Joanna Liu Chapter 4: DNA & Gene Expression

What is DNA?

The molecule that carries the genetic instructions

What is DNA made of?

Nucleotides, Phosphate group, deoxyribose sugar

What shape is DNA?

Double helix

What is each nucleotide made of?

5 carbon sugar, a phosphate group, and a nitrogenous base

What is the backbone of DNA?

Phosphate

How are the rings of the ladder connected together?

The hydrogen bonds between base pairs

What are the four nitrogen bases?

Guanine, Adenine, Cytosine, Thymine

How do the nitrogenous bases of DNA pair?

Guanine pairs with Cytosine and Thymine pairs with Adenine

What do the sequence of bases code?

It codes for proteins

How does Biotechnology use DNA’s stability and reproducibility?

PCR, Gene sequencing, Genetic Engineering

What does understanding the structure of DNA allow?

Knowing how DNA’s structure dictates its function is the foundation for modern biotechnology and genetic medicine.

When does DNA replication occur?

During the S phase of the cell cycle

What is semiconservative replication?

Half is the old strand and half is the new strand

How does the DNA double helix unwind?

By using the DNA Polymerase

What is replication fork?

the region where DNA is unraveling/unwinding

What is the leading strand?

The strand building continuously

What is the lagging strand?

The strand building in fragments

What type of DNA does bacteria have?

Circular DNA

What is the DNA polymerase?

A enzyme that separates the DNA strands

What is the Origin Recognition Complex?

It detects and binds to the origin of replication and marks where replication begins

What is Helicase?

unwinds the DNA double helix by breaking hydrogen bonds

What is the purpose of the template DNA?

to serve as a guide to build complementary new strands

What is the Replication bubble?

forms where DNA separated and expands as replication proceeds in both directions

What is the Replication fork?

Y shaped region where DNA is actively unwound and copied

What is topoisomerases?

prevents DNA from unwinding ahead of the fork by making temporary cuts

What are single-strand binding proteins?

binds to unpaired DNA strands to keep them from reattaching

What are RNA primers?

Short RNA sequences synthesized to start DNA synthesis

What is primase?

Enzyme that synthesizes RNA primers on both strands

What are Okazaki fragments?

Short stretches of newly synthesized DNA joined later into a continuous strands

What is DNA ligase?

Enzyme that joins the okazaki fragments

What are histone proteins?

Small, positively charged proteins that bind DNA and allows it to coil tightly

What are histones?

proteins that help organize and pack DNA into chromatins

What are nucleosomes?

Basic unit of chromatin consisting of DNA wrapped around histones

What is chromatin?

The entire DNA-protein complex visible in the nucleus

What are euchromatin?

loosely packed chromatins that are active

What are heterochromatin?

tightly coiled chromatins that are inactive

Who discovered transformation?

Frederick Griffith

When was transformation discovered?

1928

What was the end conclusion of DNA transformation?

Proved that heritable information could be passed between organisms without direct reproduction

What is transcription?

The process of converting the DNA template into RNA form for creating proteins

What is mRNA?

Messenger RNA, single stranded RNA copy of DNA and carries genetic information of ribosomes

What is ribose phosphate backbone?

RNA’s sugar-phosphate backbone made of ribose instead of deoxyribose

What is a codon?

A sequence of 3 RNA bases that code for amino acids

What is a polypeptide?

What is an enzyme?

A natural catalyst formed from polypeptides

What is the central dogma of molecular biology?

DNA —> mRNA —> Protein —> Trait

Why is it important to understand the structure of RNA in biotechnology?

it’s essential for modern biotechnology and medicine

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

mRNA vaccines, gene therapy, and CRISPR

What makes RNA unstable?

The extra oxygen atom

What is the ribose-phosphate backbone?

sugar-phosphate chain that forms RNA’s structural framework

What makes DNA more stable?

The lack of an oxygen atom

When does uracil pair with adenine?

during protein synthesis

What are the three key differences between RNA and DNA?

RNA: ribose, uracil, single stranded

What is messenger RNA?

carries genetic instructions from DNA to ribosomes, used during transcription

What is a codon?

three base sequence

What are amino acids?

building blocks of proteins

What is an anticodon?

a three-base sequence on tRNA complementary to an mRNA codon

What do tRNA molecules do?

• act as adaptors that read genetic code on mRNA

• deliver correct amino acids in proper sequence

What does the cloverleaf shape of tRNA allow?

it carries a specific amino acid at one end and has an anticodon at the other that can bind to a matching codon on mRNA

What is the small ribosomal subunit?

• smaller component of ribosome

• helps position mRNA and tRNA correctly during protein synthesis

What is the large ribosomal subunit?

• contains the catalytic site for forming peptide bonds

• connects amino acids together to build protein chains

What do ribosomes do?

• read mRNA codons

• matches them with tRNA anticodons

• link amino acids into polypeptide chains that fold into functional proteins

Why is it important to understand transcription?

essential for modern medicine and biotechnology because these processes cause genetic diseases

What is RNA polymerase?

• essential enzyme that catalyzes transcription

• unwinds the DNA double helix and reads the template strand in the 3’ to 5’ direction

• synthesizes RNA in the 5’ to 3’ direction by adding complementary ribonucleotides

What is pre-MRNA?

the initial RNA transcript produced directly from DNA in eukaryotic cells, contains both exons and introns

What are exons?

coding regions of pre-mRNA

What are introns?

non-coding regions of pre-mRNA that must be removed by splicesomes

What is the 5’ cap?

• modified guanine nucleotide added to the beginning of mRNA

• required for ribosome binding and translation inhibition

What is a Poly-A tail?

• A string added to the 3’ end of mRNA

• protects mRNA from degradation and increases mRNA stability

What percent of human genetic diseases is due to improper RNA splicing?

15%

What is the ribosomal complex?

• molecular machine that reads mRNA

• assembles proteins and made of rRNA

During translation, what happens at initation?

ribosomes assembles on mRNA at start codon

During translation, what happens at elongation?

• ribosomes reads each codon

• tRNA binds with complementary anti-codon

• amino acid added to growing chain via peptide bonds, ribosome moves to next codon; empty tRNA exits

During translation, what happens at termination?

stop codon and completed poly-peptide releases

Why is gene regulation important?

essential for biotechnology because it allows scientists to control when proteins are produced

What is the regulator gene?

Encodes the repressor protein

What is the promoter region?

• DNA binding site for RNA polymerase

• Where transcription begins

What is operator region?

• Control switch for gene expression

• Repressor protein binds here to block transcription

What is an inducer?

• changes repressor shape

• prevents DNA binding

What is the repressor protein?

• Binds to operator, blocking RNA polymerase

• Prevents transcription of structural genes

What is the TRP operon?

What happens when tryptophan is absent?

It can not be transcribe

What happens when tryptophan is abundant?

It acts as corepressor, converting the inactive repressor into an active form that shuts down the operon 

What is a point mutation?

A mutation in a single base

Why is it important to understand point mutations?

single base change can have cascade effects throughout gene expression

What is polymerase chain reaction?

(PCR) Amplifies DNA

How did PCR revolutionize medicine?

Enabled rapid Covid 19 testing, cancer mutation screening, forensic DNA analysis, paternity testing, and detection of infectious diseases from small samples.

What is the starting material for PCR?

Template DNA

What are PCR tubes?

Thin-walled plastic tubes containing the reaction mixture

What are primers?

Short single-stranded DNA oligonucleotides

Where does the forward primer bind?

To the 3’ end of one strand

Where does the reverse primer bind?

To the 5’ end of the complementary strand

What are dNTPs?

Deoxynucleotides

What is Taq polymerase?

Synthesized new DNA strands

Where does Taq polymerase isolate from?

Isolated from Thermus aquaticus (bacteria that lives in hot springs)

What does thermostable mean?

Survives repeated heating to 95 degrees Celsius without denaturing

What are the three steps of PCR?

1. Denaturation

2. Annealing

3. Elongation

What temperature does denaturation happen at?

95 degrees Celsius

What happens during denaturation?

Double-stranded DNA separated into two single strands

What temperature does annealing happen at?

55 degrees celsius