Proteins 1 Flashcards
What are the major steps of protein synthesis?
DNA to RNA (transcription)
RNA to protein (translation)
What is transcription?
The first step of gene expression where a particular section of DNA is copied onto RNA
What is translation?
The process where ribosomes synthesis proteins
What does a diagram of DNA look like?
What kind of bonds link the two bases of two DNA backbones?
Hydrogen bonds
What is the backbone of DNA called?
Deoxyribose-phosphate backbone
What are the four bases present in DNA?
Adenine (A)
Cytosine (C)
Thysine (T)
Guanine (G)
What is the base pairing of DNA?
Adenine pairs with thymine
Cytosine pairs with guanine
What is the double helix?
The double stranded molecule that DNA exists as
What does the general structure of an amino acid look like?
What are the sections of an amino acid?
Amino group
Side chain
Carboylic acid group
Does each amino acid have a unique side chain?
Yes
What is physiological pH?
7.4
What happens to an amino acid at physiological pH?
The carboxyl group dissosiates forming a negatively charged carboxylate ion (-COO^-) and the amino group is protonated (-NH3^-)
What does dissociate mean?
Molecule splits
What does protonated mean?
Transfer a proton to a molecule
What does the dissociation of amino acids at physiological pH allow them to do?
Amino acids join together with a peptide bond with the loss of 1 molecule of water
What does the reaction of two amino acids joining together look like?
Where does translation occur?
In the ribosome
What determines the properties of an amino acid/protein?
The side chain
What are different side chain properties
Aliphatic (organic compounds where carbon atoms form open rings, not aromatic rings)
Aromatic
Sulphur containing
Basic
Acidic
Uncharged polar
Other (such as proline)
What do non polar side chains not do?
Bind or give of protons
Participate in hydrogen or ionic bonds
Non polar side chains can be thought of as being hydrophobic, what interactions do they promote?
In aqueous solution (polar environment) they cluster in the interior to give 3D structure
In hydrophobic environments they are on the outside interacting with the lipid environment
What does hydrophobic mean?
Repels water, tends to have no charge
What does hydrophilic mean?
Attracted to water, dissolves in water
What are the properties of uncharged polar chains?
Have a net charge of 0
Contain partial charges that can form bonds
What are the properties of sulphur containing side chains?
Contains a sulfhydroxyl group (-SH) which is often important in the active site of enzymes
What are the properties of acidic side chains?
Side chains are fully ionised, containing a negatively charged carboxylate group (-COO-)
Negatively charged at physiological pH
Are orignially proton donors (before they are ionised)
What does an amino acid with an acidic side chain look like?
What are the properties of basic side chains?
Originally accept protons (before ionised)
Positively charged at physiological pH
Are fully ionised, containing a positively charged amino group (-NH3+)
How many kinds of amino acids are coded by DNA?
20
What are the four protein structures?
Primary
Secondary
Tertiary
Quarternary
What is the primary structure of a protein?
The sequence of amino acids in a polypeptide chain
What is the primary structure the source of?
Versitility and function due to there being 20 different occupants for each position an an enormous range of sequences
What is the secondary structure of a protein?
The spatial arrangement of amino acid residues that are near each other in the linear sequence
What are the three forms of secondary structures?
Alpha helix
Beta sheet
Beta bends
What is the alpha helix structure?
A coiled structure held in place by hydrogen bonds between every N-H group and the O of the C=O group in the next turn of the helix
What is the beta sheet structure?
Composed of two or more peptide chains which are almost fully extended, the hydrogen bond is perpendicular to the polypeptide backbone
What is the tertiary structure of a protein?
Spatial arrangment of amino acid recidues that are far apart in a linear sequence
What forces hold the tertiary structure in place?
van der Waals
Ionic interactions
Hydrogen bonds
Disulphide bridges
Hydrophobic interactions
What are van der Waals?
Non specific weak attraction between atoms 0.3-0.4nm apart
They are individually weak but collectively strong
What are ionic interactions?
Occurs between two oppositely charged side chains
These are strong
What are hydrogen bonds?
Occur when H is bonded to O, N or F and lone pair of electrons are present
Similar to van der Waal but are stronger and more permanent
They are 1/20 the strenth of covalent bonds
What are examples of molecules that form hydrogen bonds?
Water and ammonia
What is a disulphide bridge?
Strong covalent bond between two cysteine residues
Can occur within and between a polypeptide
What are hydrophobic interactions?
Intra-polypeptide interactions occuring in an environment with proteins which water is excluded
Where are hydrophilic and hydrophobic side chains found within a protein?
Hydrophillic side chains are found on the outside interacting with the environment (making the molecule soluble)
Hydrophobic side chains are found on the inside interacting with each other (giving 3D structure)
What is the quarternary structure of a protein?
Spatial arrangement of individual polypeptide chains in a multi sub unit protein
How are the subunits in the quarternary structure held together?
Non covalent interactions, they may function independently or in collaboration
What is denaturing?
Disruption and possible loss of both the secondary and tertiary structures
Leads to the loss of 3D structure and function
Are denaturing reactions enough to break the peptide bonds of the primary structure?
No
What is renaturation
Gaining of a proteins 3D shape and function after denaturation
It is rarely possible as the effects of denaturation are often permanent
What are some causes of denaturation?
Acids
Heat
Solvents (ethanol, methanol)
Cross linking reagents (formaldehydes)
Chaotropic agent (urea)
Disulphide bond reducers
What are some effects of denaturation?
Decreased solubility
Altered water binding capacity
Loss of biological activity
Improved digestability
What is protein digestion?
Cleavage of the peptide bonds within the primary structure
What are types of protein digestions?
Peptidases (cleavage of peptide bonds)
Endopeptidases (cleave of internal bonds)
Exopeptidases (cleavage of one amino acid at a time)
Carboxypeptidases (cleaves at the -COOH terminal)
Aminopeptidases (cleavage at the -NH2 terminal)
What is protein structure dependent on?
DNA sequence coding for amino acids
Interactions of amino acids
structure determines function
What happens when proteins are denatured?
Structure and function are lost
