Biochemistry Chapter 4 Flashcards
Classification of proteins based on overall shape and protein, name the two kinds
Fibrous
Globular
Fibrous Protein
Elongated in shape, extracellular proteins and provides mechanical strength to cell and are insoluble in water
Globular protein
Globular proteins have more compact roundish shape, usually water soluble (eg many enzymes)
Examples of fibrous protein
Keratin (hair), myosin (connective tissue) tropomyosin,
What dictates how a protein will fold?
Chemical nature of side chain (is it polar or non polar) and the local environment (ie is it a polar or non polar solvent)
Examples of Polar solvent versus non polar
Polar: water. Non polar-Chloroform
Organization of proteins
Primary
Secondary
Tertiary
Quaternary (Not present in all proteins)
Primary Sequence (structure) of proteins
Dictates the secondary structure and All proteins have this
Secondary structure is the ____total of
All proteins have this, requires NMR and crystallography to determine
Tertiary Protein structure
All proteins have this, requires NMR and crystallography to determine
Quaternary structure
Only multi-subunit proteins have this structure
A multi-subunit protein with quaternary structures consists of
multiple polypeptide chains
Condensation reaction, to join two things…you have to remove
water
condensation reaction is also called the _____ reaction or _____synthesis
dehydration
Peptide bond, also called an _____ bond is formed between the a(- nitrogen atom of one amino acid and the carbonyl carbon of a second.
amide
Leucine has a hydro___ side chain
phobic
N-terminus is:
the end chain of the amino acid that is an Amino terminal residue (look for the NH3+ bond)
C terminus is:
Carboxyl terminal residue (look for the C=OO bond
Peptide is a very _____ ____ amino acids
short sequence of 8-10
Protein chain or polypeptide chain, it is usually ___, or ___ or even ____ amino acids
100, 200 or 1000
_____ is the largest protein
Titin
Titin
has a kinase domain for signaling and also functions mechanically as a molecular spring to provide muscle with elasticity, allow postcontraction recovery, and prevent overextension
1 Dalton = weight of One ___ atom
Hydrogen
Molecular weight of 1 amino acid= _____ g mol -1 which equals ____ Dalton.
1000 Dalton = ___kDa
110
110
1 (kilo Dalton)
Different combinations of polypeptide chains formed = 20^n, where n is the number of ___ ___ involved in building a polypeptide chain
amino acids
Linear polypeptide chain can be cross linked by _____ crosslinks
disulfide
Oxidation to create a new bond results in a loss of ____
hydrogens
Reduction of a chemical is the gaining of_____ to break apart the bond
hydrogens
Cysteine is the ______ form, as ____ atoms are attached
Reduced
Hydrogen
Cystine is the ______ form, due to the new bonding and loss of ____
Oxidized
Hydrogens
Protein modification (Oxidation-reduction reactions) take place in the _____ _____
rough ER
Inside the cell, the cytoplasm is very ___ so you will never have oxidation there, as oxidation would take place inside a compartment
Reducing
You will never find ____ bonds in the soluble part of the cytoplasm
disulfide
The first protein to be sequenced is___
insulin
_____bonds help to modify protein and fold proteins so that it can function properly
Disulfide
Protein ___ plays a major role in the function of a protein
modification
Peptide bonds have _____ double bond characteristics that prevents ___ about the peptide bond. It is also uncharged, allowing formation of globular structures
partial
rotation
Peptide bonds are:
- Planner
- ____
- Partial double bond characteristics
- Very rigid
Uncharged
Peptide bonds in proteins are almost always _____, as steric hindrance would prevent it from being cys as the side chains of the amino acids can be very bulky
trans
Bond between the alpha carbon and the Nitrogen (amino) is the ____
phi (a circle with a line through it)
Bond between the alpha carbon and the Carbon (carbonyl) group is the ___
Psi (Looks like a cactus or a trident)
If the rotation is in a clockwise rotation it is represented by a ____ value. and if it is rotating in an anti clockwise rotation it is represented by a ____ value
Positive (+)
negative (-)
Hydrogen bonding scheme for Alpha Helix formula is: Carbonyl group of amino acid (n) forms Hydrogen- bond with NH(Amino) group on the (n + ___) amino acid on the ____ strand. Only one strand is involved in Alpha Helix!
4th
SAME
If you see a rod shaped protein chain, it is called an _____ _____
alpha helix
Valine, Threonine and isoleucine can not be in an alpha helix due to _____at the beta carbon
branching
Serine, Aspartate and asparagine can not be in an alpha helix due to side chains containing ____ donors and acceptors very close to the main chain
Hydrogen
Proline can not be in an alpha helix as it lacks an NH group and ____ alpha helix. It has a ____ ring structure and cannot assume the phi value to fit into a helix
breaks
rigid
Due to Prolines rigid ring like structure, nature uses Proline to form a ____ in the structure of a protein
bend/fold
Determining direction of helix, look at if the “screw”and ______ from the top, is it going clockwise or anti-clockwise.
tracing
Alpha helix that are ____ handed are more common
right
