Ch 4



BB 2 - DNA to protein synthesis 



Grifths experiment 1928

  • Showed genetic material could be passed between organisms 

  • OTHER experiments showed it was genetic material 


Streptococcus pneumoniae- a disease caused in human and mice, used in experiments. Has different strands smooth and rough.  


Smooth- made smooth-looking colonies - Protective capsule 

  • smooth have a capsule, that protects the colonies. The capsule protects bacteria from hosts immune system 

  • Griffith noticed mice infected with live S strain, died

  • -While Heated killed s strain mice  survive d


Rough colonies looked rough, with no capsules. 

  • Griffith noticed mice survived, were harmless to mice 



He killed S strain MIXED  live R strain, mouse died. G was surprised 

  • He looked  at bacteria from mouse blood, found live S bacteria. But they did not come back to life Instead, The R picked up genetic material from the S to create the capsule, and created disease. Shows genetic material can be passed between bacteria, called “ - - G called it transformation in micriobiology 

  • Did not prove dna was what made us, only provided that genetic info could be passed between bacteria, took another 25 years with watson crick 



James Watson and Francis crick structures or DNA in 1953, won Nobel prize 

  • Built on the work of rosalind franklin



Rosalind Franklin helped use x ray diffraction, and helped determine structure of dna 


DNA and RNA Made of nucleotides, which are subunits, composed of- 

  1. base (adenine, uracil, thymine, cytosine, guanine) (

  2. Sugar (purple) 

  3. Phosphate (yellow) 



Sugar-Phosphate backbone, what it’s know as  on both sides, bases are in the middle, attached by hydrogen bond


 


GC have 3 hydrogen 

AT have 2 hydrogen bonds 


Sugar in DNA is called deoxyribose 




  • chromosomes are primarily composed of histones and DNA

  • - histones are primarily structural for condensing the dna


Duplicated chromosome ^ 


Chromosomes are made of Chromatin- DNA double helix + protein 

  • Protein cluster- histone, dna wraps around them and is compressed to create chromatin 



Ribose has an extra oxygen, Deoxyribonucleic acid  for DNA (lacking 1) 


DNA and rna can create a hybrid , a bonds with u 



RNA is single stranded, still has phosphate, sugar and base 





**DNA replication, known as semi conservative. 

  • double stranded dna pulls apart,  by the breaking of hydrogen bonds, 2 strands are created parental and the newly synthesized strand,  parental act as templates 

  • If theres a g there will be a c, if theres a T there will be a an a 

  • Dna polymerase an enzyme that copies DNA, reads template strain and adds the appropriate nucleotid



Dna double helix replication before ell division creates sister chromatid. Sister chromatid aare separated during cell division


Mutations - changes in dna sequence

  • during replication- wrong base pair put in during replication 

  • Exposure to physical or chemical agents, known as mutagens 



Uv light is a mutagen 

  • cause bulge in backbone of dna, enzymes scan through and replace it 

Xeroderma pigmentosum - recessive autosomal disorder ; dna cannot repair damage from uv light 




Start of chapter 5 Lec 1 - gene expression and regulation 


Genetic info in the dna is stored in the sequence of the nucleotides


Expression (taking info and creating a protein)  of a gene involves transcription and translation 


 Proteins are the link between genotype and phenotype 


Proteins have diverse functions

  • Structural (collagen, keratin) 

  • Enzymes (lactase which breaks down lactose ) 

  • Hormones (insulin, human growth)

  • Receptors (acetylcholine receptors in the nervous system help with muscle contraction)

  • Movement (myosin, muscle contraction)



Chemica structure of amino acid 


Building block of dna is nucleoid, building block of protein is an amino aicd 




Amino group, nitrogen w/ 2 hydrogens.(-NH2)

 carboxyl grouop,  Carbon, 2 oxygen, and hydroxide (-COOH)

Alpha carbon - central carbon

Hydrogen - attached to alpha carbon


R group - varies between every 20 amino acid, what makes amino acid unique, 



Polypeptide is a chain of amino acids that are attached by peptide bonds 

Amino acid joined together known as peptide bond 

  • Polypeptide is not functional protien structure depends on the shape, determines the function. Enzyme will not function correctly if not folded correctly. Shape is very important 




Flow of genetic info in a cell- central dogma of biology PIC

DNA (transcription occurs within nucleus) > mRNA> (translation, happens in cytoplasm) protein 



4 nucleotides that incode info for all 20 amino acid (A,T,G,C), unique due to R group 


Sequence of 3 nucleotides or a Codon encodes a specific amino  acid

Order of nucleotides in Dna, than RNA, determines order of amino acids in the protein 


Part one of central dogma of bilogy : transcription

  • When info from dna is transcriped/ copied into messenger RNA, happens in nucleus 

  • What converts dna to mRna is RNA polymerase (compared to DNA polymerase that copies dna to dna)

  • RNA polymerase uses DNA as a template to create complementary (complememtry in terms of sequence of a,t,g,c’s)  Mrna 



Transcription step- 


Initiation- RNA polymerase finds the start of a gene (gene what encodes protein) 

  • at the start of every gene Promoter sequence where RNA polymerase attaches to DNA to begin transcription 

  • Termination sequence - How RNA polymerase knows to stop transcribing 

Elongation- DNA double helix is broken apart by their hydrogen bonds (blue and yellow)

  • RNA polymerase uses yellow strand as the template, tells enzyme what nucleotide to the newly made RNA 

  • mRNA and all RNA contains U instead of thymine. If there is an A a uracil is ut there, “complemtry strand”  Pre mRNA transcript. 

Termination- pre mRNA, end of transcription 


Completed pre mRNA is released, but…



Modifications mRNA is modified in 2 ways before going to the cytoplasm 


 In eukaryotic only, mRNA is modified before being translated which occurs in the nucleus 

mRNA in red, protein coding segment which is the info to make protein, bordered by start and stopped codon 

  • Two sequences are added to the ends of mRNA before leaving nucleus 

    • 5’ (Prime) cap- facilitates mRNA binding to  ribosome (where translation occurs) 

    • 3’ (prime) tail- protection from enzymes, allows export to nucleus into cytoplasm, where translation takes place 



 In eukaryotes, parts of the mRNA need to be removed before translation, known as Introns “in” for interfering sequence 

  • Introns are inbetween exons, which is the expressed sequence

  • Part that encodes the protein 

  • Introns are structural, but need to be removed, dont make sense 

  • Introns need to be removed so exons can be pierced together. After it would than be an mRNA transcript that can be translated in the cytoplasm into protein 


- summary- what happen to pre mRNa after transcription> 5’Cap & 3’cap added> introns removed, so exons can fuse



Lecture 2- 


Previously, Flow of genetic information- central dogma of biology. DNA contains genetic information and during transcription dna is converted to mRNA. Happens in nucleus, after, pre mRNA is processed in the nucleus (2 processes) . In rhe cytoplasm mRNA is converted to protein in the process of translation 


Part two translation- mRNA> protein, in the cytoplasm


  • Translation involves ribosome (site of translation) mRNA from transcription, tRNA (transfer), pool of free amino acids in the cytoplasm 


Each amino acid is encoded by a codon (3 nucleotides) 


3’ is the parent strand

RNA is single stranded 


First two letters are same, last letter differs

  • AUG in the start codon methionine,


  • 3 Stop codons signal end of translation, dont code for anything  



tRNA has double stranded regions (rna is single, tRNA has complimentary base pairs ), allowing to form 3d shape known as clover leaf shape, which is important for function 

Important region- where amino acid can attach and anti codon 


Accurate translation requires two things 

  1. Correct match between tRNA and amino acid 

  2. Correct match between tRNA anticodon and codon in the mRNA. Anticodon is complementary to the codon 



Initiation of translation- occurs in cytoplasm, on the ribosome 

  • Ribosomes on rough ER and in cytoplasm are both sites of translation

  • Ribosome clamps on mRNA after leaving nucleus> Aug tells tRNA that it needs a methionine as the first amino acid> tRNA brings amino to the ribosome

  • Anti codon on tRNA must be complimentary to the mRNA 


Elongation - polypeptide starts to form 

  • Second tRNA enters ribosome complex carrying the second amino acid 



Termination- translation terminates when the ribosome gets to the stop codone in the mRNA

  • Tells ribosome to stop and dissociate from the mRNA. Abd to release the polypeptide and mRNA

  • Horizontal line is the mRNA, vertical lines are the polypeptide/ string of amino acid


Polypeptide vs functional protein 

  • Shape of protein is important

  • Polypeptide is just a string of amino acids, does not equate to a functional protein. Must be folded into correct shape to be functional protein


What determines protein structure?

  • Primary amino acid sequence 

  • Physical and chemical environment (ph, temp, salt concetration, etc)

Denaturation- protein unfolds into a non functioning protein when conditions are not ideal, but if environment becomes favorable again



Primary structure- determined from inherited genetic info. Comes from the sequence of the codons in DNA and RNA determine sequence of amino acid in protien 



Secondary  strcuture- where protein folds,  either Alpha helix held by hydrogen bond between amino acid. Or beta pleated sheet also held by hydrogen bonds 

  • Different from peptide bonds, which holds amino acid as a back bone. These one are between amino acids and different parts of the protein 



Prions - importance of secondary 

  • Prions neurogenerative disease ex. Mad cow

  • Caused by a misfolfed protien, mostly alpha helix

  • If protein is misfolded (more beta) sticks, cause big clumps of protien 



Tertiary structure- 3D shape stabilized by different bonds between amino acid R groups

  • R groups what makes amino acid different.

  • Can be neg/pos charged, acidic/ basic 

  • Creats bonds between r groups, that folds protein into 3d shape 



Quaternary structure - association of multiple protein subunits

  • Hemoglobin. Carries oxygen in red blood bells, made of 4 protein sub-units in quaternary structure 




Summary of gene expression- 


DNA (Transcription ex. Oral to written comms:, dna read by RNA polymerase, becomes trancribed into..)> mRNA> mRNA becomes modified 2x ways> exported into cytoplasm where it interacts with ribosome and tRNA that carriers amino acids> translation of mRNA to polypeptide > polypeptide folded to become functional 



















CH5 L3- gene expression and regulation


Gene expression is controlled on/off

  • Almost are genes are off most of the time

  • 5-10% of the genes are being expressed (transcribed and translated i to protein)

  • Genes expressed contribute to phenotype 

  • Ex. liver cell is different from nueron, even tho they have the same set of genes (same dna, different phenotypes because of which genes are expressed)


Regulation at transcription- in the nucleus 



  1. Degree of chromatin condensation- determines which genes are transcribed and whats not 

  • Euchromatin- expressed region, available for transcription (newmonik “U are expresed”)

  • Heterochromatin- not expressed, not available for transcription. Telomere and centromere is heterochromatin

  • Degree of condensation - how tightly dna is wrapped around histone. Euchromatin is more loosely wrapped. 


  1. Chemical modification of histone - can loosen the dna, promoter becomes accessible. Heterochromatin > euchromatin  




  1. DNA methylation- Chemical modification of the Nucleic acid bases at the promoter region 

  • Dna methylation is a mechanism of gene inactivation 

  • Cytosine can get a Methyl group (Ch3) to the carbon 5. Masks promoter region, inactivates promoter region  

  • Ex. x inactivation if female mammals, epigenetic regulation 

  • X INACTIVATION



Regulation in translation 






  1. RNA interference (miRNA and siRNA micro/small interfering)

  • MicroRNA - blocks translation by binding to target mRNA sequence, Almost complementary to target mRNA. Method of silencing the mRNA so no protein is made

  • Small interfering RNA- Binds to mRNA and cuts it into pieces, by enzyme called Dicer 

  1. Changes in rate of initiation of protein synthesis 

  2. Post-translational regulation can also occur (protien degradation 



Ch5 L4


How altered protein results in genetic disorder


  • A Single nucleotide change can lead to a nonfunctional protein 

    • Can leads to changes in phenotype 

    • Changes in dna sequence are mutations 

  1. Change in dna sequence > misfolded protein 




  • Cystic fibrosis (autosomal reccessive)- 

    • Most common mutation- deletion amino acid 508 (Delta, F508) in the CFTR gene

      • CFTR protein, creates channels in membrane of cell. CFTR channel transports chroide ions out of the cell, fluids like water follow. Focus on Ion concentration regulation. Important in lungs and intestines. 

      • Missing cftr causes build up of sticky mucus outside the cell leads to the symptoms of CF

      • Missing DeltaF508(not always caused this way)  causes protien to be misfolded, Misfolded proteins are often marked for destruction 




  • Ubiquitin a chemical modifer,  Tags/Attatches to misfolded protein. Directs misfolded protein to the Proteasome complex, which is full of enzymes, Proteasome and ubiquitin are recycled, protein fragments (peptides) remain 

- Misfolded protein can accumulate and lead to disease, if theres issues with the ubiquitin and proteasome processes. Alzhiemers, ALS, varianceCJD





  1. Change in dna seq> shortened (truncated) protein 

  • Familial hypcholesterolemia (FH, autosom dom) FH gene encodes the LDL (low density lipoparticle “bad”,  compared to High which is good)  protein, a cholesterol receptor 

  • Mutation in the FH gene introdocues a premature stop codon in the middle of the polypeptide, translation stops early, result is in complete protein 




  • LDL receptor present in the membrane of the cell, receptor for LDL, takes extra LDL cholesterol and brings it into the cell for recycling. Helps remove excess bad cholesterol. 



  • Since LDL cant be removed, excess cholesterol causes plaque build up in the artery, narrows the arties. High risk of heart attack, especially in homo/ heterozygotes 

    • Homozygotes are rare, fatal early in life since they have none of 

    • the receptor. Homozygotes have some functional receptor 




  1. Change in dna seq> non functional protein 


  • Sickle cell anemia (autosom recc) - mutation occurs in the gene that encodes hemoglobin. Hemoglobin helps carry oxygen throughout the body



  • HEMGLOBIN is the misfuntioming protein, caused my SINgle codon change 

  • GLU IS CHANGED to VAL CASING IT TO BE MISFUNTIONAL 

  • Protein becomes folded incorrectly, pic below