Overall Quiz Flashcards
How is DNA packaged?
Beads on a string, wrapped around histone into
? Solenoid comes in
What is the limit of resolution?
The minimum distance at which two objects can be distunguished
What is limit of resolution proportional to?
The limit of resolution is proportional to wavelength.
Light microscope 2 micrometers
Electron microscope 0.002nm
What are the parts of a phospholipid molecule?
Choline, phosphate, glycerol - polar hydrophilic head
Fatty acid - non polar hydrophobic tail
What are the functions of the plasma membrane? (7)
Selective permeability Transport of materials along a cell surface Endocytosis Exocytosis Intercellular adhesion Intercellular recognition Signal transduction
Where would you find smooth endoplasmic reticulum?
Liver, mammary glad, and in ovary, testes, adrenal gland
What does the golgi apparatus/body do? (4 things)
Modifies
Sorts
Concentrates
Packages proteins synthesised on the rough endoplasmic reticulum.
What is a lysosomes function? What is the pH in the lysosome?
Contain many hydrolytic enzymes. They fuse with material requiring digestion.
PH around 5.
What do peroxisomes do?
Peroxisomes detoxify (oxidise) a number of molecules including alcohol, phenols, formic acid and formaldehyde.
What is a mitochondrias function?
Primary function- generation of ATP by oxidative phosphorylation.
Double membrane - inner membrane thrown into folds (Cristae)
What are microtubules?
Long, hollow cylinders made of the protein tubulin. Found at sites where structures are moved i.e. In nerve fibres, the mitotic spindle, cilia and flagella. Diameter 25nm.
What are the nitrogenous base purines? Do they have two rings or one?
Adenine and guanine. Two rings.
What are the pyramidine bases? Do they have two rings or one?
C and T. One ring.
Which bases form 3 hydrogen bonds?
C and G.
A and T form two hydrogen bonds.
What could cause DNA replication stress? (3)
Replication machinery defects
Factors hindering replication fork progression
Have defects in response pathways
What allows DNA polymerase to cut from the end?
As well as adding bases DNA polymerase also has an exonuclease function allowing it to cut DNA from the end.
What are telomeres?
Repeated sequences (e.g. TTAGGG) at the end of the chromosome/chromatid. Important in relation to ageing and cancer.
What are the 5 phases of mitosis:
Prophase- nuclear membrane disappears, chromosomes condensed.
Metaphase- chromosomes line up at metaphase plate.
Anaphase- each part of the chromosome pulling apart.
Telophase- spindles disappear, nuclear membrane appears, middle of cell cleaved.
Cytokinesis
During interphase the chromosomes are no condensed.
What is an allele?
A different variant of the same gene.
When does crossing over take place in meiosis?
In prophase 1 - when the homologous chromosomes ‘find each other’ in the cell.
Overview of meiosis 1 and meiosis 2:
Meiosis 1: crossing over in prophase 1 (causing genetic diversity). Homologous pairs of chromosomes line up and separate.
Meiosis 2: chromosomes line up and chromatids separate.
How many chromosomes are in a primary spermatocyte?
How many sperm does a spermatocyte produce?
There are 46 (62 chromatids).
4 sperm.
1 spermocyte (2n) produces 4 sperm (n).
What does an oocyte produce?
1 egg (n) and 3 polar bodies. - all the energy packaged into one big cell- the egg. If the egg is not fertilised it will never finish meiosis.
Describe the different phases of the cell cycle:
G0, G1, S, G2, M
G0 - resting phase. Differentiated cells stay in G0 - no signals to start cells to divide, e.g. Skeletal muscle.
G1- cell content replication, not DNA replication.
Checkpoint here.
S phase- DNA replication.
G2- double check and repair before division. Checkpoint here.
M- mitosis
Checkpoint here.
What does non-disjunction lead to?
Aneuploidy.
What is mosaicism? Can it be throughout the body or tissue limited? What can cause differences in the degree of mosaicism?
The presence of two or more cell lines in an individual.
Can be throughout the body or tissue limited.
Degree of mosaicism is dependent on the first post-zygotic division and later mitotic division.
Along with crossing over, what is also important for genetic diversity?
Random assortment of chromosomes at meiosis 1 (often very underestimated)
At what types of chromosome would you get a translocation?
Acrocentric chromosomes - the centromere located towards one end of the chromosome.
How do the autosomes ‘find each other’?
Sequence identity.
What is chiasma?
The point at which paired chromosomes remain in contact during the first metaphase of meiosis and at which crossing over and exchange of genetic material occur between the strands.
What happens at each of the checkpoints?
G1 checkpoint- is the environment favourable (before entering S phase)
G2 checkpoint- is all DNA replicated, is all DNA damage repaired?
M checkpoint- are all the chromosomes properly attached to the mitotic spindle? Pull duplicated chromosomes apart.
Checkpoints = temporary arrest. Provides time for the DNA to be repaired.
What happens if DNA damage is too high or persists?
Apoptosis- cell death
Or senescence- permanent cell cycle arrest
What are examples of exogenous and endogenous things that damage DNA?
UV light Alkylating agents Anti-cancer agents DNA replication errors V(D)J recombination Free radicals
What are the different DNA repair mechanisms?
Base excision repair
Mismatch repair
Nucleotide excision repair
Double strand break repair: NHEJ and HDR
What is the key point at which tumours can go from pre-malignant to malignant?
When the DNA damage response is turned off.
What is the significance of p53?
Guardian of the genome - involved in many aspects of damage response.
DNA damage response suppresses cancer development.
What is intracellular-tumour heterogeneity and what is its relevance?
Can chemotherapy affect heterogeneity?
Sub-clones of a tumour within the same tumour.
Development of new phenotypes may be resistant to cancer therapy and also could metastasise.
Chemotherapy can induce heterogeneity- however we can also study how they evolve and guide tumours to mutate a certain way to treat the next mutation.
What ensures the accuracy of chromosome segregation?
The mitotic spindle- the microtubules move the chromosomes around.
Why is the mitotic spindle a good target when treating cancer?
If you stop the microtubules growing toy cant make spindle and cells cant divide.
however- this doesn’t work in all patients.
Do oncogenes promote or prevent cancer?
Oncogenes promote cancer.
You have 2 copies- one on each chromosome.
Why are cancer cells considered ‘plastic’?
Cancer cells lose accuracy of segregating chromosomes = chromosome instability.
Constant changes mean cells get genetically different,
What is the relevance of increased centrosomes and using them as a target for cancer?
Cancer cells frequently have amplified centrosomes. THis can lead to a multipolar spindle.
Cancer cells overcome this by clustering into two areas to make the cell bipolar however if we stop centrosomes clustering we can have multipolar spindles and cause the cell to go into the dying state.
What things need to be right to pass the G1 checkpoint?
Nutrients are sufficient
Growth factors (signals from other cells are present)
Cell size is adequate
DNA is undamaged (mature cells don’t pass this checkpoint)
What needs to have happened to pass G2 checkpoint?
Chromosome replication completed successfully
No DNA damage
What has to have happened to pass the metaphase checkpoint (in mitosis)?
All chromosomes are attached to the mitotic spindle.
What holds the two sister chromatids together?
Cohesin- 4 proteins held in a ring structure.
What is a zwitterion?
A zwitterion is a molecule that has separate positively and negatively charged groups.
Describe peptide bonds:
Rigid single bond
However can have resonance (a double bond) as electrons move across
The carbon-nitrogen has partial double bonds- cant rotate around it
Trans- R groups on opposite side - always exhibit this
Cis- R groups same side- steric clashes as atoms too close together
Bonds either side of the peptide bond are free to rotate- however not always possible as they may clash
What is the isoelectric point (pI) of proteins?
The point at which there is no overall net charge.
Basic proteins have a pI of >7
Contain many positively charged (basic amino acids)
Acidic proteins have a pI of <7 - contain many negatively charged amino acids
(need to think about a protein that has already donated its protein so it is now negatively charged)
What are conjugated proteins?
Proteins which have covalently linked chemical components in addition to amino acids:
Lipoproteins with lipids
Glycoproteins with carbohydrates
What type of structure is an alpha helix classified as? What are the properties of an alpha helix?
Secondary structure.
3.6 amino acids per turn.
R handed helix. (Imagine going up stairs holding on the R hand rail)
0.54 nm pitch - one complete turn
Hydrogen bonds between N-H and C=O stabilise the structure (the backbone C=O group of one residue is H bonded to the -NH group of the residue 4 amino acids away)
R groups on the outside
What are strong alpha helix formers?
Ala and Leu are strong helix formers due to their small hydrophobic residues
What are strong helix breakers?
Pro - because the rotation around the N-CH is impossible
Gly- the tiny R group supports other conformations
What bonds are involved in each the protein structures (e.g. Primary, secondary, tertiary and quaternary)
1- covalent
2- H bonds
3- covalent (disulphide), ionic, H bonds, van der waals, hydrophobic- side chains become important)
4- covalent (disulphide) , ionic, H bonds, van der waals, hydrophobic
What do cysteine residues do?
Produce disulphide (covalent) bonds. Limits folding but increases strength.
What are electrostatic interactions?
Formed between charged groups (strong in solids, weak in water)
E.g. Glu- asp- , arg+, lys+ his+
What are van der waals forces?
Dipole-dipole interactions
Important when surfaces of 2 large molecules come together.
Small changes in charge, uneven charge distribution, property of any bond type therefore add them up in a large molecule and they become important.
What is protein denaturation? How can you denature a protein?
The disruption of protein structure.
Caused by breaking of forces that hold proteins together.
E.g. Heat - increased vibrational energy, pH - alters ionisation states of amino acids, changes ionic/H bonds
Detergents/organic solvents interfere with hydrophobic interactions.
How do biological catalysts work?
By increasing the rate of a reaction by reducing the activation energy.
Facilitate formation of the transition state.
An enzyme will often provide a binding site and bring substrates together.
What are some features of enzymes?
Highly specific (usually)
Unchanged after a reaction
Don’t affect the reaction equilibrium
Increase rate of reaction
Proteins (usually) - also some RNA molecules
Many require associated co-factors - additional groups
What would a low Km value tell you?
That there was high affinity for the substrate.
What is Km?
Substrate concentration that gives half the maximal velocity.
What is the rate of an enzyme catalysed reaction proportional to?
The concentration of the enzyme.
What are enzyme inhibitors?
Molecules that slow down or prevent an enzyme reaction - including many drugs.
Can be irreversible or reversible.
What does competitive binding affect?
Affects Km but not Vmax.
Adding enough substrate will always overcome the effect of the inhibitor so no effect on Vmax.
What does non-competitive binding affect?
It affects Vmax but not Km.
What does the promotor region do?
Acts as a recognition site for RNA polymerase to bind.
RNA polymerase can block the promotor region.
What happens at the terminator region of the DNA
Transcription is complete and the RNA polymerase, the DNA strand and the messenger RNA strand dissociate from each other.
What happens at intron splicing?
Spliceosome (complex of proteins and RNA) performs splicing add poly-a-tail and 5' cap Introns removed Joins adjacent segments = production of MATURE MRNA STRAND
What happens at the start of translation?
The small ribosomal unit binds to the 5’ end of the mRNA upstream of the start codon
Each amino acid is brought to the ribosome by a specific tRNA (determined by the anticodon sequence)
After the initiator tRNA binds to the start codon, the large ribosomal subunit binds to form the translation complex and initiation is complete.
What are the ribosomal units called? (Think initials)
E, P and A
What happens during elongation?
Individual amino acids are brought to the mRNA strand by a tRNA molecule through complimentary base pairing of the codons and anticodons.
Each anticodon corresponds to a particular amino acid
A charged tRNA binds to the A site and a peptide bond forms between its amino acid and the one attached to the tRNA molecule at the P site.
The complex slides down one codon to the right and the uncharged tRNA molecule leaves from the E site.
Elongation will continue until a stop codon is reached.
A release factor binds to the A site at a stop codon and the polypeptide is released from the tRNA in the P site.
The entire complex dissociates and can re-assemble to begin the process again at initiation.
The purpose of translation is to produce polypeptides quickly and accurately.
What is the promotor region on the mRNA
The TATAAA box- this is where RNA polymerase binds to DNA
Where are lots of stem loops found? Why?
On tRNA- H bonds formed between anti-parallel complimentary sequences
Does the main chemistry take place in the minor or major groove of DNA?
Major groove.
What is it called when a centromere is located right in the centre of the chromosome?
Meotcentric
What is it called when the centromere is found quite close to the end of a chromosome?
Acrocentric
What are the types of RNA?
Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) Micro RNA (miRNA) non-coding RNA
What do you need to make a polynucleotide or polypeptide?
Need an enzyme- DNA polymerase/RNA polymerase
Need an activated substrate- dNTPs or NTPs
Need a template- DNA or RNA
3 stage process: initiation, elongation, termination
- What is the enzyme for making a protein?
- What is the active substance for a protein?
- What is the template?
A ribosome
An amino acid
MRNA
When does termination occur in DNA replication?
When does termination occur in transcription?
When replication forks meet.
Sequence dependent.
What does the promotor do?
Binds to a specific sequence (TATAA box), recruits RNA polymerase and churns out mRNA
Why does RNA need to be protected straight away after transcription and how is this done?
Capping at the 5’ end protects against degradation
Poly-A-tail at the 3’ end protects against degradation
Splicing in the middle removes introns
What does polyA polymerase do?
Elongates the strand with lots of AAAAAA strands. Very long strands to protect RNA. Regulation of the polyA strand can determine the half life of the molecule.
What happens at translation?
The mRNA code is converted to a polypeptide chain.
What is the start codon?
AUG - methionine
Not all proteins keep this, may be cleaved off but all start with it.
What are the termination codons?
UAA
UAG
UGA
True or false: tRNA becomes charged when an amino acid group has been attached
True
Amino acids bind to the 3’OH group via carboxylic acid group, ester bond formed, H20 produced
What side does the amino acid bind to on the tRNA?
The 3’ end
What does tRNA synthase do?
Facilitates amino acid binding to the tRNA
What does peptide transferase do?
Forms the peptide bonds between the growing chain of amino acids
How are the sugars linked in DNA/RNA?
Through phosphoric acid groups attached to the 5’ position of the sugar and the 3’ position of the other.
The phosphate backbone bears a negative charge.
How does a nucleoside become a nucleotide?
Phosphorylation
What does post-translational modification describe the process of?
Altering the polypeptide to become active.
What is a zymogen?
A pre-cursor of an enzyme in its inactive form.
What is required for protein sorting? (4 things)
- signal (address) intrinsic to the protein
- A receptor recognising the signal + directs it to correct membrane
- A translocation machinery- to get protein across membrane
- Energy- to transfer to protein to its new place
What do peroxisomes do?
Break down large fatty acids.
What is constitutive secretion?
Can you give any examples?
Continuous process
Proteins packaged into vesicles and release continuously by exocytosis.
E.g. Serum albumin and collagen.
What is regulated secretion?
Proteins released in response to a signal e.g. Hormone
Proteins packaged into vesicles but not released until stimulus received. E.g. Hormone.
What modifications occur in the ER?
Signal cleavage (signal peptidase) Disulphide bond formation (protein disulphide isomerase) N-linked glycosylation (oligosaccharide-protein transferase)
What modifications occur in the golgi?
O-linked glycosylation (glycosyl transferase)
Trimming and modification of N-linked oligosaccharides
Further proteolytic processing (some proteins only)
How does lack of vitamin C cause scurvy?
Prolyl hydroxylase is the enzyme that produces hydroxyproline residues which increase the amount of inter-chain hydrogen bonds.
Prolyl hydroxylase requires vitamin C and Fe2+ ions for activity.
Because hydroxyproline residues aren’t being formed this causes weak tropocollagen triple helices.
