Unit 7 Biology - Continuity and Change: Molecules

DNA Replication

the process of copying the genome within a cell

DNA Replication: Meselson and Stahl experiment

concluded that DNA is semi-conservative

DNA Replication: semi-conservative

after DNA replication, one strand is original and one is new

DNA Replication: complementary base pairing

each base must pair exactly the same

DNA Replication: replication fork

the region where the original DNA double helix splits into two strands

DNA Replication: single strand binding proteins

bind to the single-stranded DNA to keep the strands separate by preventing hydrogen bonds form reforming

DNA Replication: gyrase

moves in front of helicase to relieve the tension

DNA Replication: helicase

binds to the origin of replication → begins to unzip the double helix by breaking the hydrogen bonds between the bases → creates replication fork

DNA Replication: DNA Polymerase III

the enzyme that will read the template and build the complementary strand

DNA Replication: why DNA Polymerase III works in one direction…

builds the new DNA strand in the 5’ - 3’ direction, it has an active site that is specifically shaped

DNA Replication: primase

creates an existing strand for DNA Polymerase III to add to the 3’ end

DNA Replication: primer

made of short sequences of RNA nucleotides

DNA Replication: DNA Proofreading

DNA Polymerase III has the ability to proofread the newly formed DNA strand as it is being built

DNA Replication: DNA Polymerase I

removes the RNA nucleotides and replaces them with correct DNA nucleotides

DNA Replication: antiparallel orientation

when the helicase unzips the double helix, one strand runs 5’ to 3’ and the other runs 3’ to 5’

DNA Replication: leading strand

DNA Polymerase III can synthesize one of the strands continuously following the same direction as helicase

DNA Replication: lagging strand

one strand is synthesized discontinuously away from the replication fork

DNA Replication: replication process: leading strand

1 primer required → primer created → DNA Polymerase III follows the direction of the helicase until the whole molecule has been unzipped

DNA Replication: replication process: lagging strand

replicated in sections with DNA Polymerase III moving away from the replication fork → fragments called Okazaki fragments → each fragment needs its own primer

DNA Replication: Okazaki fragments

short, discontinuous segments of DNA synthesized on the lagging strand during DNA replication

DNA Replication: enzyme activity: leading v. lagging strand

lagging strand has more primase activity for each Okazaki fragment, more DNA Polymerase I activity → more primers

DNA Replication: Ligase

catalyzes formation of phosphodiester bonds between Okazaki fragments forming a continuous strand

DNA Replication: PCR

Polymerase Chain Reaction → used to amplify small fragments of DNA

DNA Replication: Taq polymerase

DNA polymerase that is heat stable

DNA Replication: PCR: denaturation

DNA is heated to about 98 C to break hydrogen bonds

DNA Replication: PCR: annealing

sample cooled to 60 C → allows primers to bond to complementary DNA

DNA Replication: PCR: extension

at temperatures about 72 C, Taq Polymerase replicates DNA

DNA Replication: gel electrophoresis

often done after PCR → uses an electrical current to move DNA fragments through a gel → fragments are separated based on size

DNA Replication: restriction enzymes

cut DNA molecules at specific sequences to be able to travel through a gel

DNA Replication: DNA fingerprints

restriction enzyme cut sites create a unique pattern of bands when a sample is run through a gel “DNA fingerprint”

• single nucleotide polymorphisms can change cut sites which causes no enzyme activity at that location, thus changing the banding pattern

DNA Replication: applications of PCR and gel electrophoresis

• PCR Covid-19 testing

• paternity testing

• forensic investigations

transcription: central dogma

describes the flow of genetic information

DNA → RNA → protein

transcription: processes of central dogma

DNA is transcribed into mRNA → mRNA is translated into a polypeptide chain

transcription: location of transcription

eukaryotes - nucleus

prokaryotes- cytoplasm

transcription: why is transcription necessary?

• only a portion of the genome to be copied - resource efficiency

• DNA to remain protected in the nucleus of eukaryotes

transcription: RNA Polymerase

performs transcription (elongating the mRNA strand) using DNA template strand as a guide

• 5’ to 3’ direction

transcription: 3 phases of transcription

initiation, elongation, termination

transcription: promoter and TATA box

non-coding region of DNA in front of the gene of interest that begins with TATA box

transcription: initiation phase

transcription factors bind to promoter → TFs recruit RNA Polymerase to the promoter → RNA Polymerase begins to temporarily unzip a small section of the double helix to expose the bases

transcription: elongation phase

RNA Polymerase “reads” the template stand to synthesize mRNA → RNA nucleotides will temporarily hydrogen bond with template strand → growing mRNA strand exits RNA Polymerase and DNA rezips

Transcription factors

proteins that bind to the promoter

transcription: template strand

(antisense strand) strand of DNA that RNA Polymerase “reads”

transcription: coding strand

(sense strands) complementary DNA strand to the template strand

transcription: termination phase

terminator sequence at the end of the gene is reached → signals for RNA Polymerase to release the mRNA and detach from DNA

transcription: enhancers

increase rate of transcription

transcription: silencers

decrease rate of transcription

transcription: mRNA processing

• converts pre-mRNA into mature mRNA

• mRNA splicing

• addition of the 5’ cap and poly-A tail

transcription: 5’ cap

modified nucleotide that is added to the 5’ end of the mRNA

• helps with ribosome binding

transcription: poly-A tail

string of adenines attached to the 3’ end of the mRNA

transcription: exons

base sequences that are expressed (coding regions within a gene)

transcription: introns

base sequences that are removed before translation

transcription: snRNPs

small nucleotide ribonucleoproteins that bind to either side of the introns and assemble into splicesomes

transcription: splicesomes

remove the introns and ligate the exons together

transcription: alternative splicing

different introns are removed → creates unique mature mRNAs which also means unqieu polypeptides