Biological Molecules 2 Flashcards
What do nucleotides provide?
- the energy currency of cells in the form of adenosine triphosphate (ATP)
- the building blocks for the mechanism of inheritance in the form of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
What are the three parts of each nucleotide?
- A 5-carbon pentose sugar
- a nitrogen containing base
- a phosphate group
What is the pentose sugar in RNA and DNA and what is the difference between them?
- RNA: ribose
- DNA: deoxyribose
- deoxyribose contains one fewer oxygen atom than ribose
What are the two different types of bases and what are their structures?
- purine and pyramidine bases
- they are both weak bases
- purine has two nitrogen containing rings wheread a pyramidine base only has one
What are the most common purines?
Adenine (A) and Guanine (G)
What are the most common pyrimidines?
Cytosine (C), thymine (T) and uracil (U)
What property does the phosphate group give the nucleotide?
It is the result of the phosphate group (-PO43-) that the nucleotides are acidic molecules and carry a negative charge
How are the sugar, the base and the phosphate group joined together to form a nucleotide?
By condensation reactions, with the elimination of two water molecules to form a nucleotide
What molecule is the universal energy supplier in cells and what is it in this molecule that allows it to supply energy?
Adenosine triphosphate (ATP). It is the potential energy in the phosphate bonds that is made available to cells for use in breaking bonds in a chemical reaction
How does ATP differ from most nucleotides?
It has three phophate groups attached
When energy is needed in a cell how does ATP provide it?
- the third phosphate bond in the molecule is broken in a hydrolyisis reaction catalysed by the enzyme ATPase
- the products of this reaction are adenosine diphosphate (ADP) another nucleotide and a free inorganic phosphate group
- one phosphate group is broken, this uses energy
- two further bonds are made to produce the ADP and the stable phosphate group and this releases energy that is needed to drive other reactions.
- some of this energy is lost to heat but the rest isnused for any energy-requiring biological activity in the cell
Draw a nucleotide, ribose, deoxyribose and ATP molecule
Look in snap camera roll
What does the energy needed to drive the synthesis of ATP come from?
Redox reactions
How is ATP synthesised?
The breakdown of ATP into ADP is a reversible reaction. ATP can be synthesized from ADP and a phosphate group in a reaction that requires an input of energy. ATpase catalyses this reaction
What are nucleic acids also known as and what are they?
Polynucleotides. Theyre the information molecules of the cell
Nucleic acids are polymers. What monomer are they made up of?
Many nucleotide monomer units
In what form is the information to make a new cell displayed in nucleic acids?
They take the form of a code in the molecules of DNA. Parts of the code are copied into messenger RNA (mRNA) and used to direct the production of the proteins that build the cell and control it’s actions
How is genetic information stored in eukaryotes and prokaryotes?
- in eukaryotes it is stored in chromosomes in the nucleus
* in prokaryotes a single length of DNA is found floating freely in the cytoplasm
How do you build nucleic acids?
- they are chains of nucleotides linked together by condensation reactions that produce phophodiester bonds between the sugar on one nucleotide and the phosphate group on the next nucleotide
- both DNA and RNA have this sugar-phosphate backbone
- because the sugar of one nucleotide bonds to the phosphate group of the next nucleotide polynucleotides always have a hydroxyl group at one end and a phosphate group at the other.
- long chains of nucleotides containg C,G, A and T join together to form DNA
- chains of nucleotides containing C,G,A and U make RNA
What is the structure of RNA?
RNA molecules form single polynucleotide strands that can fold into complex shapes, beld in place by hydrogen bonds or remaining as long thread-like molecules
What is the structure of DNA?
- DNA molecules consist of two polynucleotide strands twisted around eachother
- the sugars and the phophatss form the backbone of the molecule and pointing ineards from the two sugar-phophate backbones are the bases which pair up in specific ways.
- a purine base always pairs with a pyramidine base
- in DNA adenine paris with thymine and cytosine with guanine
- this results in the DNA double helix
- the two strands of the DNA double helix are held together by hydrogen bonds between the complementary base pairs
- these hydrogen bonds form between the amino and carbonyl geoups of the purine and pyramidine bases on the opposite strands
- there are three hydrogen bonds between the C and G but only two between the A and T
- there are 10 base pairs for each complete twist of the helix
- the two strands are known as the 5’ (5 prime) and 3’ (3 prime) strand, named according to the number of the car on aroms in the pentose sugar to which the phosphate group is attached in the first nucleotide of the chain
- it is the phosphate that is free ar the 5’ end of the 5’ carbon and it is the free -OH group that is attached to the 3’ on the 3’ end
Draw a polynucleotide strand
Look at snap camera roll
Draw the double helix of DNA
Snap camera roll
What feature of DNA means that it can pass on genetic information from one cell or generation to another?
It can replicate or copy itself exactly
Who produced the double helix model for the structure of DNA?
Watson and crick
What were the two main ideas about how DNA replication happened and what were these ideas?
- Conservative replication model: the original double helix remained intact and in some way instructed the formation of a new, identical double helix, made up of entirely new material
- Semiconservative replication model: assumed that the DNA ‘unzipped’ and new nucleotides aligned along each strand. Each new double helix contained one strand of the original DNA and one strand of the new material. This was the Watson and Crick hypothesis - the double helix would unzip along the hydrogen bonds in their structural model, allowing semiconservative replication to take place
Describe the set of experiments carried out by Meseleson and Stahl that led to semiconservative replication being the accepted model for DNA replication
- they grew several generations of e.coli in a medium where their only source of nitrogen wwe the isotope 15N from 15NH4Cl. Atoms of 15N are denser than those of the isotope usually found, 14N. The bacteria grown on this medium took up the isotope to make the cell chemicals including proteins and DNA. After several generations the entire bacterial DNA was labelled with 15N
- they moved the bacteria to a medium containing normal 14NH4Cl as their only nitrogen source and measured the density of their DNA as they reproduced.
- They predicted that if DNA was produced by conservative replication then some DNA would have the density expected if it only contained 15N and some would have the density expected if it only contained 14N. However if DNA reproduced by semiconservative replication then all of the DNA would have the same density, half-way between that of 15N and 14N containing DNA
- they found that all of the DNA had the density half way between that of 14N and 15N containing DNA and so must replicate semiconservatively
When the DNA replicated what enzyme brings about the unzipping of the two strands?
DNA helicase
When the DNA is unzipped what do the strands act as?
Templates for the new DNA strands
After the DNA has been unzipped what happens in DNA replication?
- the exposed bases attract free nucleotides and new hydrogen bonds are formed between matching base pairs
- DNA polymerase lines up and catalyses the linking up of the nucleotides along the template strand
- DNA ligase catalyses the formation of phosphodiester bonds between the two strands of DNA
Draw the difference between what you would see in conservative replication and semiconservative replication
Snap camera roll
What is the process of joining together amino acids to make proteins called and where does it take place?
Translation that happens on the surface of the ribosomes
What is a triplet code?
A code of three bases that is the basis of the genetic information in the DNA
What is a gene?
A sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain, that affect a characteristic in the phenotype of the organism
What do triplet codes code for?
Most code for a particular amino acid but some triplets signal the beginning or end of one particular amino acid sequence
What is a sequence of three bases on DNA or RNA known as?
A codon
Why was most of the work done on codons done on codons of mRNA?
Because the codons of DNA are difficult to work out because the molecule is so large
The mRNA that we study for it’s codons is formed as a complementary strand to DNA. What does this mean and how does it enable us to work out the DNA sequence?
- it is the reverse image of the original base sequence
* we can work out the DNA sequence because of the way the bases always pai4 T/U with A and G with C
What has the result of codon work been?
• a sort of dictionary of the genetic code
What is 98% of the human DNA
- it is non-coding
- some are involved in regulating the protein-coding sequences (effectively turning the genes on and off) but others we do not know what the non-coding sequences do
Describe the genetic code
It is a triplet code that is non-overlapping and degenerate as well
What would an overlapping code be?
- it overlaps
* e.g. the mRNA sequence UUUAGC could code for four amino acids (UUU) (UUA) (UAG) (AGC)
What is a non-overlapping code?
- does not overlap
* the mRNA sequence UUUAGC can code for two amino acids (UUU) and (ACG)
What would the advantages and disadvantages be of an overlapping code?
- it would be very economical - short lengths of DNA could carry the instructions for many different proteins
- however it would be limiting because the amino acids that could be coded for side by side would be limited
How did scientists decide whether the code was overlapping or not?
They knew that:
• if a codon consisted of 3 nucleotides and was completely overlapping and a single nucleotide is altered by a point mutation then 3 amino acids would be affected
• if it was partly overlapping then a point mutation would affect two amino acids
• if it didn’t overlap then a change in a single nucleotide would only affect one amino acid which has been observed in sickle cell disease
• this is what happens so it must be non-overlapping
What is a degenerate code and why is it useful?
- the genetic code contains more information than you need. It is normally just the first two nucleotides in a codon that determine what amino acid results
- it means that if there was a mutation and the final base in the triplet is changed, this mutation could still produce the same amino acid and have no effect on the organism
In eukaryotes where is the DNA and where are the ribosomes on which protein synthesis takes place and how is the message from the DNA carried to the ribosomes?
- DNA is in the nucleus
- ribosomes are in the cytoplasm
- DNA have never been detected in the cytoplasm. RNAs carry the information from the nuclear DNA to the ribosomes
What are the differences of RNA to DNA?
- contains a different sugar (ribose)
- has a different base (uracil instead of thymine)
- consists of a single helix
- does not form enourmous complex molecules like DNA
What are the three main functions of RNA in the process of protein synthesis?
- it carries the instructions for a polypeptide from the DNA in the nucleus to the ribosomes where the proteins are made
- it picks up specific amino acids from the protoplasm and carries them to the surface of the ribosomes
- it makes up the bulk of ribosomes themselves
What is messenger RNA, how is it formed and what does it do?
- it is formed in the nucleus
- it usually carries the instructions for one polypeptide
- it forms on the template or antisense dtrand of the DNA. The mRNA formed codes for a polypeptide
- parts of the DNA molecule unravel and are transcribed onto strands of mRNA by an enzyme called DNA-directed RNA polymerase (RNA polymerase)
- the complementary bases in the nucleotides of the DNA and RNA line up alongside each other.
- RNA nucleotides from the nucleoplasm line up alongside the exposed DNA.
- initially hydrogen bonds hold the complementary RNA bases in place. Then DNA-directed RNA polymerase catalyses the formation of phophodiester bonds between the sugar and phosphate groups.of the bases to form a strand of mRNA
- the bases of the mRNA form a triplet code and each triplet of bases is a codon
- the relatively small mRNA molecules pass easilu through the pores in the nuclear membrane, carrying the instructions from the genes in the nucleus to the cytoplasm
- they then move to the surface of the ribosomes where protein synthesis takes place
What is transfer RNA, how is it formed and what does it do?
- tRNA is found in the cytoplasm.
- it has a complex shape, often described as a clover leaf which enables it to carry out its function
- its shape is the result of hydrogen bonding between different bases
- one part of the tRNA molecules has a sequence of three bases that matches the genetic code of the DNA and corresponds to one particular amino acid. This sequence of bases is called the anticodon.
- each tRNA molecule also has a binding site where it picks up one particular amino acidnfrom the vast numbers always free in the cytoplasm
- the tRNA molecules, each carrying a specific amino acid, line up alongside the mRNA on the surface of the ribosome.
- The anticodons of the tRNA line up with the codons of the mRNA, held in place by hydrogen bonds between the corresponsing bases.
- because the anticodon has a sequence of bases that align with the corresponding bases in the mRNA on the ribosomal surface, the correct sequence of amino acids is assembled
- once the amino acids are lined up together, peptide bonds form between them building up a long chain of amino acids
What is ribosomal RNA, where is it found and what does it do?
- rRNA makes up about 50% of the structure of a ribosome and is the most common RNA found in cells.
- it is made in the nucleus under the control of the nucleoili and then moves out into the cytoplasm where it binds with proteins to form ribosomes
What are ribosomes and what do they do?
- they are formed from the binding of rRNA with proteins
- the ribosomes consist of a large and a small subunit
- they surround and bind to parts of the mRNA that are actively being translated and then move along tonthe next codon
- their job is to hold together the mRNA and tRNA and act as enzymes controlling the process of protein synthesis
Summarise protein synthesis
- the genetic code of DNA is transcribed onto mRNA
- the mRNA moves out of the nucleus, into the cytoplasm and becomes attached to a ribosome
- molecules of tRNA carry individual amino acids to the surface of the ribosome
- the tRNA then breaks away and returns to the cytoplasm to pick up another amino acid
- the ribosome moves along the molecule of mRNA until it reaches the end, leaving a completed polypeptide chain
What is trancription and translation?
- Transcription is where the DNA information is copied to mRNA
- Translation is where mRNA information is translated into a specific sequence of amino acids on the ribosomes
What is a mutation and what affect does it have on the body?
A mutation is a permenant change in the DNA of an organism
• it could have no noticeable affect at all or it may have devastating effects on the whole organism. Many human genetic diseases come from mutations
What do gene mutations involve?
Changes in the bases making up the codons
What are the bodies’ repair systems for mutations?
Specific enzymes cut out or repair any parts of the DNA strand that have become broken or damaged
What are point or gene mutations?
Small mutations that occur when just one or a small number of nucleotides are miscopued during transcription
What do point mutations include?
- substitutions where one base substitutes for another
- deletions where a base is completely lost in the sequence
- insertions when an extra base is added which may be a repitition of one of the bases already there or a different base entirely
What do chromosomal mutations involve?
Changes of the positions of genes within the chromosomes
When do mutations occur?
When the gametes form or during the division of somatic (body) cells
What are whole chromosome mutations?
Where an entire chromosome is lost during meiosis or duplicated is one cell by errors in the process
Why do point mutations sometimes have no effect?
If different arrangements of nucleotides code for the same amino acid
What results if a mutation occurs that results in the production of a new superioir protein?
It may help the organism gajn a reproductive advantage so that it leaves more offspring than other individuals of that species, particularly if environmental conditions change
In what case would the effect of a mutation be catastrophic?
If a base mutation change is in a protein that plays an important role in the cell such as an enzyme
What is sickle cell disease and how does it arise?
- it is a genetic disease that affects the protein chains making up the haemoglobin in the red blood cells
- it is the result of a point mutation
- a change of one base in the codon changes a single amino acid in a chain of 147
- but this alters the nature of the protein
- the haemoglobin molecules stick together to form rigid rods that give the red blood cells a sickle shape
- they do not carry oxygen efficiently and block the smallest blood vessels
When do mutations most commonly occur?
During the copying of DNA for cell division
Where do the mutations that give rise to genetic diseases take place and why are they most damaging?
- they take place in the gametes
* they are the most damaging because they will be passes on to future offspring
What does exposure to mutagens do and give examples of mutagens
- increases the rate at which mutations occur
* mutagens include x-rays, ionising radiation and certain chemicals
