Biology - Nucleic Acids and Protein Synthesis

Cells have…

…information they can pass onto each other that could direct their function

Results of the Fredrick Griffith Experiment (1928)

Found out that cells have information they can pass onto each other that could direct their function

Process of the Fredrick Griffith Experiment (1928)

1. Mixed a strain of dead disease causing bacteria (pathenogenic/virulent) that caused pneumonia with harmless bacteria.
2. Some of the harmless bacteria were transformed into the disease-causing form.
3. When the transformed bacteria reproduced they passed on this ability to cause disease

Result of the Hershey and Chase Experiment (1952)

DNA is the hereditary material and not proteins

Process of the Hershey and Chase Experiment (1952)

1. Grew two batches of virus one with radioactive protein (sulfur) and the other with radioactive DNA (phosphorus).
2. Allowed the two batches to infect bacteria.
3. Found radioactive DNA in the bacterial cells but not radioactive proteins.
4. Viruses were then allowed to reproduce within the bacterial cells and new viruses had some radioactive DNA in them.
5. Showed that a virus (T2 bacteriophage) uses DNA to infect E. coli bacteria and reproduce

Result of the Double Helix Discovery (1953)

Determined that DNA was a double helix structure and showed the structure of DNA within chromosomes

Process of the Double Helix Discovery (1953)

1. Rosalind Franklin- took pictures of DNA using X-ray crystallography
2. James Watson and Francis Crick figured out the structure of DNA using Franklin’s images.
3. Findings were published in 1953
4. Won the Nobel prize in 1962 along with Maurice Wilkins (Franklin’s partner) but Franklin died in 1958 of cancer and they don’t give the prize to the deceased

Importance of DNA

* Codes for proteins that determine our traits.
* Stores genetic information.
* Passed on from one generation to the next (Cell to cell, organism to organism)

DNA and RNA are nucleic acids…

…that carry code

Nucleotide

building block (monomer) of DNA or RNA

* Phosphate group
* sugar molecule
* nitrogen base molecule (held together by covalent bonds)

2 types of nucleotides:

DNA (deoxyribonucleic acid)

* Deoxyribose sugar
* T A C G bases

RNA (ribonucleic acid)

* Ribose sugar
* U A C G bases
* Copy of DNA used in protein synthesis

Pyrimidines

1 carbon ring nitrogen bases (T, U, C)

Purines

2 Carbon ring nitrogen bases (A, G)

Double Helix

DNA is composed of 2 chains that are twisted together to form a spiral (staircase)

* Each chain is composed of a sugar-phosphate backbone connected by covalent bonds with the nitrogen bases (rungs of the ladder) of each chain joined together by hydrogen bonds

Base pairing rules (complementary)

* Adenine with Thymine (2 bonds)
* Guanine with Cytosine (3 bonds)

antiparallel

Chains run in opposite directions

One of the chains determines…

…the code for a trait (gene) based on the sequence and length of nitrogen base segments

* AGTACG on the 1st chain would be part of a gene code
* Actual code can be thousands of nucleotides long
* 2nd Chain is there to protect the nucleotides of the 1st chain

5’ (5 prime) end of the nucleotide

5th carbon on the sugar molecule with the phosphate (P) coming off of it (Top)

3’ (3 prime) end of the nucleotide

3rd carbon on the sugar molecule with the OH off of it that connects to the next nucleotide of a chain (Bottom)

Chargaff’s Rule

Earlier experiments on cells showed equal amounts of A and T and equal amounts of C and G within the cell

A purine bond with a pyrimidine because…

… it would maintain the width of the Helix being measured to 2 nm (nanometers) wide

Atom arrangements within the nitrogen bases allow…

…A and T to bond best (2 hydrogen bonds) and C and G to bond best (3 hydrogen bonds)

DNA Replication occurs

before cell division can occur (S phase)

Each half of the helix serves as…

…a template for adding new nucleotides

A supply of new nucleotides are added at about…

…50 per second on a strand in mammals and 500 per second in bacteria

Semiconservative model

Half of the parental molecule is maintained in each daughter molecule

Appears simple but…

to do untwisting, copying both strands simultaneously in multiple locations and speedy it is rather complex

Origins of Replication

Multiple places along DNA where replication begins (makes the process faster)

Replication Bubbles

Created when existing DNA separates and replication occurs in both directions away from the origin

Replication Forks

where the existing DNA separates (2 forks at each replication bubble)

Bubbles merge once…

replication has completed and two new double helices are made

Leading Strand

DNA polymerase builds toward the fork as it opens

Lagging Strand

DNA polymerase builds away from the fork as it opens which causes it to be built in segments (Okazaki fragments)

Helicase

Enzyme that unzips the helix

Primase

enzyme that synthesizes RNA primer

DNA polymerase III

enzyme that adds free nucleotides to existing strands in the 5’ (phosphate) to 3’ direction (OH)

DNA polymerase I

replaces RNA primer with DNA nucleotides

DNA Ligase

enzyme that connects the Okazaki fragments

DNA can only be built in the…

5’ to 3’ direction of a nucleotide

Accuracy of Replication

1 mistake per billion base pairings

DNA polymerase…

…proofreads and corrects most mistakes with the help of other enzymes (mismatch repair)

* These enzymes also repair damaged DNA caused by harmful radiation such as UV light or by harmful chemicals (excision repair)
* Repair ensures that new cells that form have the correct copy of genetic material

Occasionally mistakes are not fixed properly which results in…

mutations to the genes

* Usually mutations are bad but occasionally they can make a change that can be beneficial

DNA codes for proteins, which determine…

phenotypic traits

Genotype to phenotype

DNA (gene) 🡪 RNA🡪 Polypeptide(Protein)

* Making a protein from a gene

Transcription

Making a copy of a gene into RNA form

RNA Processing

Pre-mRNA is modified into mRNA

Translation

mRNA is read by ribosomes to make proteins

The three basic steps to protein synthesis:

1. Transcription
2. RNA Processing
3. Translation

Genetic information written as codons translates into…

…amino acid sequences

Genes are written…

in a specific code thousands of nucleotides long

Triplet code

Three DNA nucleotides corresponds to three mRNA nucleotides

Codon

Three mRNA nucleotides that codes for a particular amino acid

Number of Possible RNA codons:

64

Number of codons that code for an amino acid:

61 codons that code for 20 different amino acids

1 Start codon

AUG

* Every gene on mRNA starts with AUG
* Also codes for the amino acid methionine (so every protein starts with the amino acid methionine)

3 Stop codons

UAA, UAG, UGA

* End of a gene code on mRNA
* Does not code for any amino acid

Repeat codons

Codons that code for the same amino acid (Wobble base pairs)

Transcription take place…

…in the nucleus

template (Antisense strand)

One DNA strand used for making the RNA copy

Sense strand

unused DNA strand

RNA polymerase

adds complementary RNA molecules to the template strand of DNA

3 types of RNA made:

* mRNA (messenger) – carries gene copy
* tRNA (transfer) – brings in amino acids
* rRNA (ribosomal) –helps create ribosome

Initiation

RNA polymerase attaches to a promoter (start of a gene)

Elongation

RNA chain created and pulls away from DNA template so that DNA helix can reconnect

Termination

RNA polymerase reaches the terminator/termination signal (end of a gene), and transcribed RNA detaches

Parts of Transcription

1. Initiation
2. Elongation
3. Termination

Extra nucleotides are added…

to the ends of the mRNA

* Small 1 G nucleotide 5’cap and a long tail of 50-250 A nucleotides
* Protect and direct the mRNA to the ribosomes (are not part of the code)

RNA splicing

Messenger (mRNA) has RNA sections removed called introns (noncoding segments) before exiting the nucleus leaving the coding regions called exons that become the mRNA code

alternative splicing

can create different mRNA codes (different intron sections removed)

Parts of RNA Processing

1. Extra nucleotides are added
2. RNA splicing
3. mRNA leaves the nucleus and travels into the cytoplasm

mRNA to ribosome process

mRNA read at the ribosome one codon at a time to create an amino acid chain (becomes the protein)

tRNA

* transfer RNA
* Acts as an interpreter
* Has a specific anticodon that is a triplet of bases complimentary to the codon on the mRNA
* Carries a specific amino acid to the ribosome that it has picked up from the cytoplasm

Amino acids come from…

…food or is made by the cell from food

tRNA structure

* Twisted strand of about 80 RNA nucleotides
* Amino acid attachment site at top
* 20 different types of enzymes attach the 20 different types of amino acids to the different types of tRNA
* Anticodon at the bottom of tRNA which attaches to each mRNA codon

tRNA can be…

reused to pick up another amino acid of the same type

* Like a dump truck

Enzymes and energy (ATP) is used to…

…connect specific amino acids to each tRNA

* Specific enzyme for each tRNA and amino acid
* Help the tRNA find it’s amino acid

Ribosome structure

* Large and small subunits
* Proteins + rRNA (ribosomal RNA) make up these subunits
* mRNA binding site
* Located where the subunits are attached

3 tRNA sites

1. A Site
2. P Site
3. E Site

A site

Arrival site for tRNA

P Site

Holds the growing polypeptide

* Amino acids from tRNA at the A site are joined to the growing polypeptide chain attached to the tRNA at the P site

E site

Exit site

* Empty tRNA leaves the ribosome

Initiation Process:

1. mRNA molecule binds to a small ribosomal subunit
2. Initiator tRNA carrying Methionine (Met) binds to the start codon with its anticodon
3. Using energy (GTP) the large and small ribosomal units join (the two subunits are detached when not being used)
4. Initiator tRNA fits into the P site and awaits the next tRNA bringing in the next amino acid into the A site

Elongation Steps:

1. Codon recognition
2. Peptide bond formation
3. Translocation

Codon recognition

anticodon of incoming tRNA carrying its amino acid pairs with the mRNA codon in the A site

Peptide bond formation

amino acid in the A site bonds to the polypeptide chain forming at the P site

Translocation

* both tRNAs along with the mRNA move to the left opening the A site
* 1st tRNA leaves and the process continues

Termination Process:

* Stop codon (UAG, UAA or UGA reaches the A site signals the end of translation)
* Polypeptide, ribosome units and mRNA detach mRNA message may be read by multiple ribosomes before being broken up (trail behind the 1st ribosome) – lifetime of mRNA can be anywhere from minutes to weeks before being broken up

Functional Protein Formation

The polypeptide chain folds up due to horizontal bonding between amino acids and may attach to other folded chains before functioning

If the DNA of a gene is mutated…

…different amino acids may be coded for and the polypeptide chain could fold differently changing how it functions

Gene Mutations

Changes to DNA sequences that may cause different proteins to be created (and as a result new traits)

* Can create a new protein that helps an organism survive and reproduce better
* Most mutations create defective proteins harm a person

Two types of Mutations

1. Base substitution mutations (point mutations)
2. Frameshift mutations

Base substitution mutations (point mutations)

a nucleotide is changed causing one codon to change

* Silent mutation
* Missense mutation
* Nonsense mutation

Silent Mutation

doesn’t change the amino acid (repeat codon created)

Missense mutation

changes an amino acid

Nonsense mutation

changes an amino acid to stop (premature stop)

Frameshift mutations

addition (insertion) or deletion of a nucleotide(s) causing multiple codons to change

* Ex. Crohn’s disease, Breast Cancer (BRCA1), Huntington, Hemophilia

Base Substitution mutation example

Sickle cell shape of red blood cells is caused by a mutation in the code for hemoglobin protein (part of a red blood cell)

* The amino acid Glutamic acid is replaced with the amino acid valine when triplet code CTC is changed to CAC (MISSENSE). This then changes how the polypeptide chain folds up to make hemoglobin and causes the red blood cell to have a sickle shape

Other disease examples : Tay Sachs, Colorblindness

Sickle cells live between…

…10-20 days and are destroyed (normal is 120 days)

Sickle cell anemia

two sickle cell alleles

Sickle cell trait

one normal and one sickle allele (have both normal and sickle cells)