Amino acids/ proteins Flashcards
Amino acids
what is the importance of amino acids?
the amino acids are important in biological systems
what are the two functional groups that make up the amino acid?
- primary amine group (-NH2) attached to the carbon atom adjacent to a carboxylic acid (COOH)
draw a prototype amino acid?
what is the r group?
Variable group - can be a hydrogen or something more complex
different amino acids have…?
different R groups
what is the position adjacent to the carboxylic acid group called?
the(alpha) α-position
so amino acids are often called..?
α - amino acid or α-aminocarboxylic acids
are all the 20 naturally occurring amino acids all α- amino acids?
yes all 20 naturally occurring amino acids are α-amino acids
which amino acid does not have the primary amine group (-NH2)
proline (secondary amine)
what is the simplest amino acid?
glycine
Draw the structure of glycine.
What is the IUPAC name for glycine
NH2CH2COOH - aminoethanoic acid
how are amino acids often named?
often called by their trival names but can be named systematicaly
Draw the structures of and give the IUPAC name for the following amino acids:
Alanine, Valine, Serine, aspartic acid, phenylalanine and proline
alanine - 2-aminopropanoic acid
valine - 2-amino 3-methylbutanoic acid
Serine - 2-amino 3-hydroxypropanoic acid
aspartic acid - 2-aminobutandioic acid
phenylalanine - 2-amino 3-phenylpropanoic acid
proline - pyrrolidine-2-carboxylic acid
all amino acids have a chiral centre except..?
glycine
this means that all amino acids apart from glycine are..?
optically active
How many enantiomers are made in nature?
in nature, only one amino acid enantiomer is made
how many enantiomers are made in a laboratory?
this mixture is optically…?
when amino acids are made in the laboratory a racemic mixture is produced. a racemic mixture is a 50:50 mixture of both enantiomers. therefore racemic mixtures are optically inactive
what two properties do amino acids have?
have both acid and base properties
what are substances that can act as acid and bases called?
amphoteric
How do amino acids act as acids?
amino acids contain the carboxylic group (-cooh) that is an acidic group and can donate protons (H+)
How do amino acids act as bases?
amino acids have the amine group (-NH2) that is a basic group and it can accept electrons
Write an equation to show how amino acids act as acids?
RCH(NH2)COOH) + OH- —> RCH(NH2)COO- + H20
(as acids amino acids donate protons)
write an equation to show how amino acids react as bases?
RCH(NH2)COOH + H+ —-> RCH(NH3)COOH
(accept protons)
what are amino acids at room temperature?
white crystalline solids
this gives them properties such as?
- being able to dissolve in water
- high melting points
what type of ion do amino acids exists as?
Zwitterions
Draw the structure of a zwitterion?
why do amino acids have such a high melting points?
amino acids are all solids at room temperature with much higher than expected melting points because they exist as zwitterions. Zwitterions have ionic bonding which is stronger than hydrogen bonding
what is the normal pH of amino acids?
pH = 7
What is the effect of decreasing the pH (adding acid e.g HCL) of an amino acid?
as pH is decreased, (H+ added) the zwitterions - COO- group gains a proton (acts as a base)
What is the effect of increasing the pH (adding alkali e.g NaOH) of an amino acid?
As pH increases the zwitterion - NH3 group loses a proton (acts as an acid)
Draw the general Zwitterion structure in a strong acid and in a strong base
Proteins
amino acids join together to form?
polypeptides
amino acids link together by…?
peptide links
what are peptide links also known as?
amide bonds
by which process do amino acids join together by?
condensation polymerisation
what is eliminated?
water
Draw the formation of a dipeptide from two amino acids of glycine
2 amino acids units make a..?
3 amino acid units make a …?
Many amino acid units make a..?
dipeptide
tripeptide
polypeptide
Draw the formation of the dipeptide Ala.Val from alanine and valine
draw the formation of the dipeptide Val.Ala from the amino acids valine and alanine (opposite ends of the molecules can form a different dipeptide)
show the formation of the tripeptide Ser.Phe.Cys from serine, phenylalanine and cysteine?
what are protiens?
proteins are naturally occurring polymers of amino acids joined together by peptide links (amide bonds)
why are proteins considered complex?
proteins are thought of as complex naturally-occurring polypeptides which are made up to about 40-400 amino acids
in the body condensation polymerisation is catalysed by what..?
enzymes
why are proteins important polymers?
muscles, skin and hair contain structural proteins. Hormones and enzymes are complex proteins that control the body’s metabolism
what is the primary structure of a protein?
the sequence of amino acids in a protein chain is called the primary structure
why are there different proteins?
different proteins have different order of amino acids and therefore have a different primary structure
which small protein was the fist to be sequenced? How many amino acid units does it contain?
insulin in the 1950’s - contains 51 units with 17 different amino acids
what is the secondary structure of a proteins?
the amino acid chain in a protein is held in a particular shape by an orderly arrangement of hydrogen bonds
when and where does hydrogen bonding occur?
hydrogen bonding can occur between the amide hydrogen of one peptide link and the carbonyl oxygen of another peptide link
Draw a diagram to show how hydrogen bonding can occur
hydrogen bonding arrangements give rise to two different types of secondary structure what are they?
- the chain can be coiled into an Alpha helix
- the chain can be folded into a beta pleated sheet
Explain how hydrogen bonds are weak but can be strong?
hydrogen bonds are relatively weak but when there are many hydrogen bonds, the structure is stable
what is the tertiary structure of a protein?
is the final 3-dimentional shape of a protein. the tertiary structure still has a single polypeptide
what bonds can be formed between different parts of the polypeptide chain?
disulphide bridges - are known to help stabilise tertiary structures
what can the tertiary structure contain more than 1 of?
the tertiary structure can have more than 1 secondary structure
what are the alpha helixes and beta pleated sheets folded into?
folded into a 3-dimentional compact globular protein or (fibrous protein)
what are disulphide bridges?
sulphur-sulphur bonds
which amino acid has a thiol functional group?
cysteine
draw the structure of the thiol
what does a thiol and a thiol react together to make?
one thiol (R-SH) can react with another thiol (R-SH) to form a disulphide (R-S-S-R)
draw the word equation to show how a thiol and a thiol react?
R-SH + R’-SH –> R-S-S-R’ + 2H+ + 2e-
a cysteine part of a protein chain can therefore react with another cysteine to form..?
a disulphide bridge
Draw this out to show the formation of the disulphide bond
how does this occur?
this can occur within a single protein chain or between one protein chain and another
what is the use of the disulphide bridge?
these disulphide bridges have a significant effect on protein shape and help stabilise the tertiary structure
what affects the formation of the disulphide bridge and hydrogen bonds?
temperature and pH -
what does temperature and pH affect?
so temperature and pH changes affect protein shape
Hydrolysis of the peptide bond linkage
when a peptide or protein is hydrolysed what does it break down to produce?
Hydrolysis breaks the peptide links (amide bonds) to form constituent amino acids
how is hydrolysis of proteins/peptides carried out in a lab?
hydrolysis in a laboratory is carried out by boiling the protein with a strong acid or alkali
How is hydrolysis of enzymes carried out in the body?
by enzymes
what is the hydrolysis of proteins in food called?
digestion
How can a mixture of amino acids be separated?
a mixture of amino acids (e.g from peptide hydrolysis) can be separated and identified by thin-layer chromatography
How can amino acids be located and identified?
amino acids can be located on a chromatogram using developing agents such as ninhydrin or ultraviolet light and identified by using the Rf values
Draw out the hydrolysis of the dipeptide Val.Ala into its two constituent amino acids (Valine and Alanine)
Draw the word equation to show the condensation reaction of amino acids to form a peptide
amino acids ——condensation polymerisation—-> peptide + water
draw a word equation to show the hydrolysis of a peptide to form constituent amino acids
Peptide —-hydrolysis (heat with acid or alkali) —-> amino acids
Enzymes
what type of molecules are enzymes?
proteins
what is the role of an enzyme?
enzymes are biological catalysts which help to speed up chemical reactions in biological systems (without lowering the activation energy)
each enzyme has a specific..?
purpose/ role
which reactions do enzymes catalyse?
enzymes catalyse all metabolic reactions in the bodies of living organisms
what is the name of the molecule that enzymes act upon?
the substrate
which part of the enzyme does the substrate bind to?
the active site
the enzymes active site is part of what structure?
3D (3-dimentional) part of the tertiary structure
explain how enzymes are specific in their action?
enzymes only work with specific substrates (usually one)
explain how enzymes are specific in their action using the lock and key model?
- the ‘lock and key model’ states that for an enzyme to work, the substrate has to fit inside the enzymes active site perfectly
- if the shape of the substrate does not mach with the enzymes active site shape then the reaction will not be catalysed (the key has to match the shape of the lock or the door will not open)
explain how an enzyme can work both ways?
enzymes can catalyse reactions, breaking up substrate molecules , however can also join together two substrate molecules or change the functional group of the substrate
explain how an enzymes active site is stereospecific?
- enzymes active site is stereospecific.
- enzymes active site only works on on enantiomer of a substrate
- only one enantiomer fits in the enzymes active site
- the other enantiomer does not fit properly so the enzyme can not catalyse the reaction
what is an enzyme inhibitor?
molecules that have a similar shape and seize to the substrate can act as enzyme inhibitors
explain how they may interfere with enzyme reactions.
- these molecules compete with the substrate to bind to the active site
- so the inhibitor molecule blocks the active site of the molecule
- if the inhibitor molecule binds to the active site, no reaction occurs
if there are a lot of inhibitor molecules..?
(compared to substrate molecules) there will be more active sites blocked and very little substrate will be able to get to the enzyme to react
what is the amount of inhibition also affected by?
the amount of inhibition is also affected by how strongly the inhibitior binds to the active site
What can inhibitors be used for?
Drugs (medicines) - so block the active site and stop it from working
explain how antibiotics work to kill bacteria?
some antibiotics work by blocking the active site of an enzyme in bacteria that helps make their cell walls. this causes their cell walls to weaken over time so that the bacteria will eventually burst
why does it take a long time to find a drug molecule to fit into an enzymes active site?
the enzymes active site is very specific so will take a lot of effort to find a drug molecule that will fit snuggly into the active site.
what else might make the process longer and challenging?
if the molecule is chiral - then only one enantiomer will fit into the active site, because the active site of enzymes is stereospecific
how can drug molecules be found?
using trial and error
what is a disadvantage of this?
takes too long
what is a new way of finding drug molecules that is much faster?
scientists speed up the process by using computers to help design inhibitor drugs
How can we use computers to find an exact drug molecule?
computers can model the active site shape and predict how well potential drug molecules will interact with it
explain the advantage of this?
- scientists can test many potential molecules this way - helping narrow down the search before laboratory testing starts
What are ACE inhibitors?
Angiotensin Converting Enzyme Inhibitors
what is the role of ACE inhibitors?
slow (inhibit) the activity of the enzyme ACE
What is Angiotensin?
is a hormone that acts to narrow blood vessels
explain how exactly ACE works?
ACE inhibitors reduce the production of Angiotensin, as a result blood vessels enlarge or dilate and blood pressure is reduced.
which medical condition requires people to take ACE inhibitors?
patients with high blood pressure (hypertension)
what are some examples of ACE inhibitors?
ramipril and perindopril
DNA
what is DNA?
Deoxyribonucleic acid
where is DNA found?
DNA is found in all cells and contains the genetic information of an organism
what is DNA’s role?
provides the instructions to build, maintain and regulate cells and organisms and is passed on when cells divide and when organisms reproduce
what is DNA made up of?
Many monomers called nucleotides
what does a nucleotide consist of?
- phosphate group
- pentose sugar
- a base
what is the phosphate group?
Draw the structure.
the phosphate group is a negatively charged phosphate ion
what is a pentose sugar?
Draw the structure of a pentose sugar in DNA
made up of 5 carbons, all pentose sugars in DNA are 2-deoxyribose
Draw Haworth projections for 2-deoxyribose and glucose
what are the 4 different bases in DNA, draw their structures?
Adenine, guanine, cytosine and thymine
when a phosphate and a sugar bond, and when a sugar and a base bond, what is formed and what is lost?
- covalent phosphodiester bond
- water is lost
nucleotide monomers join together to form a…?
polynucleotide chain
what is the covalent linkage between nucleotide monomers and phosphate group of one nucleotide and the pentose sugar of another nucleotide called?
sugar-phosphate backbone
what is the sugar-phosphate backbone?
this is a sugar-phosphate-sugar-phosphate polymer chain with bases attached to the sugar in the chain
on the formation of each phosphate-sugar linkage what is lost and what is formed?
a molecule of water is lost (condensation) and a covalent phosphodiester bond is formed
write out a word equation to show the formation of a dimer?
Nucleotide + Nucleotide –> Dinucleotide/(dimer) + water
DNA double helix
what is DNA formed by?
2 polynucleotide strands
the 2 polynucleotide strands coil together to form a..?
double helix
what is the double helix held by?
hydrogen bonds between the bases
each base pairs with..?
a complimentary base
A-T and C-G
so each strand is…?
complimentary to the other strand
what is hydrogen bonding?
hydrogen bonding is the attraction between a lone pair of electrons on a very electronegative atom (O,N or,F) and a nearby hydrogen which is directly bonded to a O, N, or F, on a neighbouring molecule
why does complimentary base pairing happen?
due to the arrangement of atoms (capable of forming hydrogen bonds) in the base molecules
How many hydrogen bonds do Adenine and Thymine form?
Draw hydrogen bonding between these two bases.
forms 2 hydrogen bonds
how many hydrogen bonds does Guanine and Cytosine form?
Draw hydrogen bonding between these two bases.
3 hydrogen bonds
why does only A pair with T and G pair with C?
- other base pairing would put the partially charged atoms too close to each other (repulsion) or too far away and not lined up properly
- the twists put bases the correct distance apart and lines then up properly so that hydrogen bonds can form
DONE
