Protein Basis If Life Flashcards
Proteins shapes and surfaces allow:
-Interact selectively with other molecules
-High degree of specifity
Protein functions
1- Enzymes
2- Structural
3- Motility
4- Regulatory
5- Transport
6- Signaling
7- Receptor
8- Defensive
9- Storage
Amino acid sequence —> 3D structure of proteins —> Determines the protein function
Memorize :)
Amino acids polymers
Protein
number of standard amino acids
20
All amino acids have
- carboxyl group
- amino group
- alpha-carbon
- unique side chain
At PH=7
Carboxyl group= losses proton= negatively charged
Amino group= accepts proton= positively charge
Asymmetric alpha carbon
All amino acids except glycine have one
Each amino acid except glycine has
Asymmetric alpha carbon —> in D or L form
Amino acids in synthesis of a protein always
L-amino acids
Properties of amino acids depend on:
-size
-shape
-charge
-HB
-hydrophobic character
Acidic AA
Negatively charged
Basic AA
Positively charged
Polar amino acids location
Found on surface
Non-polar AA
Usually buried in the core of proteins
How stepwise addition of new amino acids occus?
Condensation/Dehydration
Process of elongating a chain of amino acids
Protein synthesis
Immediate product of proteins synthesis
Amino acids
When poly peptide become a protein
Assumed unique and stable 3 dimensional shape
Primary structure
-Linear strand of AA
-Size can vary 2–33000
Folding important bonds
-covalent bonds — disulfide bonds between sulfur atoms of two cysteine
-not covalent bonds - 4 types
*covalent is much stronger
Disulfide bond
Between two sulfur atom of two cysteine
*can be intra- or intermolecular bonds
Secondary Structure (stable types)
- alpha helix
- betta sheet
- turn
- loop
What generate secondary structures?
Local Hydrogen Bonds among AA (polypeptide backbones)
Alpha helix
-spiral in shape
-peptide backbone
-R groups jutting out from the spiral
-HB between NH group of one AA and CO group of second AA (only one turn away)
-can be hydrophobic/hydrophilic
** alpha helix is not hollow
Hydropolarity in Alpha helix
-Non polar in the middle of
phospholipid — non-polar tails
-Polar in both ends — polar heads
Constraints of alpha helix
1- repulsion or attraction of AA residues
2- bulkiness of adjacent R groups
3- interactions between R groups 3-4 residues apart
4- HELIX FORMING AA: L/M/E
5- HELIX BREAKERS AA: P/G
What determine structure
Primary sequence determine structure (identity and sequence of AA)
Beta sheet
Sheet like conformation with Several polypeptide (strand) side by side in a folded or pleated conformation
-characterized by maximum number of HB
-Beta sheet formers: I,V,F
Beta sheet kinds
1-parallel
2-antiparallel
Alpha helix and Beta sheet
-Major internal supportive elements
-60% of a protein
Motif
Units of secondary structure consist of short stretches of alpha helix and beta sheet
DNA binding protein motif type
Helix-turn-helix
Protein can be classified as —
Combination of secondary structures (motifs)
Tertiary structure
1- conformation of the entire polypeptide
2- stabilized by covalent and non-covalent bonds between side chains
3- tertiary structures are unlimited
Two identification way for proteins
- X-ray crystallography (protein should form pure crystals)
- NMR spectroscopy (difficult to use with larger proteins)
T or F
Proteins with different primary sequence level may have similar tertiary structure
True
Similar structure
Similar function
Domain
-Substructure of overall tertiary structure with a specific function
-50-350 AA
-regions with alpha and beta packed compactly
-Proteins with same function may have same domain
-protein with different functions have separate domain for each function
T or F?
Protein are capable of internal movement
True
Every activity in which protein take part
Accompany by conformational changes
Alpha helix breakers
Proline — too bulki
Glycine — too small
Quaternary structure
More than one subunit held together by non covalent interactions or disulfide bonds between R-group
Quaternary structure kinds:
1- Homodimer : two identical subunits
2- Heterodimer: two non-identical subunits
Hemoglobin
Heterotetramer
2 alpha-globin
2 betta-globin
Titin (human)
Tertiary structure but biggest protein
Stable three dimensional structure
Native conformation
Proteins categories
1- Fibrous
2- Globular
Fibrous proteins
1- extensive regions of secondary structure — highly ordered — repetitive structures
2- common in structural materials
— hair
— skin
— blood vessels
Globular proteins
Different segments of polypeptide chain fold back on each other creating a compact structure
- maybe mainly alpha helical, mainly beta sheet, or mixture
- each type has unique tertiary structure
- most proteins are globular
-Ex. Enzymes/Transport proteins
Denaturation by
1- detergent
2- radiation
3- heat
Self assembly
Primary sequence has all the information of 3D conformation
Final confirmation
- most energetically favorable
- folding happens fast
Chaperones
Short stretches of hydrophobic AA that are exposed in non-native protein to facilitate proper folding
Chaperons of Hsp70
Prevent them to bind to other proteins in the cytosol
Chaperones will be released if
Protein spontaneously fold into native state
Chaperones larger
Chaperonins
Prion
Proteinaceous infectious particle
- bad protein convinces good proteins to reform
