DNA and RNA

Question 1

Double Helix

Answer 1

DNA is composed of two strands that coil around each other

Question 2

DNA Sugar-Phosphate Backbone

Answer 2

Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups

Question 3

DNA Nitrogenous Bases

Answer 3

○ Adenine (A)
○ Thymine (T)
○ Cytosine (C)
○ Guanine (G)

Question 4

DNA Base Pairings

Answer 4

A-T Pairing : 2 hydrogen bonds
C-G Pairing : 3 hydrogen bonds
Antiparallel strands: both run in opposite directions (5’ to 3’ and 3’ to 5’)

Question 5

Single strand

Answer 5

RNA is typically single stranded

Question 6

RNA Sugar-Phosphate Backbone

Answer 6

Each strand has a backbone made of alternating sugar (ribose) and phosphate groups

Question 7

RNA Nitrogenous Bases

Answer 7

○ Adenine (A)
○ Uracil (U)
○ Cytosine (C)
○ Guanine (G)

Question 8

RNA Base Pairing

Answer 8

● A-U Pairing: two hydrogen bonds.
● C-G Pairing: three hydrogen bonds.
● Single Strand with Secondary Structures: RNA can fold into complex shapes allowing it to have structural and catalytic
functions.

Question 9

What are the 4 types of RNA and their functions

Answer 9

● mRNA (Messenger RNA): Carries genetic information from DNA to the ribosome
● tRNA (Transfer RNA): Brings amino acids to the ribosome during protein synthesis.
● rRNA (Ribosomal RNA): Forms the core of the ribosome’s structure and catalyzes protein synthesis.
● miRNA (Micro RNA): Involved in regulating gene expression by interfering with mRNA

Question 10

Difference between stability of DNA and RNA

Answer 10

○ DNA: More stable due to its double-stranded structure and the presence of deoxyribose.
○ RNA: Less stable, more reactive due to the presence of ribose and single-stranded nature.

Question 11

What are Purines

Answer 11

Double-ring structure (Adenine (A) and Guanine (G))

Question 12

What are Pyrimidines

Answer 12

Single-ring structure (Cytosine (C), Thymine (T), and Uracil (U))

Question 13

What is the melting temp and what are the factors that influence it

Answer 13

= The temperature at which half of the DNA molecules in a sample become single-stranded (denatured)
Factors :
○ Base Composition: Higher GC content increases Tm because G-C pairs form three hydrogen bonds, compared to two
hydrogen bonds in A-T pairs.
○ Length of DNA: Longer DNA strands have higher Tm.
○ Ionic Strength: Higher salt concentration stabilizes the DNA helix and increases Tm.
○ pH: Extreme pH values can destabilize hydrogen bonds, lowering Tm.

Question 14

5’ End def and function

Answer 14

● Definition: The end of the nucleic acid strand that has a free phosphate group attached to the 5’ carbon of the sugar.
● Function: Important for processes like DNA replication and RNA transcription initiation. Enzymes recognize the 5’ end to start
these processes.

Question 14

3’ End definition and function

Answer 14

● Definition: The end of the nucleic acid strand that has a free hydroxyl (OH) group attached to the 3’ carbon of the sugar.
● Function: Critical for the addition of new nucleotides during DNA replication and RNA synthesis. DNA polymerase and RNA
polymerase add nucleotides to the 3’ end.

Question 15

DNA Forms

Answer 15

B-DNA
A-DNA
Z-DNA

Question 16

B-DNA

Answer 16

most common and right handed helix
-10 base pairs per turn
-Major and minor grooves are distinct and easily identifiable

Question 17

A-DNA

Answer 17

right hand helix, shorter and more compact than B-DNA
-11 base pairs per turn
-Major grooves are deep and narrow, while minor grooves are shallow and broad
Found in dehydrated conditions and some hybrids

Question 18

Z-DNA

Answer 18

left-handed helix
-12 base pairs per turn.
-zigzag backbone gives it a distinctive appearance.
Can form transiently in regions of DNA that are being actively transcribed and don’t know what it does

Question 19

Major Groove

Answer 19

○ Definition: The larger of the two grooves that spiral around the DNA double helix.
○ Function: Provides a binding site for proteins, such as transcription factors, which can read the base sequence and
regulate gene expression

Question 20

Minor Groove

Answer 20

○ Definition: The smaller groove of the DNA double helix.
○ Function: Also serves as a binding site for certain proteins and drugs, but it is less accessible than the major groove
due to its size.

Question 21

Persistence Length

Answer 21

Measure of the stiffness of a polymer chain, such as DNA. It is the length over which
the direction of the polymer backbone becomes correlated with itself.
For DNA the persistence length is approximately 50 nm or about 150 base pairs (bp)

Question 22

Gene

Answer 22

○ Definition: A sequence of nucleotides in DNA that is transcribed to produce a functional RNA.
○ Function: Contains the instructions for building proteins and functional RNA molecules.

Question 23

Promoter

Answer 23

○ Definition: A sequence of DNA where RNA polymerase and associated transcription factors bind to initiate
transcription.
○ Function: Initiates transcription of a gene.

Question 24

Operator (prokaryotes)

Answer 24

○ Definition: A segment of DNA to which a repressor binds, regulating the expression of genes in an operon. ○ Function: Controls the transcription of adjacent genes.

Question 25

Enhancer/Silencer (eukaryotes)

Answer 25

○ Definition: Short regions of DNA that can be bound by proteins (activators or repressors). ○ Function: Increases (enhancer) or decreases (silencer) the likelihood of transcription of a particular gene.

Question 26

Terminator

Answer 26

○ Definition: A section of nucleic acid sequence that marks the end of a gene or operon during transcription. ○ Function: Signals the end of transcription.

Question 27

5’ / 3’ UTR

Answer 27

○ Definition: Untranslated regions at the 5’ and 3’ ends of an mRNA. ○ Function: Regulate mRNA stability, localization, and translation efficiency.

Question 28

Exon

Answer 28

○ Definition: A segment of DNA or RNA containing coding information for protein synthesis. ○ Function: Codes for amino acids in the protein.

Question 29

Intron

Answer 29

○ Definition: A non-coding segment of DNA or RNA that is removed during RNA processing. ○ Function: Allows for alternative splicing, increasing protein diversity.

Question 30

Poly-A tail

Answer 30

○ Definition: A stretch of adenine nucleotides at the 3’ end of an mRNA molecule. ○ Function: Enhances the stability of mRNA and facilitates its export from the nucleus.

Question 31

Prokaryotic Genome size

Answer 31

around 4300

Question 32

Eukaryotic Genome Size

Answer 32

varies from 6000 to 20000

Question 33

Nucleosome

Answer 33

○ Definition: The fundamental unit of chromatin, consisting of DNA wrapped around a core of histone proteins. ○ Function: Compacts DNA to fit within the nucleus and regulates access to DNA for transcription, replication, and repair

Question 34

Regulatory structures in Eukaryotes

Answer 34

● Promoters: bind transcription factors and RNA polymerase to initiate transcription. ● Enhancers/Silencers: to modulate transcription levels by increasing (enhancers) or decreasing (silencers) the likelihood of transcription. ● Transcription Factors: proteins that bind to specific DNA sequences to regulate transcription.

Question 35

Regulatory structures in Prokaryotes

Answer 35

● Operons: =Clusters of genes transcribed as a single mRNA molecule, regulated together. used to coordinate the expression of genes with related functions. ● Promoters: sites where RNA polymerase binds to start transcription. ● Operators: regions where repressors bind to inhibit transcription.

Question 36

mRNA Structure and Function

Answer 36

● Structure: ○ 5' Cap: Protects mRNA from degradation and assists in ribosome binding during translation. ○ Coding Region: Contains the nucleotide sequence that is translated into a protein. ○ 3' Poly-A Tail: Enhances mRNA stability and regulates its export from the nucleus. ● Function: Carries genetic information from DNA to the ribosome, where it is translated into a protein.

Question 37

what is mRNA splicing

Answer 37

process by which introns are removed from the pre-mRNA transcript, and exons are joined together to form a mature mRNA molecule that can be translated into a protein

Question 38

What are the 4 steps of mRNA splicing

Answer 38

1. Transcription: ○ Pre-mRNA is synthesized from a DNA template in the nucleus. 2. Spliceosome Assembly: ○ Spliceosome: A large RNA-protein complex composed of small nuclear RNAs (snRNAs) and small nuclear ribonucleoproteins (snRNPs). ○ The spliceosome recognizes specific sequences at the intron-exon boundaries (splice sites). 3. Splicing Process: ○ Branch Point: specific adenine nucleotide within the intron that plays a critical role in splicing. ○ Cleavage and Ligation: 1. The spliceosome cleaves the 5' end of the intron (at the 5' splice site) and attaches it to the branch point, forming a lariat structure. 2. The 3' end of the intron is then cleaved (at the 3' splice site) and the two exons are ligated together. 4. Release of Spliced mRNA: ○ The mature mRNA, now devoid of introns, is released from the spliceosome.

Question 39

What is the importance of mRNA splicing

Answer 39

1. Gene Expression Regulation: ○ Splicing allows for the regulation of gene expression by determining which exons are included in the final mRNA transcript. 2. mRNA Stability and Export: ○ Proper splicing is essential for the stability of mRNA and its export from the nucleus to the cytoplasm for translation.

Question 40

Exons

Answer 40

○ Definition: Coding regions of a gene that are expressed in the final mRNA product. ○ Function: Code for the amino acid sequence of a protein.

Question 41

Introns

Answer 41

○ Definition: Non-coding regions of a gene that are removed during RNA processing. ○ Function: Allow for alternative splicing, which can generate multiple protein variants from a single gene

Question 42

Alternative Splicing

Answer 42

○ Definition: The process by which different combinations of exons are joined together to produce multiple mRNA variants from a single gene. ○ Function: Increases protein diversity and allows for regulation of gene expression

Question 43

tRNA Structure and Function

Answer 43

● Function of tRNA: ○ Transfer Function: Transports specific amino acids to the ribosome during translation. ○ Role in Translation: tRNA molecules match their anticodons with the codons on the mRNA strand, facilitating the assembly of amino acids into a polypeptide chain. ● Anticodon: ○ Definition: A sequence of three bases in tRNA that is complementary to a codon in mRNA. ○ Function: Ensures the correct amino acid is added during protein synthesis by matching the tRNA anticodon with the appropriate mRNA codon.