Lecture 2 Flashcards
Genomics
− The study of the set of genes contained in the chromosomes
Transcriptomics
The study of the set of genes being expressed (as mRNA molecules) in a specific cell at a given time under specified conditions
Proteomics
The study of the set of proteins being expressed in a specific cell at a given time under specified conditions and the state of modification
Metabolomics
The study of the set of small molecules (fats, vitamins, sugars, amino acids etc) in a specific cell at a given time under specified conditions
Functions of DNA
- To store information
- To replicate faithfully
- To allow for slow changes over time (mutations)
Expression Proteomics
- Define all gene products present in a cell and their modifications
Cell-Map Proteomics
- Define the spatial & temporal positions of all proteins and interactions
Functional Proteomics
- Define the biological function of all proteins within their networks and complexes
Structural Proteomics
- Determine the structure of all proteins, alone and in complexes
Population Proteomics
- Large scale version of expression proteomics for disease studies
Post-translational modifications
- Proteolytic cleavage- Fragmenting protein
- Addition of chemical groups (Read slide 8 know definitions)
what is proteomics used to investigate?
- When and where proteins are expressed
- Rates of protein production, degradation, and stead-state abundance.
- How proteins are modified (For example, post-translational modifications)
- The movement of proteins between subcellular compartments
*The involvement of proteins in metabolic pathways - How proteins interact with one another
Plasma Components
- 40,000 forms of proteins secreted into plasma.
(500 gene variants, x2
splices, x20 glycoforms,x 2
clip forms)
*500,000 forms of tissue proteins
(23,000 genes, 5 splice variants, 5 PTMs)
*10,000,000 clonal forms of immunoglobulins
(Look at Slide 12 for examples of plasma protein composition)
Protein Structure can be divided into…
- Primary (amino acid sequence)
- Secondary (local folding structure)
- Tertiary (overall fold of amino acid chain)
- Quaternary (subunits composing functional protein)
Secondary Structure - Alpha Helices
- In an α helix, the carbonyl
(C=O) of one amino acid is
hydrogen bonded to the
amino H (N-H) of an amino
acid that is four down the
chain. - This pattern of bonding pulls the
polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix
containing 3.6 amino acids.
Secondary Structure - Beta Sheets
- In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming
a sheet-like structure held together by hydrogen bonds. - The hydrogen bonds form between carbonyl and amino groups of the backbone, while the R groups extend above and below the plane of the sheet.
- The strands of a β pleated
sheet may be parallel, or antiparallel
Tertiary Structure
Tertiary structure - fold of a give (R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, hydrophobic interactions
and disulfide bonds.
Quaternary Structure
- protein functional unit - many proteins are made up of a single polypeptide chain and have only three levels of structure
- However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure.
CFTR Protein
- The CFTR protein functions as a channel for the movement of chloride ions in and
out of cells, which is important for the salt and water balance on epithelial surfaces,
such as in the lungs or pancreas. - Changes in the CFTR gene can affect the structure of the CFTR protein.
What do Class I, II and III mutations of CFTR protein lead to?
Class I, II and III mutations generally lead to complete loss of function and a more severe disease.
What do Class IV and V lead to?
Class IV and V cause a reduction in function and have a milder effect.
