Molecular Biology 1-4 Flashcards
Describe the structure of DNA
Sugar phosphate backbone - outside
Bases - inside
2 complementary strands of DNA bind together.
The DNA double helix is held together by HYDROGEN BONDS formed between the base-pairs across the 2 different strands.
Explain how DNA is packaged within the cell
Short region of DNA double helix
“Beads on a string form of chromatin”
30nm Chromatin fibre of packed nucleosomes
Section of chromosome in extended form
Condensed section of chromosome
Entire mitotic chromosome
DNA
deoxyribonucleic acid
RNA
ribonucleic acid
What links DNA bases together on the DNA chain ?
5-3 prime phosphodiester linkage
Name the 4 main bases of nucleic acids
Adenine
Thymine
Cytosine
Guanine
What are purines ?
Adenine and Guanine
What are pyrimidines ?
Thymine and Cytosine
What is the difference between RNA and DNA ?
RNA has : Cytosine, Guanine, Adenine and Uracil
DNA has : Adenine, Thymine, Cytosine and Guanine
What is adenine lacking ?
Oxygen
Describe the polarity of the double helix
The cell reads the helix from left to right (5-3 prime)
On the opposite side of the strand (3-5 prime)
How many hydrogen bonds are between A and T ?
2
How many hydrogen bonds are between C and G ?
3
What is the term used to describe the inheritance of changes in base sequence ?
Genetics
What is important for replication ?
Major and minor grooves
How can chromosomes be distinguished by ?
Size
G-banding : Staining pattern : interacts with DNA produces darker and lighter areas
What is higher DNA in the form of ?
Chromosomes
As cells divide what happens to chromosomes ?
They become condensed.
How is DNA organised within the interphase nucleus ?
They are spread out in nuclear zones.
Inside the nuclear envelope in the nucleus
Structural features of histones
Positively charges
Long N-termini
What is a nucleosome ?
A set of histone proteins
H2A, H2B, H3, H4
Makes an octameric histone core
147 base pairs of DNA
Wrapped around histone proteins (H1)
1.7 left-handed turns
How are nucleosomes formed ?
The opposite charges of histones (+) and DNA (-) attract, so the double helix wraps twice around each group of 8 histones, forming a nucleosome.
Nucleosomes look a bit like beads on a string, and they can snuggle closer together and be further packaged as chromatin fibers.
What do the histone tails in the structure do ?
The amino-terminal tails of histone proteins protrude from the nucleosome
What is the function of histone H1 ?
Helps form 30nm fibre
Extra linking histone
Links nucleosomes together in a more compact high end structure
What are the ‘beads on a string’ packaged into ?
30nm chromatin fibre of packed nucleosomes and further condensed
How big is the short region of DNA double helix ?
2nm
How big is the ‘beads on a string’ form of chromatin ?
11nm
What do chromosomes need to allow protein access ?
They need to be remodelled by the remodelling complex.
ATP —-> ADP
Condensed chromatin —-> Decondensed chromatin
What is access/lack of access related to ?
The histone tails
What % of the genome of genes comprise ?
<5% of total content of DNA
Describe the organisation of the human genome
3 billion base pairs of DNA
Genes <5%
‘Junk’ DNA
Often repetitive
Heterochromatin location
Tends to be at the ends of a chromosome or near the centre (centromere)
Heterochromatin
More compact
Telomeres at the end
Centromere - where the mitotic spindle binds
With heterochromatin, on the other hand, nucleosomes are more densely packed, because it contains genes that the cell rarely or never uses.
Euchromatin
Most of the genes
Open configuration
Nucleosomes are more loosely packed, because it contains the genes - or regions of DNA - that the cell frequently uses to make proteins that help the cell perform its day to day job.
Repetitive types of DNA
Interspersed repeats
Tandem repeats
Interspersed repeats
SINE and LINE often derived from retroviruses
Tandem repeats
Satellite - telomere TTAGGG
Mini-satellites 7-100 bases repeated up to 40,000 bases
Micro-satellites 1-6 bases repeated >100 bases
What is myotonic dystrophy ?
Muscle wasting condition
Can be inherited in families through generations
What is the cause of myotonic dystrophy ?
Tri-nucleotide repeat expansion in 3’ UTR of MD gene
More repeats = worse
Mitochondrial DNA
mtDNA
What is mitochondrial DNA ?
Circular
Maternally inherited
Implications for disease
Can be used in forensics
‘Out of Africa’
Why are DNA strands antiparallel ?
The antiparallel nature of DNA strands is needed to form the hydrogen bonds between the nitrogenous bases.
How are 2 strands copied ?
The semiconservative model
What is the experiment to determine the way that strands are copied ?
Matthew Meselson & Frank Stahl’s experiment
What is the semiconservative model ?
In this model, the two strands of DNA unwind from each other, and each acts as a template for synthesis of a new, complementary strand.
This results in two DNA molecules with one original strand and one new strand.
Each strand of DNA serves as a template to make a new, complementary strand, seemed most likely based on DNA’s structure.
How long does it take to replicate the human genome ?
8 hours
Briefly describe the Meselson-Stahl’s experiment
They labeled the DNA of bacteria across generations using isotopes of nitrogen.
From the patterns of DNA labeling they saw, Meselson and Stahl confirmed that DNA is replicated semi-conservatively.
In what direction does DNA strand grow ?
From 5’ to 3’
What is the function of the template strand ?
Specifies which base is to be added next
What is the difference between the leading and lagging strand ?
The replication fork is asymmetrical
Leading strand
DNA opens up
5’ to 3’ direction
DNA polymerase forms
Lagging strand
Synthesised in short fragments (Okazaki)
RNA primer required
Werners syndrome
A premature aging syndrome
Defect in how the ends of chromosomes are replicated
What are the ends of our chromosomes called ?
Telomere
What happens at a DNA end ?
Telomerase binds.
Telomerase adds additional repeats to the template strand.
Completion of lagging strand by DNA polymerase.
What are mutations ?
Mistakes in base pairing, can lead to changes in the DNA sequence.
When are errors in DNA corrected ?
During synthesis during proofreading
After DNA replication has occurred
Hereditary non-polyposis
A genetic disease of autosomal dominant inheritance
What is the normal mutation rate ?
About 1 error for every 3 genomes replicated
PCR
Polymerase Chain Reaction
Function of PCR
Polymerase chain reaction (PCR) amplifies DNA using complementary primers for specific target sequences.
Repeated cycles of heating and cooling amplify the target region of DNA.
Function of DNA polymerase
DNA polymerase adds DNA nucleotides, using complementary base pairing, to the deoxyribose (3’) end of the new DNA strand which is forming.
What is produced in the 1st cycle of PCR ?
2 double stranded DNA molecules
What is produced in the 2nd cycle of PCR ?
4 double stranded DNA molecules
What is produced in the 3rd cycle of PCR ?
8 double stranded DNA molecules
What are some uses of PCR ?
Detection of presence of infectious agents
Inheritance patterns
Looking for changes in chromosome copy numbers
DNA sequencing - chain termination: Sanger method
Looking for mutations
Alexander disease
glial fibrillary acidic protein (GFAP)
Intron
The introns of the primary transcript are non-coding regions and so are removed.
Exon
The exons are coding regions and are joined together to form the mature transcript.
Describe the majority of gene encoding proteins
Contain regions of DNA which encode proteins (exons), dispersed by regions which do not encode proteins.
Splice site
Determined by sequences around each intron/exon junction
Promoter
Promoters are fairly large nucleotide sequences that initiate the process of transcription.
Repetitive non-coding regions of nucleotides.
Enhancer
Enhancers are short nucleotide sequences that enhance the transcription rate in the genome.
Transcription
DNA is used as a template
Complementary to one strand
RNA polymerase (5’ to 3’)
Not as accurate as DNA replication
What do transcription factors have ?
2 Domains :
- DNA binding domain
- Activation domain
Why is mRNA processed ?
To protect from exonucleases
Aid transport
Identify as mRNA
Fraiser syndrome
Affects the kidneys
Defect in the glomerulus of the kidneys
What is the gene number paradox ?
Making many different proteins from limited number of genes.
What is transcription ?
DNA is converted into useable form via transcription
How many bases code for an amino acid ?
3 - triplet code
What does gene expression involve ?
Transcription and translation of DNA sequences.
mRNA
Messenger RNA carries a copy of the DNA code from the nucleus to the ribosome.
tRNA
Transfer RNA folds due to complementary base paring.
Each tRNA molecule carries its specific amino acid to the ribosome.
rRNA
Ribosomal RNA and proteins form the ribosome.
Function of RNA splicing
Forms a mature mRNA transcript
Describe translation
Translation begins at a start codon and ends at a stop codon.
Anticodons bind to codons via complementary base pairing, translating the genetic code into a sequence of amino acids.
Peptide bonds join the amino acids together.
Each tRNA leaves the ribosome and the polypeptide is formed.
What are frame shift mutations ?
Occur as a result of nucleotide insertions or deletions.
Name some nucleotide substitutions
Missense
Nonsense
Splice-site mutations
What is the difference between a a mutation and polymorphism ?
Mutations are associated with changes in phenotype.
Only mutations affect gene expression.
Polymorphisms are common and do not contribute to disease.
What is the initiation codon ?
Defines the beginning of open reading frame.
What are the 3 phases of translation ?
Initiation
Elongation
Termination
Elongation
RNA polymerase unzips the coding strand from the template strand, by shearing the hydrogen bonds between complementary nucleotides.
Terminator sequence
Contains 2 complementary sequences in a row, on a single strand.
When they get transcribed onto the mRNA, the nucleotide sequences bond to each other, forming a Hairpin loop, making the RNA polymerase detach from the DNA strand.
Effects of mutations
No transcription
Protein incorrectly processed
Inappropriate function
Unstable protein
Splisosome
Cuts introns out of the mRNA sequence
START CODON
AUG
Methionine
STOP CODON
UAA
UGA
UAG
What are the 3 amino acid sites for the tRNA to bind on the ribosome ?
Aminoacyl site
Peptidyl site
Exit site
Termination
Ribosome reaches stop codon and releases the polypeptide.
