2.3- nucleic acids Flashcards
What is a double helix
The shape of a DNA molecule, due to the coiling of the two sugar-phosphate backbone strands into a right-handed spiral configuration
What is a monomer
A molecule that when repeated, makes up a polymer- nucleotides are the monomer of nucleic acids
What is a nucleotide
A molecule consisting of a 5 carbon sugar, a phosphate group, and a nitrogenous base
What is a polynucleotide
a large molecule containing many nucleotides
Describe nucleotides
- Biological molecules that participate in nearly all biological processes
Describe the general structure of nucleotides
- Phosphate esters of pentose sugars- where a nitrogenous base is linked to the C1 of the sugar residue
- a phosphate group is linked to either the C3 or the C5 of the sugar residue, by covalent bonds formed by condensation reactions
What do nucleotides form
- The monomers of nucleic acids- DNA and RNA
What is the pentose sugar in DNA and RNA
- DNA= Deoxyribose
- RNA= Ribose
What do nucleotides become when they contain more than one phosphate group- give 3 named examples
- Phosphorylated nucleotides
- Adenosine- ribose and adenine
- Adenosine monophosphate- ribose, adenine and 1 phosphate (AMP)
- Adenosine diphosphate- ribose, adenine and 2 phosphates (ADP)
- Adenosine triphosphate- ribose, adenine and 3 phosphates (ATP)
What is ATP
An energy-rich end-product of most energy-releasing biochemical pathways- used to drive most energy-requiring metabolic processes in cells
What do nucleotides help regulate
-Many metabolic pathways, for example by ATP, ADP, and AMP
What coenzymes are adenine nucleotides part of, and what are these involved in
NADP- nicotinamide adenine dinucleotide phosphate- used in photosynthesis
NAD- nicotinamide adenine dinucleotide- used in respiration
FAD- flavine adenine dinucleotide and coenzyme A- both used in respiration
List 4 general functions of nucleotides
- Form monomers of nucleic acids
- become phosphorylated nucleotides when they contain more than one phosphate group
- help regulate many metabolic pathways
- May be components of co-enzymes
What is a nucleoside
Consist of a sugar and base- no phosphate group
Where is DNA found
In the nuclei of all eukaryotic cells, within the cytoplasm of prokaryotic cells and in some types of viruses
What is DNA
- the hereditary material and carries coded instructions used in the development and functioning of all living organisms
What is DNA an example of, and what are the others
- Macromolecules (large numbers of atoms) that make up the structure of living organisms
- proteins
- carbohydrates
- lipids
What type of structure is DNA and why
- a polymer
- it is made up of many repeating monomeric units- nucleotides
What does a molecule of DNA consist of
Two polynucleotide strands running in opposite directions- antiparallel
What does each DNA nucleotide consist of
- phosphate group
- 5-carbon sugar- deoxyribose
- one of 4 nitrogenous bases- adenine, guanine, thymine or cytosine
What does DNA stand for
Deoxyribonucleic acid
Name and explain the covalent bonds in nucleotides
- between sugar residue and phosphate group is phosphodiester
- between sugar and base is glycosidic
- broken when polynucleotides break down, formed when synthesised
Describe the length of DNA molecules and what this means
-long- can carry a lot of encoded genetic information
What type of reaction is used to form a nucleotide- describe it
Condensation- 2 x OH from deoxyribose, 1x H (from OH) from phosphate, and 1x H from base forms 2 water molecules
What are the 2 types of bases, what is the difference, an which of the 4 bases does each include
Purines- 2 hexagonal rings- adenine or guanine
Pyrimidines- 1 hexagonal ring- thymine or cytosine
Describe base pairing
Complimentary- one purine with one pyrimidine- equal sized ‘rungs’ on DNA ladder- can then twist into double helix- gives molecule stability
Adenine with thymine- 2 x hydrogen bonds
Guanine with Cytosine- 3 x hydrogen bonds
What is the upright part of the large DNA molecule formed by
- sugar-phosphate backbones of the antiparallel polynucleotide strands
What does the ‘opposite direction’ of the 2 strands refer to
The direction that the 3rd and 5th carbon molecules on the 5 carbon sugar are facing
Where do you count from to identify carbon numbers on the sugar, and where is the 5th carbon
clockwise from oxygen
attached upwards from the fourth
What us the 5’ and the 3’ end of the molecule
5’- where the phosphate group is attached to the 5th carbon atom of the deoxyribose sugar
3’- where the phosphate group is attached to the 3rd carbon atom of the deoxyribose sugar
How is the structure of DNA suited to its function
Strong covalent bonds between sugar and base- the integrity of coded info from bases protected
Hydrogen bonds weak- easy to break in replication
Covalent bonds in backbone strong- stable
Complimentary bases- stability
How is DNA organised in eukaryotic cells
- majority of DNA content (the genome) in nucleus
- each large molecule of DNA tightly wound around special histone proteins into chromosomes
- each chromosome is therefore one molecule of DNA
- also a loop of DNA without the histone proteins inside mitochondria and chloroplasts
What is a gene
a section of DNA that codes for a polypeptide or for a length of RNA that is involved in regulating gene expression
How is DNA organised in prokaryotic cells, and what is this similar to
- DNA in a loop within cytoplasm- not enclosed in a nucleus
- not wound around histone proteins- described as naked- same as viruses
Describe the process of DNA replication
- Gyrase unwinds the DNA
- Helicase unzips the 2 strands- the replication fork moves along the molecule
- Primase makes primers (RNA) to signal where the nucleotides need to be added
- DNA polymerase adds the nucleotides on the leading strand continuously (as it’s in the 5’-3’ direction) - using each single strand as a template
- The lagging strand travels in a 3’-5’ direction, so DNA polymerase works discontinuously
- This means nucleotides are added as Okazaki fragments, which are stuck together by DNA Ligase- which takes longer
- The strands are held apart by SSB proteins
What is meant by semiconservative replication
One parent DNA strand, and one new daughter strand
When 2 original strands separate and each acts as a template for a new, complementary strand
Why does DNA need to be replicated
So that when a cell divides, each new daughter cell receives a full set of genetic instructions
When does DNA replication occur
during interphase, before the cell divides
What does cell division result in eukaryotes
- each chromosome having an identical copy of itself
- At first they are joined together, at the centromere, forming 2 sister chromatids
- The DNA within mitochondria and chloroplasts also replicates each time these organelles divide- just before the cell divides
What is added to the unzipped strand during DNA replication
Free phosphorylated nucleotides- present in the nucleoplasm within the nucleus are bonded to exposed bases, following complementary base pairing rules
What specific thing requires energy in DNA replication, and what provides this
-hydrolysis of the activated nucleotides, to release extra phosphate groups, supplies the energy to make phosphodiester bonds between the sugar residue of one nucleotide and the phosphate group of the next
What is the end result of DNA replication
- 2 DNA molecules- identical to each other and the parent molecule
- each of these molecules contains one new and one old strand- it is semi-conservative replication
Describe DNA replication in prokaryotes
- The loops of DNA in prokaryotes, and inside mitochondria and chloroplasts, also replicate semi conservatively
- a bubble sprouts from the loop and this unwinds and unzips, and then complementary nucleotides join to the exposed nucleotides
- eventually, the whole loop is copied
What are mutations, and how often do they occur
- When errors are made during replication and the wrong nucleotide is inserted
- 1 in 10’8 base pairs
What is it called when a mutation changes the genetic code
a point mutation
What reduces mutation risk
Enzymes that can proofread and edit out incorrect nucleotides
What are different versions of particular genes called
Alleles
What can mutations be
- harmful
- neither advantage nor disadvantage
- advantageous
In which ways is RNA different to DNA
- the sugar molecule in each nucleotide is ribose- not deoxyribose- has no O on 2nd carbon
- The nitrogenous base uracil (a pyrimidine) replaces thymine
- the polynucleotide chain is usually single-stranded and shorter
- 3 forms mRNA, tRNA, rRNA
What is a polypeptide
A polymer made of many amino acid units joined together by peptide bonds
What does each gene contain
A code that determines the sequence of amino acids in a particular polypeptide or protein
What percentage of an organisms dry mass do proteins account for
75%
Give examples of proteins
- Structural- cytoskeleton threads
- enzymes
What determines the primary structure of a polypeptide
DNA base triplets
How is a polypeptides tertiary structure created
The folding of a polypeptide chain
What are examples of how the tertiary structure of a polypeptide determines its function
- Shape of the active site on an enzyme must be complementary to the shape of the substrate molecule
- Part of an antibody molecule must have a complementary shape to antigens
- Receptor on the cell membrane must have a complementary shape to the cell signalling molecule to detect
- Ion-channel protein must have hydrophilic amino acids lining inside and lipophilic amino acids on the outside that will be next to lipid bilayer of plasma membrane
Describe the nature of the genetic code
- near universal- almost all living organisms have the same triplet of the base to code for amino acid
- Degenerate- other than methionine and tryptophan, there is more than one base triplet for the amino acid- reduces effect of point mutations, as the change in one base of triplet could produce another base triplet that still codes for same AA
- Non-overlapping- still read starting from a fixed point in groups of 3 bases- if bases are added or deleted it causes a frameshift- as every base triplet after that, and hence every amino acid coded for is changed
What are the 2 stages of protein synthesis
Transcription and translation
Describe transcription
- gene unwinds and unzips
- Hydrogen bonds between complementary nucleotide vases break
- RNA polymerase catalyses the formation of temporary H bonds between RNA nucleotides and their complementary, unpaired DNA bases
- A with U (not T)
- T with A
- C with G
- molecule being paired with is called the template strand
- Complementary length of RNA produced is the same as the coding strand other than T
- mRNA passes out of the nucleus through the nuclear envelope and attaches to a ribosome
Describe how ribosomes are formed
- made in the nucleolus in 2 smaller subunits
- pass separately out of the nucleus through pores in the envelope and come together to form a ribosome
- Magnesium ions help to bind 2 subunits together
- made of ribosomal RNA and protein in roughly equal parts
Describe tRNA
- tRNA molecules are made in the nucleolus and pass out to the cytoplasm. They are single-stranded polynucleotides but can twist into a hairpin shape
- at the end is a trio of nucleotide bases that recognises and attaches to a specific amino acid
- at the loop of the hairpin there is a triple of bases called an anticodon that is complementary to a specific codon of bases on the mRNA
Describe translation
- tRNA molecules bring the amino acids to find their place when the anticodon binds by temporary H bonds to the complementary codon on the mRNA molecule
- as the ribosome moves along the length of mRNA, it reads the code, and when 2 amino acids are adjacent to each other peptide bonds form between them
- Energy (in form of ATP) is needed
- The amino acid sequence for the polypeptide is therefore ultimately determined by the sequence of triplets of nucleotide bases on the length of DNA- the gene
- After the polypeptide has been assembled, the mRNA breaks down- its component molecules can be recycled into new lengths of mRNA, with different codon sequences
- The newly synthesised polypeptide is helped, by chaperone proteins in the cell to fold correctly into its 3D shape ( tertiary structure) in order to carry out its function
