Week 2: Intro to Protein Structure Flashcards
What are the levels of protein structure?
Primary > Secondary > Tertiary > Quaternary > Multiprotein complexes
Which levels of proteins do only SOME proteins have?
Quaternary and multiprotein complexes
What are proteins composed of?
Amino acids
What differentiates amino acids from each other?
The side-chain/R group
What are the major categories of amino acids?
Acidic, basic, uncharged polar, nonpolar
What are the parts of an amino acid?
Amino group, alpha carbon, carboxyl group, R-group
True or False: The grouping of genetic codes is perfect
False
What makes cysteine stand out?
Its ability to create disulfide bonds
Where are regular cysteine (no disulfide bonds) regularly found?
In reduction conditions in the cytosol
Where are the cysteine that form disulfide bonds regularly found?
In oxidation conditions in the ER outside the cell
What is an important property of disulfide bonds?
They have strong covalent bonds
Disulfide bonds act as braces, which helps to hold the _________ in proper configuration
Protein shape
What kind of bond holds amino acids together?
Peptide bond
What are examples of more proper names for the components of an amino acid, post-peptide bond?
R-group + main parts = reisdue
Carboxyl carbon = carboNYL carbon
Amino group nitrogen = amiDE nitrogen
What happens when a peptide bond forms (besides the joining of two amino acids)? What kind of reaction is this?
The OH from one AA’s carboxyl group and the hydrogen from another AA’s amino group make water. This is a condensation reaction
What is considered a polypeptide chain?
2 or more AA together
What is lies at the end of polypeptide chains?
An amino end (N-terminus) and Carboxyl end (C-terminus)
True or False: Differences in primary AA sequence DO NOT matter
False
True or False: The order of AA acids are important
True
How many residues do you need to create an alpha helix?
> 4 residues
What properties differentiate alpha-helices from DNA double-helices?
Alpha-helix:
- R-groups OUTWARD
- R-groups DO NOT hold it together (No H-bonds)
- SINGLE strand
- N-end, C-end
DNA double helix:
- Base pairs face INWARDS
- Base pairs HELP hold it together
- DOUBLE strand
- Anti-parallel
What bonds stabilizes the beta sheet?
H-bonding between carbonyl oxygen (C=O) of 1 AA and amide hydrogen (N-H) of AA in NEIGHBOURING strand
True or False: R groups are involved in the stability of beta sheets
False
What are the two types of beta sheets?
Anti-parallel and parallel
What is the difference between the two types of beta sheets?
Anti-parallel face the opposite directions while parallel face the same directions
True or False: A coiled coil is a tertiary protein structure
False!!!!!!!!
What does it mean when an alpha helix is amphipathic?
Two different biochemical/biophysical properties on two different sides. One side is hydrophobic while the other is hydrophilic.
Where can coiled coils be found?
alpha-keratin of skin, hair, and myosin motor proteins
Why does the hydrophobic strand coil inwards?
There is H2O all around the cell, the hydrophobic strand coils inward to get away from the water.
What is the tertiary structure of a protein?
The overall 3D structure of the protein
What is the tertiary structure of a protein held together by?
Hydrophobic bonds, non-covalent bonds, covalent disulfide bonds
Proteins generally fold into the conformation that is the most __________ _________
energetically favourable
Proteins will fold into the shape dictated by their amino acid sequence. What makes this process more efficient and reliable in living cells?
Chaperone proteins
What are protein domains in tertiary structures?
Domains are portions of a protein that has its OWN tertiary structure, often functioning in a SEMI-INDEPENDENT manner
Eukaryotic proteins often have 2 or more domains connected by ___________ ____________ ____________
intrinsically disordered sequences
True or False: Connectors are not really part of the domain
True
What makes protein families alike?
Similar sequences and tertiary structures
What makes protein families different?
They often evolve to have different structures
What subunits make up the hemoglobin protein?
2 alpha helices, 2 beta sheets
True or False: 1 polypeptide chain can make up one protein
True
What makes up multiprotein complexes & molecular machines?
Many identical subunits, mixtures of different proteins and DNA/RNA, and very dynamic assemblies of proteins to form molecular machines
What are examples of multiprotein complexes & molecular machines?
Actin filaments, viruses and ribosomes, machines for DNA replication initiation or for transcription
What are the steps for studying a single or a few proteins?
- Purify protein or proteins of interest (i.e. various types of electrophoresis & affinity chromatography
- Determine amino acid sequences (e.g. Mass spectrometry)
- Discover precise 3D structure using techniques such as: x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cry-electron microscopy and other techniques
What is proteomics?
Large scale study of proteins
Researchers usually use a range of “____-____” and computational approaches to collect & analyze data on the set of proteins in a sample
Wet-lab
What are some examples of the types of data of analyses performed?
- Protein-protein interactions, regulation of these interactions, & their position within a pathway
- Abundance & turnover to protein
- Location within a cell or tissue
- Bioinformatics, statistics, & artificial intelligence (e.g. machine-learning-based algorithms), often in combination with other “omics” data sets
