APS138 Cell And Molecular Biology - Scholes Flashcards
How many chromosomes do humans have?
46 (23 pairs)
What is unique about nucleic acids?
They can direct their own replication
When was the chemical composition of DNA discovered?
Late 1800s.
Friedrich Miescher isolated DNA in 1874
In 1881 Albrecht Kossel isolated the nucleotide bases
Actual structure worked out in 1953
Rosalind Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce…
- That DNA was helical
- The width of the helix
- The spacing of the nitrogenous bases
- Double helix made of 2 strands
DNA is a polymer of nucleotides, each consisting of:
- A nitrogenous base (A,T,C or G)
- A phosphate group
- A deoxyribose sugar
What does 5’ refer to?
The specific carbon of the sugar molecule which the P group is attached to
What does 3’ refer to?
The carbon in the sugar molecule with the -OH group
What are the purines? How many organic rings do they have?
Adenine and Guanine.
2 rings
What are the pyramidines? How many organic rings do they have?
Cytosine and Thymine (and Uracil). 1 single ring.
How many hydrogen bonds does A pair to T with?
C to G?
2 bonds A to T, 3 bonds C to G
What direction do the 2 DNA strands run in?
An antiparallel direction
What are the base pairs on the 2 DNA strands?
complementary
Each ‘daughter’ DNA molecule consists of one …… strand and one …… strand
Parental, New
What is the model of DNA replication?
Semi-conservative
Each nucleotide that is added to a growing strand of DNA is a…
Nucleoside triphosphate (e.g. dATP, dTTP etc.)
DNA polymerases add nucleotides only to he free …. end of a growing strand. Therefore a new DNA strand can only elongate in the ….. direction.
3’
5’ to 3’
How long can E. coli’s 4.6 million nucleotide pair genome take to be replicated?
~1 hour
In eukaryotes each double helical DNA molecule is packages into a…
Chromosome within the nucleus
DNA replication begins at sites called…
Origins of replication
How many origins of replication are there in the circular of E. coli?
Only 1
What is an origin of replication?
A short stretch of DNA with a particular sequence of bases. Parental strands separate at the origin forming a replication bubble with a fork at each end.
What types of enzymes catalyse the synthesis of new DNA at a replication fork?
DNA polymerases
Which proteins participate in the unwinding of parental DNA strands?
Topoisomerases (correct overwinding), helicases (untwist double helix), single strand binding proteins (stabilise single stranded DNA)
What is the initial nucleotide strand in DNA replication called?
An RNA primer
What does the enzyme primase do?
Starts an RNA chain from scratch, adding RNA nucleotides one at a times using the parental DNA template.
To elongate the new strand, called the …… strand, DNA polymerase must work in the direction ….. the replication fork
Lagging
Away from
The lagging strand is synthesised as a series of fragments called….
Okazaki fragments
What does DNA pol I do?
Replaces RNA primer with DNA nucleotides
Which enzyme joins together the Okazaki fragments?
DNA ligase
What are telomeres?
DNA at the end of eukaryotic DNA molecules, consisting of multiple repetitions of one short nucleotide sequence. Prevents the shortening of DNA molecules and postpones he erosion of genes near the ends of DNA molecules
What has it been proposed that the shortening of telomeres is connected to?
Ageing - telomeric DNA tends to be shorter in dividing somatic cells of older individuals
Which enzyme catalyses the lengthening of telomeres in germ cells?
Telomerase
What is the region of a bacterial cell in which “supercoiled” DNA is found?
Nucleoid
What proteins are responsible for the first level of packing in chromatin?
Histones
The nucleosome consists of DNA wound twice around a protein core composed of …..
2 molecules of each of the 4 main histone types
What do the histone tails of one nucleosome interact with?
The linker DNA and nucleosomes on either side. A fifth histone is involved
What is gene expression? How many stages are there?
The process by which DNA directs protein synthesis. There are 2 stages: transcription and translation
What does transcription produce?
messenger RNA (mRNA)
What is translation?
The production of a polypeptide using information in mRNA
Where does translation occur?
At ribosomes
What is the sugar found in RNA?
ribose
What is Thymine replaced by in RNA?
Uracil
How many strands does RNA usually have?
One
What does the fact that prokaryotes lack nuclei mean for transcription and translation?
They can occur simultaneously (translation of mRNA can begin before transcription has finished) - ribosomes attach to the leading strand of an mRNA molecule while transcription is still in progress
What does the transcription of a protein coding gene result in in eukaryotes?
pre-mRNA
Modified through processing to yield finished mRNA
What is the central dogma?
Single directional flow of genetic information from DNA to RNA to protein
How many amino acids are there in humans?
20
What is a triplet of nucleotide bases called?
A codon
How many possible codons are there with the triplet code?
64 (4^3)
In which direction are mRNA codons always read in?
5’ to 3’ direction
What does each codon code for?
An amino acid, to be placed at the corresponding position along a polypeptide
Of the 64 triplets how many code for amino acids and how many are stop codons?
61 amino acids, 3 stop codons
How many types of RNA polymerase do bacteria have to synthesise RNA molecules?
One
How many RNA polymerases do eukaryotes have?
Three
Which eukaryotic RNA polymerase is used for mRNA synthesis?
RNA polymerase II
What 3 stages can transcription be separated into?
Initiation, Elongation, Termination of the RNA chain
In transcription of RNA, what is the initiation stage?
After RNA polymerase binds to the promoter, the DNA strands unwind and the polymerase initiates RNA synthesis at the start point on the template strand
In transcription of RNA, what is the elongation stage?
The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript in the 5’ to 3’ direction. In the wake, the DNA double helix reforms
In transcription of RNA, what is the termination stage?
Eventually the RNA transcript is released and the polymerase detaches from the DNA
What signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point?
Promoters
What recognises and binds to the promoter in bacteria?
RNA polymerase itself
In eukaryotes, what mediate the binding of RNA polymerase and the initiation of transcription?
Transcription factors
what is the key promoter sequence in eukaryotes called?
TATA box - a transcription factor recognising this box must bind to the DNA before RNA polymerase can do so
What is the complex of the RNA polymerase II and transcription factors called?
Transcription initiation complex
What is the rate of transcription in eukaryotes?
40 nucleotides per second
What is the mechanism of RNA transcription termination in bacteria?
The polymerase stops translation at the end of a specific RNA sequence known as the terminator and the mRNA can be translated without further modification
What is the mechanism of RNA transcription termination in eukaryotes?
RNA polymerase II transcribes polyadenylation signal sequence (AAUAAA) in pre-mRNA, and at a point about 10 to 35 nucleotides past this sequence the RNA transcript is cut from the polymerase, releasing the pre-mRNA, which then undergoes processing
How are the ends of pre-mRNA modified in eukaryotes? What benefits do these modification bring?
5’ end receives modified nucleotide 5’ cap
3’ end gets a poly-A tail
- Facilitate export of mRNA to cytoplasm
- Protect from hydrolytic enzymes
- Help ribosomes attach to 5’ end
What are UTRs?
Untranslated regions
What is RNA splicing?
When non-coding regions of pre-mRNA called introns are cut out and exons are joined to create an mRNA molecule with a continuous coding sequence
In some cases, what is RNA splicing carried out by?
Spliceosomes
What do spliceosomes consist of?
Small nuclear ribonucleoproteins (snRNPs) and other proteins - snRNA base pairs with nucleotides at specific sites along the intron, cuts and releases it for degradation and splices the exons together
Do introns have any function?
Some introns contain sequences that may regulate gene expression. Some gens can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing - called alternative RNA splicing - number of different proteins an organism can produce is much greater than its number of genes
What does each tRNA molecule carry?
An amino acid
What does a tRNA molecule consist of?
A single strand of about 80 nucleotides folded back on itself - includes a loop containing the anticodon and an attachment site at the 3’ end for an amino acid
What shape is tRNA (roughly)?
L-shaped
Can tRNA molecules be used repeatedly?
Yes
Where do tRNA molecules pick up and deposit their amino acids?
Pick up in the cytosol, deposit at the ribosome
What are the two recognition steps that accurate translation requires?
A correct match between the tRNA and an amino acid, and a correct match between the tRNA and mRNA codon
Which enzyme joins amino acids to tRNA molecules?
aminoacetyl-tRNA synthase - 20 different varieties that match the 20 amino acids - catalyses a covalent bond between them in a process driven by ATP hydrolysis
What is the flexible base pairing of tRNA and mRNA anticodons called?
Wobble
What does a ribosome consist of?
A large and small subunit, each made up of proteins and ribosomal RNA (rRNA) - the most abundant type of cellular rRNA
What are the 3 binding sites in ribosomes for tRNA?
P site - holds tRNA that carries the growing polypeptide chain
A site - holds next tRNA that carries the next amino acid to be added to the chain
E site - the exit site, where discharged tRNAs leave the ribosome
What are the 3 stages of translation?
Initiation, elongation, termination
What does the initiator tRNA carry?
Methionine (binds to start codon)
What is the start codon?
AUG
What molecule is invested to provide energy for the formation of the translation initiation complex?
GTP
Whereabouts on the polypeptide chain are amino acids added during elongation (translation)? What proteins are required?
C-terminus
Elongation factors
What are the 3 stages of elongation during translation?
- Codon recognition
- Peptide bond formation
- Translocation
During translation, when does termination occur?
When one of the stop codons reaches the A site of the ribosome - a release factor binds to the stop codon and causes hydrolysis of the bond between the polypeptide and its tRNA in the P site
Where is the polypeptide released from after translation
Ribosome exit tunnel
What does breakdown of the translation assembly require?
2 GTP molecules
Often translation is not sufficient to make a functional protein. What happens to these non-functional proteins post-translation?
They are folded and modified - amino acids interact with each other to produce a well-defined three-dimensional structure.
What are the two populations of ribosomes?
Free ribosomes (in the cytosol) and bound ribosomes (attached to the ER). But they are identical and can switch from free to bound.
What do free ribosomes tend to synthesise?
Proteins that function in the cytosol
What do bound ribosomes tend to synthesise?
Proteins of the endomembrane system and proteins that are secreted from the cell (these are marked by a signal peptide)
What is the genome?
The complete set of genes in an organism or the total genetic content in one set of chromosomes
What is genomics? Comparative genomics?
The study of whole sets of genes and their interactions
The analysis and comparison of genomes
When did the human genome project begin and when was it completed?
1990-2003
Cost $2.7 bn
In Jan 2017 Illumna announced that the company could now sequence a human genome for…
$1000
As of 2018 how many organisms’ genomes have been sequenced?
more than 24,000 - many archaeal and bacterial
Around 10% eukaryotes
How is genome sequencing prioritised?
Based on the medical, agricultural and biological opportunities expected to be created by sequencing a given organism
How many bases are in the human genome? Compared to most bacteria? Amoebae?
3000 Mb (bacteria 1-6 Mb, whereas amoebae 670,000 Mb)
The number of genes is not correlated with…
genome size
e.g. rice has 430 Mb genome and 42,000 genes, corn has a 2,300 Mb genome and 32,000 genes
What is gene density?
The number of genes present in a given length of DNA
Humans have 10,000 times as much ….. ….. as bacteria
Noncoding DNA
The genomes of humans, rats and mic show high sequence conservation for how many noncoding regions?
About 500 - more highly conserved than protein-coding genes in these species
How much of the human genome codes for proteins, rRNAs or tRNAs (exons)?
Only 1.5%
What are pseudogenes?
Former genes that have accumulated mutations and are nonfunctional
What are transposable elements?
Sequences of DNA that move from one location of the genome to another - can cause mutations by inserting into functional genes or regulatory regions
What does comparative genomics allow us to do?
- Gain a better understanding of how species have evolved
- Help explain how the evolution of development leads to morphological diversity
- Determine the function of genes and non-coding regions of the genome
What are orthologs?
Genes in different species that evolved from a common ancestral gene by speciation - normally retain the same function in the course of evolution
What percentage of genes are conserved between the fruit fly (drosophila) and humans?
60%
