| 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 |
| 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 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 |
| 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 |
| 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 |
| Describe the process of translocation (3rd stage) (4) | Ribosomes moves one codon position in a 5' to 3' direction
deacylated tRNA (no AA) in P-site = translocated to E-site = released
tRNA in A-site = now in P-site
new tRNA can be added from the A-site |
| Describe the process of termination (last stage) (3) | elongation + translocation is repeated sequentially along the mRNA
Translation is terminated when ribosome reaches stop codon
These codons call a releasing factor = disassembles the ribosome
polypeptide is released |
| Why can pros have translation immediately after transcription? (4) | polysomes: group of 2 or more ribosomes translating a mRNA sequence at the same time
in proks the polysomes can form on an mRNA strand while being transcribed from DNA
so translation can occur immediately after transcription in pros because of no nuclear membrane
possible bec transcription and translation both happen in 5'-3' direction |
| Why does genetic material have to be transported from the nucleus for translation in euks? (3) | the ribosomes are separated from the genetic material by the nucleus
after transcription, the mRNA has to be transported before translation
the transport needs mods to the RNA (5' methyl capping and 3' polyadenylation) |
| What are polysomes? (3) | group of 2 or more ribosomes translating an mRNA at the same time
can form on an mRNA strand during transcription in pros
ribosomes on the 3' end of the polysome will have longer polypeptide chains than the 5' end |
| Which two locations can protein be synthesised? | ribosomes in the cytoplasm
ribosomes bound to the rough ER |
| what is the difference between protein production in the cytoplasm and in the ER? (2) | Cytoplasm: if the protein is for intracellular use, within the cell
Rough ER: if the protein is for secretion membrane fixation or for lysosomes = proteins transported by vesicles to the golgi apparatus for secretion |
| What is protein destination determined by? | presence /absence of an initial signal sequence on a nascent (recent) polypeptide chain |
| What does the presence of the signal sequence cause? (2) | recruitment of a signal recognition particle (SRP) = stops translation
SRP-ribosome complex stops at a receptor on the ER membrane = rough ER |
| How is the protein transported out of the cell? (5) | after the SRP ribosome complex stops at a receptor, translation starts again = polypeptide chain start to grow
by a transport channel into the ER's lumen
protein is then transported by a vesicle =
golgi complex for secretion/ lysosome
signal sequence is cleaved + SRP recycled after PP is made in the ER |
| Where do proteins for membrane fixation go? (examplle) | integral proteins get embedded into the ER membrane |
| What are the 4 levels of protein structure? | primary
secondary
tertiary
quaternary |
| What is the primary structure of protein? (3) | order of AA in a PP sequence
formed by covalent peptide bond bw AA
controls all the following levels of protein structure |
| What is the secondary structure of protein? (3) | the PP chain is folded into repeating arrangements = forms stabilising H bonds bw AA not next to each other
= alpha helices / beta-pleated sheets / random coils |
| What is the tertiary structure of proteins? (5) | Describes how the chain folds into a 3D shape
forms interactions between variable groups (ionic bonds, H bonds, etc)
affinity + repulsion of diff side chains affects the overall folding
eg: fibrous protein: structural, insoluble
eg: globular protein: functional, soluble
may be important for the protein's function = specificity of active site in enzymes |
| What is the quaternary structure of proteins? | more than 1 PP chain or additional prosthetic groups in a biologically active protein
NOT ALL proteins have a quaternary structure
prosthetic group: inorganic compound in protein structure / function (heme group in hemoglobin)
protein with prosthetic group conjugated protein
held with many diff bonds |
