Module 2 - Nucleotides and Nucleic acid

What are amino acids and proteins?

building blocks of proteins which are essential macromolecules - monomers when joined to another is a dipeptide and the polymer is polypeptide (chain of amino acids form with each amino acid by peptide bond (covalent) where amino acids at each end of chain form two end terminals: N + C terminal) - proteins polymers made of chains of amino acids contain C,H,O + N some contains sulphur 

What are the roles of protein?

1.Enzymes - proteins used to breakdown + synthesise molecules
2.Antibodies - proteins involved in immune response
3.Transport - some proteins move molecules or ions across membrane
4.Structural components - protein such as keratin + collagen used to create strong fibres 
5.Hormones - some proteins act as chemical messengers in the body
6.Muscle contraction - muscles are made up of proteins

What is the structure of amino acids?

20 different amino acids + all have same general structure of - central carbon atom - amino group (-NH2) - carboxyl group (-COOH) - hydrogen atom (-H) - an R group (each amino acid has different R group which determines its properties) eg cysteine contains a sulphur atoms allowing it to form disulphide bonds - hydrogen atom (glycine) smallest amino acid and only amino acid that doesn’t carbon in R group - complex ring structures (tryptophan) very large Residual group

How are dipeptides synthesised?

dipeptides are synthesised via condensation reactions - when two amino acids join the hydroxyl (OH) in carboxyl group of 1 amino acid react with the hydrogen (H) in amino group of another - releases a water molecule and forms a peptide bond between carbon of 1 and nitrogen of another 

How are dipeptides broken down?

dipeptides are broken down via hydrolysis reactions - when a water molecule is added to dipeptide the peptide bond is broken to release the two amino acids

What is the test for proteins?

to find out whether a sample contains peptide bonds (hence proteins) you must carry out Biuret test
steps 1. place food sample in test tube 2. add equal volumw of Biuret solution (sodium hydroxide and copper sulphate) 3. if proteins are present,solution will turn from blue to purple - if no protein is present solution remains blue - intensity of violet colour is proportional to concentration of protein + can be determined using colorimetry

What are the four structures of protein?

proteins are large,complex molecules with unique 3D structures where there are four main levels: primary - secondary - tertiary - quaternary
each level has specifc bonds influencing overall shape 

What is the primary structure of protein?

made up of unique sequence of amino acids in polypeptide chain where structure held together by peptide bonds where a change to just one of the amino acids in chain can result in change to proteins structure and function - simply the order of amino acids in polypeptidechains - each amino acid joined on chain by condensation reaction
change in nucleotide sequence of genes coding region will lead to different amino acid added to pp chain

What is the secondary structure of protein?

involves hydrogen bonds forming between the amino group of one amino acid and carboxyl group of another amino acid further down chain - causes polypeptide chain to coil/fold into either an alpha helix or beta-pleated sheet structure
structure is stable as has many hydrogen bonds leading to overall high stability

What is a alpha-helix?

hydrogen bonds form between the oxygen of a -CO group of one amino acid + hydrogen of -NH2 of another holding a section of the polypeptide chain in a helical shape - held permanently in place by hydrogen bonds

What are beta-pleated sheets?

parts of polypeptide chain which are connected laterally by hydrogen bonds - folds into concertina-like way with hydrogen bonds with hydrogen bonds connecting to adjacent pleated sheets where in both hydrogen bonds are weak but number present in such protein molecules help maintain stability of molecule

What is the tertiary structure?

form when polypeptide chains folds and twists further to create a complex 3D structure - occurs when secondary structure becomes further coiled includes 4 bonds - hydrogen bonds - ionic bonds - disulfide bridges - hydrophobic + hydrophilic interaction - hydrophobic amino acids orientate themselves towards outside protein 

What are hydrogen bonds in tertiary structure?

individually weak but provide strength in numbers - attraction between slight positive amino group (-NH) + slight negative charge of another (-CO)

What are ionic bonds in tertiary structure?

these form between postive and negative R groups

What are disulfide bridges in tertiary structures?

form between positive and negative R groups that contain sulphur (such as cysteine) - covalent bond

What are hydrophobic and hydrophilic interactions in tertiary structure?

weak interactions between polar and non-polar R groups

What is the quaternary structure?

involves two or more polypeptide chains held together by same bonds found in tertiary structure of a protein - also involves addition of non-proteins groups known as prosethic groups - all proteins are the other strcutures but only some have quaternary

What are the two types of protein?

globular proteins - compact,spherical and soluble proteins - 3D shape important for metabolic processes as shape allows enzymes to have active sites - usually soluble
fibrous proteins - form long and narrow strands and insoluble proteins - have tertiary structure

What are some examples of globular proteins?

tend to have metabolic roles in the body such as 
1.enzymes - speed up chemical reactions in body
2.hormones - chemical messengers that travel in bloodstream
3.antibodies - bind to + prevent spread of pathogens

What are conjugated proteins?

some globular proteins contain non-protein known as prosthetic group - this includes lipids which forms lipoproteins - carbohydrates which forms glycoproteins - metal ions such as iron in haemoglobin

What are some examples of fibrous proteins?

tend to have structural roles in the body such as
1.keratin - found in the skin,hair and nails
2.collagen - found in connective tissues such as bone + muscle
3.elastin - found in elastic connective tissue + allows skin to return to normal apperance after being pinched
4.fibrin - blood-clotting protein 

What are some specific examples of globular protein?

haemoglobin - insulin - amylase

What is haemoglobin?

globular protein used to carry oxygen around body in red blood cells - made of four polypeptide chains meaning has quaternary structure - two of these chains are alpha chains and the other two known as beta chains - example of conjugated protein because each polypeptide chain contain a haem group (prosthetic group - non-protein part of protein permanently attached to molecule + vital for normal function) which contains an iron atom - can reversibly bind with one oxygen molecule meaning a molecule of haemoglobin (with four haem groups) can carry four oxygen molecules at a time

What are the features that allow haemoglobin to transport oxygen around the body?

1.four polypeptide chains/subunits (surrounds central haem group) - means four molecules of oxygen can be carried at a time 
2.haem group - contains iron that reversibly binds 
3.compact globular structure - allows haemoglobin to fit inside red blood cells

What is insulin?

globular protein known as a hormone + used to regulate blood glucose concentration - hormones travel in the bloodstream and so need to be soluble + also need a specific shape to fit with receptors on cell-surface membranes of their target cells
made up of two polypeptide chains with 21 amino acids residues in chain A + 30 amino acids residues in chain B held together by 3 disulfide bonds 

What are amylase and pepsin?

globular protein known as an enzymes + responsible for breakdown of starch into maltose - enzymes is made up of single polypeptide chain folded using both alpha-helixes + beta-pleated sheets 
protease enzyme made in stomach and helps digest protein - made of single polypeptide chain - has more acidic R groups than basic R groups explains why so stable in acidic environment of stomach - tertiary structure held together by hydrogen bonds and 2 disulfide bridges

What is collagen?

fibrous protein used as structural component in skin,tendons,cartilage,bones,teeth + walls of blood vessels
made up of three polypeptide chains (made of 3 repeating amino acids) wound around each other in rope-like structure - provides strength by hydrogen + covalent bonds between chains + flexibility to the molecule - high tensile strength - forms collagen fibril that links with others to form a collegen fibre

What is keratin?

group of fibrous proteins found in the hair,skin and nails
contain large number of the amino acids cysteine (contains element sulphur) which allows disulfide bonds to form creating strong + insoluble molecules + can be either flexible or rigid depending on number of bond - highly insoluble in water + organic solvents

What is elastin?

fibrous protein found in elastic connective tissue such as walls of blood vessels - elastic which allows tissues to expand and return to their original shape 

What are nucleotides?

building blocks of nucleic acids - monomers which can join together to form dimers (dinucleotides) + polymers (polynucleotides) - nucleic acid is a functional molecule made of 1 or more polynucleotide chains
made of 3 components that are bonded covalently - pentose sugar (contains 5 carbon atom) - organic nitrogenous base (contains carbon + nitrogen) - phosphate group (contains phosphate)

What are nucleic acids and how do they form?

vital molecules as carry genetic code so important for passing on information from each generation - form when 2 polynucleotide chains join together by hydrogen bonds between nitrogenous bases where double strand forms between two parallel polynucleotide strands join together by hyrdogen bonds where strands described as antiparrallel as run in opposite direction to eachother - phosphate combined with carbon 3 of one deoxyribose and carbon 5 of next - both backbones twist to form double helix

What are polynucleotides?

nucleotides joined together via condensation reactions to form a polynucleotide - phosphate group of 1 nucleotide forms a covalent bond with the sugar of another forming a phosphodiester bond - many nucleotides can join in this way to create chain of sugars + phosphates known as sugar-phosphate backbone - phosphate attaches to hydroxyl group of 5’ carbon of one sugar + hydroxyl group of 3’ carbon of sugar of next nucleotide - bond called ‘5-3’ phosphodiester linkage -phosphodiester bonds can be broken via hydrolysis reactions releasing the nucleotide monomers - nucleotides must have same pentose sugar

What is DNA?

deoxyribonucleic acid is type of nucleic acid containing instructions needed to make proteins 
made of 3 components - deoxyribose (pentose sugar) - a base (Adenine,thymine,guanine or cytosine) - phosphate group

What is the structure of DNA?

Watson + Crick credited with structure of DNA - two polynucleotides atrands lie in opposite direction known as antiparallel - two strands joined to make a double strand which twists forming a double helix - 2 sugar-phosphate backbones attached to one another by complementary base pairs

What are the features allow DNA to pass genetic information from one generation to another?

1.sugar-phosphate backbone - protects coding bases on inside of helix
2.double stranded - allows strands to act as templates in DNA replication
3.large molecule - stores a lot of information
4.double helix - makes the molecule compact
5.complementary base pairing - allows accurate DNA replication
6.weak hydrogen bonds - allows strands to separate in DNA replication

How are the four bases of DNA caregorised?

purines - larger bases that contain two carbon-nitrogen ring structures (A + G)
pyrimidines - smaller bases that contain one carbon ring structure (T+C) Uracil

What are the complementary base pairs?

hydrogen bonds between complementary bases on opposite strands
adenine pairs with thymine via 2 hydrogen bonds
cytosine pairs with guanine via 3 hydrogen bonds
known as complementary base pairing - a smaller pyrimidine base always binds to larger purine base - arrangement maintains a constant distance between two sugar-phosphate backbones + becomes stable

What is RNA?

ribonucleic acid is type of nucleic acid that uses information from DNA to synthesise proteins - transfers genetic information from DNA to the ribosomes
made of three components - ribose (pentose sugar) - bases (adenine,uracil,guanine or cytosine) - phosphate group

What is RNA structure?

contains sugar ribose rather than deoxyribose + contains uracil in place of thymine
single stranded molecule made of just one polynucleotide strand (held together by phosphodiester bonds between nucleotides) where strands are much shorter than DNA strands as only contain small portions of genetic code eg mRNA has instructions for one gene

What is DNA replicated?

copied via process known as semi-conservative replication - produces DNA molecules consisting of one original DNA strand + one newly synthesised DNA strand therefore original molecule is semi-conserved - during replication each of 2 strands used as template from which new strands are copied

How is DNA replicated?

1.enzyme DNA helicase breaks hydrogen bonds between complementary bases this unwinds double helix + seperates the strands 
2.each strand acts as a template as free nucleotides attract to their complementary bases
3.enzyme DNA polymerase joins free nucleotides (attracted to exposed bases on template strand) together via condensation reactions in the 5’ to 3’ direction - forms phosphodiester bonds to create sugar-phosphate backbone of new DNA strand
4.two identical copies of DNA are made - each copy made up of one original DNA strands + one new DNA strand (semi-conservative replication)

What forms from DNA replication and what is involved?

2 exact DNA copies are made - each copy carries one strand of original DNA that acts as a template (conserved) + 1 strand of new nucleotides
single-strand binding (SSB) proteins - keep each strand apart during replication
polymerase reads parent strand in 3’ to 5’ + build leading strand in 5’ to 3’ direction away from replication fork
in contrast lagging strand built in 3’ to 5’ direction discontinuosly in small fragments (okazaki fragments) these are joined by DNA ligase
multiple replication forks along single DNA molecule which speeds up replication when occurs in both directions called replication bubble 
DNA polymerase catalyses condensation reaction between nucleotides in DNA strand + forms phosphodiester bonds between adjacent nucleotides

What are the basic steps of replication?

double helix unzips to expose 2 single strands - attachment of complementary nucleotides to bases of exposed strands - new nucleotides added to original exposed ones 

What is computer modelling?

being able to predict shape of protein molecules from its primary structure + can be useful in medicine and drug design 
sequence of amino acids in protein can be produced by a modern large-scale DNA sequencing efforts such as Human Genome Project

What are the two types of modelling?

comparative protein modelling - uses previously solved structures as templates - effective as although number of actual proteins is vast there is a limted set of tertiary structures to which most proteins belong - suggested only around 2000 distinct protein folds in nature
Ab initio protein modelling - seeks to build three-dimensional protein models from scratch ie based on physical principles rather than (directly) on previously solved structures - tends to require vast computational resources so have only been carried out for relatively small proteins

How do you extract DNA?

1.use pestle + mortar to grind fruit to a pulp - 2.pour salt detergent solution + mix trying to avoid bubbles - 3.use filter funnel to pour through mixture + collect filtrate in boiling tube - 4.add protease enzyme to filtrate - 5.place boling tube into water bath + leave for ten minutes - 6.tilt boiling tube gently puring ice cold alcohol down sides of the tube - keep going til you see a seperate layer of alcohol on top of filtrate

What are the reasons of each DNA extraction step?

1.breaks open cell wall - 2.detergent dissolves phospholipid bilayer that makes up plasma + nuclear membrane - salt helps precipitating DNA - 3.remove insoluble material from sample just leaving soluble material in filtrate - 4.breaks down histone proteins that DNA are wrapped around - 5.optimum temperature for protease enzymes - speed up rate of histone protein breakdown - 6.precipitate DNA as not soluble in alcohol making DNA visible

How is DNA stored?

DNA molecules are incredibly long + must be tightly packed up to fit within a nucleus where each molecule wound around proteins known as histones to form DNA-histone complex - these complexes coil further to form chromatin which helps pack DNA into chromosomes - each chromosome contains just a single molecule of DNA

What is the genetic code?

refers to sequence of bases (triplet codes called codons) that code for amino acid - a gene is short section of DNA that codes for a polypeptide (protein) - each gene is located at specific position along a chromosome known as a locus - complete set of genes within cell known as a genome where full range of protein a cell capable of producing known as proteome - scientists found each amino acid is coded by a sequence of 3 DNA bases known as a triplet

What are some features of the genetic code?

universal - each DNA triplet codes for same amino acid in all organisms 
non-overlapping - each base in DNA sequence is only read once
degenerate - most amino acids are coded for more than one triplet/codon

How are amino acids used in genetic code?

DNA is a triplet code (3 bases that read along DNA strand that code for an amino acid) - 20 amino acids + 64 different combinations of triplet code meaning some triplets code for same amino acids (up to six different codes for same amino acid) although usually only differ by one base - advantages of this is if a mutation causes a base change triplet may still code for same amino acid + therefore not change protein produced

How can the length of DNA differ?

3 amino acids act as full stops signalling end of message - codes for numerous proteins where each short length of DNA known as gene is in fact sequence of bases that code for amino acids making up a single protein - no 2 proteins same so lengths of genes varies where some genes around 50 nucleotides long but most are thousands nucleotides long

How can amino acids be interpreted?

genetic codes can be summarised into a table where code often shown as mRNA bases so U shown instead of T where each amino acid is coded by a sequence of 3 mRNA bases called codon - many amino acids are coded for by multiple codons

What is mRNA?

messenger RNA is type of RNA synthesised during process of transcription - role to carry genetic information from DNA to ribosomes (where proteins are made) - transfers DNA code from nucleus to cytoplasm - complimentary to DNA code - determines sequence of amino acids during protein synthesis - easily broken down + only exist whilst needed to manufacture a protein - sequence of nucleotides in mRNA referred as genetic code

What are the features of mRNA?

single-stranded,linear molecule
contains a base sequence complementary to DNA structure
contains codons which are set of three bases that codes for an amino acid
small enough to leave nucleus/nuclear pores  

What is tRNA?

transfer RNA is type of RNA used in process of translation - role is to transport amino acids to ribosomes to build up polypeptide chain - shorter in length than mRNA - different tRNA molecules for each amino acid where anticodon ensures amino acids correctly sequenced along mRNA

What are the features of tRNA?

single-stranded molecule folded into a clover-leaf shape
use hydrogen bonds between complementary base pairs to hold in shape
contains specific sequence of three bases at one end known as anticodon
contains an amino acid binding site at opposite end

Where does transcription occur?

in eukaryotic cells takes place in nucleus - intial step in protein synthesis which involves creating an mRNA copy of a gene from DNA template - once mRNA formed leaves nucleus via nuclear pores for ribosomes where acts as template for proteins to be synthesised

What are the key events in transcription?

1.RNA polymerase enzyme binds to DNA where hydrogen bonds between bases break due to DNA helicase + two strands of double helix seperate
2.antisense strand act as template for mRNA synthesis + free RNA nucleotides align with DNA template through complimentary bases
3.u pairs with a - a pairs with t - c pairs with g 
4.RNA polymerase catalyse formation of phosphodiester bonds between adjacent RNA nucleotides 
5.complementary mRNA strand is formed carrying same base sequence as DNA sense strand
6.process ends when RNA polymerase reaches a stop codon,detaches from DNA + terminates transcription
7.mRNA is released,detaches from DNA + rewinds into double helix

What is translation?

process of decoding information in messenger RNA to synthesise a polypeptide chain with help of transfer RNA - chain then folds into functional protein - occurs in cytoplasm

What are the key events in translation?

1.mRNA thats produced during transcription binds to a ribosome in cytoplasm at start codon (AUG)
2.tRNA molecule carrying specific amino acid acid with an anticodon (UAC) that is complementary to start codon binds to mRNA
3.second tRNA molecule with anticodon attaches to mRNA meaning at any point two tRNA molecules can be attached to ribosome
4.amino acids carried by first two tRNA molecules linked together by peptide bonds using ATP
5.first tRNA molecule detaches from tRNA + free to collect another amino acid for future use
6.ribosome moves along mRNA allowing another tRNA molecule to bind to next codon on mRNA
7.process from 4 to 6 repeats elongating polypeptide chain
8.sequence continues until ribosome reaches stop codon (eg UAG) on mRNA as no corresponding tRNA molecule
9.completed polypeptide chain detaches from the ribosomes where each amino acid connected by condensation reaction to form a peptide bond - some joined to other chains or prosthetic group

What is ATP?

modified form of nucleotide - adenosine triphosphate is a compound that transfers energy within cells - often referred as energy currency - temporarily holds energy + transfers it from one part of cell to another 

What is the structure and storage of ATP?

consists of 3 parts: adenine - nitrogenous base ribose - 5 carbon sugar phosphates - 3 phosphate groups - all covalently bonded
ATP unstable molecule so cannot be stored easily - energy stored as fats and carbohydrase - during cellular respiration fats and carbohydrates are broken down to make ATP

How is ATP used in the body?

movement - muscle contration or for sperm cells to swim 
active transport - molecules go against concentration gradient such as ions entering roots
synthesis - large molecules such as DNA and proteins 
secretion - substances from cells such as releasing hormones from glands 

What are the ATP reactions?

hydrolysis - addition of water to break down ATP - breaks down into adenosine diphosphate (ADP) and inorganic phosphare (Pi) - reaction catalysed by enzyme ATP hydrolase + release energy for use in cells - 30.5 kJ
condensation - removal of water to form chemical bond which re-synthesises ATP - when phosphate group + ADP join water molecule released - reaction catalysed by enzyme ATP synthase - process requires energy + traps chemical bond

How are the properties of ATP relate to its function?

hydrolysis of ATP releases a small amount of energy meaning little energy lost as heat
ATP is broken down in one step meaning energy released quickly
ATP rapidly re-synthesised so ATP always readily available - easily regenerated 
inorganic phosphare from ATP hydrolysis can phosphorylate other components which makes them reactive
bonds between phosphate groups are unstable have low activation energy + are easily broken
ATP is soluble so it can be easily be transported around cells

What are the mark scheme descriptions of transcription and translation?

transcription - DNA copied into mRNA - free RNA nucleotides - line up by complementary base-pairing - to one/template/sense strand - catalysed by RNA polymerase
translation - mRNA moves to ribosomes - tRNA binds to mRNA - anticodons match with codons - specific amino acid attached to tRNA - formation of peptide bonds between amino acids 

What is rRNA?

ribosomal RNA are short chains of RNA which attach to ribosomal protein molecules forming ribosomes which are the site of protein synthesis

What are the short differences of DNA and RNA?

DNA - double helix of two antiparallel polynucleotide strands - long term storage of genetic information where sequence of bases codes for assembly of amino acid to make polypeptides
RNA - one polynucleotide chain twist into a helix + chain linear for variations of RNA made of RNA nucleotides joined by covalent bonds from condensation reactions - function is protein synthesis

What is energy coupling?

an example of energy coupling using ATP is transmembrane sodium-potassium pump where energy released from hydrolysis of ATP + energy needed to power the pump that drives Na+ out and K+ into the cell

What can inorganic phosphate be used for?

inorganic phosphate released in ATP hydrolysis can be used to phosphorylate other compounds making them more reactive