MCBG Flashcards
Difference between nucleotide and nucleoside?
Nucleotide is phosphate + base + sugar
Nucleoside is base + sugar
Describe processes of PMAT
Prophase - chromosomes condense and spindles appear
Prometaphase - spindles attach to chromosomes
Metaphase - chromosomes line up
Anaphase- sister chromatids separate
Telophase- nuclear membrane reforms, chromosomes decondense
+ Cytokinesis - cytoplasm divides
Difference between centrosomes and centromeres?
Centromeres join sister chromatids in a chromosome and centrosomes are what mitotic spindles are attached to at the poles of the cell
What is chromosome condensation?
During DNA replication DNA is stored as chromatin but during mitosis it condenses to become chromosomes
What is a telomere?
Repeated sequence at the end of chromatids (e.g. TTAGGG) that will protect it from damage like the caps at the end of shoelaces
When do crossing over and random assortment occur?
Crossing over in prophase I, random assortment is metaphase I
What is karyotyping?
Number and appearance of chromosomes
What is mitotic nondisjunction?
Where a chromosome doesn’t split into sister chromatids and get pulled to separate poles, so it results in aneuploidy (cell with more or less than 46 chromosomes)
What is mosaicism?
Presence of cells with different number of chromosomes than other cells in same body
Roughly describe meiosis
Meiosis I - diploid cell divides into 2 haploid cells
Meiosis II - 2 haploid cells become 4 haploid cells (essentially mitosis)
What is the official name for “jumping genes”?
Transposable element (transposons)- can change their place in the genome, sometimes to create or fix mutations
Which direction is mRNA synthesised?
5’ to 3’
Which direction is DNA read?
3’ to 5’
What are histones?
DNA is wrapped around histones to make a nucleosome (the structural unit of chromatin)
RNA polymerase
Poly A tail and cap
Types of RNA?
messenger, transfer, and ribosome
What is splicing?
Introns are removed from preRNA but exons stay, forming an mRNA (still with poly A tail and cap)
What happens after splicing?
mRNA leaves through nuclear pore
What does tRNA do?
Each tRNA attaches to one amino acid in the cytoplasm
amino acyl tRNA synthetase attaches a tRNA to an amino acid. Then a ribosome (rRNA) will join together the tRNA:amino acid with mRNA
Where does ribosome attach?
Ribosome attaches to cap region of mRNA moving towards the polyA tail
What are the EPA sites of a ribosome?
A is attachment, E is exit; ribosome moves towards the polyA tail. If
What are codons and anticodons?
3 nucleotides on mRNA are codons and 3 nucleotides of tRNA are anticodons
What are the EPA sites of a ribosome?
A is attachment, P is polypeptide, E is exit; ribosome moves towards the polyA tail. If a tRNA matches the codon the ribosome is on it will attach at A site
What are codons and anticodons?
3 nucleotides on mRNA are codons and 3 nucleotides of tRNA are anticodons
Where does RNA polymerase bind?
Binds to mRNA at the TATA box (signals where transcription should begin)
Describe the rough processes involved in making proteins
DNA replication in nucleus, then transcription where DNA is converted into pre-mRNA then splicing to remove introns then mRNA formed (transcription), then mRNA exits the nucleus and tRNA with amino acid joins and ribosome makes it happen, makes a chain of amino acids.
What is the wobble position?
5’ base of anticodon and 3’ base of codon where more than one codon can be recognised
What enzyme joins tRNA with its amino acid?
Aminoacyl tRNA synthatase
Tell me about formation of rRNA and its structure
Made in the nucleolus, 2 subunits (one large one small), formation with RNA polymerase I
How is translation terminated?
With stop codons e.g. UAA, UGA, UAG
Name sources of ionising radiation
Radon gas, gamma rays, CT scan, cosmic rays
Give examples of types of single nucleotide mutations (point mutations)
Transition mutation: change to same type of base e.g. purine-purine (AG) or pyrimidine-pyrimidine (CTU)
Transversion: change to different type of base
May be a silent, neutral or synonymous change
What are purines?
Pure As Gold (AG)
Name the four types of chromosomal mutations
Deletion, insertion (sister chromatid gives some of itself to other), inversion (some attaches backwards), translocation (part of one chromosome gives to another chromosome)
Why is mtDNA more prone to somatic mutations?
Limited repair abilities (x10 higher mutation rate!)
Symptoms of mitochondrial disease?
Muscle weakness, cardiomyopathy, WPW, liver failure, kidney problems, exercise intolerance, sensorineural deafness
How do primordial germ cells proliferate?
Mitosis
In general, what effect do AR and AD mutations have?
AR decreased function of gene, AD increased function of gene
What is sickle cell?
Mutation in HBB gene that codes for beta-globin with a single base substitution (missense mutation) on chromosome 11 that changes codon 7 of HBB from Glutamate-Valine.
What is a missense mutation?
One that changes the amino acid that is coded
How do you test for sickle cell?
Use Southern blot with a restriction enzyme (called MstII) to bind to the mutated DNA sequence. Can also use electrophoresis
What are the types of chromatin?
Heterochromatin (more condensed, inactive, has methyl groups) and euchchromatin (active, light, less condensed, has acetyl).
What is a solenoid?
Type of DNA organisation with heterochromatin (the inactive heavy type) formed by the winding of 5 nucleosomes. 30nm size
Name the nucleosides and nucleotides for RNA and DNA
RNA:
adenosine AMP, guanosine GMP, uradine UMP, cytidine CMP
DNA:
deoxyadensine dAMP, deoxyguanosine dGMP, deoxythymidine dTMP, deoxycytidine dCMP
What is a phosphodiester bond?
Links the 3’ of the above ribose/deoxyribose with the 5’ of the ribose/deoxyribose below , including the two ester bonds between the phosphate and each sugar
At what stages does cell content and DNA get replicated?
Cell content replicated in G1, DNA replication is S
How do you get to be a leading strand?
DNA polymerase only adds nucleotides on the 3’ end of the template so this strand leads and the other one lags
What enzymes are involved in DNA replication?
Helicase unzips, DNA polymerase adds nucleotides to copy strand, primase generates small RNA strands that DNA polymerase can then add to, ligase binds up Okazaki fragments on the lagging strand
Why do we make dNTPs?
So deoxyribose nucleoside triphosphate- need 3 phosphates when we are building a DNA strand because DNA polymerase will then use the energy from those two extra phosphates for the phosphodiester bond that creates the backbone
Name types of DNA replicative stress (insufficient replication leading to slowing or breaking)
Replication machinery defect e.g. SLIPPAGE where nucleotide is missed or added
Hindered fork progression e.g. DNA lesions, fragile/oncogene sites
Defect in response to problem e.g. Base excision repair defect so SSBs persist, BRCA deficiency so DSBs persist
Give an example of a disease caused by DNA replicative stress
Werner’s - progeroid syndrome (premature ageing) caused by defect in Werner protein which is a helicase
BRCA-deficiency associated breast and ovarian cancer: BRCA involved in DNA repair of DSBs
What is the most common cause of polyploidy?
Polyspermy (arises from non-disjunction at meiosis)
What causes mosaicism?
MITOTIC non-disjunction
What is robertsonian translocation?
In 2 acrocentric chromosomes (i.e. long q arms) the two long arms fuse together and the short arms fuse and are lost
What is FISH?
Fluorescence In Situ Hybridisation- probe DNA e.g. green signal for normal control and red signal for probe of interest e.g. use it for DiGeorge syndrome with deletion on chromosome 22
What is uniparental disomy?
Both sets of chromosomes inherited from one parent (happens after trying to repair a trisomy)
What is non invasive prenatal testing (NIPT)?
Detect cell-free fetal DNA in maternal plasma for likelihood of common aneuploidies: Down’s, Turner’s, Edwards
Tell me about Huntingdon’s
CAG repeat on HTT gene, onset earlier each gen, test with PCR, get seizures, personality changes, dementia
What is translocation and what problems can result from it during meiosis?
Part of one chromosome swapped for part of another. If the translocation is alternate (i.e. giving rise to one fully normal pair and one completely translocated pair) it is viable. If it is adjacent (i.e. you get half and half translocated with a large amount deleted and a large amount duplicated) this is not viable.
Name types of DNA repair for single stranded breaks and what they are used for
BER Base excision repair for weird stuff e.g. U in DNA
MMR Mismatch repair e.g. G + T
NER Nucleotide excision repair for UV damage T-T dimers
Name DSB repair mechanisms
NHEJ (non-homologous end joining)- Ku70/80 attaches to both ends of the DSB and they are joined together. Its non-homologous because we’re not using another identical strand to repair, we’re just pasting them together.
The other methods are all homologous:
SSA (single strand annealing)- exonucleases chop more off each strand until they reach a repeat sequence and those repeat sequences will anneal together
SDSA (synthesis dependent strand annealing)- one of the strands uses another chromosome to make a copy and when it finds a homologous segment will bind, copy, then unbind and then its partner that is also broken will copy from its fixed partner.
DSBR- follows SDSA initially with resection, strand invasion and DNA synthesis, but then differs as the other broken partner also comes in for DNA synthesis, creating 2 Holliday junctions. They then resolve by moving back or crossing over.
Do SDSA and DSBR lead to crossover or non crossover products?
SDSA always non-crossover (because only 1 Holliday junction)
DSBR either crossover or non-crossover
How does p53 link to cancer?
Its a tumour suppressor gene mutated in many cancers
What causes HNPCC (hereditary non-polyposis colorectal cancer)
A mutation in a gene e.g. PMS2, which is a mismatch repair gene
Characteristics of most cancer cells?
Aneuploid and chromosomally unstable with centrosome amplification and oncogenes
What is centrosome amplification?
Multiple centrosomes which then leads to multipolar spindles and then aneuploidy
How can cancer cells hide their centrosome amplification?
By centrosome clustering: the multiple centrosomes cluster in poles to appear pseudo-bipolar. Chemotherapy can inhibit centrosome clustering so the centrosome amplification is easier to spot
What are blood types A and B and what are they coding for?
Codominant. Both are dominant over O. Coding for glycoproteins on the surface of RBCs
Males are _____ for any alleles on their one X chromosome
Hemizygous (only 1 allele)
How is albinism inherited?
Recessive but polygenic (can be mutated in 4 different genes)
Where are sources of genetic diversity?
Independent assortment (metaphase I) where chromosomes could attach to different spindles and therefore end up in different cells Crossing over (prophase I) where parts of a chromosome is swapped with another chromosome)
What are linked genes?
Genes on the same chromosome at different loci that are usually inherited together- they are NOT affected by independent assortment because they’re on the same chromosome, but it’s possible to separate them via crossover which is more likely if they are further apart.
What’s osteogenesis imperfecta?
Type I collagen defect (dense collagen found in bone, skin, cornea, tendons), AD inheritance due to glycine problem where it can’t form triple helices. “brittle bone disease”, blue sclera, easy bone breaking
What’s alkaptonuria?
AR disease where body can’t complete breakdown of phenyalanine and tyrosine, leading to a build up of homogentisic acid (due to defect in homogentisic acid oxidase) which can be excreted in urine –> black wee in babies, dark earwax in older children. Can also bind to collagen, causing progressive arthritis in adults
What are the groups of an amino acid?
R, carboxyl, NH2 (amino group), H
How can you classify amino acids?
By their side chains (R side group which is CH2):
Acidic = if they have a negatively charged side chain (COO-)
Basic = if they have a positively charged side chain (NH2+)
Nonpolar (hydrophobic) = doesn’t have polar molecules
Polar (hydrophilic) = have OH, SH of NH2 (at CH2)
Aromatic = contains benzene ring (6 carbon atoms)
Aliphatic = non-aromatic
What is a peptide bond?
Carboxyl group of one aa reacts with NH2 group of another aa, loses a H20 and binds
What is pKa?
Acid dissociation constant. Helps you predict whether an acid will donate or accept protons at a specific pH. The lower the pKa, the stronger the acid and the more likely it is to give away protons and thus be deprotonated
Glutamate’s pKA is 4.3, and your pH is 6. What will happen to glutamate?
It will give away its protons from its R group i.e. is deprotonated
What is the henderson-hasselbalch equation used for?
If you have pKa or pH can work out the other
What are the 4 degrees of protein structure?
1- amino acid sequence
2- spatial arrangement of polypeptides e.g. helices
3- overall 3D protein structure
4- association between polypeptides to make multi-subunit protein
What is the isoelectric point?
The pH where a protein has no overall electric charge. So for acidic proteins this will be more than 7 (because will balance out and they give their charge away) and for basic will be less than 7.
What type of bond holds the primary structure of proteins together?
Covalent peptide bonds
What type of bonds stabilise a-helix and are inter-strand in B sheets?
H bonds
What is an amino acid residue?
What is left of each amino acid after two have bonded to form a peptide (they together lose H20)
Compare fibrous and globular proteins
Fibrous (keratin, collagen) support, function to BE something i.e. shape and protect. Have a single type of secondary structure arranged in long strands or sheets. Repetitive aa sequence.
Globular function is to DO something (albumin, haemoglobin, insulin) e.g. for catalysis and regulation with several types of secondary and tertiary structures. Irregular aa sequence.
Why are water soluble proteins and membrane proteins opposite?
Water soluble proteins have hydrophobic side chains buried and polar charged chains on the surface whereas membrane proteins have hydrophobic side chains on the outside
Name the five collagen types and where they’re found
I- dense CT bone, skin, tendons, cornea II- hyaline cartilage, IV discs III- loose CT aorta, blood vessels IV- BM V- placenta
What secretes collagen?
Fibroblasts
Describe the structure of tropocollagen
Right handed helix with glycine at every 3rd position, made of 3 polpeptide alpha chains coiled together (=triple helix), non-extensible or compressible with high tensile strength and H bonds between alpha chains
What are the 4 stages of collagen synthesis
Pre-procollagen, propeptide, procollagen, tropocollagen
Describe the stages of post-translational modifications of collagen
Has a signal sequence on its N-terminal which is recognised by SRP (signal recognition protein) and so enters ER and now called preprocollagen. Signal sequence is removed and now called propeptide (note!).
Next is hydroxylation of lysines (lysine hydroxylase) and prolines (proline hydroxylase) which aids alpha crosslinking via H bonds. They are glycoslated, N-linked oligopeptides added, chains align and triple helical procollagen forms. Exocytosed and procollagen peptidases cut N+C terminals to make tropocollagen. Lysyl oxidase makes covalent cross links between moles to form fibrils (aldol cross link)
What happens to make collagen into each of its different forms
Preprocollagen: once entered ER
Propeptide: once signal sequence removed
Procollagen: once triple helix formed
Tropocollagen: once N+C terminals cut off
Why do you get problems with collagen in scurvy
Need vit C as a cofactor for hydroxylation of lysines and prolines to make procollagen
What is Ehlers-Danlos
Deficiency of lysyl oxidase makes covalent links between collagen molecules to form fibrils. Stretchy skin, hypermobility
What bonds are important in collagen
Interchain H bonds
Covalent cross-linking (aldol cross-link) of collagen to form fibrils
Name key enzymes in collagen synthesis
Lysyl oxidase makes covalent cross-linking bonds for fibrils, lysyl and proline hydroxylase is needed to make procollagen, procollagen peptidases cut N and C terminals off procollagen to make tropocollagen
Name a protein that interacts with newly synthesised proteins in the ER
BiP (binding immunoglobuin protein) is a chaperone that holds newly made proteins in a state where they are ready to fold
What can target proteins for degradation by the proteasome?
Calnexin and calreticulin- hold unfolded proteins and if they can sense misfolding they return it the cytosol for degradation
Which post-trans mods happen in the golgi?
O-linked glycosylation, NANA addition, Mannose removal, Gal addition, GlcNAc addition
Insulin is ____ secretion whereas collagen is _____ secretion
Insulin regulated secretion, collagen constitutive secretion
Describe stages of insulin synthesis
Preproinsulin enters ER to become proinsulin and its signal sequence is removed. In the ER disulfide bonds form.
Goes to golgi –> B chain and carboxyl termini removed to become insulin
Compare ER and golgi post-trans mods
ER: N-linked glycosylation, acetylation, hydroxylation, proteolytic cleavage
Golgi: O-linked glycosylation, removing Mannose, adding NANA, Gal, GlcNAc
How do proteins get targeted for ER retention?
Proteins get KDEL attached as their signal on the C terminus, leave for the Golgi via COPII, move back to ER via COPI and enter ER via KDELR. KDEL signal is retained
How do proteins get targeted to lysosomes?
In the golgi they have M6P + signal patch attached and bind to M6PR in golgi, transported to endosome via clathrin coated vesicles, in the endosome the hydrolase dissociates from M6PR and M6PR is recycled back to the golgi. ATP needed to pump H+ ions into endosome to remove the hydrolase from the M6PR.
How do proteins get targeted to mitochondria?
Signal sequence MTS at N terminus, binds to the import R on the TOM (translocase of outer membrane) and then to the TIM and then is inside the mitochondria. Hsp keeps it unfolded, which costs ATP.
How do proteins get targeted to the nucleus?
Signal is NLS which binds to importins to get through the nuclear pore, then once in RanGTP causes importin to dissociate. In Swyer syndrome there is mutated NLS in SRY protein (XY genotype, outwardly female)
What signals are involved in protein targeting?
ER retention: KDEL (KDELR)
Lysosome: M6P (M6PR)
Mitochondria: MTS (importin R of TOM, TIM)
Nucleus: NLS (importins)
Name a disease associated with mutation in protein targeting
Swyer syndrome has mutated NLS on SRY which produces XY genotype but outwardly female with streak gonads
In what ways can protein function be controlled?
Product inhibition (accumulation of product inhibits making more)
Allosteric inhibition or activation e.g. PFK inhibited by ATP
Covalent modifications e.g. phosphorylation
Proteolytic cleavage e.g. zymogens
Ubiquitin targets for destruction in proteasome
Allosteric activators promote _ state, inhibitors promote _ state
Activators R state (the more active state), inhibitors T state (less active state). R for ready to go.
Which factors lead to activation of factor X (Xa)?
XI, IX, XII from intrinsic (endothelial) and VII and tissue factor (TF) from extrinsic (trauma)
What converts prothrombin to thrombin
Xa (activated X)
What does thrombin do
Converts fibrinogen to fibrin
What keeps prothrombin inactive?
Kringle domains (lol). Its protease is C terminal and its N terminal binds to the damage site
Describe the structure of fibrinogen
2 tripeptides with globular domains and A and B chains that prevent aggregation. Thrombin chops off the A + B chains
What do you need to make a soft clot and to make a hard clot?
Soft clot needs thrombin to chop off A and B chains of fibrinogen
Hard clot needs aldol cross-linking of fibrinogen by transglutaminase (activated by thrombin)
What mechanisms are in place to stop clotting?
Blood dilutes and liver removes
Protein C (activated by protein S)
Antithrombin III
Plasmin degrades fibrin clots
What is a haem group?
Protoporphyrin ring with an Fe atom that binds to O.
When O2 binds to Fe in a haem group what happens?
Fe moves into the plane of the photoporphyrin ring which causes a change in protein conformation
What is myoglobin?
Protein that binds O2 in skeletal muscle and cardiac myocytes
What is the difference between myoglobin and haemoglobin?
Myoglobin has a hyperbolic dissociation curve whereas Hb has a sigmoidal curve. This means there can be a much lower oxygen partial pressure to give same saturation with myoglobin.
What is P50?
The partial pressure giving 50% saturation
What is the structure of haemoglobin?
2 alpha polypeptides 2 beta polypeptides, each with a haem group. Once it binds O2 goes to R (more active state).
What happens when O2 binds to Hb?
Fe moves into the plane of the photoporphyrin ring and changes protein conformation to R state (from T state) and it now is easier for more O to attach so promotes cooperative binding in the lungs and losing oxygen in tissues
What substances affect Hb oxygen binding?
2-3BPG, H+, CO2 all decrease affinity for oxygen so that it is given to the tissues.
CO has x250 affinity for O than Hb
What subunits does HbF have?
a2 and y2 (higher affinity than HbA)
What is a normal variant of HbA found in all adults?
HbA2
What happens in HbS?
So gluatamate is changed for valine (point mutation) in B globin to form a sticky hydrophobic pocket so HbS stick together. HbS more prone to lyse –> anemia and more rigid –> block microvasculature.
What is thalassaemia?
Either alpha or beta chain genetic imbalance
Describe B and A thalassaemias
B: decreased or absent B globin chain production, alpha can’t form stable tetramers, symptoms post birth
A: decreased or absent alpha chain. Onset pre birth
Describe energy changes between substrate and product
Brief high energy transition state and then lower energy product state
What do biological catalysts do?
Lower activation energy needed to convert substrate to product
Give an example of a disease involving protein misfolding
Alzheimer’s- amyloid can misfold to form amyloid fibres which are insoluble and can form plaques
By which bonds do substrates bind to active sites?
Non-covalent- needs to be temporary
What is Vo?
Initial rate of reaction
What is Vmax?
Max velocity mol/min
What is Km?
Substrate conc that gives you half the max velocity
What effect do competitive and non-competitive enzymes have on Vmax and Km?
Competitive no Vmax effect, increases Km (need more substrate to get half velocity)
Non-compet reduces Vmax but NOT Km
What bonds are involved in each degree of protein structure?
1- covalent
2- H
3- covalent, ionic, H, hydrophobic, Van der Waals (dipole-dipole interaction)
4- covalent, ionic, H, hydrophobic, Van der Waals
Southern blot
Find a specific piece of DNA using allele specific probes, denaturing DNA, transfer to membrane, probe with labelled ssDNA
Western blot
Find a specific Protein using gel electrophoresis and mAbs as probes
Northern blot
Find specific RNA
FISH
Fluorescence in situ hybridisation, give green control probe and red of interest probe e.g. for DiGeorge 22 syndrome
Karyotyping
Size and structure of chromosomes
Electrophoresis
Separates proteins by size
Microarray
Each slide printed with DNA as rpobes, collect mRNA and convert to DNA and flouroscent probe it, mix samples. If expression on sample increases will go red
ELISA
Ag coated well, Ab added, add secondary Ab, add substrate and colour forms
Proteomics
Digest protein with trypsin, then use mass spectronomy for list of peptide sizes you can identify
DNA profiling
Look for minisatellites (highly variable regions) w restriction enzymes (endonucleases made by bacteria) and then add a radioactive probe to reveal sequences
PCR
Heat to denature proteins, add Taq DNA polymerase, add pair of primers to define region to copy
What is a mitochondrial cristae?
Fold created by inner membrane
Do you know how to identify cis vs trans golgi on a micrograph?
Cis is fairly continous concave line, trans is more irregular with bobbles coming off
What is the function of SER?
Lipid synthesis
Will an insertion mutation result in a frameshift mutation?
Maybe, maybe not (it adds 1+ nucleotide base pairs)
What’s the difference between an oncogene and a proto-oncogene?
Oncogene has the potential to cause cancer, proto-oncogene is a normal gene that could become an oncogene
How does nitrous acid cause mutations?
Deaminates adenine or cytosine (changes to uracil) which in next round of replication pairs with adenine to produce a transition mutation
What is hereditary haemochromatosis?
Iron overload due to defect in HFE gene which controls hepcidin (high hepcidin in inflam causes iron trapping in macrophages and liver so lowers serum iron) . Iron stored in skin, heart, liver, pancreas, joints
Where does fatty acid synthesis occur?
Cytoplasm
Functions of the ER?
Post-trans protein mods
What does amphipathic mean?
Hydrophobic and hydrophilic like a phospholipid barrier!
Give two definitions of pH
Logarithmic measure of H ion concentration
-log(H+)
How would a PE change blood pH?
Hypoxia so tachypnea so respiratory alkalosis
What is telomerase?
Adds to telomeres, found in fetal tissues, adult germ cells and tumour cells. Because somatic cells do not regularly use telomerase, they age
What is xeroderma pigmentosa?
Extreme UV sensitivity caused by problem with NER
Give an example of an antibiotic that interferes with RNA synthesis
Rifampicin inhibits RNA polymerase
What makes a protein polar (and thus hydrophilic)
Off the CH2: NH2, OH, NH2, COOH
What makes a protein basic or acidic
Off the CH2: NH2 (basic), COOH (acidic)
What charge do histones have?
Positive, which makes sense because DNA is negative
What increases and decreases activity of PFK?
Activated by F6BP, AMP
Inhibited by ATP, H+, citrate
How does warfarin work?
Inhibits vitamin K (makes factors X, IX, VII, II)
Why are sclera blue in osteogenesis imperfecta?
Underlying choroidal veins show through due to thinner sclera than normal (defective type I collagen)
How does mitochondrial replacement therapy work?
Use donor egg with mtDNA and remove nucleus and replace with mother’s and fertilise with father
