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Pyrimidines Properties

Pyrimidines Properties

C, T, U, Polar, Soluble in water

Purines Properties

A, G, Water Soluble but less

What are receptors

Protein molecules that receive and respond to signals

Two types of nucleic acids

RNA and DNA

Nucleic acid structure

Made up of 3 monomers: Phosphate group, 5 carbon sugar, Base Group (Nitrogenous Base)

DNA and RNA sugars

DNA: Deoxyribose (one less oxygen), RNA: Ribose (additional hydroxyl group) DNA more stable, RNA less stable more reactive

DNA Base Groups

Adenine, Thymine, Cytosine, Guanine

RNA Base Groups

Adenine, Uracil, Cytosine, Guanine

Assembly of Nucleic Acids

Phosphate group bonds to 5-carbon sugar of another monomer (sugar-phosphate backbone) (phosphodiester bond). 5’ attaches to the phosphate group and 3’ attaches to the next nucleotide) Aka 5’ to 3’

RNA Structure

Single stranded nucleic acid

DNA Structure

Double-stranded nucleic acid. Two strands are connected by hydrogen bonds connecting between two base groups. One strand runs from 5’ to 3’ while the complementary runs 3’ to 5’

Why prokaryotes and eukaryotes need to respond to external signals

Cells need to respond to coordinate responses to environments, share resources, and respond to change

Direct intercellular signaling

Signals pass directly through cell junctions

Contact-dependent signaling

Requires cells to touch

signals bind to receptors on adjacent cells

Autocrine signaling

Cells send signals to themselves and nearby cells

Paracrine signaling

Signals affect nearby cells and do not last long

Endocrine signaling

Long-distance signals, such as hormones, spread through the bloodstream

Surface receptors

Located on the cell membrane for large, polar molecules

Intracellular receptors

Inside the cell for small, hydrophobic molecules

Stages of cell signaling -

1. Reception

2. Transduction

3. Response

Reception

Ligand binds to a receptor

Transduction

Relay molecules carry the message without the actual signal

Response

Activation of cellular response, often from the nucleus

Why do cells respond to certain signals while others do not

Specific receptors on cells determine their response to certain ligands

Role of Transcription Factors

Transcription factors are proteins that bind to specific DNA sequences to control the transcription of genetic information from DNA to mRNA. In cell signaling, they are often the end-point effectors of signal transduction pathways, activating or repressing genes in response to a signal

Experiment of Wattson and Crick

Described double helix using Chargaff’s rules and Franklin’s X-Ray Data

Franklins experiment

Showed that DNA is a 3D structure

Chargaff’s Rules

A=T G=C

Griffiths Experiment

Worked w/ R & S cells (strains of bacteria). Transformed R cells into S cells. Show that genetic info could be transferred

Avery’s Experiment

Breaks down DNA, RNA, Protein, etc. Showed you need intact DNA to transform R cells into S cells

Meselson and Stahl’s Experiment

WATCH VIDEO Grew e-coli in a heavy nitrogen isotope, then switched to a lighter one. After replication, DNA was analyzed, and the results supported the idea that each new DNA molecule consists of one old and one new strand. Fed them a heavier isotope and they followed the Semi-Conservative model

What way does DNA polymerase synthesize

5’ to 3’

Helicase

Unwinds DNA double helix

Primase

Lays down RNA primers

DNA Polymerase III

Extends the DNA from the RNA primer

DNA Polymerase I

Replaces RNA primers w/ DNA

DNA Polymerase II

Responsible for transcribing the mRNA from eukaryotic protein-coding genes

Template/Coding strand

The template is used in RNA synthesis, Coding is the one opposite to the template

Ligase

Joins Okazaki fragments on lagging strand

Leading strand

Continuous

Lagging strand

Synthesized in short Okazaki fragments

Replication bubble

Be able to draw this bro

Why is DNA repair Important?

Is DNA repair random?

No, If it was random then it would increase our mutations

Mismatch repair

Proofreading from DNA polymerase

Base Excision Repair

Removes and replaces damaged bases

Central Dogma

Refers to the steps of gene expression at the molecular level: DNA is transcribed into mRNA, and mRNA is translated into a polypeptide

Gene

A unit of heredity. At the molecular level, a gene is an organized unit of base sequences in a DNA strand that can be transcribed into RNA and ultimately results in the formation of a functional product

Promoter

A sequence of DNA within a gene that controls when and where transcription begins

Terminator

A sequence of DNA within a gene that specifies the end of transcription

Transcription steps -

1. Initiation: Recognition step

   1. Sigma factor (prokaryotes only) binds to the base sequence of a promoter causing RNA polymerase to bind there

      1. In Eukaryotes primary factors bind to the promoter and then recruit RNA polymerase II, forming a pre-initiation complex w/ 5 transcription factors which then unwinds the DNA to initiate transcription

      2. In Eukaryotes, RNA polymerase II requires 5 transcription factors to initiate transcription

   2. Stage is completed when DNA strands are separated near the promoter forming an open complex

2. Elongation: RNA strands or polypeptides are made

   1. RNA polymerase slides along the DNA while still maintaining an open complex

   2. DNA is used as a template strand for RNA synthesis

   3. Coding strand has same sequence of bases as the resulting mRNA

      1. Except for the fact that the RNA has Uracil instead of the Thymine found in RNA

   4. Nucleotides bind to the template strand and are covalently connected in the 5’ to 3’ direction

   5. Behind the open complex DNA is rewound into a double helix

3. Termination: RNA dissociation from DNA

   1. RNA polymerase reaches a termination sequence causing itself and the RNA transcript to dissociate from the DNA

Translation steps

Done by ribosome, helped by tRNA and rRNA, builds proteins out of amino acids

1. Initiation

   1. Small subunit binds mRNA

   2. Scan for start codon (AUG)

   3. Brings in first tRNA

2. Elongation

   1. Large subunit joins

   2. Brings in tRNAs w/amino acids

   3. Read 3 at a time by a new tRNA every time

   4. Brings in an amino acid adding to a longer chain of amino acids

3. Termination

   1. Stops at stop codon

RNA Modifications in Eukaryotes

Capping (5’), Tailing (3’)

Splicing

In eukaryotes, splicing removes non-coding sequences (introns) from pre-mRNA, leaving only coding regions (exons) in the mature mRNA. This process is carried out by the spliceosome, a complex of proteins and RNA

Why is splicing important?

Increases diversity of proteins you can get from 1 gene

Genetic Code

Set of Codons that correspond to amino acids. Be able to draw out

Codons

A codon is a sequence of three nucleotides in mRNA that specifies an amino acid or a stop signal during translation. Each codon is matched with an amino acid by the tRNA's anticodon

Start Codon

AUG

Transfer RNAs (tRNAs)

tRNAs are crucial for translating mRNA sequences into proteins. They serve as adaptors, carrying specific amino acids to the ribosome and matching them with the appropriate codons in the mRNA through complementary base-pairing

Charging RNAs

“Charging” tRNAs is the process by which a tRNA molecule is linked to its corresponding amino acid. This reaction is catalyzed by a family of enzymes known as aminoacyl-tRNA synthetases

Ribosomes

Composed of ribosomal RNA (rRNA) and proteins, the ribosome facilitates mRNA translation into protein. It has two main subunits (large and small), each involved in coordinating tRNA binding and peptide bond formation

Promoter

A sequence of DNA within a gene that controls when and where transcription begins

Terminator

A sequence of DNA within a gene that specifies the end of transcription

Spliceosome

A complex of several subunits known as snRNPs that removes introns from eukaryotic pre-mNRA

1. First two snRNP’s bind to the 5’ splice site and branch site

2. Then additional snRNP’s bind to 3’ splice site and other locations to create a loop

3. 5’ splice site is cut, 5’ end is then covalently attached to branch site

4. Then 3’ splice site is cut, and exon 1 and 2 are attached

Silent Mutation and effect on protein structure

A change in a nucleotide that does not alter the amino acid sequence of a protein due to the redundancy of the genetic code. Typically has no effect on protein function or structure.

Missense Mutation and effect on protein structure

A single nucleotide change that results in the substitution of one amino acid for another in the protein sequence. The effect on protein structure depends on the properties of the substituted amino acid and its location in the protein.

Nonsense Mutation and effect on protein structure

A nucleotide change that converts an amino acid codon into a stop codon, leading to a prematurely truncated protein. This often results in a nonfunctional protein.

Frameshift Mutation and effect on protein structure

An insertion or deletion of nucleotides that changes the reading frame of the gene. This mutation alters all downstream amino acids, often resulting in a completely nonfunctional protein.