Dr Kramers Bit Flashcards
What is the difference between the major groove and the minor groove?
Major groove is wider, transcription factors are more likely to bind the major groove.
What is the appearance and function of euchromatin and heterochromatin?
Euchromatin is expressed and not condensed into solenoids, appears lighter
Heterochromatin is not expressed, not in solenoids. Appears darker.
What is the structure of histone?
Octamer of proteins consisting of a H3 H4 tetramer and 2 H2a H2b dimers
How does DNA form beads on a string?
DNA forms a nucleosome by winding twice around each histone, then joined by linker DNA.
How is beads on a string DNA packaged?
Into solenoid 30nm fibre.
What is the mutation in sickle cell anaemia?
Chromosome 11 11p15.5
A>T results in glutamate to valine.
Gene coding for beta haemoglobin.
What is the mutation in cystic fibrosis.
Chromosome 7 7q31.2
3bp CTT deletion between 5th and 6th position. Deletion of phenylalalanine, misfolded protein.
Mutation in gene coding for CFTR.
What is the human genome?
Entire DNA sequence (22 plus X and Y = 24 chromosomes)
How many base pairs in the genome of:
A human
A fruit fly
E. coli
- 2 x 10^9
- 4x10^7
- 6x10^6
What is the difference between a nucleoside and a nucleotide?
Nucleoside has a sugar and a base
Nucleotide has a sugar, a base and a phosphate.
What is the difference between ribose and deoxyribose?
Ribose is 5C, has inline oxygen and 4 OH groups including on methyl group.
Deoxyribose is the same but doesn’t have an OH group on carbon 2.
Ribose is in RNA, deoxyribose is in DNA.
Why is DNA and RNA negatively charged?
Phosphate group is negatively charged.
Where does phosphate group bind in a nucleotide?
5’ carbon
Where does the base bind in a nucleotide?
1’ carbon
How does phosphate bind the sugar?
Phosphate ester bond
Which bases are purines?
Adenine and guanine
What bases are pyrimidines?
Cytosine, thymine, uracil
What is the structure of a purine?
Nitrogenous, 2 rings
What is the structure of a pyrimidine?
Nitrogenous, single ring.
For A, give the base, and nucleoside and nucleotide for DNA and RNA
Adenine Adenosine (RNA) Adenosine monophosphate (RNA) Deoxyadenosine (DNA) Deoxyadenosine monophosphate (DNA)
How are nucleotides joined?
Phosphodiester bonds
What groups are at the 5’ and 3’ ends of DNA?
5’ phosphate
3’ OH
How many hydrogen bonds form between C and G?
3
How many hydrogen bonds between A and Ta
2 hydrogen bonds
What is the benefit of the hydrogen bonds between bases in a base pair being almost the same length.
Strength
What is a duplex?
Double stranded structure of DNA - two complementary antiparallel strands.
Can form two DNA, two RNA, or one of each.
What is an RNA stem loop?
Loops formed when hydrogen bonds form between complementary antiparallel sequences in RNA
What is the pitch of DNA?
3.4nm
What is the diameter of a DNA Double helix?
2nm
What is the distance between adjacent DNA bases?
3.4nm
How many DNA bases per turn of the helix?
10
In what direction is DNA notated?
5’ to 3’
What are the phases of the cell cycle?
Mitosis Then either G0 (cell cycle stops, cell performs function) Or: G1 - cell contents replicates Cell cycle checkpoint S - DNA replicates G2 - checking and repair of DNA Cell cycle checkpoint Mitosis
What catalyses DNA polymerisation in DNA replication?
DNA polymerase
How are bases added to DNA during replication?
Added as deoxynucleotide triphosphates,
Added to 3’ end of primer strand
Release PPi
Forms phosphodiester bond
What is pyrophosphate hydrolysis?
Hydrolyse ATP to AMPS releases pyrophosphate (PPi, P2O7 4-)
In what direction is DNA synthesised?
5’ to 3’
How is DNA replicated in prokaryotes?
Circular chromosome.
Initiation - recognise origin of replication - requires DNA polymerase. Needs a kickstart from primase - synthesis short RNA sequence (as polymerase can only extend from 3’ end)
then replicates around the circle in both directions (elongation)
Then termination - two circular chromosomes.
How is DNA elongated during replication?
The 3’ to 5’ strand is replicated by DNA polymerase in the 5’ to 3’ direction (leading strand)
The 5’ to 3’ strand is replicated in multiple Okazaki fragments in the 5’ to 3’ direction, which are fused by DNA ligase. (Lagging strand)
What enzyme separates the two strands of DNA?
DNA helices R
How many sites of replication are there in each chromosome?
Multiple - speeds it up.
What is the structure of a replicated chromosome?
Two sister chromatids (identical) joined by centromere.
P arm is shorter
Q arm is longer
Telomeres are the ends of each chromatid.
What are the four arrangements of chromosomes and centromeres, and are they present in humans?
Metacentric - central centromere
Submetacentric - shorter p arms
Acrocentric - very short p arms
Telocentric - no p arms - not seen in humans.
Which cells use mitosis for cell division?
Somatic cells
How many mitotic rounds occur during development?
50
What occurs in prophase?
Chromosomes condense
Spindle fibres appear - centrioles
What happens in prometaphase?
Chromosomes condense further
Spindle fibres attach to chromosomes via kinetochore, centrioles migrate to poles.
Nuclear membrane breaks down
What occurs in metaphase?
Chromosomes align on the metaphase plate.
What occurs in anaphase?
Centromeres divide and chromatids move to the opposite poles of the cell
What occurs in telophase?
Chromosomes de condense
Nuclear membranes reform
Spindle fibres disappear
What happens in cytokinesis?
Cytoplasm divides, two identical daughter cells form.
What is produced via meiosis?
Germ line cells - oocytes and spermatozoa
How many chromosomes are present following replication in meiosis?
92 (4n)
What occurs in meiosis 1?
Homologous chromosomes separate - 2 identical sister chromatids of each chromosome present in daughter cells.
What causes genetic variation?
Crossing over during meiosis 1 (chiasmata form, genetic material exchanged between chromatids)
What occurs during meiosis 2?
Sister chromatids are separated, generate haploid cells.
What are the consequences of meiosis?
Generate haploid cells (maintains diploid chromosome number in somatic cells)
Generates genetic diversity - random assortment and crossing over
How long is spermatogenesis?
48 days
Outline the process of spermatogenesis
Spermatogonium goes to form primary spermatocyte (diploid)
Undergoes meiosis - spermatids (haploid)
Differentiate to mature sperm.
How long does oogenesis take?
12-50 years
Outline the process of oogenesis:
Oogonium-> primary oocyte (diploid)
Undergoes meiosis to form an ovum which matures and 3 polar bodies which do not have sufficient cytoplasm to survive so degenerate.
Why is crossing over necessary?
Homologous chromosomes don’t separate during meiosis one if crossing over hasn’t occurred.
How often are mistakes made in meiosis?
30% rate of missegregation in humans
What are the causes of missegregation?
Cause one third of identified miscarriages, infertility and mental retardation.
What is the difference between genotype and phenotype?
Genotype is an individual’s genetic sequence.
Phenotype is how this is expressed as characteristics.
How can the environment affect genotype and phenotype?
Genotype - mutagens, radiation,
Phenotype - genotype, and diet, lifestyle, chemicals etc
What is the difference between a gene and an allele?
An allele is a version of a gene - there will be many different alleles for each gene in a population, some of which may be disease causing.
What is a homozygote?
An individual with two identical alleles for a gene
What is a heterozygote?
An individual with two different alleles of a gene
What is a hemizygote?
Someone who has only one allele of a gene (on the X chromosome)
What is the difference between a dominant and recessive allele?
The dominant allele determines the phenotype.
The recessive allele in a heterozygote is the non dominant allele (doesn’t determine the phenotype)
Give an example of a trait that demonstrates codominant inheritance
ABO blood group
What does the isoglutamin gene code for?
Glycoproteins on surface of erythrocytes - determine ABO blood group
Give an example of a trait that demonstrates complementation
Albinism
What is peculiar about complementation?
Two homozygous affected individuals (it’s a recessive trait) can have an unaffected offspring if it’s two different genes.
How can more than one gene be involved in producing a phenotype?
For example, if multiple enzymes (each coded for by a different gene) are involved in a pathway to synthesise a product.
What are linked genes, and what is the implication for meiosis?
Genes on the same chromosome - do not show independent assortment at meiosis.
What does recombination frequency depend on?
Distance between genes
What is the behaviour of genes that are far apart on a chromosome?
Behave almost like unlinked genes.
What is a gene?
Stretch of DNA that codes for a protein, and regulates its production.
Has a chromosomal locus.
Unit of inheritance
Unit of transcription
What are the five types of RNA?
mRNA - messenger RNA a tRNA - transfer RNA rRNA - ribosomal RNA miRNA - micro RNA Non coding RNA
In what direction does transcription occur?
RNA is synthesised 5’ to 3’
DNA is read 3’ to 5’
In what direction does translation occur?
mRNA is read 5’ to 3’
Protein synthesised from amino terminal to carboxy terminal.
Where is the energy needed for DNA replication found?
Nucleotide triphosphates are cleaved - pyrophosphate hydrolysis.
What enzyme is used for transcription?
RNA polymerase
What is a promoter sequence?
TATA box at -30 in eukaryotes, many upstream sequences - complex regulation
Pribnow box at -10 in prokaryotes, upstream sequences at -35 - simple regulation
Binds promoter which causes RNA polymerase to bind.
What are the coding and template strands?
The coding strand holds the TATA box and as the same sequence as the mRNA that will be transcribed (except T instead of U)
The template strand has a sequence complementary to the mRNA and is the strand used to synthesise the RNA with RNA polymerase.
What is an open reading frame?
The part of mRNA that has the potential to code for a protein/peptide (from start codon - methionine - to stop codon)
How is mRNA modified post transcription?
Splicing
Polyadenylation at 3’ end
Capping at 5’ end
What is the purpose of polyadenylation (tailing)?
Protection of mRNA from degradation by exonucleases
What is the purpose of capping mRNA?
Protect mRNA from degradation.
Plays a role in translation.
What is capping?
Addition of guanosine (guanosine triphosphate GTP) via a 5’ to 5’ triphosphate linkage.
The 7 Nitrogen of guanosine is methylated.
Describe the process of polyadenylation.
When the sequence AAUAA is transcribed it is recognised by a specific endonuclease.
Causes transcription to cease, endonuclease cleaves the mRNA downstream of the sequence.
Roughly 200 adenosine bases are added (ATP -> PPi) using polyA polymerase.
What are endonucleases and exonucleases?
Endonucleases cut within a polynucleotide - can be specific or non specific.
Exonucleases degrade polynucleotides from either 5’ or 3’ end - they are 5’ or 3’ specific.
What are exons and introns?
Exons are the coding parts of mRNA, introns are removed during splicing.
How does splicing occur?
Specific sequence recognised (AGGU) by spliceosome.
RNA lariat formed and removed, two ends joined.
What is the genetic mutation in PKU and its consequences in protein expression?
Chromosome 12 12q22-q22.4
Single base substitution G>A results in intron skipping, unstable mRNA.
In what proportions are mRNA, tRNA, and rRNA found in eukaryotes?
80% rRNA
15% tRNA
2% mRNA
What does RNA polymerase 1 synthesise?
rRNA
What does RNA polymerase 2 synthesise?
mRNA
What does RNA polymerase 3 synthesise?
tRNA
Why is 80% of the RNA in a cell rRNA, 15% tRNA and 2% mRNA?
Many types of mRNA, but only a few copies of each as they are unstable and easily degraded.
Only a few kinds of rRNA, but there are very many copies of each as they are essential for translation.
Roughly 100 kinds of tRNA, but very many copies of each.
What is the structure of a ribosome in prokaryotes?
70s ribosome with 30s and 50s subunits
Consists of 3 rRNAs and 56 proteins
What is the structure of a ribosome in eukaryotes?
80s ribosome consisting of 40s and 60s subunits
Consists of 4 rRNAs and 82 proteins.
How long is a 70s ribosome?
20nm
What makes up a 50s subunit?
5S rRNA - 120 bases
23s rRNA - 2900 bases
35 proteins
What makes up a 30s subunit?
16s subunit - 1500 bases
21 proteins
How big is an 80s ribosome?
32nm
What does a 60s subunit consist of?
5S RNA - 120 bases
5.8S RNA- 160 bases
28S RNA - 4700 bases
49 proteins
What does a 40s subunit consist of?
18s RNA - 1900 bases
33 proteins
What direction is mRNA read in, and in what direction are polypeptides synthesised?
5’ to 3’, amino to carboxy terminal.
What codon marks the initiation of translation?
AUG - methionine
What are the stop codons?
UAA, UAG, UGA
What is the structure of tRNA?
Anticodon loop - sequence complementary to codon on mRNA.
DHU loop (contains dihydrouridine)
T Psi C loop (contains pseodouridine)
Variable loop
CCA terminus at 3’ end - A forms ester bond with amino acid (OH on ribose, COOH on amino acid)
How is tRNA activated?
tRNA activated to become amino acyl tRNA
Covalent ester bond between 3’ OH on 3’ adenine of tRNA and the carboxylic acid of the amino acid.
What is I?
Inosine - a nucleotide, the base is hypoxantine. It’s a purine derivative.
Which is the wobble position?
5’ base of anticodon, 3’ base of codon (3rd position)
What can I pair with?
Uracil, cytosine and adenine
What is the implication of wobble?
One tRNA species can recognise more than one codon - compensates for degeneracy in triplet code.
What is another unusual base pairing?
G and U
What enzyme catalyses the formation of amino acyl tRNA? What else is required?
tRNA synthetase
ATP > AMP + PPi
How is translation initiated?
Ribosome dissociates into two subunits
40S subunit forms ternary complex with an initiation factor, Met tRNA and GTP.
Another initiation factor interacts with cap and guides ternary complex to bind.
The complex ‘scans’ the RNA until the anticodon on tRNA binds AUG. Requires ATP and other initiation factors.
The 60S subunit binds and GDP and initiation factors are released, met tRNA is positioned in the P site on the ribosome.
How does elongation occur?
A new amino acyl tRNA binds to the A site on the ribosome (requires GTP)
The newly synthesised peptide on the amino acyl tRNA in the P site is transferred to the amino group on the new amino acyl tRNA in the A site to form a new peptide bond, catalysed by peptidyl transferase.
Translocation then occurs - the uncharged tRNA is ejected from the A site, and the tRNA carrying the polypeptide is transferred to the A site. This requires GTP.
How is translation terminated?
Stop codon is reached - no corresponding tRNA.
Eukaryotic release factors 1 and 3 form a complex with ribosome.
This stimulates the hydrolysis of the ester bond between the peptide and the tRNA, protein is released.
The factors are released from the ribosome following GTP hydrolysis.
What is a polysome?
Multiple ribosomes translating a piece of mRNA concurrently.
How are transcription and translation different in bacteria?
Transcription and translation are coupled Smaller, simpler ribosomes Different transcription factors Different mechanism of initiation Simple promoters Different translation factors Single RNA polymerase No post transcriptional processing - splicing Short lived mRNA.
