Chapter 4: DNA & Gene Expression

What is DNA/

DNA is the molecular script of lige

What is DNA made-up of

two long chains of nucleotides that wind around each other to form a double heliz

What shape is DNA?

a double helix?

What is each nucleotide made up of?

• A phosphate group

• A deoxyribose sugar

  • A nitrogenous base

What is the backbone of DNA?

the sugar and phosphate form the backbone of each strand

How are the rungs of the ladder connected together

the bases form the rungs of the twisted ladder and connect through the hydrogen bonda

What are the four nitrogenous bases?

Adenine, Thymine, Cytosine, Guanine

How do the nitrogenous bases of DNA pair?

Adenine - Thymine
Cytosine - Guanine

What do the sequence of bases code?

Base pairing enrures that when DNA replicated, each new strand is an exact Copy of the original

How does biotechnology use DNA’s stability and reproducibility?

for PCR, gene sequencing, and genetic engineering

What does understanding the structure of DNA allow?

dictates its function is the foundation for modern biotechnology and genetic medicine

When does DNA replication occur?

S-Phase

What is semiconservative replication?

contains one old strand and new strand 

How does the DNA double helix unwind?

with the help of enzymes that separate the strands

What is the replication fork?

makrs the region where the DNA is opening

What is leading strand?

built continuosly 

What is the lagging strand?

built in fragments

What type of DNA does bacteria have?

circular

What is DNA polymerase

attaches here, sperating the DNA strands and building new complementary strands

What is the orign recognition complex?

detechts and binds to the origin of replication

What is helicase

unwinds the DNA double helix by breaking hydrogen bonds between base pairs

What is the purpose of the template DNA?

orginal DNA strands serves as guides to build complementary new strands

What are topoisomerases?

prevent DNA from unwinding ahead of the fork by making temp. cuts

What are single-strand binding proteins?

bind 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 in both strands

What are okazaki fragments

short stretched of newly synthesized DNA joined later in continue strand

What is DNA ligase?

• enzyme that joins okazki fragments

  • final steps ensuring a complete strand

What are histone proteins?

small positively charged proteins that bind DNA, allowing it to coil tightly

What are histones

idk

What are nucleosomes 

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

• resembles “beads on a string”

what is replication fork?

• the y shaped region where Dna is actively unwound and copied

What is replication bubble

formed where DNA strand seperate

• expands as replication proceeds in both directions

What is chromatin?

• the entire DNA-protein complex visible in the nucleus

• euchromatin (loosely packed, active)

  • heterochromatin (tightlly pack inecti)

Whaat are euchromatin?

loosely packs, active

What are heterochromatin?

tightly pack , inactive

Who discovered transformation?

Frederick Griffin

When was transformation discovered?

1928

What was the end conclusion of DNA transformation?

revealed that genetic information could be transferred between bacteria — a process later known as transformation idk man

What is transcription?

MRNA
- a single stranded RNA Copy of DNA that carries genetic information ribose
- formed through transcription, DNAacts as a templatee for MRNA synthesis

Ribose phosphate backbone

• rnas sugar-phophate structure

Uracil

• found only in RNA; paids with adenine instead of thymine

What is MRNA

carries genetic instructions from nucleus to ribosomes

What is a ribose phosphate backbone?

structual framework of mrna made of ribose sugars linked by phosphates

What is a codon?

specific protein squences

What is a polypeptide>

multiple amino acidslinked tg by peptide bonds

What is an enzyme?

a biological catalyst formed from the populepptide

• speeds up specfic chemical reactions

What is the centeral sogma

dna → mRNA → protein → trait

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

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

How are RNA used to treat disese and create nre therapies?

• MRNA vaccines, gene therapy, and CRISPR technology all depend on manipulating RNA to treat disease and develop new therapies

What makes RNA unstable?

contains ribose, a 5-sugar carbon with an extra oxygen atom compared to DNA deoxyribose, makes rna more chemially reactive and less stable that DNA

What is the ribose-phosphate backbone

the repreating sugar phosphate chain that forms rna’s structural framework

What makes DNA mroe stable?

lack one oxygen atom on each sugar (deoxy - without) makes dna more stable for long-term genetic storage

When does uracil pair with thymine?

during protein synthesis

What are the 3 key differences between rna and dna?

• constain ribose not doxyribose

• use uracil instead of thymine

  • typically single stranded

what is messengar rna

• rna that carries genetic instructions from dna to ribosomes

  • constains genetic code copied from dna during transcription

What is a codon?

uhhh three-based sequences = 1 codon?

What are amino acids?

bulding blocks of protein

• each tRNA molecule carries one specific amino acid to the ribosome

What is an anitcodon?

a three base sequences on tRNA complementary to an mRNA codon

• ensure that the coorect amino acid is added during translation

What do trna molecules do?

red genetic code on MRNA and deliver correct amino acids

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

What does the cloverlead shape of trna allow?

• to bind to the amino acid and the complementary codons on mrna

What is the small ribosomal subunit?

• the smaller componet of a ribsome

  • helps position mrna and trna correctly during protein synthesis

what is the large ribosomal subunut?

contains the catalystic site for forming a polypeptide

connects amino acids together to build a protein chain

What do ribosoomes do?

protein factoires where mrna, trna and amino acids come together. The ribosome reads mrna codons and matched with trna anitcodons and links amino acids into polypeptide chains

Why is it imoprtant to understand transcription?

bc defects in these processes cause genetic diseases

what is rna polymerase?

unwinds the dna double helix and reads the template strand in 3 - 5 direction

synthesiszes rna in the r - 3 direction by adding complementary ribonucleotides

What is pre mrna?

intial rna transcript before being sent out, constain both coding sequences, and non coding sequences

what are exons?

uhm i will get back to this

What are introns?

non coding regiona that must be removed

cut away by the splicesomes and loop out during RNA processing

What is the 5 cap

a modified guanine nucleotide added to the begiining 5 end to the mrna

protects mrna from degradation by cellular enzymes

required for ribosome bindings and translation initiation

What is poly A tail?

added to the 3 end of mrna
prtectss from degredationa and increases stability

helps with mrna export from nucleus and enhances translation

What percent of human genetic disease is due to imporper RNA splicing?

15%

what is the ribosomal complex?

idk sigh

During translation, what happens at initatioN>

ribosome assembles on mRNA at start codon

what happens at elongation?

ribosome reads each codon
trna with anticodon binds
amino acid added → grows polypeptide chain

ribosome moves to next codon; empty trna exists

termination/

at stop codon completed polypeptide releass

why is gene regulation important?

bc it allows for scientists to control when protein are produced

What is the regulator gene?

encodes the repressor protein

located away from the operon

What is the promoter region?

dna binding site for rna polymerase

where transcription begins

operator region?

control switch for gene expression

represor protein binds to block transcription

what is an inducer?

attaches to reppressor from stoping it to bind to the operator

what is the repressor protein?

make sure the genes are now on

bidngs to the operatios to prevents polymerase from doing its thing

what is the trp operon?

reveals how bacteria efficiently manages amino acid synthesis

what happens when tryptophan is absent?

the mrna codes bc the repressor protein canot bing to operation in its conformation at that moment

trp is abundant so…?

trp molecules bind to repressor protein making it active and then binds to operator region

why is it important to understand point mutation?

imoprtant for precision medicine, gene therapy desing and predicitng disease severity from genetic testing results

what is a point mutation

foudation of genetic diseases from sickle cell anemia to cystic fibrosis

what is a polymerase chain reaction

a molecular photocopier

how did PCR revolutionze medicine?

enabled rapid covid-19 testing, cancer mutation screening, forensic DNA analysis, paternity testing, and detection of infectious dieases from tiny samplesw

what is the starting material for pcr?

DNA? Template dna.

what are pcr tubes/

thin walled plastic tubes containing the reaction mixture

what are primers?

two short sinlge-stranded dna oligonucleotides

where does the forward primer bind?

binds to 3 end od one strand

where does the reverse primer bind?

binds to the 5 end of the complementary strand

what are the dNTPS

the bulding blocks for new dna synthesis

what is TAQ polymerase?

enzyme that synthesizes new dna strands

Where is taq polymerase isolated from?

thermus aquaticus(bacteria living in hot springs)

What does thermostable mean?

survis repeated heating to 95 degrees without denaturing

what are the three steps of pcr?

1. initialization/denaturation - 95 degrees

2. annealing - 72

   1. elongation 72

what temperature does denaturation happen at?95

95

what temp does annelaing happen?

72

what happes during denaturation?

high temp breaks hydrogen bonds between complementary base pairs

dna separates into two single strands

the speratesd template strandS are now abaliable for primer binding