DNA and RNA Flashcards
DNA
-Deoxyribonucleic acid (DNA) is the basis for heredity
-composed of deoxyribose (a 5 carbon sugar) nonded to a phosphate group and one of 4 nitrugenous bases: A, T, G, C
-ability to self-replicate makes sure that the coded DNA sequence will be passed on to future generation
=Central Dogma
-DNA is mutable, and these changes alter the proteins produced and therefore the organism’s characteristics
-changes in DNA usually stable and passed down from generation to generation. this provides the basis of evolution
DNA structure
–basic unit of DNA is the nucleotide
-a nucleotide is composed of deoxyribose (a sugar) bonded to both a phosphate group and a nitrogen base-there are 2 types of bases: purines and pyrimidines
purines in DNA include adenine (A), and guanine (G)
-pyrimidines are cytosine (c) and thymine (T)
-purines are larger in structure than pyrimidines because they posses a 2-ring nitrogenous base, whereas pyrimidine have a 2-ring nitrogenous base
-phosphate and sugar form a chain with the bases arranged as side groups off the chain
-the directionality of DNA id 5’ to 3’
-double stranded DNA helices of complementary strands with the sugar-phosphate chains on the outside of the helix and the nitrogenous bases on the insde
-strands held together by H-bonds between bases: T-A, G-C
-antiparalel
discovered by James Watson and Francis Crick with the help fo Rosalind Franklin and others- a.k.a Watson-Crick DNA model
topoisomerase
-uncoils DNA strands for replication
DNA helicase
- breaks hydrogen bonds between the nitrogenous bases of each nucleotide for DNA replication -unwinds DNA
- creates the opening in the DNA molecule- called the replication fork
semiconservative model
- each single strnd acts as a template for complementary base-pairing
- this allows the synthesis of 2 new daughter strands
- each new helix contains an intact strand from the parent helix and a newly synthesized strand
- this type of replication is called the semiconservative model
DNA polymerase
- creation of the daughter strands is a result of the action of DNA polymerase
- DNA polymerase reads the parent DNA strand and creates a complementary, antiparallel daughter strand
- reads parent strand 3’->5’ direction, creating new daughter strand in 5’->3’ direction
- one daughter strand is the leading strand and the other is the lagging strand
leading strand
-is continuously synthesized by DNA polymerase, which attaches nucleotides to the exposed 3’ end of the parent strand and follows the replication fork to the 5’ end
lagging strand
- synthesized discontinuously because the 5’ end of the parent strand is the one exposed.
- therefore, DNA polymerase, which can only read in the 3’->5’ must continually reattach to the 3’ ends of the parent stand since these ends are continually exposed as new section of helices unwinds
- the short fragments that result fro this discontinuous synthesis are known as Okazaki fragments
DNA ligase
as the lagging daughter strand is being formed, DNA ligase joins these fragments together
The genetic code
- DNA is made of 4 different nuceotides: Adenine (A), Thymine (T), cytosine (C), guanine (G)
- in RNA, the nucleosides are identical except for thymine which is replaced with uracil (U)
- DNA is transcribed into mRNA and arranged into troplets also known as codons, then translated from mRNA into amino acids
- there are 20 amino acids that can be formed from all the possible combinations of the 4 nucleotides
- genetic code is universal for all organisms
- 64 different codons are possible based on the triplet code and 4 possible nucleotides, and only 20 amino acids need to be coded, the code must contain synonyms
- meaning most amino acids have more than one codon coding for them, referred to as redundancy of the genetic code
redundancy of the genetic code
- 64 different codons are possible based on the triplet code and 4 possible nucleotides, and only 20 amino acids need to be coded, the code must contain synonyms
- meaning most amino acids have more than one codon coding for them, referred to as redundancy of the genetic code
RNA structure
- Ribonucleic acid is a polynucleotide that is very structurally similar to DNA but with 3 major exceptions:
- its sugar is ribose (instead of deoxyribose)
- it contains uracil instead of thymine
- is usually single stranded
- RNA can be found in both the nucleus and the cytoplasm of the cell
- several types: all of which are involved in protein synthesis
- 3 major types are mRNA, tRNA, and rRNA
mRNA
- carries the complement of a DNA sequence (except T substituted for U)
- transports this complement from the nucleus to the ribosomes for protein synthesis
- mRNA is made from ribonucleotides complementary to the template strand of DNA= means that mRNA has the complementary code to the original DNA
- mRNA id monocistronic- meaning one mRNA strand codes for one polypeptide
Transfer RNA
-tRNA is a small RNA molecule found in the cytoplasm
-assists in the translation of mRNA’s nucleotide code into a sequence of amino acids
it brings the amino acids coded for in the mRNA sequence to the ribosome during proetin synthesis
-tRNA recognizes both the mRNA codon and its corresponding amino acid
transcription
RNA polymerase binds to the TATA box in the promoter region of the DNA template strand (only 1 strand of DNA is used for a given gene)
-nucleotides are added 5 prime to 3 prime direction
-heterogenous nuclear RNA (hnRNA) is formed
>introns are cleared and exons are spliced togehter to form the mRNA
>the 5 prime end of the mRNA is capped
>the 3 prime poly A tail is added
-finsihed mRNA leaves the nucleus through the nuclear pores
translation
the synthesis of an amino acid chain using mRNA as a template
steps:
-occurs in the cytoplasm,
-needs GTP energy
-mRNA binds to a ribosom- translation starts when ribosome encounters start codon
-tRNA delivers amino acids to the ribosome
-the tRNA/amino acid complex temporarily binds the mRNA codon
>enzyme- peptidyl transferase-forges a peptide bond between adjacent amino acids
-protein synthesis stops when stop codon is reached
-post-translational modification occurs to the protein product: 3D folding, additional carbohydrate, lipid, phosphate group, cleavage of signal sequences
peptidyl transferase
enzyme that forges a bond between adjacent amino acids
Base substitution
one base pair is subsituted for another
- transition: substitution of a pyrimidine ( C or T) by another pyrimidine, or of a purine (A or G) by another purine
- Transversion: substitution of a pyrimidine by a purine or vice versa
transition
- type of base substitution
- can cause small scale mutations
- substitution of a purine by a purine and a pyrimidine by a pyrimidine
transversion
- type of base substitution, can cause small scale mutations
- substitution of a purine by a pyrimidine or a pyrimidine by a purine
Deletion
one or more nucleotides are lost from a sequence
-can cause mutations
insertions
one or more nucleotides are added to a sequence
-can include a transposition- a sequence is inserted at an incorrect location in the DNA
Transposition
a sequence is inserted at an incorrect location in DNA
Spontaneous deamination
ex: cytosine loses its amino group to form uracil
alkylation of bases
the addition of a methyl group to a base
DNA Damage can result from these internal and environmental sources
- Mismatching during DNA replication
- spontaneous deamination or alkylation of bases
- UV light causing the formation of thymine dimers
- ionizing radiation producing double strand breaks
- chemicals causing the formation of bulky adducts
Direct repair
reverses DNA damage without cutting the deoxyribose phosphate (ex: removing a m=methyl group in order to restore the original base
Base excision Repair (BER)
is used when incorrect bases are present in DNA (ex: U is incorporated into DNA)
-the damaged base is recognized by a glycosylase and is hydrolytically removed from the dexyribose phosphate backbone. This leaves an apurinic or apyrimidic site where the purine or pyrimidine was removed.
The correct base is then inserted and the break is sealed by DNA ligase
Mismatch repair
use a method similar to BER to remedy incorrect pairings of the normal bases (A paired with C so then repaired to G will be repaired so that A pairs with T and C pairs with G)
Nucleotide excision repair (NER)
removes thymine dimers and bulky adducts.
the area of DNA surrounding and including the damaged portion is unwound and an endonuclease makes cuts on both the 5 prime and 3 prime sides of the damage
the bases are removed by an exonuclease and DNA is resynthesized, using the sister strand as a template to fill the gap
DNA ligase seals the new section into the backbone
glycosylase
involved in Base excision repair
nucleosome
the most basic unit of DNA packagining.
consists of 8 histones
DNA is wound almost 2 times around this protein core to produce a “bead like” structure
30nm chromatin fiber
nucleosomes are hoined by linker DNA and coiled into a 30nm fiber which is organized into loops
this structure is maintained by the histone H1 protein which is attached to the linker DNA
loop-scaffold complex
the loop-scaffold comples provides the compact structure of chromosomes seem during metaphase
- chromosomes have regions that stain either light or dark when observed under a microscope. the light regions are euchromatin, which is single-copy, genetically active DNA. the dark regions ae heterochromatin, which are repetitive sequences that are genetically inactive
- also important: centromeres and telomeres
centromeres
essential for proper chromosome segregation and the site of kinetochore function
telomere
cap the ends of chromosomes, maintaining structural integrity, ensuring complete replication and positioning of the chromosomes
euchromatin
the light regions in chromosomes
are single copy and genetically active DNA
heterochromatin
dark regions in chromosomes
repetitive sequences, are genetically inactive
cross-over
occurs during meiosis
occurs between homologous chromosoems resulting in genetic recombination this produces combinations of alleles not present in either parent
cross-over guidelines
- it occurs randomly along the entire chromosome
- two genes clese together on the chromosome have a low chance of cross-over (the genes are said to be linked)
- the further apart two genes are on a chromosomes, the greater the chance of these genese crossing-over
holiday model (holiday junctions)
provides an explaination for the events that occur during recombination
- homologous pairs line up
- an endonuclease nicks a single strand of DNA on each homolog at the same place
- the homologs exchange strands and are ligated together forming the Holiday structure
- branch mitigation can occur, incorporating a portion og the opposite strand into each molecule
- cleavage occurs: if the same strands are cleaved the original chromosomes are reformed. if the opposite strands are cleaved then recombinant chromosomes result
constitutional abnormality
chromosome abnormality
-the abnormality can be found in all cells of the body
somatic abnormality
the abnormality is found in only certain cells or tissues
numerical abnormality
- one of two categories of chromosomal abnormalities
numerical: the gain or loss of complete chromosomes
>Aneuploidy
-monosomy
-trisomy
>Euploidy
-polyploidy
-monoploidy
>mixoploidy
-mosaicism
-chimerism
structural abnormality
- 1 of 2 categories of chromosomal abnormalities
- the formation of abnormal chromosomes through the misrepair of chromosome breaks or a malfunction during recombination
Aneuploidy
numerical abnormality
-one or more chromosomes are missing or are present in more than the normal nu,ber
aniploidy usually results from nondisjunction, which is the failure of paired chromosomes to seperate in anaphase (usualy during meiosis 1)
Monosomy
a type of Anuploidy
the loss of a single chromosomes
-autosomal (any chromosome that is not a sex chromosome) monosomy is always lethal
monosomy of sex chromosomes X results in Turner’s syndrome (45, X)
trisomy
a type of Aneuploidy
the gain of an extra chromosome
-can cause down Syndrome (trisomy 21)
tetrasomy
the gain of an extra pair of homologous chromosomes
-tetrasomy 9p, tetrasomy 18p
Euploidy
tyoe of nnumaerical chromosome abnormality
-an extra, complete set of chromosomes is present or missing
>Polyploidy
>monolploidy
Poliploidy
a type of Euploidy
polyploidy: mor than 2 sets of chromosomes is present or missing
- triploid, tetraploid, pentaploid etc
monoploidy
type of euploidy
- monoploidy: a complete chrmsme set is missing
- lethal
mixoploidy
type of numerical chromosome abnormality
>mosaicism
>chimerism
mosaicism
type of mixoplidy
2 or more genetically different cell lines within a single individual derived from a single zygote
- being composed of cells of two genetically different types.
chimerism
2 or more genetically different cell lines within a single individual derived from different zygotes
-composed of two genetically distinct types of cells
how to structural abnormalities occur
they occur whe part of a chromosome is duplicated, deleted or has been switched to another part of the chromosome
so the chromosome number is normal but there is either excess or deficient genetic material present in the cell
2 main ways structural abnormalities occur:
-recombiation malfunction
-misrepair of chromosome breaks
results of malfunctions in chromosome
-inversions
-duplications
-deletions
-translocation
>reciprocal
>robertsonian
inversion
the chromosomal segment is rejoined opposite og its normal configuration without loss of genetic information
duplication
a segment of the chromosome is repeated
deletion
a segment of the chromosome is lost
translocation
chromosomal material is exchanged between non-homologous chromosomes
>reciprocal: there is no loss of genetic information although gene arrangement is altered (considered a balanced translocation)
>robertsonian: the short arm of two chromosomes breaks off and the long arms are fused together; this can result in a balanced
most important mode of control of gene expression
-transcription since it is the first costly step in protein synthesis is transcription= economical to control gene expression then
-2 types:
>Negative
>positive
Negative control (or repression)
A protein binds to DNA in order to interfere with the binding of the RNA polymerase to the promoter region
-prevents transcription
Positive control (or activation)
a protein binds to DNA in order to facilitate with the binding of the RNA polymerase to the promoter region
-initiates transcription
