Bio112 Exam 2 part 4

Number of genes don’t determine complexity

Humans and mice have a similar number of genes yet are seemingly different in complexity→why? Mobile elements

Mobile elements

Short segments of DNA present from a few to millions

genes that are transcribed with the only goal to make more of itself

(“selfish genes” “parasitic genes”)

Transposons

1. Can transpose DNA from one location to another

2. two inverted ends→bidirectinal transcription

3. Codes for transposase which binds onto the ends of the gene and cuts out the transposon

4. moves it to a target site and cuts that target site aswell

5. Abuses double streanded break repair→after DNA synthesis→repairs the transposons→transposon is replicated. “cut-and-paste"

Retrotransposon

1. Long terminal repeats

2. produces both a reverse transcriptase and tranposase

3. uses RNA to make cDNA of itself which then gets doubled making dsDNA

4. transposase cuts the genome and inserts this new genome.

“Copy and paste”

Retroposons

1. Codes for endonuclease and reverse transcriptase

2. DNA is directly cut by endonuclease which allows for reverse transcriptase to directly make dna strand into the genome. the complimentary strand is then made. 

3. SImilar to retrotransposon but the cDNA is made directly onto the gene

Insertion of mobile element into a coding gene effects

%5-10 of the time

• If it distrupts orhganism function than natrual selection weeds it out “loss from population”

• If it benifits the organism, the chromosome insertions are fixed with population

• No effect, likely to stay aswell

Insertions away from genes

90-95% are this (sea of mobile elements)

- the insertion are neutral (no effect on the organism).

- the chromosome with the insertion can still become fixed by genetic drift.

Mobile element regulation

Chromatin modification →DNA methylation and histone modification to prevent mobile element expression

RNA→cause Chromatin modification, block transcription, or destroy mRNA transcript.

Not 100% effective, so thats why it accumulates.

Compostion of the human genome

5-10% genes “coding/regulatory”

45% mobile elements- 300k transposons, 450k retrotransposons, 1.5 mil retroposons

50%- Older mobile elements that are older thsn 150 millons years. Unrecognizable and no function. (introns and stuff)

(introns) SnRNP or…

Spliceosome brings the ends of introns together forming a lariot and degrades it.

recognizes 5’-GU…AG-3’ ends 

Exons vs introns length and composition

Exons - 150nt avg, 5% of RNA expressed 10 exons

introns 3330 nt avg longer, 95% of RNA degraded 9 introns

(some genes are 99.7% introns so it varies)

Mobile element size in plants and animals

In animals they’re large because ME insertions can be neutral and they can accumulate

In plants they are typically selected against, so there exists smaller number of ME insertions and therefore smaller introns.

problems with Intron

They waste more energy than mobile elements.

Splicing requires high accuracy\

The required sequences at the ends of introns mean the mutation target site for a gene is larger

Alternative splicing model (model for why genes have introns)

A single gene can produce multiple different messenger RNA (mRNA) molecules and consequently multiple proteins.

This is achieved by selectively including or excluding certain exons (coding regions) from the precursor mRNA

Pros can cons of alt splicing model 

Pros: Easy to explain, already shown to exist in a few genes, lets us feel better about our measly 22k genes, 

Cons: Plants have introns but no alt splice, The level of alt splicing is usally low, Introns appear randomly in genes, intron location varies based on organism, no suggestion for origin of introns

Alternative model (Mobile element II model)

Introns possibly originated from mobile elements, “Self-splicing introns”.

Makes reverse transcriptase and Reverse splices* into DNA and makes a CDNA strand directly in the gene and then makes the second strand.

Behaves like retroposons but self-splices instead of endonuclease, and Splices out of a gene transcript instead of having its own transcript

Pros and cons of mobile group II intron hypothesis

Pros: Spliceosome mechanism is similar to group II introns, Explains the presence of useless DNA (selfish gene), Explains random locations, Explains why all eukaryotes have introns even though many do not use alternative slicing.

Cons: MGII introns are not currently found in plants and animals ,Requires that all current introns lost their ability to self-splice, their ability to encode a reverse transcriptase, and now rely on spliceosomes.

The arguments are not simple.

Peptide vs Protein

Peptide- short, usally single chain, unstructured, hormones, toxins, anitbiotics

Protein- one or more polypeptide chains, can be structured, have other componenets.

Most proteins are made…

in the cytosol 

-some in mito or chloro endosymbioti theory. 

often folding durin protein synthesis

Reason for protein folding

to minimize energy of molecule, one structure is more theormodynamically favorible.

• folds due to inter and intra molecular interactions, H bonds, ionic, disulfide

“central dogma” of proteins

Sequence→structure→function

ex. Lysozome: has an activate that lets the cell wall of bacteria fit in

Levels of protein structure

Primary- single chain

secondary- a-helix b-sheets

teitiary→ flobal fold between pp(disulfide) 

quatenary→multiple protein subunits

A-helix

Minimizes energy →NH+ and COO- groups interactions, forming H bonds (3.6 residue turn)

Beta-strands/sheets

minimizes energy by allowing multiple bdta strands to overlap and for H bonds

Protein structure determination by X-ray crystallography steps

1. Purify the protein

2. Crystalize the protein

3. Collect diffraction data

4. Calculate electron density

5. Fit residue into density

Protein structure by Cryo-EM

Rapid flash freezing →multiple overlapping images used by computer to reconstruct protein structure, →good for bigger molecules

The Anfisen experiment

Wanted to determine if the sequence was the only factor in protein folding.

→unfolded Ribonucelease A using Urea and reducing agent causing it lose structure and function (breaks disulfide bonds)

→when both were removed protein was refolded to original function.

Conclusion:

The information needed for determining the folded (native) structure of a protein is fully contained in the primary sequence. • You should be able to predict the structure of a protein from its sequence

Problem? →likely not gonna happen for larger proteins

Computer prediction intiative (like alphafold) (list pros and describe)

Pros: chepaer faster and better

CASP competition with the protein folding problem

2020-2022 Alphafold with deepmind

won CASP for being better at other programs at predict protein structure.

Used AI and LLM to predict structure based on past similar structures.

Levinthal’s Paradox

if a protein were to sample all possible conformations randomly, it would take longer than the age of the universe to fold, yet proteins fold into their correct structures within seconds.

Protein misfolding reason

Hydrophobic groups of proteins face outwards and clump together forming amorphus aggregates and/or order fibrils

HSP molecular chaperons…

GroEL/GroES

→allows for proteins to fold inside a barrel shaped controled enviorment with no other proteins to cause it aggregate

HSP70 is human version

Do chaperons support or contradict Anf conclusion

They support his conclusion→simply assist the folding process by preventing aggregation or misfolding, ensuring the protein reaches the conformation already encoded by its sequence.

Neurodegenerative diseases and protein misfolding

Alzheimers→Amyloid B and tau 

Huntingtons disease →genetic mutation changes protein folding state

Pathogenic prions form…

Whena normal cellular prion protein (PrPᶜ) misfolds into an abnormal, β-sheet–rich structure (PrPˢᶜ),

which then induces other normal PrPᶜ molecules to adopt the same misfolded conformation,

leading to a self-propagating chain reaction of misfolding and aggregation.