amino acids, protines and enzymes

Function on herceptin

Anti cancer antibody

What % of cellular material is protien

50

Which is the most complex macromolecule

Carbohydrate

How to work out possibilities of proteins when given a. Number of amino acids

20^number fo amino acids in chain

Primary structure if protiens

Amino acid sequence

Secondary strucutre of protiens

How the peptide backbone folds to from either beta pleated sheets or alpha helices

Tertiary structure

How the protein strucutre folds to make 3D shape

Quaternary strcutre of proteins

When protien chains interact with other

When is an amino acids in the L configuration

When the amine group is on the left of the compound

When is an amino acid in its d isomer

When the amine group is on the right

How does l/d isomerism arise

Amino acids are chiral so amine group can go

On either the left of the right

What isomer are all proteinogenic amino acids in

L form

Why do only l fomrs of amino acids make up proteins

Possible that this presence was a consequence of a chance selection in nature- evidence that l amino acids are more soluble than a race mix of d and l amino acids which tend to form crystals

What kind of reaction forms apeptide bond

Condensaiton

Peptide bond occurs between

The cooh group o one aa and the amino groups in the next chain : CONH

How are the peptide bond between aa formed

Syntehisised directly hy ribomses and therefore have free amino acids and carboxylic ends

Features of the peptide bond

Rigid- partial double bond strucutre with delocalisation of electrons across the bond, can undergo cis trans isomerisms

Which is the more common form peptide bodn and why

trans_ allows for more space for amino acids side chains

How can AAs be categorised

Hydrophobic with no polar r groups,`polar with neutral r groups but with unenven charge distribution, positively changes with r groups that are Osita Ely charged at physiological pH, negatively charged with r group that have a negative charge at physiogical pH

What is physiological pH

7.4

A tphysiological pH what do aminoácido ids predominantly exist as

Zwitterions

In what direction is the polypeptide backbone formed

From the n terminus to the c terminus eg from free amine end to. Free carboxyl ends

How are proteins synthesised

Through condensation of thee peptide backbone by ribosomes

What kind o amino acid do ribosomal proteins Have

L

Where are d amino acids found

Non ribosomal proteins eg bacterial cell wlaks

What bonds hold together the peptide bonded amino acids

Covalent

How can protiens be drug targets

Anti ticos target active site of the ribosomes’ specific to bacteria

What to electron shells adopt when carbon forms 4 covalent bonds

SP3 hybridisation

What is sp3 hybridisation and why is ti beneficial for proteins

When covalent bonds point to corners of a pyramid- reduces overlap

How does the secondary strucutre of proteins have a “handednes”

Alpha helices are right handed and beta strands twist

Oligomeric state of protiens

Quaternary strcutre

How can teh 4 structure be handed

helical filaments of proteins display a hand, icsehdral viruses

Icosahedrons lviruses and there shape benefit

Virus whose outer protien shell has an icosahedrons shape= 20 equilateral triangles- is efficient T for packing dna.rna into capsid

How does chirlatiy affect protein interaction

Protiens and molecules have preference for specific chira forms of substrates

How did chira laity of thalidomide cause problems

The r enantiomer was therapeutic but s causes problesm and the body convert the r form to s form so there o was no safe way to just administer the r form

Phocomelia

Developmental disorder caused by thalidomide resulting is incorrectly formed upper-lower limb

If the pH is under the pKa of an amino acid chain what will teh charge be

Positive

What are some examples of enzymes that selenocysteine is an essential component of

Glutathione peroxidase, thioredoxin reductases, de-ions se, formate dehydrogenase

What type of compounds are Glutathione peroxidase, thioredoxin reductases, de-ions se, formate dehydrogenase

Antioxidants

Why is selenocysteine useful as an antioxidant

Has a Leonor redox potential

How is hydroxyproline produced

Not genetically encoded so produced via post translational modification of proline

Where is hydroxyproline found

In collagen, plant cell walls

What des hydroxyproline do in plant cell walls

Actas as an attatcchemnt point for glycans

What causes scurvy

Vit c deficinecy- if colágeno not made it breaks down

Residue

Each amino acid in the sequence of a polypeptide

Why is the peptide bond rigid and planar

Due to partial double character

What is the degree of rotation around the omega of the alpha carbon

180 is rtands or 0 if cis but most peptides are trans

What do protein folds do for the amount of energy is a system

Minimise it as folding involves a decrease in ram domes which causes a decrease in entropy

Features of alpha helix strcutre

Satisfies all h bonding potential within T he chain, is chiral, has the n terminus facing you as it for clockwise

Whta is the degree of repeat and what dos this mean

100 deg- there are 3.6 residues per turn of the alpha Leix

What is teh pitch in an alpha helix and what doe this mean 5.4A -

each residue is linked to the amino acid 4 along in the chains

Feature of beta strands

Has 2 residue replétales o every second side chain points int he same direction, there are hydrogen bonds every 2nd side chain, have 3 residue repeats of 7A, 2’15 strands forms a sheet, is not as stable as alpha helix and, the parallel formation is less stable than the antiparallel formation

Why is the antiparallel more stable for beta sheats

Teh hydrogen bonds from better

Why doe beta sheets have a right handed twist

To accommodate the l amino acid side chains which want to have as much space between them as possible

What do beta sheets often form

The core of globular protiens

What type of strucutre are most proteins

Globular

Why si x ray crystallography helpful

Can determine protein structures

Why was myoglobin one of the first proteins to have is strucutre determined

Is it highly abundnat in whales

How can proteins be modified

By binding other smal moelcuels of metals to enhance- differ this functions

Difference between myoglobin and haemoglobin

myoglobin has 1 subunit, haemoglobin has 4, myoglobin has a tertiary strucutre, haemoglobin has a tertiary and a quaternary strcutre

Whta do proteins often fold into

Domains- independently folding units of strucutre a bout 100’200 amino acids long, most proteins have multiple

Which is better conserved between proteins strucutre of sequence

Strucutre

What determines the unction of a protein

The strucuter

Quaternary strucutre of a protein

Arrangement of proteins with other proteins and small moelcuels

Homo oligomers

Proteins formed by 2 or more identical subunits with the same sequence

Dimer

2 proteins working together

What does a 30% amino acid ID or more mean between 2 protiens

They have. Similar strucutre and function