Chapter 4: DNA & Gene Expression

What is DNA?

molecular script for life

what is DNA made up of?

2 long chains of nucleotides

what shape is DNA?

double helix

what is each nucleotide made up of?

• a phosphate group

• a deoxyribose sugar

• a nitrogenous base (A, T, C, G)

what is the backbone of DNA?

sugar-phosphate

how are the rungs of the ladder connected together?

hydrogen bonds

what are the 4 nitrogenous bases?

• adenine

• thymine

• cytosine

• guanine

how do the nitrogenous bases of DNA pair?

• A = T (2 bonds)

• C = G (3 bonds)

what do the sequence of bases code for?

instructions for building proteins

how does biotech use DNA’s stability and reproductibility?

• PCR

• gene sequencing

• genetic engineering

what does understanding the structure of DNA allow?

when does DNA replication occur?

S phase of cell cycle

what is semiconservative replication?

new strand of DNA contains 1 old strand and 1 new strand

how does the DNA double helix unwind?

DNA polymerase attaches to Origin of replication and separates the DNA strands

what is the replication fork?

the Y shaped region where DNA is actively unwound and copied

what is the leading strand?

• strand synthesized continuously, away from the fork

• requires one primer

what is the lagging strand?

• strand synthesized discontinuously, away from the fork

• built in short pieces known as Okazaki Fragments

what type of DNA does bacteria have?

circular

what is DNA polymerase?

• adds new nucleotides to the 3’ end of each primer

• builds new DNA in the 5’ —> 3’ direction

• proofreads for errors

what is the Origin Recognition Complex?

• detects and binds to the Origin of replication

• marks where replication begins

what is Helicase?

enzyme that unwinds DNA by breaking hydrogen bonds between base pairs

what is the purpose of the template DNA?

origin DNA strands serves as guides to build complementary new stands

what is the Replication Bubble?

• formed where DNA strands separate

• expands as replication proceeds in both direction

what is the replication fork?

the Y shaped region where DNA is actively unwound and copied

what are topoisomerases?

• prevents DNA from unwinding ahead of the forx by making temp. cuts

• essential for relieving torsional stress during replication

what are single-strand binding proteins (SSBPs)?

• bind to unpaired DNA strands to keep them from reattaching

• stabilize the open replication fork

what are RNA primers?

short RNA sequences synthesized to start DNA synthesis

what is primase?

enzymes that synthesizes RNA primers on both strands 

what are Okazaki fragments?

short stretches of newly synthesized DNA joined later into a continuous strand

what is DNA ligase?

• enzyme that joins O. Fragments

• final step ensuring a complete strand

what are histone proteins?

• small (+) charged proteins that bind DNA, allowing it to coil tightly

• 8 histones form a core around which DNA unwinds

what are histones?

what are nucleosomes?

• the basic unit of chromatin, consisting of DNA wrapped around histones

• resembles “beads on a string“

what is chromatin?

entire DNA - protein complex visible in the nucleus

what are euchromatin?

loosely packed & active chromatin

what are heterochromatin?

tightly packed & inactive chromatin

who discovered transformation?

Fredrick Griffith

when was transformation discovered?

1928

what was the end conclusion of DNA transformation?

the discovery laid the foundation for identifying DNA as the molecule of heredity

what is transcription?

the process of creating mRNA copy of a gene from a DNA template

what is mRNA?

a type of single-stranded RNA involved in protein synthesis

what is a ribose phosphate backbone?

the structural framework of RNA, consisting of alternating ribose sugar molecules and phosphate groups linked by phosphodiester bonds

what is a codon?

a group of 3 nucleotide bases

what is a polypeptide?

long chain of amino acids linked by peptide bonds, which is a fundamental component of proteins

what is an enzyme?

an organic catalyst that speeds up chemical reactions

what is the central dogma of molecular biology?

DNA —> mRNA —> proteins —> traits

why is it important to understand the structure of RNA in biotech?

how are RNA used to treat disease and create new therapies?

mRNA vaccines (like for covid-19), gene therapy, and CRISPER all depend on manipulating RNA

what makes RNA unstable?

it has an extra oxygen atom

what is the ribose-phosphate backbone?

the structural framework of RNA, consisting of alternating ribose sugar molecules and phosphate groups

what makes DNA more stable?

it doesn’t have an oxygen

when does uracil pair with thymine?

never

what are the 3 key differences between RNA and DNA?

DNA: double stranded, no oxygen atom, stable

RNA: single stranded, oxygen atom, unstable

what is messenger RNA?

carries protein info from the DNA to the cytoplasm

what is a codon?

what are amino acids?

what is an anticodon?

what do tRNA molecules do?

what does the cloverleaf shape of tRNA allow?

what is the small ribosomal subunit?

what is the large ribosomal subunit?

what do ribosomes do?

why is it important to understand transcription?

what is RNA polymerase?

what is pre-mRNA?

what are exons?

what are inrons?

what is the 5’ cap?

what is a Poly-A tail?

what % of human genetic diseases is due to improper RNA splicing?

what is the ribosomal complex?

during translation, what happens at initiation? 

during translation, what happens at elongation? 

during translation, what happens at termination? 

why is gene regulation important?

what is the regulator gene?

what is the promoter region?

what is the operator region?

what is an inducer?

what is the repressor protein?

what is the TRP operon?

what happens when tryptophan is absent?

what happens when tryptophan is abundant?

what is a point mutation?

why is it important to understand point mutations?

what is polymerase chain reaction?

how did PCR revolutionize medicine?

what is the starting material PCR?

what are PCR tubes?

what are primers?

where does the forward primer bind?

where does the reverse primer bind?

what are dNTPs?

what is Taq polymerase?

where is Taq polymerase isolated from?

what does thermostable mean?

what are the three steps of PCR?

what temperature does denaturation happen at?

what happens during denaturation?

what temperature does annealing happen at?