Chapter 4: DNA and Gene Expression

1. What is DNA?

molecular script of life

2. What is DNA made up of?

two long strands, nucleotides, wound together in a double helix structure

3. What shape is DNA?

Double helix

4. What is each nucleotide made up of?

A phosphate group, a deoxyribose sugar, and a nitrogenous base

5. What is the backbone of DNA?

a sugar-phosphate backbone

6. How are the rings of the ladder connected together?

hydrogen bonds

7. What are the four nitrogen bases?

adenine, guanine, cytosine, thymine

8. How do the nitrogenous bases of DNA pair?

A-T, C-G

9. What do the sequence of bases code?

Proteins

10. How does Biotechnology use DNA's stability and reproducibility?

PCR, gene sequencing, and genetic engineering

11. What does understanding the structure of DNA allow?

Foundations for modern biotech and genetic medicine

12. When does DNA replication occur?

S phase

13. What is semiconservative replication?

contain a parental strand and a daughter strand

14. How does the DNA double helix unwind?

helicase (enzymes)

15. What is the replication fork?

where DNA is opening

16. What is the leading strand?

one of the strands created continously

17. What is the lagging strand?

one of the strands creates in fragments

18. What type of DNA does bacteria have?

singular, circular and double-stranded DNA

19. What is DNA polymerase?

enzyme that separates DNA strands and builds new complementary strands

What is the Origin Recognition Complex?

a protein complex essential for initiating DNA replication in eukaryotes by binding to origins of replication

What is Helicase?

enzyme that uses the energy from breaking down nucleoside triphosphates to unwind double-stranded DNA and RNA into single strands.

What is the purpose of the template DNA?

to provide the genetic instructions for creating new strands of DNA or RNA

What is the Replication bubble?

region of DNA where the double helix unwinds and separates to allow for DNA replication.

What is the replication fork?

where DNA is opening

What are topoisomerases?

prevent DNA from unwinding ahead of the fork

What are single-strand binding proteins?

Bind to unpaired DNA proteins 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?

enzyme that synthesizes RNA primers on both strands

What are Okazaki fragments?

short stretches of newly synthesized DNA joined later in a continous strand

What is DNA ligase?

enzyme that joins Okazaki fragments, final step in ensuring a complete strand.

What are histone proteins?

 What are histones?

histone complex after DNA loops around them

What are nucleosomes?

basic unit of chromatin consisting of DNA wrapped around histones and resembles beads on a string.

What is chromatin?

entire DNA protein complex visible in the nucleus

What are euchromatin?

loosely packed and active

 What are heterochromatin?

tightly packed and inactive

Who discovered transformation?

Frederick Griffith

When was transformation discovered?

1928

What was the end conclusion of DNA transformation?

DNA is the molecule for heredity

What is transcription?

creating a complementary RNA molecule from a DNA template

What is MRNA?

single strand RNA copies DNA that carries genetic info to ribosomes

What is a ribose phosphate backbone?

RNA’s sugar phosphate structure

What is a codon?

sequence of 3 RNA bases that code for a specific amino acid

What is a polypeptide?

chain of amino acids linked by peptide bonds folds into functional protein

 What is an enzyme?

biological catalyst formed from the polypeptide. Speeds up specific chemical reactions

What is the central dogma of molecular biology?

DNA→ mRNA→Protein→Trait

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

critical intermediaries between our genetic code and the proteins that perform nearly every cell function.

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

Used for mRNA vaccines, gene therapy, and CRISPR

What makes RNA unstable?

Has extra oxygen atom

What is the ribose-phosphate backbone?

repeating sugar-phosphate chain that forms RNA’s structural framework

What makes DNA more stable?

Lacks an oxygen atom

When does uracil pair with thymine?

In RNA

What are the three key differences between RNA and DNA?

contains ribose, uses uracil, is single-stranded

What is messenger RNA?

carries genetic instructions from DNA to ribosome

What is a codon?

three-base sequence on mRNA coding for a specific amino acid

What are amino acids?

building blocks of proteins

What is an anticodon?

three-base sequence on tRNA complementary to mRNA

What do tRNA molecules do?

“read” genetic code on mRNA and deliver correct amino acids

What does the cloverleaf shape of tRNA allow?

allows binding to both specific amino acids and complementary codons on mRNA

What is the small ribosomal subunit?

positions mRNA and tRNA correctly during protein synthesis

What is the large ribosomal subunit?

contains catalytic site for forming peptide bonds

What do ribosomes do?

makes proteins and reads mRNA codons

Why is it important to understand transcription?

to understand how defects in these processes cause genetic disease

What is RNA polymerase?

enzyme that catalyzes transcription

What is pre-MRNA?

initial RNA transcript that is produced directly from DNA in eukaryotic cells 

What are exons?

coding regions of mRNA

What are introns?

Non-coding regions of mRNA

What is the 5' cop?

protects mRNA from degradation

What is a Poly-A tail?

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 and assembles proteins

During translation, what happens at initiation?

ribosome assembles on mRNA at start codon

During translation, what happens at elongation?

ribosome reads each codon

During translation, what happens at termination?

polypeptide releases at stop codon

Why is gene regulation important?

ensures cells have the right proteins at the right time

 What is the regulator gene?

gene that controls the expression of other genes by producing a regulatory protein, such as a repressor or activator

 What is the promoter region?

a region of DNA that is located upstream of a gene and serves as the binding site for RNA polymerase and transcription factors, which initiate the process of transcription

 What is the operator region?

a segment of DNA within an operon that acts as a binding site for regulatory proteins, which control the transcription of adjacent genes

 What is an inducer?

a molecule or substance that triggers a specific process, most commonly gene expression or the operation of a mechanical system

 What is the repressor protein?

a type of protein that inhibits gene expression by binding to a specific DNA sequence called an operator, which blocks the RNA polymerase from transcribing the gene

What is the TRP operon

a group of bacterial genes that are transcribed together to produce enzymes for synthesizing the amino acid tryptophan

what happens when tryptophan is absent

a lack of tryptophan can lead to a recurrence of depressive symptoms and may increase anxiety, irritability, and pain sensitivity

what happens when tryptophan is abundant

its production in a cell is shut down through gene regulation mechanisms like the trp repressor and attenuation, which prevent the transcription of genes needed for synthesizing more tryptophan

what is a point mutation

single base changes

why is it important to understand point mutations

they can have a lot of effects throughout gene expression

What is polymerase chain reaction?

Molecular “photocopier” that revolutionized medicine

How did PCR revolutionize medicine?

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

What is the starting material for PCR?

Template DNA

What are PCR tubes?

Thin-walled plastic tubes containing reaction mixture

What are primers?

Short single-stranded DNA oligonucleotides

Where does the forward primer bind?

Bind to 3 prime

Where does the reverse primer bind?

Bind to 5 prime

What are dNTPs?

Building blocks for new DNA synthesis: dATP, dGTP,dCTP,dTTP

What is Taq polymerase?

Enzyme that synthesizes new DNA strands

Where is Taq polymerase isolated from?

Thermus aquaticus

What does thermostable mean?

Survives repeated heating to 95 degrees Celsius without denaturing

What are the three steps of PCR?

Denaturation, Annealing, and Elongation

What temperature does denaturation happen at?

~ 95 degrees Celsius

What happens during denaturation?

Double-stranded DNA separates into 2 single strands

What temperature does annealing happen at?

55 degrees Celsius