Lecture 5: Proteins Flashcards
(25 cards)
Amino acids
> Amino acids (aa) are polymers containing amino and carboxylic acid groups
Central carbon bound to amino and carboxylic acid groups plus hydrogen and ‘R’ group.
‘R’ group side chain differs for each aa
aa linked together by peptide bonds to form proteins
Nucleotides
> Building blocks for DNA ad RNA
RNA= ribose
DNA= deoxyribose
Phosphate groups attached to 5’ carbon
Base attached to 1’ carbon
Nucleotides are composed of a sugar, a base, and 1-3 phosphate groups
Cells contain distinct structures that perform specialised functions
> To accomplish the tremendous number of tasks necessary to remain alive, cells practice division of labour and specialise
Membranes separate cellular components into distinct regions that perform specific functions
Some proteins cluster together to form complex structures on the plasma membrane or in the cytosol
Eukaryotic cells contain membrane-bound organelles in the cytosol that are highly specialised
Proteins
> The most abundant organic molecule in cells
Humans have app. 25000-30000 genes which encode for proteins
Functional diversity of proteins
> Structural
-keratin, collagen, actin,
myosin
Transport
-haemoglobin, transferrin,
ceruloplasmin
Hormonal
-insulin, thyroid stimulating
hormone (TSH),
adrenocortiotrophic
hormone (ACTH),
papthyroid hormone (PTH),
growth hormone (GH)
Regulatory
-enzymes
Size/molecular weight
> Usually given in Daltons or kDa
Dalton definition- one hydrogen atom has a mass of 1Da
Protein or polypeptide?
> The difference between proteins and polypeptide is their size (length)
Polypeptides are small proteins, molecular weight <less 5K Da
Polypeptide or peptide used to describe just a chain of amino acids linked together. Proteins usually used to describe a fully functional macromolecule
Composition of proteins
> Proteins are made up of repeating units- amino acids joined via a covalent peptide bond
There are 20 common (standard) amino acids
Conjugated proteins contain a prosthetic group
Conjugated proteins
> Metalloproteins- Metal group, very common
Glycoproteins- sugar group
Phosphoproteins- phosphate groups
Lipoproteins- lipid group
Nucleoproteins- associated with a nucleic acid (DNA or RNA)
Protein structure
> Primary structure
-amino acid sequence
Secondary structure
-alpha helix, beta pleated
sheet
Tertiary structure
-3D conformation (globular,
fibrous)
Quaternary structure
-Multi-protein assemblies
Amino acids
> Each R group is a different side chain
Substances that can either donate or accept a proton are called ampholytes
Stereochemistry
> 4 different groups around a carbon atom – chiral carbon
2 different ways to arrange in space - enantiomers
All naturally occurring amino acids found in proteins of living individuals have the “L” configuration (note glycine R=H not chiral)
D = Dextro, L = Levo
R for alanine = CH3
R for aspartic acid = see the other slides
Example of utilizing Aspartic Acid D / L features of amino acids in forensic science
> Can be applied in precise age determination of human remains
Teeth, disinfected in 10% formalin
Dried and enamel removed
Dental drill with diamond disc
Washed with acid, ethanol and water
Dentin powder
Special amino acids
> Cysteine has sulphur
Glycine only has H (very small)- not chiral
Proline is cyclic
Peptide bond
> Condensation reaction- loss of water
In a protein backbone there are restrictions as to which bonds can be rotated
The conformation of the main chain atoms is therefore determines by the values of these two angles for each amino acid
Why the proteins fold
> Protein 3⁰ structure is influenced by alpha and beta regions
Proteins fold in order to expose hydrophilic regions, and bury hydrophobic regions
Typically enzymes can have an inner core with large hydrophobic regions and/or protected regions to perform enzymatic reactions needed in the cell
α-helix (2° structure)
> Pro and OH-Pro break the αhelix
Ser, Ile, Thr, Glu, Asp, Lys, Arg,
and Gly destabilize the α-helix
Folding (3° structure)
Globular proteins have stable 3-
dimensional conformations at
physiological pH, temperature
Secondary Structure - α-helix
has φ and ψ angle pair
approx -60o and -50o with
3.6 residues per turn and
hydrogen bonds between C=0
of residue i and NH of residue i+4
Secondary Structure – β strand
> A β sheet is built up from a combination of several regions of the polypeptide chain. Β strands are usually from 5 – 10 residues long and are in almost fully extended conformation. > The β strands are aligned adjacent to each other such that hydrogen bonds can form between C=O and NH
groups.
β strands can either form parallel or antiparallel and each has a distinct hydrogen bonding pattern
Hydrophobic effect influences protein folding
> Hydrophobic amino acids tend to cluster in the interior of the protein molecule, avoiding contact with water
Hydrophilic amino acids tend to be arranged on the outside of proteins in contact with aqueous medium
4° structure of proteins
> Hemoglobin has four subunits
- Two α chains
- Two β chains
- a heme group associated with
each subunit
Many enzymes have quaternary structures
Ancient DNA and forensic scientists are particularly interested in Hb reactions in the dry state because both regularly encounter aged, dried bloodstains.
Determining protein
structure requires very
large equipment
> Synchrotron:
- X ray beam line
- X-ray crystallography
Magnet :
- Nuclear Magnetic
Resonance (NMR)
Forensics- finding evidence with proteins: Luminol
> the test is based on the ability of the luminol molecule to be oxidised by the reaction of sodium perborate with an oxidising agent such as haemoglobin
False positives with household chemicals
