Nucleic acids and their functions

What type of molecules are nucleic acids

- polynucleotides

State types of nucleic acids

DNA and RNA

What monomer makes up DNA and RNA?

- nucleotides

What is a nucleotide

- phosphate group, pentose sugar(deoxyribose/ribose), organic nitrogenous base

Pentose sugar in DNA

Deoxyribose

Pentose sugar in RNA

Ribose

State shapes of parts of nucleotides

- phosphate groups = circle

- pentose sugar = pentagon

- organic nitrogenous base = rectangle(ish)

State types of organic nitrogenous bases

- purines

- pyramidines

State purines

Adenine and guanine

Describe purines

- short word = big molecule

- 2 ring structure

State pyramidines

- cytosine and thymine (and uracil)

- ('y' containing words)

Describe pyramidines

- long word = small molecule

- 1 ring structure

Describe polymerisation of nucleotides

- the nucleotides are joined by condensation reactions between the sugar and the phosphate

Describe structure of DNA

- deoxyribose sugar and phosphate groups are on outside = backbone

- double helix

- 2 complementary bases face each other pointing inwards = H bonds

- nucleotides in 1 strand are arranged in opposite direction from those in the complementary strand = antiparallel

- phosphate group joined on C3' and C5' of pentose sugar, base joined on C1'

What maintains the double helix shape of DNA

- H bonds between bases

Describe hydrogen bonding in DNA

- 3 between cytosine and guanine

- 2 between adenine and thymine

Define what is meant by 'antiparallel'

- parallel strands but facing in opposite directions

How are carbons classified on pentose sugar in DNA/RNA

- number' = primary

- why: to distinguish from C in base group

DNA functions

- replication: cell division, complementary bases allows accurate copying of genetic material

- holds information for protein synthesis in all cells

Define exons

- regions of DNA that contain the code for proteins

Define intrions

- non-coding regions of DNA

Where are intrions found

- between exons

How many possible codons are there?

- 64

One word to describe that DNA is a polymer made of nucleotides?

- polynucleotide

Why RNA can get out easily from the nucleus

- single strand

The rule of complementary base pairing?

- A,T

- C,G

The organelle where proteins are made?

Ribosomes

Term used instead of DNA copying itself?

Replication

What DNA stands for?

- deoxyribose nucleic acid

The sugar in RNA

Ribose

Bonds formed during protein synthesis

- peptide

What makes the sides of the ladder of DNA

Sugar-phosphate backbone

Function of mRNA

- copies part of the genetic code

How many mRNA bases code for an amino acid?

3 bases

Old theory of mRNA

- copy of 1 gene and codes for 1 protein

New theory of mRNA

- copy of 1 gene and codes for 1 polypeptide

Why is the statement: 1 gene codes for 1 protein, wrong

- some proteins are made up of multiple polypeptide chains (haemoglobin) and 1 gene can only code for 1 polypeptide chain

Function of tRNA

- transfers amino acids to ribosomes to make proteins

State types of RNA

- messenger RNA

- transfer RNA

- ribosomal RNA

Describe ribosomal RNA

- large and complex molecule

- made of both double and single helixes

- makes up ribosomes along with protein

Where is mRNA found

- made in nucleus and leaves to cytoplasm through nuclear pore

Where is tRNA found

- cytoplasm

Where is rRNA found

Part of ribosomes

Shape of mRNA

- single strand, short, carries codons

Shape of tRNA

- clover leaf shape, single strand, anticodons and amino acids binding sites

Shape of rRNA

- single and double strand

- complex structure

Function of mRNA

- carries genetic code from DNA to ribosomes

Function of tRNA

- connects amino acids to ribosomes

Function of rRNA

- part of ribosome so involved in protein synthesis

Similarities between DNA and RNA

- polynucleotides

- sugar phosphate backbone

- 4 types of nitrogenous bases

Differences between DNA and RNA

- DNA is double helix vs RNA is single strand

- sugar in DNA is deoxyribose, RNA - ribose

- DNA - thymine nitrogenous base vs uracil in RNA

Outline DNA replication

- Helicase enzyme unwinds double helix and breaks H binds (unzips) between 2 strands, making short and single stranded region

- nucleotides made in G1 in cytoplasm enter nucleus via nuclear pore

- free nucleotides are attracted to complementary bases in single strands and will form H bonds

- DNA polymerase join nucleotides together forming sugar phosphate backbone (phosphodiester bonds) = becomes new DNA strand

State proposed DNA models

- conservative

- semi-conservative

- dispersed

Outline conservative model of DNA and how it would appear in Meselson and Stahl's practical

- DNA molecules made up of 2 old strands and then 2 new strands each time

- results: 1st culture has N15, second would have N15 at bottom, then a N14 band above, then 1 N15 molecule and 3 N14 molecules - small band at bottom, bigger band near top

Outline semi-conservative model of DNA and how it would appear in Meselson and Stahl's experiment

- each molecule has 1 old strands and 1 new strand

- 1st gen - 2 molecules each with N14 and N15 strands, band near middle (above gen0 band)

- 2nd gen - 2 molecules each with N15 and N14 strands, another 2 molecules with only N14 strands - 2 equal width bands on bottom and top

Outline dispersive replication and how it would appear in Meselson and Stahl's experiment

- mixture of old and new DNA make up each molecule

- gen 0: only N15

- gen 1: 2 molecules mixed with N14 AND N15 - band in middle

- gen 2: 4 molecules with both N14 and N15 but progressively more N14 as the source N15 runs out - band slightly higher than in gen 1

Outline Meselson and Stahl's experiment

- cultured bacteria E.coli for several generations in a medium containing amino acids made with the heavy isotope of nitrogen = N15. Bacteria made nucleotides with this. DNA was extracted and centrifuged = settled at a low point in the tube (as N15 is heavy)

- bacteria was washed (no contamination of N14 medium with N15) then put in N14 medium, allowed to divide

- DNA from 1st gen centrifuged = mid point density, ruling out conservative which would show an entirely heavy band - could be semi-conservative or dispersive

- DNA from second gen grown in N14 = settled at the mid-point and high point in the tube in equal amounts. Supports semi-conservative not dispersive where all strands would be mixed and only 1 mid-point band would appear

Define an enzyme

- a protein which catalyses a metabolic reaction

Polypeptide definition

- a polymer with amino acid monomers joined together by peptide bonds

Histone definition

A protein associated with the chromosomes in a eukaryote

Gene definition

- a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain

Transcription defnition

- the creation of a single-stranded mRNA copy of the DNA coding strand

Triplet code defintion

The sequence of 3 nucleotide bases which coded for 1 amino acids

What is meant by the term 'degenerate' or 'redundant' genetic code

- it can be referred to as this because more than 1 triplet code can encode each amino acid

State terms used to describe triplet code

- redundant/degenerate

- universal

- non - overlapping

Why are the codons referred to as non-pverlapping

- they are each read separately

Why are triplet codes called universal?

- the same triplet codes for the same amino acids in all known organisms

Where dies transcription take place in eukaryotes

- nucleus

Why is the code called a triplet code

- each amino acid is coded for by 3 bases (codon)

What structure of a protein is coded for by the genetic code

- primary structure (sequence of amino acids)

Why does it have to be a triplet code

- 4 different bases and 20 amino acids need to be coded for

- if the code was 1 base = 4^1 =4 amino acids

- if code was 2 bases = 4^2 =16 amino acids

- code is 3 bases = 4^3 =64 amino acids (enough for 20 amino acids)

Outline stages of transcription (in both prokaryotes and eukaryotes)

- DNA helicase breaks the H bonds between the bases in a specific region of DNA

- so 2 strands separate and unwind, exposing nucleotides

- 1 DNA strand acts as a template

- RNA polymerase binds to the template strand on DNA at the start of the sequence to be copied

- free RNA nucleotides align opposite the template strand based on complementary pairings

- RNA polymerase moves along DNA strand, joining adjacent/complementary nucleotides = forms RNA strand

- DNA strand rewinds to reform double helix behind RNA polymerase

- RNA polymerase separates from the DNA template when it reaches a stop signal and transcription is complete = (pre) mRNA detaches

Outline extra stage in transcription in eukaryotes

- Eukaryotic genes contain coding sequences, exons and non coding sequences, introns

- introns need to be removed from pre-mRNA strand formed in transcription

- introns cut by endonuclease enzymes

- exons then join to form mature mRNA which is translated

- exons spliced together by ligase enzyme

What are spliceosomes?

- the protein complexes that remove introns and splice exons together to form the mature mRNA that leaves the nucleus via the nuclear pores and moves to the cytoplasm to be translated

What is needed for translation?

- mRNA

- ribosomes

- tRNA

- amino acids

What is the site of translation?

- ribosomes

Where are ribosomes found?

- cytoplasm or the rough endoplasmic reticulum

State stages of translation

- initiation

- elongation

- translocation

- termination

Outline initiation stage

- small subunit of ribosome binds with mRNA at a start codon

- an initiator tRNA molecule with an anticodon complementary to the first codon on the mRNA, attaches to the ribosome. The 3 bases of the codon on the mRNA bond to the 3 complementary bases of the anticodon on the tRNA, with H bonds

- A 2nd tRNA, with an anticodon complementary to the second codon on the mRNA attaches to the other attachment site and the codon and anticodon bond with H bonds

Describe elongation and translocation stages

- 2 amino acids are now sufficiently close together for ribosomal enzyme to catalyse the formation of a peptide bond between them

- the 1st tRNA leaves the ribosome, leaving its attachment site (A) vacant. It returns to the cytoplasm to bind to another cope of it specific amino acids

- translocation: the ribosome moves along mRNA strand to next codon releasing the unattached tRNA from its exit site

- the growing peptide chain is positioned in site P

Outline termination stage

- the sequence repeats until a 'stop' codon is reached

- the ribosome - mRNA - polypeptide complex separates

Outline the 1 gene - 1 polypeptide hypothesis

- it was prposed that 1 gene would always make 1 enzyme

- was then modified to 1 gene, 1 polypeptide at the result of work by Beadle and Tatum

- as research continued, we have found exceptions to the rule: some genes control the expression of others (no polypeptide produced)

- some genes code for mRNA that is modified in the cytoplasm and go on to prodcue different polypeptides eg lymphocytes to make range of antibodies

What is a polysome

- several ribosomes can bind to a single mRNA strand, each reading the coded information at the same time

- each ribosome produces a polypeptide, so several are made at once