BIOLOGY TOPIC 7 NUCLEIC ACIDS (HL)
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BIOLOGY TOPIC 7 NUCLEIC ACIDS (HL) - Leaderboard
BIOLOGY TOPIC 7 NUCLEIC ACIDS (HL) - Details
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| Definition of nucleic acids? (4) | Genetic material made of recurring monomeric units (nucleotides): a phosphate group (circle) 5-carbon pentose sugar (pentagon) nitrogenous base (A, C, G, T) |
| Draw a nucleotide (3) | 5-carbon sugar , phosphate group and a nitrogenous base (A, T, G , C) Nitrogenous base attached to 1' carbon atom Phosphate base attached to 5' carbon atom |
| How are the nucleotides bonded? | Covalently bonded |
| Definition of DNA (2) | Deoxyribonucleic acid: stable double stranded form = stores genetic blueprint of cells made up of polymers of nucleotides |
| Describe the process of transcription | RNA sequences are produced from a DNA template0 |
| Definition of RNA | Ribonucleic acid: versatile single stranded form = transfers genetic info for decoding from nucleus to cytoplasm made up of polymers of nucleotides |
| What is produced with the phosphodiester bond? | Water is produced when there is a phospho bond between two nucleotides |
| What are the 5 different nitrogenous bases? | Adenine, Thymine, Guanine Cytosine, Uracil |
| How are the nucleotides linked together? | Linked into a strand by condensation reactions which forms long polynucleotides |
| How are the nitrogenous bases bonded? | Hydrogen bonding |
| Number of bonds between AT and GC? | AT = 2 GC = 3 |
| What is the structure of DNA? (4) | Sugar phosphate backbones strands run in opposite directions (antiparallel) made up of polynucleotide strands double helix |
| Differences between RNA and DNA? (3) | DNA = deoxyribose, ATGC, double stranded RNA = ribose, AUGC, single stranded |
| What did Watson and Crick propose about the DNA molecule? (4) | Made models of DNA based off of findings from other researchers: bond angles + molecular distances by Pauling DNA is made of nucleotides (sugar, phosphate and base) equal number of purines (A + G ) and pyrimidines (T + C) organized into a helical = Franklin |
| What was included in their DNA model? (3) | Antiparallel and form a double helix complementary base pairing (AT GC) outer edges of bases exposed for replicative and transcriptional proteins |
| Problems with earlier models of the DNA molecule? | Triple helix bases on the outside and sugar-phosphate residues in center bases didn't show complementarity |
| How did Rosalind Franklin contribute to the DNA molecule? | X-ray crystallography data that showed the DNA arrangement as a helical structure shared without Franklin's permission but helped a lot to the final model of DNA |
| What do mRNA do? (messenger) | Transcripts a gene copy that encodes for a specific polypeptide |
| What is an rRNA? (ribosomal) | In ribosomes for catalyctic activity |
| What is a tRNA? (transfer) | Carries PP subunits (AA) to ribosome for synthesis |
| Outline DNA replication (3) | DNA is copied during the formation of new cells in the nucleus before cell division (with enzymes) |
| Outline transcription (3) | DNA codes for RNA transcripts with the mRNA continuously in the nucleus (with enzymes) |
| Outline translation (3) | MRNA transcripts code for protein production continuously after transcription in the cytoplasm (With ribosomes) |
| Why is DNA replication a semi-conservative process? | Bec when new DNA molecules form they're made of one original strand and one new strand |
| How does the semi-conservative method work? (3) | Bec each base can only pair with its complementary base pair (AT, GC) = base sequence is conserved during replication as each new strand formed will be identical to the original strand which separates from the template |
| What were the three models to explain how the new molecules formed? | Conservative model: entire new molecule from original DNA molecule Semi-conservative model: ever new molecule comes from one new strand and one template strand dispersive model: new molecules made from new and old DNA segments |
| Describe the Meselson-Stahl experiment (7) | 2 radioactive isotopes of N were used during replication (15N and 14N) DNA molecules were first incorporated with 15N and then replicated in the presence of the 14N (nitrogen makes up DNA and can be either 15N or 14N) DNA samples were separated to see the composition of DNA in replicated molecules 1st division: DNA molecules had both 15N and 14N = disproves conservative 2nd division: Some molecules only had 14N = disproves dispersive = supports the semi conservative model |
| What does helicase do? (3) | Unwinds double helix to separate the 2 PN strands by breaking hydrogen bonds between complementary base pairs the separated PN strands = templates for new strand synthesis |
| What does DNA polymerase (III) do? | Makes new strands from 2 template strands free deoxynucleoside triphosphates aligns with complementary base pair with hydrogen bonding covalently joins the DNA nucleotides together to form a new strand (phosphodiester bond) |
| What is PCR? (polymerase chain reaction) (3 steps) | Artificial method of replication to make large quantities of a DNA sequence. happens in a thermal cycler at different temps 1) Denaturation: heat separates strands (95 degrees) 2) Annealing: cooled so primers make copying sequence (55 degrees) 3) Elongation: TAQ polymerase copies sequence (72 degrees) = 1 billion copies |
| What does DNA replication do? (2) | Semi conservative process whereby DNA is copied to create identical sister chromatids before cell division. The key enzymes used are: Helicase (separate DNA strands) and DNA polymerase (copies new strands) |
| Describe the process of polymerisation (w DNA polymerase (III) (4) | New nucleotides align with complementary pairs as (deoxynucleoside triphosphates) DNA pol III cleaves 2 phosphates = releases energy energy is used by enzyme = covalent phosphodiester bond w/ nucleotide chain 5' - 3' direction ON NEW STRAND |
| What are codons? (2) | How the mRNA is read by ribosomes as triplets of bases = each triplet = 1 AA order of codons = order of AA in a PP chain |
| What is the genetic code? (5) | Rules by which mRNA sequences are converted into protein identifies the corresponding AA for each codon 64 codon possibilities Coding region always begins with the START codon (AUG) and ends with the STOP codon key features: Universality: all organisms use the same code Degeneracy: more than 1 codon can code for the same AA (only 20 AA) |
| Translation overview | MRNA goes to Ribosome, which reads sequence as Codons recognised by Anticodons on TRNA which carries AA which joins with PP bonds to form Polypeptides |
| Why is genes transferrable between species? | Because the same codons code for the same AA in all living things |
| Where has gene transferability been used? (6) | To produce human insulin in bacteria for mass production gene for insulin production is removed from a human cell spliced and put in a plasmid vector = autonomous replication and expression then put in a bacterial cell (E-Coli) the transgenic bacteria is then cultured in a fermentation tank (increase numbers) bacteria= produces human insulin = used for diabetics |
| Describe Hershey and Chase's experiment (5) | Radio-labelled viruses were used to infect bacterium bec viruses inserted their genetic material into cells, then separated by centrifugation T2 Bacteriophage grown w/ 2 mediums to radio-label Viruses in 35S = RL proteins in supernatant (liquid above residue) Viruses in 32P = RL DNA in pellet (transferred to bacteria) = DNA is the genetic material not protein |
| Franklin's X-Ray diffraction method and inferences (3) | X-ray beam was targeted at a crystallized DNA molecule Beam was diffracted = scattering pattern recorded on film pattern shows structural features of DNA molecule Composition: double stranded, tightly packed, regular Orientation: Sugar-phosphate backbone, bases inside Shape: double helix Data shared by Wilkins to Watson and Crick without her permission to create a DNA model |
| What was found to be radioactive in the Hershey and chase experiment (pellet or supernatant)? | Found to be radioactive by the 32P but not the 35S which shows that DNA has the genetic material = DNA was transferred |
| How does the structure show DNA replication? (2) | Complementary base paring = sequence is conserved during replication as each strand acts as a template for the other antiparallel strands = replication is bidirectional so it is more quick |
| What are the enzymes used in DNA replication? (6) | Helicase DNA Gyrase DNA primase DNA polymerase III DNA polymerase I DNA ligase |
| What does DNA gyrase do? | Reduces strain from unwinding by relaxing + supercoils by - supercoils |
| What are the purines and pyrimidines? | Purines = A+G pyrimidines = T + C |
| What does SSB proteins do? (3) | Binds to DNA strands to stop recoiling stops single stranded DNA from being digested by nucleases. Removed when a new complementary strand forms from DNA pol III |
| What does DNA primase do? | Creates short RNA primer for DNA pol III to start extending the chain on each template strand |
| What does DNA polymerase III a do? (6) | Free nucleotides align with complementary base pairs. Covalently joins free nucleotides in 5'-3' direction Attaches to the 3' END OF THE PRIMER DNA pol III moves in opposite directions on the 2 strands leading strand: towards rep fork = extends continuously lagging strand: moves away from rep fork = extends in pieces (okazaki fragments) |
| What does DNA polymerase I do? | Removes the multiple RNA primers from the okazaki fragments and replaces them with with DNA nucleotides on the LAGGING STRAND |
| What does DNA ligase do? (2) | Joins the okazaki fragments = continuous strand covalently joins the sugar-phosphate backbones w/ phosphodiester bond |
| How does DNA polymerase add nucleotides? (6) | CAN'T start replication, only add new nucleotides attaches to the RNA primer and extends from 5'-3' direction adds nucleotides to the 3' primer of the template strand Free Nucleotides = deoxynucleoside TRIphosphates (dNTPs) DNA pol cleaves 2 extra phosphates from dNTPS and uses energy released = phospho bond with the 3' end of the chain |
| In which direction does DNA Polymerase III move on the leading strand? | Towards the replication fork = synthesises continuously |
| What is sequencing? | How the base order of a nucleotide sequence is explained using chain terminating dideoxynucleotides |
| What does Helicase do? | Unwinds and separates the strands of DNA by breaking H bonds bw base pairs = replication fork of 2 strands in antiparallel directions |
| In which direction does DNA polymerase III move on the lagging strand? | Away from the replication fork and is made in okazaki fragments |
| Why is the lagging strand discontinuous? | DNA pol is moving away from the helicase = has to return to copy new sections of DNA copied in short okazaki fragments = each w a primer primers are then replaced with DNA bases with pol I and are joined together w/ DNA ligase |
| How do dideoxynucleotides prevent further elongation? (2) | They can't form a phospho bond as they don't have the 3'-hydroxyl group = terminate replication So the length of the DNA sequence will show the nucleotide position which the ddNTP was used |
| Sanger Method (7) | Used to determine DNA sequence 4 sets of PCR with normal nucleotides and 1 dideoxynucleotide is used (ddATP, ddTTP, ddCTP, ddGTP) whenever the DDON is used the sequence is terminated bec PCR = 1 billion copies so every possible fragment will be made for a base When the fragments are separated by GEL ELECTROPHORESIS base sequence is determined by ordering the fragments according to their lengths fragments fluorescently tagged for automated sequencing |
| What are 5 types of non coding DNA? (5) | Satellite DNA: short tandem repeats (STRs) used for DNA profiling Telomeres: regions at the end of chromosomes to protect chromosomal deterioration during replication Introns: non coding sequences within genes, removed by RNA splicing before forming mRNA Non-coding RNA genes: codes for tRNA or rRNA Gene regulatory sequences: sequences used in transcription (promoters) |
| What does DNA structure do? Exceptions? | DNA structure has a role in genetic material, 4 bases form sequenced that encode for specific proteins but some sequences don't encode for protein such as: Satellite DNA Telomeres Introns Non-Coding genes Gene regulatory sequences |
| How is non coding DNA used in STR profiling? (3) | Satellite DNA: long lengths of short tandem repeats (STRs) differs between diff people = unique DNA profiles can be made by comparing the STR location tandem repeats can be cut out w/ restriction enzymes + separated with gel electrophoresis for comparision |
| What are nucleosomes?(4) | In Eukaryotic cells DNA is bound by histone proteins to form nucleosomes = compacts the DNA packaging for more effective storage supercoiling protects DNA from damage and allows chromosomes to be more mobile during mitosis and meiosis nucleosomes are then linked + compressed to form chromatin |
| How are nucleosomes held together? (3) | Made of DNA molecule wrapped around an octamer (8) of histone proteins - charged DNA associates w/ + charged AA on the surface of the histone proteins Nucleosomes link with an additional H1 histone protein |
| Order of organisation from DNA -> Chromosome? | DNA = Nucleosome = Chromatosomes = Solenoid = 30 nm Fibre = Chromatin = Chromosome |
| What is transcription? | The process whereby a DNA sequence is copied into a RNA sequence by RNA polymerase which can be translated into a polypeptide chain |
| What is a gene? | DNA section which is transcribed into RNA with 3 main parts: Promoter: non-coding sequence that starts transcription (binding site for RNA polymerase) Coding sequence: region of DNA that is transcribed by RNA polymerase terminator: terminates transcription |
| What is the difference between the antisense and sense strand? (2) | Antisense: transcribed (complementary to RNA transcript) - template strand sense: not transcribed (identical to RNA transcript except T instead of U) = coding strand |
| Describe the process of (5) | RNA polymerase binds to the promoter and separates DNA strands = 5' - 3' direction Nucleoside triphosphates (NTPs) bind complementary bases from the antisense strand covalently binds the NTPs together and releases the two extra phosphates for energy Once RNA pol reaches terminator sequence, the pol and RNA sequences dissociates from DNA = DNA reforms into double helix |
| What are 3 post-transcriptional modifications? | To form mature mRNA: Capping: 5' methyl (CH3) cap added to = prevents degradation by exonucleases Polyadenylation: 3' end is polyadenylated = poly-A tail added (AAAAA = adenines) improves stability and export from nucleus Splicing: introns (non coding sequences) are removed = continuous mRNA sequence from exons Introns = INTruding sequences and Exons = EXpressing sequences |
| What is alternative splicing? | Selective removal of exons in addition to removal of introns = different polypeptides can be made from the same gene = larger proteome |
| What is gene expression determined by? | Level of transcriptional activity = higher mRNA transcript production = increased proteins levels |
| What is gene expression? | Gene expression: how a cell controls which genes, out of the many genes in its genome, are expressed. each cell type in your body has a different set of active genes even though almost all the cells contain same DNA. |
| How is gene expression regulated? (2) | By 2 groups of proteins that bind to specific base sequences in DNA regulatory proteins and transcription factors |
| What are the two groups of proteins that regulate transcriptional activity? (+2 sub groups) (4) | TRANSCRIPTION FACTORS: form a complex with RNA pol at the promoter, needed to start transcription = their levels regulate gene expression REGULATORY PROTEINS: bind to DNA sequences outside the promoter + interact w/ the transcription factors. Such as: Activator proteins: bind to enhancer sites = increases transcription rate (moderates complex formation) Repressor proteins: bind to silencer sequences = decreases transcription rate (prevents complex formation) |
| What does the presence of transcription factors / regulatory proteins depend on? | They could be tissue specific chemical signals (hormones) can moderate protein levels = moderate a change in gene expression |
| What are control elements? (3) | DNA sequences that regulatory proteins bind to proximal elements: close to the promoter distal elements: more distant |
| Which control elements do the two different types of protein bind to? | Regulatory proteins bind to distal control elements transcription factors bind to proximal elements |
| Why is gene expression a controlled process? | Bec most genes have multiple control elements |
| How does the external/ internal environment of a cell affect gene expression? (4) | Chemical signals within the cell = triggers changes in levels of regulatory proteins / transcription factors bec of stimuli = gene expression changes because of changes in intracellular extracellular conditions |
| What are some examples of organisms changing gene expression? (2) | Hydrangeas change colour based on the pH of soil (acidic = blue, alkaline = pink) humans produce diff amounts of melanin (skin pigment) based on light exposure |
| How do nucleosomes help regulate transcription in eukaryotes? (4) | Histone proteins have protruding tails that determine how DNA is packaged within euk nucleosomes Acetylation: DNA LESS tightly packed and MORE accessible to transcription machinery Methylation: DNA is MORE tightly packed = LESS accesible ro transcription machinery = regulates transcription |
| How are nucleosomes held together? | Bec histone tails are positive and DNA is negatively charged = associate tightly |
| How does acetylation affect transcription? | Acetylation: adding an acetyl group to the tail = neutralizes charge = less tightly coiled = increases transcription |
| How does methylation affect transcription? | Methylation: adding a methyl group to the tail = maintains positive charge = DNA becomes more coiled = reduces transcription |
| What are the two types of chromatin? | Heterochromatin: DNA is supercoiled = no transcription (methylation) euchromatin: DNA is loosely packed = transcription (acetylation) some DNA segments are permanently supercoiled while other segments can change |
| How does direct methylation affect gene expression patterns? (2) | Increased methylation = decreases gene expression as it stops the binding of transcription factors so genes that aren't transcribed show MORE DNA methylation than genes that are actively transcribed |
| Factors that affect DNA methylation patterns? | Pregnancy: maternal diet Infancy: early exposure to microbes Young adult: lifestyle and diet Senior: age related changes |
| What is epigenetics? | Study of changes in phenotype because of variations in gene expression levels |
| What does epigenetic analysis show? (4) | LIFETIME: shows that DNA MP can change over a lifetime HERITABILITY: influenced by heritability but not genetically pre-determined CELL TYPES: diff cell types in the same organism can have diff DNA MP ENVIRONMENTAL FACTORS: diet, pathogen exposure influence level of DNA methyl within cells |
| Study 1: What does comparing twins of different ages show? | Shows that DNA methyl patterns differ bw twins but change over time = methyl patterns have a genetic basis but are influenced by the environment |
| Study 2: What does comparing methyl patterns in twins with diff health patterns show? | DNA methyl patterns differ bw healthy + unhealthy twins = methylation controls transcription = phenotypic expression of disease |
| What is translation? | MRNA sequences are translated into AA sequences (polypeptides) |
| What are ribosomes? (4) | Made of protein (Stability) and rRNA (catalytic activity) and is where translation occurs. They have 2 subunits: Small subunit: mRNA binding site Large subunit: 3 tRNA binding sites (A, P, E) found in cytoplasm or bound to rough ER pro = 70S euk = 80s |
| What are tRNA? (5) | Carries specific AA to the ribosome and have 4 regions: Acceptor stem (carries AA) Anticodon (complementary to mRNA codon T arm: associates with ribosome (A,P,E binding sites) D arm: associates with tRNA-activating enzyme (adds AA to the acceptor stem) = clover structure |
| Describe tRNA activation (7) | AA attaches to tRNA with tRNA activating enzymes enzyme = + ATP to AA (phosphorylation) = charged AA-AMP complex the phosphorylated AA is then linked to a SPECIFIC tRNA molecule = AMP released phosphorylation creates hi energy bond that is transferred to tRNA energy used for peptide bond formation |
| What are the stages of translation? (4) | Initiation: assembly of active ribosomal complex on an mRNA sequence Elongation: new AA is added to a developing peptide chain Translocation: ribosome moves to the next codon position Termination: ribosomal complex + polypeptide separates from mRNA |
| Which stages in translation is repeated? | Elongation and translocation is repeated in the same order as the ribosome moves along the transcribed mRNA sequence in a 5' to 3' direction |
| Describe what happens during initiation (1st stage) (4) | Involves assembly of the components that carry out translation (mRNA, tRNA, ribosome) small r subunit binds mRNA = moves to start codon (AUG) tRNA binds to start codon w/ complementary anticodon large r subunit binds tRNA (w/ P site) = completing ribosome translation occurs |
| Describe what happens during elongation (2nd stage) (4) | 2nd tRNA pairs w/ next codon (w/ ribosomal A-site) AA in P-Site is transferred to AA in A-site ribosome covalently joined the AAs together with a peptide bond tRNA in A site carries the peptide chain |