week 3 Flashcards
what is mitochondrial DNA, where is it found and what are the consequences of mutations
found near mitochondrial membrane and is called mtDNA
it is like bacterial DNA
mutations cause diseases centred around inability to generate enough energy
what is the error rate of DNA repair and why
very low as the cell goes to lengths to keep genetic material correct
what is the one gene one mutant theory and what is its importance
in experiment each mutant could only grow if supplied with a compound made after the defective step
showed that each gene codes for a single polypeptide, and that genes control metabolism
what are the main structural differences between dna and rna
Uracil instead of thymine, bonds with Adenine
made of ribose, doesn’t have a regular 3d structure but can form a 3D shape
single stranded
what is transcription and its catalyst
synthesis of RNA, catalysed by RNA polymerase
what are the steps of transcription
3 stages - initiation, elongation and termination
what occurs during initiation (transcription)
happens at a promoter site containing a particular sequence of bases
in prokaryotes the rna polymerase recognises and binds to promoter site
in eukaryotes a set of proteins called transcription factors are involved in the binding of rna polymerase to the promoter (TATA box)
what occurs during elongation (trascription)
local unwinding of 102 turns of DNA and addition of nucleotide units
DNA rewinds as the RNA polymerase proceeds along the template strand
many RNA polymerase molecules can be transcribing a particular gene simultaneously, allowing large amounts of protein to be made
what occurs during termination (transcription)
not well understood, appears to be signalled by the sequence of the RNA transcript itself
after this sequence has been transcribed proteins bind the growing transcript and cut it free from the polymerase, the transcript is released and the RNA polymerase detaches from the DNA
what are the three main types of RNA
mRNA - messenger
rRNA - ribosomal
tRNA - transfer
what makes RNA in prokaryotes
a single RNA polymerase
how is the primary RNA transcript modified before leaving the nucleus in eukaryotes and what is their affect
a cap is added to the 5’ end
polyA tail is added to the 3’ end
they protect the mRNA from degrading, aid export from the nucleus and help the mRNA to anchor to the ribosomes
what is mRNA splicing
the removal of non-coding regions, leaving exons
carried out by snRNP’s, which consist of small nuclear RNA and various proteins
several snRNP’s and other proteins form a spliceosome complex
how are splice sites marked
short nucleotide sequences at the end of introns mark the splice sites for recognition of snRNP’s
often there are more untranslated pre-mRNA sequences like introns, 5’ cap, polyA tail - than translated sequences like exons
why is splicing important
helps increase the range of possible protein products from a given gene (alternative)
alternative splicing of RNA leads to male and female Drosophila, and switches between classes of certain antibodies for examples
final transcript after splicing = mature mRNA
what was Garrod’s work to do with metabolism about
studied rare genetic diseases and discovered that some disorders were caused by faulty metabolism due to missing or defective enzymes.
what is the overall process of translation
mRNA is moved through a ribosome, codons are translated into amino acids one by one
tRNA codons add amino acid cargo to growing polypeptide chain when anticodon recognises codon
what happens during initiation (translation)
occurs in ribosome, ribosome binds to the mRNA at the start codon (AUG)
tRNA attaches to AUG using its anticodon (UAC)
describe elongation (translation)
inside ribosome
tRNA molecules bring amino acids based on the mRNA codons
ribosomes forms peptide bonds between amino acids, creating a growing polypeptide chain
ribosome moves along the mRNA 5’-3’
what occurs during termination (translation)
ribosome reaches the stop codon
release factor binds to the stop codon instead of tRNA
ribosome disassembles and the new protein is released
protein undergoes folding and modification
what enzyme is responsible for loading of a tRNA molecule with its correct amino acid
aminoacetyl-tRNA
how do enzymes interact with amino acids
there are 20 enzymes - one for each amino acid, each one has an active site that houses a specific combination of tRNA and amino acid
what are ribosomes made up of
2 subunits, large and small, and they only join together then mRNA is present
65% of the mass of a ribosome is rRNA, the rest is proteins
they have a p site, an a site and an e site
what does each site on a ribosome do
P site: peptidyl-tRNA site: binds to the growing peptide chain
A site: aminoacyl-tRNA site; binds the incoming aminoacyl-tRNA
E site - exit site to allow the discharged tRNA to leave the ribosome
how is protein structure stabilised
non-covalent interactions eg H bonds, ionic bonds and hydrophobic bonds
how do hydrophobic interactions on proteins work
non-polar side chains cluster themselves together excluding water and allow water molecules to form H bonds between themselves
give a few examples of proteins and their functions
enzymes = biological catalysts
structural proteins for supporteg collagen
hormones for signalling eg haemoglobin
recpetors for signalling eg insulin receptor
do all proteins look the same?
no, their structures vary in relation to their function
what are proteins made up
polymers of amino acids liked by peptide bonds
how are peptide bonds formed
condensation between the alpha amino group of one amino acid and the carboxyl of the next one
they are planar and very stable
how many amino acids make up a protein
20, each protein also has different side chains
how are the unique amino acid sequences of each protein determined
by the DNA sequence of its gene
how is the 3D structure of a protein determined
by its amino acid sequence, allowing the protein to bind specifically to other molecules
how are the 2 ends of a polypeptide chain defined
N or amino terminus (NH3) , and C or carboxy terminus (COOH)
what are main functions of proteins in the body
communication, movement and defence
what is the general formula for an amino acid
NH2 - RCH - COOH
what is the general formula for a peptide bond
C-N bond resulting from a reaction between an amine and carboxylic acid group
what is the average number of amino acids in a protein, an what is unusual
average = 500
less than 20 amino acids are called aligopeptides
why do sidechains arise
non-polar side chain cluster together due to hydrophobic interactions, due to H bonds formed between water molecules and other polar molecules
what is the primary structure of a protein
the amino acid sequence
what is the secondary structure of a protein
the way the backbone folds regularly, stabilised by H bonds between backbone C=O and N-H groups
what is the tertiary structure of a protein
the way the polypeptide chain folds into a compact 3D shape, stabilised by H bonds, ionic bonds, hydrophobic interactions and disulphide bonds involving backbone or sidechain groups
what is the quaternary structure of a protein
arrangement of subunits in proteins containing 2 or more polypeptide chains, stabilised as tertiary structure
not in all proteins
what is the alpha helix and beta sheet
both types of secondary protein
different proportions exist in different proteins
alpha helix = rigid rod with sidechains on the outside
beta sheet forms a flat surface that can be twisted into a cylinder, with sidechains alternatively above and below the sheet, and chains running parallel or antiparallel
what strength of interactions stabilise a protein and what are the implications
held by a number of weak interactions
means protein conformation is flexible
also conformation can be easily destroyed/denatured eg heating
also means the function of a protein can be regulated by events that cause a change in conformation eg binding to another molecule
what causes denaturation
high temps, detergents, changes in pH
in some proteins, what aids folding
chaperone proteins
what is a protein domain
they are an independently stable part of the polypeptide, usually with a specific function
most proteins contain 2 or more domains, each often corresponding to an exon
how can evolution of new proteins happen
via domain swapping
how do proteins bind to other molecules
by making many precise weak interactions with their target
- ionic bonds to the negatively charged phosphate groups
- H bonds to the OH groups pf ribose
- hydrophobic interactions with the adenine ring
- H bonds to the N atoms of the adenine
what is de novo protein synthesis
synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation
how is de novo synthesis used in vaccine progression
to generate a better immune response to RSV a resp virus
use proteins to breakdown gluten in the stomach for a treatment for celiac disease
what are challenges and aims in using de novo synthesis
finding a universal flu vaccine to find a lifetime
using new version of amino acids
new proteins to help ecological problem
what are possible new drug developments using constrained peptides
peptide library creation
novel amino acids
tight structure - resistant to breakdown
protein inhibitors or molecular glue
what are the characteristics of enzymes as catalysts
very successful and specific
speed up reactions and reduce activation energy
each enzyme can catalyse several hundred reactions per second
they bind to their substrate and catalyse the reaction at the active site
explain induced fit model
- substrates enter active site, enzyme changes its active site shape to enfold substrate
- substrate held in the active site by weak hydrogen and ionic bonds
- active site can lower activation energy and speed up reaction via a few methods
- substrates are converted to products
- products are released
- active site is now available for 2 new substrate molecules
how can active sites lower activation energy and speed up a reaction
acting as a template for substrate orientation
stressing the substrates and stabilising transition state
providing a favourable microenvironment
participating directly in a catalytic reaction
how are enzymes used in industry
proteases and lipases in biological detergent and glucose isomerase to product fructose corn syrup
name some places enzymes are regulated
proteases in the blood
end product inhibition
binding of another molecule eh phosphate group
what is the structure of antibodies
2 heavy and 2 light chains joined together by disulphide bridges
both types of chain have variable and constant regions
antigen specificity is conferred by the variable regions
an antibody recognises just a small part of the antigen called the epitope
how is protein funtion regulated
regulatory proteins can occur in two or more conformations with different properties
regulation is crucial in homeostasis
a single mutation can have severe consequences
which proteins are usually spanning membranes
alpha helices or beta Barrells
the parts exposed to the membrane is hydrophobic, the parts exposed to the inside and outside of the cells are hydrophilic
name functions of membrane proteins
they have many, some include cell-cell recognition, signal transduction via hormone receptors and transport
many hormone receptors are targets for drugs eg beta blocker
how do fibrous proteins contribute
strength or flexibility
some proteins associate to form filaments eg myosin and actin in muscles
