Proteins Flashcards
what is a gene
sequence of nucleotide bases in DNA molecules that codes for the production of a specific sequence of amino acids to make up a specific polypeptide (protein)
what is transcription
DNA is transcribed and an mRNA (messenger RNA) molecule is produced
what is translation
mRNA is translated and an amino acid sequence is produced
what is the role mRNA
carry the information encoded in the DNA from the nucleus to the site of translation on ribosomes
explain transcription
Part of a DNA molecule unwinds and the hydrogen bonds between the complementary base pairs break
exposes the gene to be transcribed
A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA which is catalysed by RNA
Free activated RNA nucleotides pair up, via hydrogen bonds, with their complementary bases on the exposed strand of the ‘unzipped’ DNA molecule
The sugar-phosphate groups of these RNA nucleotides are then bonded together in a reaction catalysed by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule
When the gene has been transcribed and the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule reforms
The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope
what is the strand called which the RNA nucleotides pair with
antisense or template strand, and it is used to produce the mRNA molecule.
The other strand is known as the sense or coding strand
how does RNA polymerase move along template strand
in the 3’ to 5’ direction
what happens after the mRNA leaves nucleus
the mRNA molecule attaches to a ribosome in the cytoplasm
what is tRNA
tRNA is a single stranded molecule of RNA that folds into a clover-like structre
triplet of unpaired bases at one end, known as the anticodon, and a region at the other end where a specific amino acid can attach
what do tRNA molecules do
bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome
The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet on the mRNA molecule called the codon
what is there at the beginning of each mRNA
Near the beginning of the mRNA is a triplet of bases called the start codon (AUG)
This is a signal to start off translation
what bond is formed between two amino acids and what is produced by the end
A peptide bond is then formed, via a condensation reaction
continues until a ‘stop’ codon on the mRNA molecule is reached
The amino acid chain then forms the final polypeptide
what direction does the ribosome move along the mRNA in translation
5’ - 3’
describe the genetic code
non overlapping
degenerate: multiple codons can code for same amino acid limiting effect of mutation
universal
what are proteins
polymers made of monomers called amino acids
what is the structure of an amino acid
amino group H-N-H
R group: H - C - R
carboxylic acid O=C-OH
what happens when a peptide bond is formed
A hydroxyl (-OH) is lost from the carboxylic group of one amino acid
A hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid. This is a condensation reaction so water is released
what happens during a hydrolysis reaction
he addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids
what are the first three levels of structure in proteins related to
Three are related to a single polypeptide chain
The fourth level relates to a protein that has two or more polypeptide chains
what is the primary structure
The sequence of amino acids bonded by covalent peptide bonds
what is the secondary structure
relates to hydrogen bonds forming between the amino group and the carboxyl group
weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
when does α-helix shape occur
when the hydrogen bonds form between every fourth peptide bond
when does the β-pleated sheet form
when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
what is tertiary structure
change of the secondary structure leads to additional bonds forming between the R groups
what are examples of addition tertiary bonds
Hydrogen (these are between R groups)
Disulphide (only occurs between cysteine amino acids)
Ionic (occurs between charged R groups)
Weak hydrophobic interactions (between non-polar R groups)
is common in 3D globular proteins
what is quaternary
Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule eg. haemoglobin
what structures contain hydrogen bonds
secondary and tertiary
what are the structure of globular proteins
Compact
Roughly spherical (circular) in shape
Globular proteins form a spherical shape when folding into their tertiary structure
why do globular proteins form spherical shape when folding into tertiary structure
Their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings
Their polar hydrophilic R groups orientate themselves on the outside of the protein
what is the function of globular proteins
The orientation of their R groups enables globular proteins to be (generally) soluble in water as the water molecules can surround the polar hydrophilic R groups
easily transported around organisms and be involved in metabolic reactions
give an example of a globular protein and explain its function and structure
Haemoglobin
It has a quaternary structure as there are four polypeptide chains
The four globin subunits are held together by disulphide bonds
haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red
binding oxygen in the lungs and transporting the oxygen to tissue to be used in aerobic metabolic pathways
what is the structure of fibrous proteins
long strands of polypeptide chains that have cross-linkages due to hydrogen bonds
do fibrous proteins have tertiary structure
little or no tertiary structure
function of fibrous proteins
large number of hydrophobic R groups, fibrous proteins are insoluble in water
Fibrous proteins are strong suitable for structural roles
examples of 2 fibrous proteins
Collagen is a connective tissue found in skin, tendons and ligaments
Elastin is found in connective tissue, tendons, skin and bone
describe collagen
Collagen is an insoluble fibrous protein
formed from three polypeptide chains closely held together by hydrogen bonds to form a triple helix
In the primary structure of collagen almost every third amino acid is glycine
Along with hydrogen bonds forming between the three chains there are also covalent bonds present
how are collagen positions
The collagen molecules are positioned in the fibrils so that there are staggered ends
When many fibrils are arranged together they form collagen fibres
function of collagen
staggered ends????
structural protein forming connective tissues
The presence of the many hydrogen bonds within the triple helix structure of collagen results in great tensile strength
The staggered ends of the collagen molecules within the fibrils provide strength
compare collagen and haemoglobin
triple helix / 4 polypeptide chains
long and thin / spherical round
structural / functional
receptive amino acid variation / variable
insoluble / soluble
what does biological catalyst mean
they function in living systems
‘Catalysts’ because they speed up the rate of chemical reactions without being used up or undergoing permanent change
They speed up reactions by reducing the activation energy of reactions
are enzymes globular or fibrous
with what type of structure
globular proteins with complex tertiary structures
made up of two or more polypeptides and therefore have a quaternary structure
are enzymes globular of fibrous and what does this mean
globular proteins
This means their 3D shape is determined by the complex tertiary structure of the protein that makes up the enzyme and is therefore highly specific
enzymes have a unique….
active site where specific substrates bind forming an enzyme-substrate complex
for a reaction to occur what conditions?
Substrates collide with the enzymes active site and this must happen at the correct orientation and speed
how does the 3d shape of active site change
Proteins are formed from chains of amino acids held together by peptide bonds
The order of amino acids determines the shape of an enzyme
If the order is altered, the resulting three-dimensional shape changes as determined by complex tertiary structure of protein that makes enzyme
what does higher enzyme concentration lead to
The higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation
what is a limiting factor
If the amount of substrate is limited, at a certain point any further increase in enzyme concentration will not increase
method for investigating the effect of enzyme concentration on the rate of reaction
Add a set volume of hydrogen peroxide solution to a boiling tube
Add a set volume of buffer solution to the same boiling tube
Invert a full measuring cylinder into a trough of water
Place the end of the delivery tube into the open end of the measuring cylinder and attach the other end to a bung
Add a set volume of one concentration of catalase to the boiling tube and quickly place the bung into the boiling tube
Record the volume of oxygen collected in the measuring cylinder by the water displaced every 10 seconds for 60 seconds
Repeat the whole experiment for the different concentrations of catalase
results of investigating enzyme concentration on the rate of reaction
As the concentration of catalase increases the volume of oxygen produced would increase
This is because there would be more available active sites for hydrogen peroxide to use
The volume of oxygen would plateau out after the initial rate of reaction due to the substrate decreasing, having been converted into the product (oxygen)
how does primary structure of leptin allow it to be water soluble
{primary structure / sequence of the amino acids} determines the folding (of the polypeptide)
forming a globular structure
hydrophobic (R) groups located in the centre of the protein / hydrophilic (R) groups located on the outside of the protein
water forms hydrogen bonds with { protein / hydrophilic groups}
How does removing and substituting have different affects on protein structure
deletion could affect every codon (on the mRNA) / substitution will only affect one codon (1)
deletion more likely to affect the position of { stop codon / start codon } (1)
deletion results in a different sequence of amino acids / substitution may not affect the sequence of amino acids (1)
substitution may code for the same amino acid (1)
(same amino acid) due to the degenerate nature of the genetic code (1)
how doe substitution affect the function of haemoglobin
(because) {one tripletis affected / a different triplet code is produced } (1)
* (the mutation) could change one of the amino acids (1)
* this would (change the bonds formed betweer the R groups / cause a change in the tertiary structure! (1)
* the haemoglobin would no longer be able to bind to oxvaen (1)
importance of primary structure for function of enzyme
(primary structure) determines interaction between {amino acids / R groups} (1)
(primary structure) determines { folding / tertiary structure }
(1)
(therefore) affecting the shape of the active site
(1)
* (active site is) complementary to ATP (1)
how can a base mutation lead to altered primary structure of an enzyme
changes in base will alter the triplet code which changes the codon and hence different amino acid sequence in primary structure
how can an enzyme break down polysaccharide
hydrolysis of glucosidic bonds
compare structure of globular and fibrous
both are chains of amino acids joined by peptide bonds (1)
both contain named bonds (holding molecule in its three dimensional shape) (1)
globular proteins have hydrophilic groups on the outside whereas fibrous proteins have hydrophobic groups on the outside (1)
globular have tertiary or quaternary structures whereas fibrous have little or no tertiary structure (1)
globular are folded into compact shapes whereas fibrous have long chains (1)
how amino acids would be incorporated into a surfactant protein
mRNA of surfactant protein is attached to ribosome
pairing of anticodons on tRNA and mRNA and a tRNA is specific to one amino acid. Amino acids join by peptide bonds and a tertiary structure is formed
what is an allele
is it an alternative version of a gene found at the same locus on a chromosome
Vinegar contains ethanoic acid. why would vinegar result in anthocyanin pigments leaving onion cell
increased permeability of (cell surface) membrane
the low pH would {change the shape of / denature} proteins (in cell surface membrane)
(as vinegar) affects bonds (in protein)
explain how the primary structure of an enzyme determines its three dimensional structure and its properties
(primary structure) {position / sequence / order /eq} of the {amino acids / R groups} / eq;
idea that this determines the {positioning / type} of the {bonds / folding / eq} ;
determining the {shape / properties} of the active site / eq;
idea of interaction of active sites and substrates e.g. enzyme substrate complex forms
idea of {polar / hydrophilic} on the outside of enzymes / {non polar / hydrophobic} on the inside / eg;
Describe the structure of an enzyme.
ref to an enzyme as a protein ;
- ref to {3D / tertiary / globular} structure ;
- ref. to named bonds (holding structure in
place) ; - between the R groups ;
- ref to active site ;
- idea of specificity of active site
