genes and transcription Flashcards
Structure of DNA
- double-stranded and complementary but anti-parallel
- each nucleotide is bonded together with a phosphodiester bond
what is complementary base pairing
- advantage of having complementary DNA strand
- One side of DNA is 5 prime
- The other side of DNA is 3 prime
- direction is always 5 to 3 prime
complementary base pairing transcribing
T-A
G-C
- MRNA is complementary to DNA when transcribed
what is a gene
- a functional unit of hereditary (DNA) which carries information from one generation to the next (or from 1 cell to another during cell replication)
- they occur on chromosomes and are short segments of DNA
what is a chromosome
- where genes are located
- packaging unit of DNA located in the nucleus
- nucleus component is inherited from both parents
chromosomes in prokaryotic organism
- DNA is located in the CELL not the nucleus
- single circular DNA naked as its not wrapped around proteins
chromosomes in eukaryotic individuals
- made up primarily of linear DNA and bound to proteins called histones
genome
all genetic information inside a cell
- one cell has half of the chromosomes from each parent (each chromosome has 2 copies)
Whats transcription
DNA in the nucleus is transcribed by RNA and translated to a polypeptide protein
- (mRNA is transcribed in the nucleus and exits the nucleus to the cytoplasm when it’s ready for translation)
gene expression key process
INPUT DNA, OUTPUT is RNA
1. Initiate (transcription)
2. elongate
3. termination
initiate/ transcription
- plus 1 nucleotide will be transcribed
- unwinds DNA and starting at +1 uses TEMPLATE strand to produce complementary RNA (based on complementary base pairing) until reach terminator
- RNA uses uracil instead of thymine
RNA
is the main component of ribosome used as a translationary machinery (how mrna can be translated into a protein)
Trna
transfer rna (single strand) transfer amino acid for making polepeptide
gene expression in prokaryotes vs eukaryotes
- pro: transcription happens from circular DNA
- euka: needs processing and moving from nucleus to cytoplasm
why is there modified ends to DNA
- to promote export of mrna from the nuclues and protect from degradation
- cap is located at 5 prime siteand poly-a to 3 prime
- in order to translate properly
splicing
- removal of INTRONS which are noncoding regions interspersed within the encoding regions called EXONS
INTRON: after pre mature mrna is transcribed cap and poly a is added and then remove intron to make mature RNA
EXON: expressed part (we want)
why is splicing needed
- we can use one coding sequence (template) to create different VARIATIONS of protein for different purposes
- (not in prokaryote)
Not all genes are expressed all the time…
eg:disease defense
- it is controlled so it can be expressed in the right time and place (we want disease resistant gene to function when the pathogen attacks, not be delayed)
- also energy saving as it comes with a metabolic cost
Activator binding site
- will only be expressed (transcripted) if this activator exists (protein binds to activator site)
eg: if the pathogen attacks plant produces protein which activates transcription
(positive regulation)
repressor binding site
STOP trasncription
(negative regulation)
ribosomes
- composed of rRNA and proteins
- large and small subunits
- contains P and A sites for tRNA binding during translation
the genetic code
AUG is START codon (starting point of tranlation)
STOP codon UGA,UAG,UAA
- translation initiation
- When the mRNA is released from the nucleus it goes to the cytoplasm
- The small subunit will bind to the mRNA and scan to find the start codon
- The tRNA will bind as a complementary to the start codon so UAC
Then they recruit their large subunit, the tRNA located in the P site of the large subunit
- translation elongation
- Then the A site on the large subunit will use trna to be complementary on the mrna site
- Each trna has its own unique amino acid (the condensation reaction occurs and the 2 amino acids bind together
- Then the disarmed trna will be released
- The p side is then empty and the translation can move forward
This process continues until reach stop codon (as there is no trna that can bind to the stop code)
- translation termination
- RNA subunits release
- the polypeptide chain is released into the cytoplasm
mutations (genetic variation)
- they are alterations to DNA sequences
- they are genetic variation
MUTATION IS CAUSE, GENETIC VARIATION IS CONSEQUENCE
why is complementary base pairing important
- vital for accurate conservation of informationduring the production of DNA, RNA and protein
- DNA-> DNA base pairing during DNA replication
- DNA-> RNA base pairing during transcription
RNA-> RNA base pairing during translation
structures of polypeptide
Primary structure
- Simple chain of amino acids (each amino acid has its own properties)
Secondary structure
- Can make a beta sheet (3 strands)
- Can make an alpha helix
Tertiary structure
- Can be a combination of sheet, alpha helix and loops
- The loop is the most unstable part of the protein
The final product (not necessarily functional) sometimes binds to other proteins and makes another structure
- 3 copies of the same protein or 2 different proteins come together
functions of protein
- can be tragted to particular organelles
- can store nutrients
Consequence of mutation in DNA
- may change the protein function
- if there is a mutation in DNA it will be transcribed to the mRNA and will create a different protein
(could be more or less efficient)
spontaneous mutation
mutation that arises naturally and not as a result of exposure to mutagenic agents
(occur due to natural causes)
induced mutations
- mutation that is produced by treatment with a physical or chemical agent that affects the dna or an organism
- occurs due to exposure to mutagens
what are mutagens
- electromagnetic radiation like X rays, Gamma rays, UV
- chemicals like thy
- natrual disasters
consequences of mutations are dependent on
where (cell/tissue) the mutation occurs (somatic vs germline mutation)
- if the mutation is NOT genetically inherited its no use for agriculture
Somatic mutation
- does NOT transfer to progeny (won’t inherit it to the next gen)
Germ-line mutation
- is the mutation which happens in the germ-line, the entire organism carries the mutation which will be passed onto the next gen
where the mutation occurs?
- mutation can occur in the coding region or the non coding region
coding mutation
- may affect the gene product
noncoding mutation
may affect the expression of the gene
small scale mutation
- single or small scale changes in the nucleotide of the DNA
point mutations
Silent mutation: no change in gene product
Missense mutation: amino acid changes, likely affect protein tertiary structure and change the protein function
Nonsense mutation: truncated (or shorter) protein, most likely reduced function or no function
Frameshift mutation: change in amino acid sequence, most likely reduced or no function or change of function
why is DNA replication important
- is the basis for biological inheritance
what is DNA replication
biological process by which produces 2 identical replicas of DNA from one original DNA molecule
process of dna replication
- the ori sequence binds the pre-replication complex
- two replication forks move away from one another and unwinds the DNA
(1 replication origin)
(bi-directional synthesis) - needs rermination replication
role of helicase
- helicase seperates strands of dna
- creates a single stranded dna in the localised area (which is very vulnerable)
- other proteins keeps the strand open and protects from other enzymes
DNA polymerase
- reads template 3-5
- adds bases to the 3 end of the growing strand
- needs a short double stranded region to start DNA replication
primase enzyme
- read the bottom strand and synthesis a short primer RNA
B clamp
keeps the DNA polymerase in place (allowing for smooth progression)
Lagging strand
5-3 (polymerase can’t read this strand)
- primase adds RNA primers to start replication
- dna POLYMERASE 3 will form new strands on the complementary template
- okazaki fragments are formed on the lagging strand
Okazaki fragments
- are joined by ligase
- gaps are filled with complementary basis by dna pol 1
Errors in dna (nucleotide mismatches) (DNA polymerase)
- have proofreading mechanisms for newly synthesised dna
- if mismayching was found cuts out the error and replaces with new base
DNA repair by mismatch repair (MMR)
- MMR proteins excise sections of dna
- DNA pol 1 adds correct sequence
DNA ligase repairs
telomeres
- protective chromosome ends
- protects ends of chromosomes from deterioration
chromosoemns need 3 elements
- origins of replication- DNA replication
- centromers- essential for segregation at cell division
- telomeres- crucial for structural stability
difference between prokaryotic and eukaryotic replication
in p dna synthesis is not cell cycle dependednt, whereas for e it is
