Textbook 1.1 Flashcards
pg. 48-60, 71-72, 373-377, 726-728
in neutral aqueous solution…
the alpha carboxyl group loses its proton and exists as COO- and alpha amino group accepts a proton
Amino acids exist as
stereoisomers except glycine
How long is the average polypeptide chain?
450 amino acids
Can proteins contain components other than amino acids?
Yes, after polypeptide has been synthesized other things like carbohydrates (to form glycoproteins), metal- containing groups (to form metalloproteins), and organic groups (to form flavoproteins).
Polar charged amino acids
In physiologic pH, side chains of these amino acids are able to form ionic bonds with other charged species in the cell.
ex. aspartic acid
Polar uncharged amino acids
side chains can have partial pos. or neg. thus can form H bonds with other molecules (including water)
ex. tyrosine
Non polar amino acids
hydrophobic side chains, usually lack oxygen and nitrogen. Interactions are restricted to hydrophobic interactions and Van der Waals forces.
ex. Alanine
Other amino acids
Glycine - only has one stereoisomer (side chain is just H)
Proline - doesn’t really fit into any secondary structures and its alpha amino group is part of a ring (produces kinks and folds)
Cysteine - forms disulfide bridges
Post-translational modifications (PTMs)
proteins with different amino acids that arise from alteration of side chain of one of normal 20 amino acids AFTER its incorporation into a polypeptide chain
How can a single polypeptide chain exist as a number of distinct biological molecules?
Post-translational modifications can alter its biological activity
Examples of post-translational modifications
- reversible addition of phosphate group to a serine, threonine, or tyrosine residue
- lysine acetylation affects thousands of proteins in a mammalian cell
Where are polar residues usually found?
Situated near the surface of molecule where they can associate with nearby water molecules and contribute to solubility.
Primary Protein Structure
specific linear sequence of amino acids that constitute the chain
Secondary Protein Structure
describes conformation (spatial arrangement) of portions of the polypeptide chain
What did Linus Pauling and Robert Corey propose?
That polypeptide chains exist in preferred conformations that provide maximum number of possible H-bonds between neighbouring amino acids.
Alpha helix and beta sheet.
Alpha helix
backbone lies on inside of helix, side chains project out. In water soluble proteins, the outer surface of the alpha helix often contains polar residues in contact with the solvent (inward facing contains non-polar side chains).
Beta sheet
Consists of several segments of a polypeptide lying side by side. Backbone assumes folded or pleated conformation. Beta sheet also has hydrogen bonds but they are oriented perpendicular to the long axis of polypeptide chain and project across from one part of the chain to another.
Silk has a lot of…
beta sheets which make it resistant to pulling
Tertiary Structure
describes conformation of entire polypeptide. This kind of structure is virtually unlimited—many possible conformations.
Tertiary structures are stabilized by…?
Non covalent bonds between side chains of protein.
How is tertiary structure usually determined?
X-ray crystallography: crystal of protein is bombarded by thin beam of x-ray radiation that is scattered by electrons of the proteins which then strike radiation sensitive detector in an array of spots. Computer program is then used to convert the spatial arrangement of dots into protein structure.
Fibrous proteins
elongated shape
globular proteins
compact structure
Where are fibrous and globular proteins found?
Fibrous proteins are usually the structural material outside the living cell (collagens and elastins of connective tissues, keratins of hair, skin, and silk). They resist pulling or shearing forces. Most proteins within the cell are globular proteins.
Can proteins with different primary structure have similar biological functions?
Yes. Even if the primary linear sequence differs, structural similarity between the tertiary structure indicates the possibility that the functions of the proteins are similar. Function follows structure.
How are x-ray crystallographic images of proteins not necessarily accurate?
They are static images and proteins are dynamic. Its like saying one resonance structure represents the molecule when really it represents only a portion of the true structure.
Homodimer
protein complex of two identical subunits/chains
heterodimer
protein complex of two nonidentical subunits
conformational changes
predictable movements within a protein that are triggered by the binding of a specific molecule
Proteome
the entire inventory of proteins that is produced by an organism. Also applies to inventory of proteins present in a particular tissue, cell, or cellular organelle.
TAP-tag mass spectrometry
Used to study interactomics (protein interactions). DNA from gene of interest is fused to DNA encoding for protein tag (called a TAP tag) that is easily purified using affinity chromatography.
- TAP tagged gene is expressed in cell
- cell is lysed and tagged protein + interacting protein is purified
- set of accompanying proteins can be identified using mass spectrometry
hub proteins
More likely to be of higher importance biologically. Have multiple binding partners. Some have multiple binding surfaces and can bind with many at once while others have one surface capable of binding with many different proteins (at different times).
Distance between nucleotides on a strand of DNA
0.34 nm
How frequently does a large structural repeat occur?
Ever 3.4 nm of helix or every 10 base pairs
What about DNA is constant for a specific species?
base composition (proportion of each base)
A nucleoside is a nucleotide without…
the phosphate
What causes DNA to have a negative charge?
The phosphate groups
What’s the width of the double helix?
2 nm
Proteins can fit in…of DNA and can read the sequence without…?
- the major and minor grooves
- separating the strands
Can PCR be used for RNA?
Yes, if RNA template strands are converted to complimentary DNA strands using reverse transcriptase
Final product of PCR
(2^n double stranded DNA molecules)(however many strands you started with). For example if you started with ten and you did four rounds of PCR you would have
(2^4)(10) = 160
