DNA + RNA - Structure, Function, Processes

DNA

DNA

deoxyribonucleic acid; composed of nucleotides

Components of a Nucleotide

• Sugar-phosphate (backbone)

• Nitrogenous base

Functions of DNA

• Controls cell activities (protein synthesis)

• Cell replication through mitosis

• Undergo mutations for genetic diversity (evolution)

  • Typically rare, recessive, random

Okazaki fragments

Short DNA fragments synthesized on the lagging strand during replication, later joined by DNA ligase.

Leading strand

The continuously synthesized DNA strand in the 5' to 3' direction toward the replication fork.

Lagging strand

The discontinuously synthesized DNA strand built in short Okazaki fragments away from the replication fork. (5’ to 3’ direction)

DNA polymerase

The enzyme that adds nucleotides to a growing DNA strand and proofreads for errors during replication.

helicase

The enzyme that unwinds the DNA double helix by breaking hydrogen bonds at the replication fork.

single stranded binding proteins

bind to single-stranded DNA to stabilize it and prevent it from re-annealing or forming secondary structures during replication.

Topoisomerase

relieves the supercoiling and tension in the DNA ahead of the replication fork by cutting and rejoining DNA strands.

transcription

• Synthesis of RNA from a DNA template where the code in the DNA is converted into a complementary DNA code

• Occurs in the nucleus

translation

process by which a cell converts the information encoded in mRNA into a specific sequence of amino acids to form a protein.

• occurs in cytoplasm and on the rough ER: ribosomes read mRNA in codons —> tRNA bring corresponding amino acids to build polypeptide chain —> key steps of translation are: initiation, elongation, termination

wobble pairing

phenomenon in translation where non-standard base pairs form between the 3rd codon position of mRNA and the corresponding anticodon in tRNA. This allows some tRNAs to pair with multiple codons, increasing translation efficiency.

ex: (G) can pair with (U) in the tRNA anticodon

Given the following DNA strand:
5' - ATG GGC TTA - 3'
What is the corresponding mRNA strand and tRNA anticodons?

• mRNA: 5' - AUG GGC UUA - 3'

• tRNA Anticodons: 3' - UAC CCG AAU - 5'

Given the DNA strand:
5' - ATG GGC TTA TAA - 3'
What would happen if the codon "TAA" was replaced with "TAC"? How would this affect the mRNA strand and the resulting amino acid sequence?

• The original mRNA codon for "TAA" would be "UAA," which is a stop codon, signaling the end of translation.

• If "TAA" is replaced with "TAC," the mRNA codon would become "UAC," which codes for the amino acid tyrosine (Tyr).

• Result: The mRNA sequence would change from "UAA" (stop codon) to "UAC" (tyrosine), causing translation to continue/extension of the protein

what direction does DNA polymerase synthesize a strand of DNA?

can only add nucleotides in the 5' to 3' direction. This means it adds nucleotides to the 3' end of the new DNA strand as it builds.

• If the template strand is: 3' - A T G C - 5' DNA polymerase will read it 3' to 5' and add the complementary nucleotides to the growing strand: 5' - T A C G - 3'

RNA Polymerase

enzyme that synthesizes RNA by reading a DNA template during the process of transcription. It unwinds the DNA locally and builds a complementary RNA strand using the DNA sequence as a guide

tRNA (transfer RNA)

• small RNA molecule that helps decode mRNA into a protein by carrying specific amino acids to the ribosome during translation. Each tRNA matches to a codon on the mRNA using its anticodon

• found in the cytoplasm

rRNA (ribosomal RNA)

structural and functional component of ribosomes. It helps align mRNA and tRNA and catalyzes the formation of peptide bonds during protein synthesis.

• formed in the nucleolus

purines

double ringed nitrogenous base

• adenine and guanine

“AG is pure” (silver is pure)

• “AG” —> two letters = double ringed

pyrimidines

single-ringed nitrogenous base

• cytosine, thymine, guanine

“CUT the Py”

mRNA

• single-stranded RNA molecule that carries genetic information from DNA to the ribosome, where it serves as a template for assembling a protein.

Steps of Protein Synthesis

1. Transcription (in the nucleus)

• DNA —> mRNA. RNA polymerase builds mRNA, introns are removed, and a cap/tail are added

2. Translation (cytoplasm)

   • Ribosome reads mRNA, tRNA delivers amino acids, and a polypeptide is built. Process ends at a stop codon

After these steps, the polypeptide folds into a functional protein; modifications may occur

Start codon

AUG

Purines always match with a...

Pyrimidine (Adenine pairs with Thymine, Guanine pairs with Cytosine in DNA).

Chromosome

threadlike structure made of DNA and proteins that carries genetic information. Humans typically have 46 chromosomes (23 pairs) in each cell.

Chromatin

complex of DNA and histone proteins found in the nucleus of eukaryotic cells. It condenses to form chromosomes during cell division.

histone proteins

Proteins around which DNA winds to form chromatin. They help package DNA into a compact structure and play a role in gene regulation.

Sugar-Phosphate Backbone

structural framework of nucleic acids (DNA and RNA), made up of alternating sugar (deoxyribose in DNA, ribose in RNA) and phosphate groups. It provides structural stability to the nucleic acid chain.

Primase and its role

• enzyme that synthesizes RNA primers during DNA replication

• provides a starting point for DNA polymerase to begin synthesizing the new DNA strand.

topoisomerase vs. single-stranded binding proteins (SSBs)

Topoisomerase: enzyme that prevents DNA from supercoiling by creating temporary cuts in the DNA strand to relieve tension

SSBs: Proteins that bind to single-stranded DNA to keep it from re-annealing or degrading during replication.

supercoiling and topoisomerase

Supercoiling: overwinding or underwinding of the DNA double helix, causing tension.

Role of topoisomerase: prevents supercoiling by cutting and rejoining DNA strands, allowing the DNA to unwind without becoming too tangled

why does primase have to be replaced?

Primase adds RNA primers to initiate DNA replication, but these primers are later replaced by DNA nucleotides.

• RNA primers are short-lived, and DNA polymerase cannot start replication without them, but they are not part of the final DNA sequence, so they need to be replaced with DNA.

when does dna replication occur?

occurs during the S phase of the cell cycle, before a cell divides (either mitosis or meiosis).

where does replication occur?

ccurs in the nucleus of eukaryotic cells and in the cytoplasm of prokaryotic cells (since they lack a nucleus)

ribosomal subunit (small and larger)

Anticodons

sequence of three nucleotides in tRNA that is complementary to a codon in mRNA. The anticodon allows the tRNA to match with the correct codon during translation to ensure the proper amino acid is added to the growing polypeptide chain.

• example: if the mRNA codon is AUG, the tRNA anticodon would be UAC

both RNA polymerase and DNA polymerase synthesize their respective strands in what direction?

5' to 3' direction

What is the first step in transcription initiation?

Transcription factors bind to the promoter region of DNA.

What is the promoter in transcription?

a specific sequence of DNA that signals the start of a gene and where RNA polymerase binds to begin transcription.

What role do transcription factors play in transcription?

proteins that help RNA polymerase bind to the promoter region of the gene to initiate transcriptio

function of RNA polymerase in transcription

the enzyme that synthesizes RNA by reading the DNA template strand and adding complementary RNA nucleotides.

How does DNA unwind during transcription?

RNA polymerase unwinds a small section of the DNA double helix to expose the template strand for RNA synthesis.