Lecture 4: Proteins (Part 2) Flashcards
1
Q
What determines tertiary structure?
A
- 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
2
Q
Disulfide bridge
A
- 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.
3
Q
Hydrophobic interactions
A
- 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)
4
Q
Coiled Coils
A
- 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.
5
Q
Diversity of tertiary structures
A
- 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
6
Q
Cro Protein
A
- 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
7
Q
Amino Acid sequence
A
ex. sickled cell anemia • Normal red blood cell: Pro-Glu-Glu • Sickles red blood cell: Pro-Val-Glue - 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
8
Q
Ribonuclease Protein Experiment
A
- 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
9
Q
Protein turnover
A
- 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.
10
Q
Chaperones
A
- 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
11
Q
Nucleotide
A
- 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)
12
Q
Pryimidines
A
- have one aromatic ring
- Cytosine
- Uracil (the pryimidine for RNA)
- Thymine (the pryimidine for DNA)
- smaller than purines
13
Q
Purines
A
- Have two aromatic rings
- Guanine
- Adenine
- Purines are larger than pyrimidines
14
Q
Phosphodiester linkage
A
- 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
15
Q
Sugar-phosphate backbone of RNA
A
- 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
16
Q
Rosalind Franklin
A
- collected the X-Ray diffraction pattern of DNA
- found sometime in 50s
17
Q
Nucleotide Pairings
A
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
18
Q
DNA form
A
- 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)
19
Q
Major Groove & Minor Groove
A
• 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.
20
Q
DNA FORMATION
A
- Strand seperation (5’ to 3’)
- Base-pairing with template
- Polymerization (the original molecule has been copied
21
Q
Loops in DNA
A
- 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
22
Q
The O.G DNA
A
- 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
