Nucleic acids and protein synthesis

genetic material has to have which two features?

the ability to store information

the ability to copy itself accurately

general structure of DNA and RNA?

macromolecules are polymers

nucleic acids because they were originally found in the nucleus

the monomers are nucleotides. DNA and RNA are polynucleotides

nucleotide?

a molecule consisting of a nitrogen containing base, a pentose sugar and a phosphate group

polynucleotide?

a chain of nucleotides joined together by phosphodiester bonds

bases in DNA?

adenine, thymine

guanine, cytosine

all bases contain nitrogen

bases in RNA?

adenine, uracil

guanine, cytosine

purines?

adenine and guanine

2 rings in its structure

pyrimidines?

thymine, cytosine, uracil

one ring

pentose sugars?

2 pentoses in nucleic acids, ribose and deoxyribose

deoxyribonucleic acid?

a nucleic acid containing deoxyribose

ribonucleic acid?

a nucleic acid containing ribose

difference between deoxyribose and ribose?

deoxyribose has one fewer oxygen atoms in its molecule

phosphate group?

the phosphate group gives nucleic acids their acid nature

what do nucleotides comprise of?

nitrogen containing base

pentose sugar

phosphate group

what does ATP comprise of?

adenine, ribose and phosphate

adenine + ribose =

adenosine

can be combines with one, two or three phosphate groups to give, adenosine monophosphate, adenosine disphosphate and ATP

two nucleotides can be joined together by a..

condensation reaction

process can be repeated to make and polynucleotide which has the form of a long, unbranching strand of nucleotides

the sugars and phosphates are linked by the phosphodiester bonds to form a backbone from which the bases stick out sideways at right angles to the backbone

dinucleotide?

: two nucleotides joined together by a phosphodiester bond

phosphodiester bond?

a bond joining two nucleotides together; there are two ester bonds, one from the shared phosphate group to each of the sugars either side of it

who published a correct model structure for DNA?

James Watson and Francis Crick

Rosalind Franklin?

X-ray diffraction photos

suggested that DNA had a helical structure

what is the correct model structure?

two polynucleotide chains held together by hydrogen bonding between the bases of the two chains by twisting each of the two strands into a helical shape (double helix) and to run the strands in opposite directions

five prime and three prime?

refer to carbon atoms 5 and 3 of the sugar

the two ends of a DNA strand are called the 5' end and the 3' end

at the 5' end is phosphate and at the 3' end is sugar

features of the DNA molecule?

2 polynucleotide chains

each chain is a right handed helix

the 2 chains coil around each other to form a double helix

the chains run in opposite directions - antiparallel

each chain has a sugar-phosphate backbone with bases projecting at right angles

the bases in one chain are attracted to the bases of the other chain by hydrogen bonding between the bases

because of the way they fit together, adenine pairs with thymine and guanine pairs with cytosine

A links with T by 2 hydrogen bonds, G links with C by three

adenine and guanine are purines, thymine and cytosine are pyrimidines, a purine always pairs with a pyrimidine

purines are two rings wide and pyrimidines are one ring wide, the distance between the two backbones is constant and always 3 rings wide

a complete turn of the double helix takes place every ten base pairs

complementary base pairing?

the hydrogen bonding of A with T or U and of C with G in nucleic acids

the sequence of bases in one strand...

determines the sequence of bases in the other strand

the two strands are complementary

the information is the sequence of bases

any sequence is possible within one strand but the other strand must be complementary. The sequence acts as a coded message

how does the molecule copy itself?

by "unzipping" down the middle. This is relatively easy because the two strands are only held together by weak hydrogen bonds

each half can then make a complementary copy of itself, thus, two identical molecules of DNA are produced

general structure of RNA?

a single polynucleotide strand

protein synthesis involves which types of RNA?

mRNA (messenger), tRNA (transfer), rRNA (ribosomal)

tRNA and rRNA fold up into complex structures but mRNA remains as an unfolded strand

unwinding of the 2 strand of DNA?

breaks the hydrogen bonds that hold the two strands together which is done by helicase

what does DNA polymerase do?

used for the copying process, a molecule of DNA polymerase attaches to each of the single strands, it adds one new nucleotide at a time, which is held by hydrogen bonding to the strand being copied

DNA polymerase can only copy..

in the 5' to 3' direction along each strand. The DNA polymerase follows the unwinding process, copying the DNA as it is unwound. The new strand being formed in the leading strand

in contrast to the top parent strand, for the bottom parent strand the 5' to 3' direction of copying is in the opposite direction to the unwinding

DNA polymerase has to copy an unwound piece of DNA and then go back and copy the next piece of unwound DNA.

it keeps repeating this process

results is a series of short fragments of copied DNA

okazaki fragments, the new strand being formed is the lagging strand

what does DNA ligase do?

finishes the process, connects all the new nucleotides with covalnet bonds

before this they are only holding on to the parent strand with hydrogen bonds between complementary bases

it connects neighbouring nucleotides with phosphodiester bonds to form the sugar phosphate backbone of the new DNA molecule

fragments are connected in the same way at the same time

DNA polymerase?

an enzyme that copies DNA; it runs along the separated DNA strands lining up one complementary nucleotide at a time ready for joining by DNA ligase

leading strand?

during DNA replication, the parent strand that runs in the 3′ to 5′ direction is copied to produce the leading strand

lagging strand?

during DNA replication, the parent strand that runs in the 5′ to 3′ direction is copied to produce the lagging strand

DNA ligase?

an enzyme that catalyses the joining together of two nucleotides with covalent phosphodiester bonds during DNA replication

semi-conservative replication?

the method by which a DNA molecule is copied to form two identical molecules, each containing one strand from the original molecule and one newly synthesised strand

each time a DNA molecule is replicated...

half the original molecule is conserved in each of the new molecules

if replication was conservative, the parent DNA molecule would remain at the end of the process and the new DNA molecule would have two newly made strands

gene?

a length of DNA that codes for a particular polypeptide or protein

if you control the sequences of amino acids in the cells proteins..

you control the enzymes that are made and thus you control the cell.

the sequence of bases in the DNA of a cell is the code for all the proteins of that cell and organism. The code for one polypeptide is a gene

there are 20..

common amino acids found in proteins, but only 4 different bases in DNA to code for them

the code is a triplet code so three bases are the code for one amino acid

there are 64 possible combinations of 3 bases

most of the amino acids have more than one code

features of the genetic code

3 letter (triplet) code

universal code, each triplet codes for the same amino acid in all living things

the code has punctuations. 3 of the DNA triplets act as full stops in the message. During protein synthesis, these stop triplets mark the end of a gene. some triplets can act as 'start signals' where the process of copying a gene starts

the code is degenerate/redundant so some amino acids are coded for by more than one triplet

the process by which DNA makes mRNA is called..

transcription

transcription?

copying the genetic information in a molecule of DNA into a complementary strand of mRNA; a single strand of the DNA is used as a template (this is called the template or transcribed strand) - the enzyme responsible is RNA polymerase

the process by which the message is carried by mRNA is decoded to make protein is called..

translation

translation?

a stage in protein synthesis during which a sequence of nucleotides in a molecule of messenger RNA (mRNA) is converted (translated) into a corresponding sequence of amino acids in a polypeptide chain; it takes place at ribosomes

first step of transcription?

takes place in nucleus

RNA polymerase attaches to the beginning of the gene to be copied

starts to unwind DNA

helicase breaks hydrogen bonds between the two strands2 single stranded sections of DNA with the normal double helical structure on either side of the unzipped section

second step?

only one of the exposed strands is copied. This is the template/transcribed strand. the other strand is the non-transcribed strand

a complementary RNA copy of the template strand is made

3rd step?

the bases A,G,T and C are copied in the RNA as U,C,A and G respectively.

each set of the three bases codes for one amino acid

the lower strand is the template strand

reading from the left hand end of the template strand, the first triplet shown is CAA

this is the DNA code for the amino acid valine

4th step?

mRNA is made from nucleotides found free in solution in the nucleus

as the RNA polymerase moves along the gene, the nucleotides approach and hydrogen bond with their complementary nucleotides in the DNA

as each nucleotide arrives, RNA polymerase joins it to the growing mRNA molecule with a phosphodiester bond

once phosphodiester bonds are formed, hydrogen bonding of that part of the mRNA to the DNA is no longer necessary and the hydrogen bonds are broken

5th step?

eventually a stop message will be reached

at this point, the RNA polymerase releases the completed mRNA

the RNA polymerase leaves the DNA

6th step?

the mRNA leaves the nucleus through a nuclear pore in the nuclear envelope

it is a single polynucleotide chain which, unlike the 2RNA's involved in translation does not fold up into a more complex structure after it has been made

codon?

sequence of three bases on an mRNA molecule that codes for a specific amino acid or for a stop signal

function of the ribosome in translation?

used to bring all the molecules involved together

have a small and a large subunit and that they are made of rRNA and protein

function of tRNA in translation?

transfers amino acids to the ribosome

each amino acid has a different tRNA molecule to carry it

the amino acid is attached at one end of the molecule

at the other end of the molecule three projecting bases form an anticodon

anticodon?

sequence of three unpaired bases on a tRNA molecule that binds with a codon on mRNA

1st step of translation?

when an mRNA molecule arrives at a ribosome, it enters a groove between the 2 subunits of the ribosome where it is held ready to receive the first tRNA molecule

2nd step?

the tRNA with the anticodon complementary to the first codon on the mRNA enters the ribosome and attaches to the codon by hydrogen bonding

3rd step?

two tRNA molecules can fit into the ribosome at any one time, so the second tRNA enters the ribosome

this has the anticodon which matches the second codon in the mRNA

the amino acids carried by the two tRNA's are now side by side and a peptide bond is formed between them.

4th step?

the first tRNA now leaves, the ribosome 'clicks' forward one codon and the third tRNA enters, carrying the next amino acid

this process is repeated until a stop codon is reached

5th step?

the completed polypeptide leaves the ribosome and folds up into its secondary and tertiary structures

the folding may be assisted and controlled by special proteins

the polypeptide may enter the endoplasmic reticulum for transport to another part of the cell

the process of modification is called..

RNA processing

in eukaryotes..

mRNA is modified before it leaves the nucleus

original molecule is the primary transcript

RNA splicing?

the removal of sections of the primary transcript

the sections removed are introns

the nucleotide sequences that remain after the introns are removed are called exons

they have to be joined together after the removal of introns

introns in DNA help to..

regulate the activity of genes

a primary transcript molecule can be spliced in different ways to result in different..

mRNA's being made form the original primary transcript

these different mRNAs will produce different proteins when translated

one gene can code for several different proteins or different forms of the same protein

gene mutation?

a change in the base sequence in part of a DNA molecule

chromosome mutation?

a random and unpredictable change in the structure or number of chromosomes in a cell

mutation occurs when..

a wrong nucleotide is inserted. this may be because of errors during DNA replication or because damage is done to the DNA by radiation or carcinogens

a change in the base sequence of the DNA..

may cause a change in the amino acid sequence of the polypeptide coded for by the mutated DNA

mutagens cause mutation

a change in the amino acid sequence..

affects the way a polypeptide folds up and in turn changes the tertiary structure of the protein

this could affect the functioning of the polypeptide

this is harmful

what are the types of mutation

substitution

deletion/insertion

substitution?

may or may not affect the sequence of amino acids coded for

structure of haemoglobin?

two alpha polypeptide chains

two beta polypeptide chains

each chain has one iron containing haem group in the centre

sickle cell anaemia?

mutation in the beta chain

the mutation responsible is a substitution

the first T in the triplet is replaced by an A

glutamine becomes valine

frame-shift mutation?

a type of gene mutation caused by insertion or deletion of one or more nucleotides, resulting in incorrect reading of the sequence of triplets in the genetic code due to a shift in the reading frame

for insertion/deletion..

the whole of the rest of the code is altered the frame has been shifted by one base

all the triplets from the mutation onwards are affected

all the amino acids coded for will probably be incorrect so the polypeptide or protein made as a result is likely to be non functioning