Week 2 Flashcards
example of primary protein structure
AA sequence
what is a primary protein structure
a linear chain of amino acids
amino acids can be described as the __________ _______ of protein
building blocks
what part of the amino acid is variable
side-chain/r group
what determines the type of amino acid
the side chain/r group
name all components of an AA
amino group (NH2), carboxyl group (COOH), and side chain all attached to an alpha carbon
what are the 4 major categories of AA
acidic, basic, uncharged polar (ionization depends on pH of the solution that they are in), non polar
how many aa are there
20
where are non polar aa usually found
forms the inner core of proteins (eg pocket where a metabolite may bind) and often associated w lipid bilayer and membranes
where are uncharged polar aa usually found
usually on the outside of a protein
where are charged polar aa usually found
enzymatic functions and in charge of the shape of the protein
acidic r groups have a + or - charge
negative (side note, the also have the same first two nucleotides in the codon)
describe why is cysteine (aa) special
- strong cov bond
- non polar
- SH r group
- under correct conditions, you can form disulfide bond BETWEEN cysteines
- interchain for between and intrachain for within the aa
- the bonds happen bc of oxidation and removed due to reduction
why are disulfide bonds important for proteins
Disulfide bonds imp for proteins that are likely to undergo mechanical or chemical stress - eg proteins excreted outside a cell, sitting outside a plasma membrane, proteins in hair (curly) <== the ones that need to handle the stress
name the 2 classes of the secondary structure of protein
alpha helix and beta pleated sheets
describe peptide bonding
- Peptide bonds join the linear sequence/primary structure of protein
- rxn between carboxyl group and amino group - the OH and H makes water as a byproduct and a strong covalent peptide bond
- condensation rxn
- Strong and rigid, cannot rotate the atoms around this bond
what is a n and c terminus
the n terminus is the amino end of an aa and c terminus is the carboxyl end
in a polypeptide chain what is the polarity maintained by
Polypeptide chain completed and polarity maintained by distinct amino and carboxyl ends
when does an aa become an aa residue
once an aa is joined in a peptide bond
when are the terms carbonyl oxygen and amine hydrogen used
when aa are joined tgt in a peptide bond, the cooh is left with a c-o and the nh2 becomes a n-h
t/f is the shape of the protein important for how it binds to the receptor
yes
t/f do differences and order of aa matter in the sequence
yes
how do we number aa
starting from the amino end
whats the difference between secondary and tertiary protein structures
secondary is local folding and tertiary is long range folding
what bonding is responsible for the structure of the alpha helix, and between which atoms
hydrogen bonding - carbonyl oxygen and amide hydrogen in the peptide backbone
what is the difference between regular protein structures (specifically alpha helix) and dna
the polarity and strand #.
- Both have polarity but they have diff types
○ 5’ and 3’ vs the terminals
- Bases facing in for DNA but alpha helix R-groups are facing out
Alpha helix is single stranded and DNA is double
between how many aa apart are alpha helixes joined (within the same segment of polypeptide chain)
4 aa apart (n and n+4)
what is a key difference in the h bonding of alpha helices and beta pleated sheets
for beta, its between carbonyl oxygen and amide hydrogen of aa in a neighboring strand instead of 4 aa residues away
alpha helices bonding is within same segment of polypeptide chain and beta sheet has it in diff segments/strands of the polypeptide chain
in which direction are r groups projected in beta pleated sheets
alternately up and down
how many beta strands are typically in a sheet
4-5 but can have up to 10+
what are the two types of beta sheets and described the difference
- antiparallel: Arrows point towards c-terminus by convention, and the yellow is connecting amino acid residues between beta strands
- Parallel is longer because you have all the extra looping and you need for aa
why are beta sheets commonly found in all types of proteins
because they make a strong rigid type structure and you can also find stacked beta sheet in amyloid proteins (have both negative and positive functions - in neurodegenerative disorders and also helped to store things)
described what a coiled coil is
- 2-3 alpha helixes that are wrapped around each other
- Not all alpha helix can achieve this, you need repeating pattern of residues with particular r-groups
- amphipathic: when you have a coiled coil, the hydrophobic stripe gets pushed to the middle and so all hydrophilic are on the outside
- found in alpha keratin of skin, hair, and also myosin motor proteins
t/f can you have amphipathic beta sheets
true
what type of protein structure makes up the 3d structure of proteins
tertiary
list the type of interactions that tertiary structures are held by
hydrophobic interactions, non-covalent bonds, covalent disulfide bonds
what bondings occur between
backbone - backbone
backbone - side chain
side chain - side chain
all of them have hydrogen bond
proteins will generally fold into the most ____________ _________ conformation
energetically favorable (all the info comes from linear aa seq)
what type of proteins make the shape folding process more efficient and reliable
chaperone proteins
t/f once a protein starts to fold into its 3d structure, can you fix it
false
t/f tertiary structures can be dynamic
true
t/f shape will always be related to function
true
protein domains are often specialized for diff ________
functions
describe protein domains and how are they important
- they are a portion of a protein that has its own tertiary structure, often functioning in semi-independent manner
- important for the evolution of proteins: esp w only point mutations, it will take awhile for evolution of diff process but with diff domains it expedites the process
eukaryotic proteins often have _____ domains connected by intrinsically disordered sequences
2 or more
conditions/descriptions for a protein family
- have similar aa seq and tertiary structures
- members have evolved to have diff functions
- most proteins belong to families with similar structural domains
protein domain example - src protein kinase:
- purpose
- how many lobes are there
- signalling protein: the kinase domain is important bc responsible for phosphorylating proteins and regulates protein activity
- has 2 lobes
- The SH3 and 5H2 help regulate the kinase
describe the quaternary protein structure
multimeric organization - more than 1 polypeptide chain
quaternary protein example: hemoglobin
- how many subunits
- sickle cell anemia is caused by a mutation in which subunit
- 2 alpha and 2 beta subunits <– each subunit is a separate polypeptide
- caused by a mutation in the b subunit
describe what could make up multiprotein complexes/molecular machines
could be:
- many identical subunits (eg actin filaments)
- mixtures of diff proteins and dna/rna (eg viruses and ribosomes)
- very dynamic assemblies of proteins to form molecular machines - machines for dna replication initiaition or for transcription
Main idea is that it is a bunch of proteins together working as a machine and that they are dynamic
describe examples of multiprotein complexes/molecular machines: scaffold protein
Ex of molecular machine: A couple of proteins (the top) uses atp to do work - conformational change of one part in the protein (highlight the fact that energy is needed)
scaffold protein has binding sites for binding other types of protein; when you have complex biochem happening in a part of the cell (you know how packed proteins are) and you need all the proteins that are relevant nearby –> the binding sites will all be held close together possibly as a part of molecular machine
state the name of the database that helps you predict protein structure
alphafold - AI program machine learning that predict protein structure just on AA sequence
what is proteomics
the large scale study of proteins
what might be some approaches to collect data in proteomics
identity + structure of proteins, protein-protein interactions, abundance + turnover, location in cell or tissue
list at least 2 protein properties (dimensions)that you can look at
physical: all the structures, mass
chemical: charge distribution, activity, solubility, surface hydrophobicity, activity
a bit of both: flexibility, pH
“proteins differ in size, shape, charge, hydrophobicity, and their affinity for other molecules”
what is the first thing you do when studying proteins and how
first thing you do is protein separation/purify protein(s) of interest through various types of electrophoresis and affinity chromatography –> determines aa seq (through mass spec: Break up peptide, send through mass spec and compare with known) and can discover precise 3d structure using techniques such as x-ray crystallography, NMR spec, or cryo electron microscopy and/or alphafold 1 and 2
