UCSC BIOL 101

Molecular Biology Summer 2026

Proteins

made of amino acids

made of carboxylic acids

chemical synthesis

Any sequence can be made fast and cheaply

• limit in # of nucleotides

• good for primer sequence ~60 bp

enzymatic synthesis

Uses DNA polymerase to copy a sequence

• fast, cheap

• limit in length and you NEED a template DNA/RNA

• makes ~20,000 bp

biological synthesis

Let cells make nucleic acids & proteins

• cheap, fast, have to separate many protein or nucleic acid from other proteins in nucleic acid in cells

gel electrophoresis

Separates molecules by “size”

• Uses SDS-PAGE denaturant

• longer DNA molecules travel faster towards the positive end

Southern Blot

nucleic acid probe with complementary sequence, DNA target

Northern Blot

nucleic acid probe with complementary sequence, RNA target

Western Blot

antibody probe, protein target

genetic code

3 codons used to specify an amino acid

• universal and redundant

reading frame

coding sequence, defining where to begin the code

• ORF is the whole segment

Genomes v Genes

genomes: species DNA sequence that’s passed onto offspring

• organized into chromosomes and have many genes in them

genes: segment of DNA sequence corresponding to a protein

• Offspring is composed of a set of genes with variations/ mutations

LUCA

last universal common ancestor

• Original single-celled organism that sits at the top of the tree of life

recombinant DNA process

• DNA pol remakes a DNA strand

• 3’ end of one strand needs to be next to a 5’ overhang

  • Primer is added on the 3 ′- 5 ′ side

• Primer extension has a template with radioactive addition to mark it

• DNA pol synthesizes new nucleotides, dATP, dGTP, dCTP, dTTP

PCR {polymerase chain rxn]

Amplifies a specific DNA sequence

• needs 8 biomolecules to work

• denatures and anneals a primer to the template strand in multiple rounds

sanger sequencing

Determines the next nucleotide after the primer and how far DNA polymerase works; used to isolate nucleotides

• Primer extension reaction where all incoming DNA lacks a 3’ OH

• An incoming nucleotide can link, but the following cannot

transcription

DNA template turns into mRNA

translation

mRNA codes for proteins

column chromatography

Separation of molecules via a column filled with a porous mixture

• ion-exchange, gel-filtration, affinity binding

vector

special DNA sequences that have the ability to be transferred into other cells

• circular, have a selectable marker, origin of replication

transfection

introducing DNA with a nanoparticle

integration/ infection

“forever” implementation where a virus or retrovirus integrates viral genome into a host cell

“old school” recombinant DNA

• Cut, then mold vectors where DNA is cut and new DNA is attached

  • Uses sticky ends and DNA ligase to bond parts together covalently

  • restriction digest is used to cut target sequence

RT PCR

Special DNA polymerase that uses RNA as a template for an assay to replace Northern blots

• RNA sequence needs to be in the sample & pair with the probe/primer

• Ethidium bromide label used

central dogma

D —> R —> P

• DNA, RNA, protein

Sliding clamp

Keeps DNA polymerase from falling off every 10-50 nucleotides

• makes probability every 50,000

• uses ATP and needs clamp loader enzyme

helicase

unzips DNA/ exposes it for replication

telomerase

brings its own template to extend 3’ end of the strand, used for lagging strand and okazaki fragments

RNAse H

destroys extra DNA during replication

polymerase

makes DNA by adding nucleotides

exonuclease

destroys DNA by removing nucleotides on new strand, increases fidelity

fidelity

discrimination in replication

ORY

origin of replication

ORC

open reading complex

cis-elements

DNA sequence that “marks” the site of DNA replication to start

trans-elements

molecule that recognizes the cis-element

gel shift assay [ EMSA ]

Purpose: Does the sample contain a protein that binds my labeled DNA fragment to my sequence of interest?

• tests for presence of a trans factor or importance of a specific DNA sequence

initation

RNA polymerase “finds” a promoter & engages with DNA

elongation

joining nucleotides based on a DNA template

termination

ddNTPs, RNA polymerase ends transcription

consensus

-35—>-10 base-pairing region of a gene sequence

• Any errors in the region lead to dysfunctional genes

• in promoter region

core promoter

lets RNA polymerase know there is a gene

sigma factor σ

Works with RNA polymerase for the initiation of transcription

fidelity in RNA transcription

Discrimination in replication

• high fidelity= good

gene regulation in bacteria

Cells choose when to express a specific gene

• has ORF, operons code for a gene

intrinistic termination

Internal base-pairing loop, leads to disruption in the pairing sequence

• RNA polymerase gets knocked off

rho-dependent termination

sequence recruiter rho moves faster than RNA polmerase; disruptions base pairs

• knocks RNA polymerase off

foot printing assay

Purpose: to see if the sample protein binds to the DNA sequence of interest

• Need end-labeled restriction fragments

• Protein gets digested by the DNA-binding protein

  • Gaps seen in the gel, show where the protein of interest is interacting