Bio Unit 4- Molecular Genetics

Nucleotide

One individual unit/building block of DNA or RNA, made up of

• one nitrogenous base of any kind

• a sugar

• phosphate group (on the sugar)

Chargaff’s Rule

Chargaff discovered the Chargaff’s Rule (base pairing) by looking at the chemical make up of DNA. He found that:

• Adenine is always found with Thymine (and vice versa)

• Guanine is always found with Cytosine (and vice versa)

Complementary Base Pairing

The pairing of complementary bases between the two strands of DNA as shown by Chargaff’s rule

Anti-parallel

Refers to the orientation of the two DNA strands against each other. They are parallel to each other but face opposite directions, meaning that when one strand runs 5' to 3', the other strand runs 3' to 5'. Referring to the carbons on the sugar from the ether group, from top to bottom of the strand.

genome

the total genetic material of an organism, the “Instruction book” on the entire body in DNA

gene

A distinct functional region within DNA that holds genomes.

Griffith’s Experiment

Griffith tested 2 forms of the same bacterium on mice: an S-strain that was pathogenic (carries the virus that would kill the mice) but could be made non-pathogenic by heating it, the other, R-strain, being non-pathogenic and harmless. When he injected the heated S strain and the R strain into the mice, the mice died. This indicated that there was something being transferred from the dead bacteria in the S-strain to the R-strain. This transfer is referred to as transformation.

Transformation

The movement of genetic material from a dead organism to a live one, altering their DNA. Found in Griffith’s Experiment

Initiation Phase

First phase of semi-conservative replication. A portion of the double helix is unwound to expose the bases for new base pairing

Elongation Phase

Phase 2 of semi-conservative replication. 2 new strands of DNA are put together using the individual parent strands as a template. The new DNA molecules (made of one parent and one new strand) wind back into helix shape.

Termination Phase

Last phase of semi-conservative replication. The new DNA molecules separate from each other completely. The replication machine is dismantled

Origin of Replication

The specific nucleotide sequence at which the process of replication starts.

Helicase

Type of enzymes that unwind and separate the double-stranded DNA during semi-conservative replication.

They cleave the h-bonds between the complementary base pairs to allow the strands to separate.

Semi conservative replication

The proved method of DNA replication in which each new DNA molecule consists of one original strand and one newly synthesized strand due to each new strand being made by using a parent strand as a guideline

DNA polymerase III

The enzyme that catalyzes the addition of new nucleotides one at a time to create a new strand based off of the parent strand.

• III only attaches to the 3’ hydroxyl end of pre-existing nucleotides

• Can only synthesize a new strand from a parent strand in the 5’ to 3’ direction

primer

The short strands of RNA used to start the replication process by providing a free 3' hydroxyl group for the nucleotide addition done by DNA polymerase III

Okazaki fragments

Short DNA fragments created when a nucleotide is added to the various primers of the lagging strand

The use of primers means that the fragments always start with an RNA section

lagging strand

The second strand, ordered from 3’ to 5

needs several primers for replication which leads to the creation of Okazaki fragments

leading strand

needs only one primer for DNA replication

ordered 5’ to 3’

DNA polymerase I

• enzyme that removes the RNA primers from the Okazaki fragments of the lagging strand, and fills that space by extending the neighboring DNA nucleotide. This causes the Okazaki fragments to be just made of DNA which are then joined together by DNA ligase

• can also recognize mistakes in replication, cutting out the incorrect or extra base from the new strand and replacing it with the correct one (works with DNA polymerase II to do this) using the parent strand as a template

DNA ligase

the enzyme that catalyzes the joining together of Okazaki fragments that have only DNA nucleotides

Creates a continuous DNA strand

replication machine

protein-DNA complex at the end of each replication fork that carries out replication

DNA polymerase II

recognizes mistakes in replication and cuts out the incorrect base from the new strand, replacing it with the correct one using the parent strand as a template

Mismatch repair

A replication error fixing method in which specialized enzymes recognize the deformities in newly formed molecules that have mismatched base. These enzymes then bind to the DNA to remove the incorrect base from the new strand and replace it with the correct one

Errors in replication that pass the DNA polymerase and mismatch repair are called what?

Mutations

telomere

A repetitive DNA sequence at the end of a strand added to avoid the loss of important genetic information loss when the RNA section of the very last Okazaki fragment is removed and cannot be replaced

one gene/one polypeptide hypothesis

The theory that each gene only holds the information needed to produce a single polypeptide.

mRNA

• “Messenger RNA”

• RNA that contains the genetic information of a gene and carries it to the protein synthesis machinery

  • provides information that determines the amino acid sequence of a protein

  • acts as an intermediary

genetic code

• a set of rules for determining how genetic information in the form of nucleotides are transferred into amino acid sequences in proteins.

• a code specifying the relationship between a nucleotide codon and an amino acid

Triplet Hypothesis

• Only 4 nucleotides in RNA, but 20 different amino acids. To produce 20 different combination, a minimum of three nucleotides needs to be used (4 times 4 times 4 = 64 vs 4 times 4 = 16) leading to the name TRIPLET HYPOTHESIS

• States that genetic code consists of 3 different nucleotides

gene expression

• the transfer of genetic information from DNA to RNA to protein, leading to it determining the phenotype (and being expressed)

transcription

• the transferring of genetic information from DNA template to RNA

  • the mRNA is synthesized using the DNA as a template

translation

• the transferring of genetic information from mRNA to protein

  • the protein is synthesized using mRNA as a template