Molecular Bio Flashcards
What is molecular biology?
**concerns the molecular basis of biological activity that occurs between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, proteins and their biosynthesis, as well as the regulation of these interactions
study of the molecular foundation of the processes of transcription, translation, replication, cell function
The ‘central dogma’ of molecular biology, where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding this field. This picture, however, is undergoing revision in light of emerging novel roles for RNA”**
- The central dogma of molecular biology explains the flow of genetic information within a biological system. It was first stated by Francis Crick in 1956, and re-stated in a Nature paper published in 1970
- “The central dogma of molecular biology deals with the detailed residue-by- residue transfer of sequential information. It states that such information cannot be transferred back from protein to nucleic acid.”- Francis Crick-
- Crick’s use of the word ‘dogma’ was unconventional, and has been controversial.
This genetic material must be able to do what?
- have info. necessary to construct an entire organism
- pass from parent to offspring; cell to cell, cell division
- An accurate copy
- Account for the known variation within and between species (be able to help in differentiating itself from another species)
a. History: from 1920s to 1940s scientists thought which portion of chromosomes to be the genetic material?
protein
Frederick Griffith: what’d he do?
(ff = cc in streptococcus; c -> capsule)
- “bacterial transformation”
- he worked with streptococcus pneumonia
- rough strains (R) without capsules are non-fatal as the R strain bacteria (s. pneumonia) doesn’t have a capsule to protect itself from immune cells
- Smooth strains S have capsules thus are fatal however heat-killed type S not fatal
- BUT THEN AGAIN when R mixed with heat-killed S found that living type R cells have been transformed into virulent type S cells as this trait gave the R the capsule and was passed down to their offspring
he didn’t know the “transforming principle”’s biochemical basis (he still thought this transforming thing was protein)
Building off of Griffith’s work on transforming bacteria, what did Avery, MacLeod and McCarty (north Americans) find and how?
- Only purified DNA from type S strain which could transfer to type R
- Purified DNA might still contain traces of contamination that may be the transforming principle
- added (cell lysates from the pathogenic type) DNAase to digest DNA, RNase and proteases
- only w/ DNase no transformation as it had removed DNA thus it was concluded that DNA was the GENETIC MATERIAL (transforming principle)
Solving DNA structure
what did Watson and Crick propose the structure of and which method/structures did they use?
Did they receive any prize for it?
who else worked with them and what’d they do?
they proposed the structure of the DNA double helix and they used Linus Pauling’s method of working out the protein’s structure using ball and stick models; found ball and stick model consistent with data
They received the noble prize for this discovery
Rosalind Franklin: helped visualize the structure using x-ray diffraction that also provided imp. info.
Franklin died prematurely and nobel prize is NOT awarded posthumously.
Erwin Chargaff (Ukrainian guy): analyzed base composition of DNA that also provided imp. info.
Structure of nucleic acid
nucleic acid is a what?
what does it consist of “A”? what does this “A” consist of?
nucleic acid is a polymer
it consists of a chain of nucleotides which contains 3 basic building blocks:
phosphate
sugar
nitrogenous base
DNA’s structure has/is?
double-stranded
helical
sugar phosphate backbone
“bases on the inside (nitrogenous bases)!” which are stabilized by H bonding
specific pairing of nitrogenous bases (AT/GC)
(H bone can be easily broken)
3 components of DNA and RNA
phosphate group
nitrogenous base
- purines (“double/two ring” - IMP!): A & G
- pyrimidines: C & T
Deoxyribose sugar (pentose sugar)
RNA: same except “U instead of T” (IMP!) and ribose sugar (also pentose) instead of deoxyribose sugar
Conventional numbering system of DNA? e.g. phosphate on which # of C and nitrogenous on which ?
phosphate on the 5th carbon
nitrogenous base on 1st C (see screenshot)
Strands
how are they bonded?
which bond links sugars?
which 2 components of DNA form backbone?
bases project from backbone?
directionality from 5 to 3
or 3 to 5?
nucleotides covalently bonded so pretty strong
phosphodiester bond (between 3rd (top) and 5th carbon of sugars)
phosphate and sugar
yes
5 prime to 3 prime (TACG)
“Chargaff’s Rule”
it is also known as? (hint: nitrogenous base)
how many base pairs turn?
the DNA strands are what and what?
AT/GC
10 base pairs
complimentary (nitrogenous base); antiparallel
(lesser AMINO ACIDS than codons)
What are the buildings of DNA and RNA?
DNA is associated with an array of diff. what?
what is the complete complement of an organism’s genetic material?
nucleotides
proteins (histones etc.)
genome
n which groove does protein bind to to regulate transcription or replication?
major groove
DNA replication: what happens? short summary
what is the site of start point for replication known as?
is it uni or bidirectional? replication proceeds in same or opposite directions?
how many origin does bacteria and eukaryotes have?
The parental strands separate and serve as template strands
new nucleotides must obey the AT/GC rule
End result 2 new double helices with same base sequence as original
- origin of replication (note: not promoter as its not transcription)
- bidirectional; opposite
- bacteria has one and eukaryote has multiple
DNA replication a little more in detail?
and the enzymes involved?
origin on replication provides an opening called a replication bubble that forms two replication forks
DNA replication occurs near the fork
synthesis begins with a primer from 5’ to 3’
leading strand - one long continuous molecule whereas lagging strand - okazaki fragments connected by DNA ligase
enzymes:
DNA helicase binds to DNA and travels 5’ to 3’ separating strands using ATP
DNA topoisomerase: relieves additional coiling ahead of replication fork
single strand binding proteins: keep parental strands open to act as templates
DNA polymerase: forms bonds between new and parental strand
https://www.youtube.com/watch?v=T1aR77FLdi0
DNA replication is v accurate y?
H bonding more stable than mismatches (ensure that the correct base is incorporated by the enzyme DNA polymerase).
active site of DNA polymerase unlikely to form bonds if pairs mismatched
DNA polymerase removes mismatched pairs;
-it digests mismatched pairs’ linkages during proofreading
-other DNA repair enzymes
Central Dogma - Crick (formation of a functional product that makes the cell work)
what do transcription and translation produce?
eukaryotes have an additional intervening step called ? where pre-mRNA is processed into functionally active mRNA
transcription
- produces an RNA copy or transcript of a gene
- structural genes produce mRNA that specifies the amino acid sequence of a polypeptide
translation
- the process of making specific polypeptide on a ribosome
eukaryotes have an additional intervening step called RNA processing where pre-mRNA is processed into functionally active mRNA
Genes to Proteins
what is necessary to make an organism and allow it to favourably interact with its environment
structural genes code for “A”?
“A” becomes a ?
“B” determines the structure and function of cells?
what else is “B” the basis of?
Information in Genes
polypeptides
polypeptides become a protein
proteins’ activities
traits or characteristics of an organism
In transcription, DNA is transcribed into an ?
In translation, mRNA is translated into a ? at the
?
RNA copy or transcript of gene or mRNA (eukaryote, extra step, RNA processing where pre-mRNA to functional active mRNA)
polypeptide at the ribosome
what is an organized unit of DNA sequences?
what do these organized units of DNA sequences enable?
what percent of all genes are structural? Other genes code for the RNA itself
what does transfer RNA (tRNA) do?
Ribosomal RNA (rRNA) -
gene
the organized units of DNA sequences enable segments of DNA to be transcribed into RNA and ultimately results in the formation of tRNA, mRNA, rRNA
90%
tRNA links mRNA and amino acid sequence in proteins (transports amino acids to the ribosome)
rRNA (transcribed in nucleolus, prior to pre-ribosome construction) is part of ribosomes
what are the 3 types of RNA?
and their functions
- rRNA gene: constructs w other ribosomal protein/forms the core of cell’s ribosomes
- tRNA gene: links mRNA and amino acid sequences; carry amino acids to the ribosomes
- mRNA: carry codon sequences or protein information from cell’s nucleus (DNA) to cytoplasm
what does RNA polymerase do?
RNA polymerase catalyses the chemical rxn that synthesis the the RNA from DNA template
How many polymerase in prokaryotes v/s eukaryotes? and are they I, II OR II OR IV
RNA pol II needs how many general transcription factors to initiate transcription in eukaryotic cells?
prokaryotes only a single one - similar to polymerase II
eukar:
RNA poly II - transcribes mRNA
RNA pol I & III - transcribes non-structural genes for tRNA and rRNA
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