2. Protein Structure Flashcards
Example of primary protein structure
AA sequence
Example of secondary protein structure
Local scaffolding (alpha helix & beta sheet)
Example of tertiary protein structure
long-range folding (3D structure)
Example of Quaternary protein structure
multimetric organization (more than 1 peptide chain)
Example of multiprotein complexes (molecular machines)
multiprotein complexes & molecular machines
Major categories of amino acids:
- Acidic
- Basic
- Uncharged polar
- Nonpolar
What determines the type amino acid
the R group
The 3 parts of amino acids
- Alpha carbon
- Amino group
- Carboxyl group
A unique amino acids
CYSTEINE (DISULPHIDE BONDS/ DISULPHIDE BRIDGE)
how are peptide bonds formed?
there is a reaction between the carboxyl group on the lysine & the amino group on the phenylalanine
Residue
amino acids within a peptide chain (not a full amino acid anymore- because of the loss of H20)
what are the 2 ends of an alpha helix called?
N terminal end
C terminal end
what are the 2 ends of a DNA double helix called?
5’
3’
What is the difference between protein & DNA
- *Protein is single stranded- bases point outwards of helix
- *DNA is double stranded- bases point into centre of helix
What is DNA synthesised from?
deoxyribonucleoside triphosphates (dNTPs)
What is RNA is synthesized from
ribonucleoside triphosphates, or:
➢ NTPs
Ionic bonds, interactions between oppositely charged atoms, happens within a molecule or between
Electrostatic attractions
much weaker than covalent bonds, fond in water, also found when and H+ comes close to an electronegative atom ie: O or N
Hydrogen bonds
whenever atoms are close together, are transient fluctuations in electron distributions
Van der Waals attractions
pushing nonpolar parts of molecules out of H-bonded water network)- ie. Hydrophobic interior of cell membrane
Hydrophobic force
A-T have ___bonds
2 hydrogen
G-C have ____ bonds
3 hydrogen
3 Forces that keep DNA strands Together
- Hydrogen bonds
- Hydrophobic interactions
- Van der Waals attractions
__________ covalently link nucleotides together to make DNA or RNA
Phosphodiester bonds
____________ covalently link together amino acids into polypeptides
peptide bonds
Beta Sheets
- Not as compact as alpha helix
- R groups not involved but notice they alternately project up and down
Beta sheet typically contains 4-5 beta strands but can have 10+!
- R groups not involved but notice they alternately project up and down
Bonds within beta sheets
H -bonding between carbonyl oxygen (C=O) of 1 aa and amide hydrogen (N -H) of aa in neighboring strand
2 types of beta sheets
- anti-parallel
- parallel
Hydrogen bonds are ____ to axis to actual helix
parallel
Which atoms are H-bonded?
- Carbonyl oxygen
- amide hydrogen in peptide backbone
Where are hydrogen bonds located in alpha helices?
4 AA’s apart and within the same segment of pp chain
Where are hydrogen bonds located in beta sheets?
Between AA’s in different segments or strands of pp chain (is one polypeptide-3 beta strands- parallel or anti-parallel)
Amphipathic
contain both hydrophobic & hydrophilic parts
Amphipathic alpha helix
coiled coils (in myosin motor proteins, skin & hair)
3 Ways Protein structures are held together by
- hydrophobic interactions
- non-covalent bonds
- covalent disulfide bonds
Proteins generally fold into the conformation that is the most ________
energetically favorable.
Proteins will fold into the shape dictated by their amino acid sequence, but _________ help make the process more efficient and reliable in living cells
chaperone proteins
Protein Domains
are often specialized for different functions
- Portion of a protein that has its own tertiary structure, often functioning in semi- independent manner (one part of the protein can function independent of the other protein)
Eukaryotic proteins often have_____domains connected by intrinsically disordered sequences (connecting sequences of amino acids)
2 or more
Protein Families
are groups of proteins with a common evolutionary origin (clear that overtime, proteins that have evolved to a stable structure- the DNA sequence has copied & passed on with new structure & function)
Protein Families have similar…
sequences & tertiary structures
Quaternary Structures are made of
- More than 1 polypeptide chain (example: hemoglobin)
Examples of multi protein complexes & molecular machines
- mixtures of different proteins and DNA/RNA— e.g. viruses and ribosomes
- very dynamic assemblies of proteins to form molecular machines—e.g. machines for DNA replication initiation or for transcription
Scaffold
an entity that Is used to bind proteins by putting them in close proximity (usually RNA)
Interactome
Protein-protein interactions
- Abundance & turnover
