

• There is an inevitable loss of genetic material during replication

• Telomeres are used to protect chromosome ends

Telomeres

Repeats of the sequence TTAGGG in humans

Telomerase

Extends telomeres

DNA replication in prokaryotes

• Prokaryotes have circular double-stranded DNA (dsDNA)

• Do not require telomeres to prevent loss of genetic material

Baltimore classification

Used to categorize viruses according to their method of mRNA production

What do viruses do after infecting host cells?

Viruses use host machinery to replicate their genetic material

Classes of DNA viruses

1. double-stranded DNA (dsDNA (class I))

2. single-stranded DNA (ssDNA (class II))

Where does genome replication occur in viruses?

It occurs in the host cell’s nucleus using a combination of viral and host proteins

DNA-dependent DNA polymerase

• An important enzyme used in replication

• Produced by either the host or the virus

RNA-dependent RNA polymerase

Catalyzes genome replication in viruses

Types of RNA viruses

dsRNA, (+)ssRNA, (-)ssRNA

(+)ssRNA

functions as mRNA, so can be immediately translated

(-)ssRNA

complementary to mRNA, so cannot encode proteins

Reverse transcribing viruses

• (+)ssRNA-RT and dsDNA-RT

• Genome replication involves reverse transcription of the viral genetic material

Retrovirus

Has a DNA intermediate in its replication cycle

Pararetrovirus

Has an RNA intermediate its replication cycle

Transcription in eukaryotes

RNA transcripts must undergo processing to become mature mRNA

5’ cap

A modified guanine triphosphate added to the 5’ end of the transcript

Poly(A) Tail

A string of adenine nucleotides added to the 3’ end of the transcript

What do the 5’ cap and poly(A) tail do in transcription in eukaryotes?

The 5’ cap and poly(A) tail protect mRNA from degradation and aid in its export from the nucleus to undergo translation

Splicing

The process of removing certain sections (introns) of pre-mRNA, leaving the remaining sections (exons) to be linked together

Alternative splicing

Allows different proteins to be made from the same gene

Kozak consensus sequence

Protein translation initiation site in most eukaryotic mRNAs

• Surrounds the start codon

• Ensures that a protein is correctly translated

• Can be modified to alter the level of protein synthesis

Operon

• Collection of genes under control of one promoter

• All genes here are transcribed into one polycistronic mRNA

Polycistronic mRNA

An mRNA that encodes for multiple proteins

Shine-Dalgarno sequence

• Ribosome binding site in prokaryotes

• Multiple of these sequences are used to express proteins in polycistronic mRNA

Reading frame

• A method of dividing a sequence of nucleotides in an mRNA molecule into a set of consecutive triplets without overlaps

• The first AUG on the mRNA normally determines this

• Some viruses can shift the standard ____________ to produce multiple unique proteins