BIOLOGY 2B03 Study Guide - Spring 2018, Comprehensive Midterm Notes - Protein, Gene, Phosphorylation
12 Oct 2018
School
Department
Course
Professor
BIOLOGY 2B03
MIDTERM EXAM
STUDY GUIDE
Fall 2018
Polypeptide to Protein - Amino Acids and Chemical Interactions
Functions of Proteins
structural component of cell •
sensors for environmental changes and mechanisms for relaying info to cell •
enzymes, catalysts for chemical reactionns •
gene regulation •
signalling molecules between cells •
molecular motors •
organelle identity and function •
Protein Structure
structure of protein related to function •
Ex. Glutamine Synthetase - donut shaped with •
active domain in the middle
proteins composed of amino acids •
amino acids attached in a linear array to ◦
create the primary structure of the protein -
this is called a polypeptide
they are held together by peptide bonds ◦
What is an Amino Acid?
each amino acid has the same basic structure, but have variable side chains (R-•
groups)
these side chains differ in: •
size ◦
shape ◦
charge ◦
hydrophobicity ◦
reactivity ◦
these properties can all have an effect on the conformation of the whole protein •
they are group based on solubility in water or polarity of the side chain •
Solubility - refers to ability of molecule to transiently bond with water via hydrogen bonding ◦
this is thermodynamically favourable ‣
Hydrophilic molecule: is charge-polarized and can H-bond with water ‣
Hydrophobic molecule: not electrically polarized and unable to form H-bonds, so water repels them in ‣
favour of bonding with itself
Hydrophobic Amino Acids
anything unable to form hydrogen bonds = hydrophobic •
i.e. oils, fats - saturated hydrocarbons (chain of carbons linked by single bonds) ◦
general formula for a hydrocarbon is CnH2n+2 = alkane •
water insoluble amino acids are also hydrophobic •
hydrophobic amino acids tend to stay in the core of soluble proteins and form hydrophobic cores •
Ex. Aromatic aminos acids - Phenylalanine (F), Tyrosine (Y), Tryptophan (W) •
Note: Tyrosine is both hydrophobic and hydrophilic due to it's -OH group ◦
Ex. Aliphatic amino acids - Alanine (A), Valine (V), Isoleucine (I), Leucine (L), Methionine (M) •
Hydrophilic Amino Acids
these are charge-polarized and capable of hydrogen bonding •
hydrophilic amino acids are charged (ionized) at pH = 7 •
-OH at one end (O-) ◦
find more resources at oneclass.com
find more resources at oneclass.com
-NH2 at other end (NH3+) ◦
hydrophilic amino acids tend to be on the surface of proteins and make proteins soluble in aqueous solutions •
Ex. Basic Amino Acids - Lysine (K), Arginine (R) •
Ex. Acidic Amino Acids - Aspartic acid (D), Glutamic Acid (E) •
these amino acids contribute to the overall charge of the protein ◦
Ex. Serine (S), Threonine (T) •
these amino acids are uncharged at neutral pH but have polar -OH groups that participate in H-bonds ◦
Ex. Asparagine (N) and Glutamine (Q) are uncharged but have polar amide groups •
Special Amino Acids
Cysteine: disulphide bridges •
Glycine: very small •
Histidine: pH dependent charge •
Proline: forces a kink in peptide chain •
Making of a Protein
amino acids can be covalently bonded together into peptides by the formation of a peptide bond •
peptide bonds formed by condensation reaction between amino group of one amino acid and carboxyl group •
of another
peptide formation occurs in the ribosome •
Primary Structure of a Protein
linear sequence of amino acids •
the amino acid sequence is determined by the nucleotide sequence of the encoding gene •
number of different sequences = 20^n •
Chemical Interactions
polypeptides spontaneously become random-coil structures •
local interactions stabilize periodically ordered structures - so can also call statistical coil •
some chemical interactions includes: •
ionic bonds - attraction between a positively charged cation and negatively charged anion ◦
hydrogen bonds - interaction between a partially positively-charged hydrogen atom in a molecular dipole ◦
and unpaired electrons from another atom
Van der Waal forces - weak, non-specific attractive forces that results from creation of a dipole when 2 non-◦
covalently bonded atoms are close enough to influence the distribution of electrons in on another
when many, they can be very strong! ‣
hydrophobic effect - aggregation of non polar molecules (side chains) in an aqueous medium to reduce # of ◦
interactions with water. Arrangement of molecules so hydrophobic area stays away from water
non-covalent interactions = weak attractive forces •
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Fall 2018 structural component of cell sensors for environmental changes and mechanisms for relaying info to cell enzymes, catalysts for chemical reactionns gene regulation signalling molecules between cells molecular motors organelle identity and function. Polypeptide to protein - amino acids and chemical interactions. Protein structure structure of protein related to function. Solubility - refers to ability of molecule to transiently bond with water via hydrogen bonding this is thermodynamically favourable. Hydrophilic molecule: is charge-polarized and can h-bond with water. Hydrophobic molecule: not electrically polarized and unable to form h-bonds, so water repels them in favour of bonding with itself. Aromatic aminos acids - phenylalanine (f), tyrosine (y), tryptophan (w) Note: tyrosine is both hydrophobic and hydrophilic due to it"s -oh group. Aliphatic amino acids - alanine (a), valine (v), isoleucine (i), leucine (l), methionine (m) Hydrophilic amino acids these are charge-polarized and capable of hydrogen bonding hydrophilic amino acids are charged (ionized) at ph = 7.
