Topic 2 Flashcards
How are Biomolecules held together?
Different types of chemical bonds
Weak bonds have more or less flexibility?
More
Polymers such as DNA are held together
covalent bonds
What is held together by covalent bonds
Backbone of polymers
Proteins
DNA
RNA
Polysacchardes
Non-covalent bonds are
Electrostatic or ionic
T or F: Non-covalent bonds break and reform more covalent bonds
True
Are covalent or non-covalent bonds stronger
Covalent
Hydrogen bonds
Hydrogen bonded to highly electronegative atom (Nitrogen or oxygen)
What liquid is good at hydrogen bonding?
Water!
What is created when Electrons spend more time around the e neg atom
a partial charge
Van der Waals
Pretty weak
Lots of low-energy interactions
Can interact with hydrophobic surfaces
works like a Velcro
Water
Partial negative oxygen
Partial positve hydrogen
Works very well as a bond donor and acceptor
entropy of water
High due to free rotation
How does water interact with ionic solutes (eg NaCl)
Electrostatically
water can form a flickering cluster
Flickering clusters can break and reform in a matter of picoseconds
What do you need to break down Ice
input of energy
Hydrophobic molecules
will arrange themselves in a way to avoid interactions with water
have hydrophilic head group and hydrophobic tail
Entropy
Dissaray in the system
The greater the disorder the……. the entropy
higher
is high entropy good?
yes
macromolecules
Nucleic acids, proteins, lipids, polysaccharides
Most Versatile macromolecules
Proteins
How are amino acid properties determined
properties determined by R group
amino acids stereochemistry
L and D isomers
amino acid L isomer
only form found in proteins produced by ribosmes
Abs config of amino acids
Corn Rule
NH3 has higher priority than COO- group (draw) slide 26
how are the 20 common amino acids grouped
On the basis of their side chains
amino acid grouping
non polar
polar
acidic
basic
Peptide bond
very stable
amino acids covalently liked vis peptide bonds
half life of peptide bonds
7 years
100 peptide bonds, after 7 years 50 would remain
Bonds within peptides
Disulfide bonds
hydrogen bonds
ionic bonds
van der Waals and hydrophobic interactions
Protein structure types
Primary structure
Secondary Structure
Tertiary Structure
Quaternary
Primary structure (proteins)
includes all covalent bonds and is defined by amino acid sequence
the sequence is determined by genes
linear sequence of amino acids in a protein
Secondary structure (proteins)
regular recurring arrangements in
space of adjacent amino acids
adopted from polypeptide
held together by hydrogen bonds between peptide bonds
Tertiary structure (proteins)
Spatial relationship among all amino acids in a polypeptide
determines the shapes of a single protein (polypeptide)
contained both 1 and 2 structures
stabilized by weak bonds
Quarternary (proteins)
Protein made up of several polypeptide chains
What are the terminuses of proteins
N (amino) terminus and C (carboxyl) terminus
Polar molecule
two different ends
2 structure alpha helix
forms by bonding every 4 atoms
2 structure beta sheet
peptide bonds lie flat so that H bonds can occur
can form parallel or antiparallel
Intramolecular
within a molecule (protein)
Intermolecular
between molecules (protein)
How are proteins organized
in domains
T or F: most protein domains are 50 to 350 amino acids
True
what can protein domains fold into
a conformationally stable discrete unit
What determines the function of a protein
The structure
Non kinase domains
Src: cytosolic kinase
VERGFR2: find a molecule that turns the kinase on
Src (cytosolic kinase)
how the protein selects a target
what do Denaturation and Renaturation determine
how the protein folds
determined by primary sequence
Denaturation
unfolds protein
Renaturation
folds protein
What needs to occur so that denatured molecule can fold back
Dialysis
Chaperones
Enzyme
utilized in cells to encourage the folding of proteins back to native conformation
required input of energy
Ubiquitin
76 a.a. protein
when tagged onto another protein, that protein gets sent for degradation
must have 4 ubiquitin tags for degradation to occur
