Lecture 4: Proteins (Part 2) Flashcards Preview

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What determines tertiary structure?

- Side chain interactions:
• H-bond between side chain and carbonyl group on backbone as well as an H-bond between two side chains
• Hydrophobic interactions + van der Waals interactions between side chains - SUPER IMPORTANT
• Disulfide bridges (covalent bonds)
• Ionic Bonds


Disulfide bridge

- only occurs with cysteine (has SH group)
- Two SH groups come together to form a disulfide bridge
disulfide bridge:
- stabilize types of proteins (ex. alpha helixes in your hair)
- getting a perm involves breaking down the D>B in your hair, then reforming them.


Hydrophobic interactions

- very important for protein folding
- has hydrophobic amino acids (red) and hydrophilic amino acids (blue)
- the red part of hydrophobic amino acids will arrange in the interior (the major driving forces that enable folding)


Coiled Coils

- arise when two α-helices have hydrophobic amino acids at every 4th position (one complete turn 3.6 amino acids)
- Fibrous structural proteins consist mainly of α-helices arranged as coiled coils, such as the keratins in hair and feathers.


Diversity of tertiary structures

- Very diverse
- The larger the protein, the more likely you’ll find a mixture of both alpha helixes and beta pleated sheets
- Can be just helices, or just sheets or a mixture of both
- D.B connect helices and sheets together


Cro Protein

- a dimer
- sometimes proteins aren’t functional on their one, so they. Must form a dimer
- Polypeptide not yet functional, so two must come together
- Ex hemoglobin is a tetramer (made up of 4 different polypeptides- can all fold independently)
- This is called quaternary structure


Amino Acid sequence

ex. sickled cell anemia
• Normal red blood cell:
• Sickles red blood cell:
- one amino acid can be mutated, which affects the folding and the
- Common in African populations (have advantages and disadvantages)
- Cannot carry o2 as well
- But have resistance to malaria


Ribonuclease Protein Experiment

- Heat up protein and causes protein to unfold.
- Unfolded cannot cut RNA anymore, but folded can
- When you lower the heat, the protein will refold and become fully functional
- Refers to ideal circumstances- in body not ideal (proteins cant refold on own due to crowded cytoplasm, once proteins unfold, they expose hydrophobic stretches, when they refold two different proteins will interfere with one another)
- When you boil egg it gets hard; initially all proteins in solution unfold, then try to refold, but connect with other proteins and you get a tangled mass)
- Passed a certain temp, you can die because proteins cant refold


Protein turnover

- the breakdown and resynthesis
- occurs constantly in cells
- proteins are constantly getting broken down and getting remade
- Half-life: time it takes for half of proteins to be broken down then reformed (can be between minutes or years)(can be regulated, or natural)
- After three weeks, you are basically a new being because all proteins are replaces except parts of eye bones and teeth.



- specialized proteins that help keep other proteins (temporarily exposed hydrophobic regions) from interacting inappropriately with one another
- They do so by sequestering some newly synthesized proteins to give them time to fold

ex. Lemon in milk it curls due to change in pH
- Rendors proteins
- Must keep pH stable (need buffers)
*Temp, pH and chemicals can denature proteins



- Good for RNA, DNA, energy carrier (ATP), signalling
- Made of:
- phosphate group (bonded to 5' carbon of sugar), have energy-rich bonds (breaking them release energy), can be mono, di or triphosphate.
- 5 C sugar (either ribose (has OH) for RNA and deoxyribose (has H) for DNA)
- Nitrogenous base (bonded to 1' Carbon sugar)



- have one aromatic ring
- Cytosine
- Uracil (the pryimidine for RNA)
- Thymine (the pryimidine for DNA)
- smaller than purines



- Have two aromatic rings
- Guanine
- Adenine
- Purines are larger than pyrimidines


Phosphodiester linkage

- Two monomers get linked with covalent bond (3’ OH and 5’ Phosphate group)- make phosphodiester linkage
- Made thru condensation reaction
- OH of phosphate group + H of 5C sugar


Sugar-phosphate backbone of RNA

- polymerization starts at 5’ , ends at 3’
- Or polymerize from 5’ to 3’ direction
-3′ end of nucleic acid:
new nucleotides are added
to the unlinked 3′ carbon

*3' and 5' carbons are joined by phosphodiester linkages


Rosalind Franklin

- collected the X-Ray diffraction pattern of DNA
- found sometime in 50s


Nucleotide Pairings

A&T (has 2 H-bonds- less stable)
C&G (has 3 H-bonds)
- must be a purine and prymadine in order to have the just right amount of space inside the sugar- phosphate backbones


DNA form

- have antiparallel arrangement
5’ and 3’
- All base pairs carry hereditary information (interior of double helix)
- Very clever arrangement because nucleotides are protected (keeps hereditary info safe)


Major Groove & Minor Groove

• Major Groove : describes where n base in middle are accessible
• Minor groove: describes narrow group where n bases are less accessible
- bind usually in Major groove.



1. Strand seperation (5' to 3')
2. Base-pairing with template
3. Polymerization (the original molecule has been copied


Loops in DNA

- can fold into this sometimes
- Often you find stemmed loop structure (single-stranded region forms a loop, double-stranded region forms a double helix)
- Molecule forms back on itself
- Sometimes RNA molecules even fold into complex molecules



- Gave rise that RNA came first
RNA to DNA to proteins
- Not possible if all 3 systems came at same time, one must have come first
- Because it can store info as well as fold into protein
- 2nd was proteins
- Last step was DNA (to store info)
- RNA molecules are much less stable due to single strands