MGD Flashcards
Name 2 uncharged amino acids
Possible answers: phenylalanine, tyrosine, tryptophan, glycine, alanine, pro line, valine, leucine, isoleucine and methionine
What stereoisomer (L or D) of amino acids are naturally found in proteins?
L
Name a negatively charged amino acid
Possible answers: aspartate and glutamate
Name a positively charged amino acid
Possible answers: lysine, arginine and histidine
Name 2 polar amino acids
Possible answers: serine, threonine, cysteine, asparagine and glutamine
What are the key features of peptide bond?
CO and NH bond in trans orientation
Cant rotate due to double bond characteristics
What are the difference between a globular and fibrous protein?
Globular: water soluble, compact and highly folded. Usually has a regulatory or enzymatic function
Fibrous: water insoluble, elongated, repeating units. Usually has a structural function
Define the isoelectric point
The pH at which a protein has no overall net charge
Define a zwitterion
A neutral ion with the positive NH3+ and negative COO- ends. Formed at the isoelectric point
What is the primary structure of a protein and what bonds are involved in its formation?
The linear amino acid sequence of a polypeptide. Covalent (peptide) bonds
What is a secondary sequence of an amino acid, what bonds are involved in its formation and what are the 2 common types?
The local special arrangement of the polypeptide backbone.
Hydrogen bonds.
Alpha helix and beta pleated sheets.
What is the tertiary structure of a polypeptide and what bonds are involved in its formation?
The overall 3 dimensional structure.
Hydrogen, van der waals, hydrophobic, covalent and ionic
How many amino acids are there in 1 turn of an alpha helix?
3.6
If a protein has an isoelectric point of 5.0 and is placed in an electric field at physiological pH would it move towards the positive or negative electrode?
Positive
What can denature a protein?
Heat, pH and detergent
What is the pitch of an alpha helix?
0.54nm
How large is a eukaryotic and a prokaryotic cell?
Eukaryotic:10-100 micrometers
Prokaryotic: 1 micrometer
What are the differences between a prokaryote and a eukaryote?
Prokaryotes have no nucleus, membrane bound organelles or cytoskeleton. They reproduce asexually and divide by binary fission as opposed to mitosis/meiosis. They have smaller ribosomes.
Which residues are strong helix formers?
Alanine and leucine because they are small and hydrophobic
Name two helix breakers and explain why they are helix breakers
Proline - the rotation around the N-C bond is impossible
Glycine - the tiny R group supports other conformations
In beta strands, what is the distance between each amino acid?
0.35nm
How is a beta sheet formed?
The beta strands run anti parallel to each other and H bonds form between them to stabilise the structure
What is a domain?
Part of a polypeptide chain that folds into a distinct shape. Usually has a specific functional role
What is a motif?
Folding pattern that contains 1 or more types of secondary structure
What residue are disulphide bonds formed between?
Cysteine
What shape would a graph showing the binding of oxygen to myoglobin exhibit?
Hyperbolic
What shape would a graph showing the binding of oxygen to haemoglobin exhibit?
Sigmoidal
Why does haemoglobin have a sigmoidal shape?
Cooperative binding - the binding of oxygen to one of the haem groups increases the affinity of oxygen to the other ones.
Why is the sigmoidal curve of haemoglobin significant?
Because it means that oxygen is easily picked up in the lungs and then easily given up at the tissues
What effect does BPG have on oxygen binding, which direction will the curve shift and why is this significant?
BPG decreases the affinity for oxygen binding. The curve will shift to the right. It is significant because more BPG is produced in higher altitudes which promotes oxygen release at tissues
How do H+ ions and CO2 affect the affinity haemoglobin has for oxygen, which direction will the curve shift and why is this significant?
Reduce the affinity. Shift to the right. Because metabolically active tissues produce both substances and will need more oxygen. This couples supply and demand. Known as the Bohr effect.
Why is carbon monoxide poisonous?
It binds more strongly and irreversibly to haemoglobin than oxygen
How do the subunits of foetal haemoglobin differ from the regular form, what effect does this have and why is it significant?
It has 2 gamma sub units instead of the 2 beta ones. This increases the affinity for oxygen. This means that the foetus can get oxygen from the mothers blood
What are Thalassaemias?
A condition where there is an imbalance between the number of alpha and beta sub units
What are the differences between alpha and beta thalassaemias?
Beta: decreased or absent beta sub units. Alpha chains can’t form stable tetramers. Symptoms onset after birth
Alpha: decreased or absent alpha subunits. Different levels of severity but beta chains can form stable tetramers with increased affinity for oxygen. Onset before birth
Define Vmax
The maximal rate when all enzyme active sites are saturated with substrate
Define Km
The substrate concentration that gives half the Vmax value
Does a low Km value represent a high or low affinity for the substrate?
High
What are the differences between competitive and non competitive inhibition?
Competitive binds at active site and effects Km but not Vmax.
Non competitive binds at a secondary site and effects Vmax but not Km
What is one unit of an enzyme?
The amount of enzyme that catalyses the conversion of 1 micro mole of substrate per minute.
What is a zymogen?
An inactive precursor of a proteolytic enzyme
What are the 5 main regulatory mechanisms that control enzyme activity
Allosteric, substrate/product concentration, proteolytic, covalent modification and enzyme amount
How would an allosteric activator affect an enzyme?
It would make the R state more stable. This shifts the curve to the left
What type of enzyme catalyses the attachment of a phosphate group? What catalyses its removal? What amino acids are phosphate groups added to?
Kinase attaches. Phosphotase removes. Can be attached to serine, threonine and tyrosine.
Give 2 examples of covalent modification of an enzyme
Attaching one of the following to a protein via an amino acid: phosphoryl, acetyl, adenyl, uridyl, methyl or ribosyl
What is proteolytic activation and why is it used?
Activating a protein by removing part of the chain. This is useful, especially for proteases (enzymes that break peptide bonds), because it allows for them to be transported without causing any damage
How can the amount of enzyme be changed?
Increase its production by increasing the rate of transcription. Increase its degradation - tag it for destruction by adding a molecule known as a ubiquitin
Define feedback inhibition and give an example
End product of a pathway inhibits its own rate of synthesis e.g. ATP inhibits catabolic pathways. Glucose 6-phosphate inhibits hexokinase.
Define feed forward activation and give an example
Increased amounts of a substrate increase the rate of the first of the first step of its pathway e.g. Ethanol increases amount of ethanol oxidising enzymes
Define counter regulation and give an example
Catabolic degradation of the product inhibits the anabolic production of it e.g. Glycogenesis/glycogenolysis
What is an isoenzyme?
Enzymes that catalyse the same reaction but have a different amino acid sequence
What is the difference between a nucleoside and nucleotide?
Both have a nitrogenous base and pentose sugar but only nucleotides have the phosphate group
List the activators and inhibitors of phosphofructokinase
Activators: AMP and fructose 1,6-bisphosphate
Inhibitors: ATP, citrate and H+
What is an enzyme cascade?
An initial enzyme will activate subsequent enzymes which in turn activate even more increasing the magnitude of an initial signal very rapidly
What is the zymogen for Pepsin, where is it synthesised and what activates it?
Pepsinogen. Stomach. pH
What is the zymogen for Chymotrypsin, where is it synthesised and what activates it?
Chymotrypsinogen. Pancreas. Trypsin
What is the zymogen for Trypsin, where is it synthesised and what activates it?
Trypsinogen. Pancreas. Enteropeptidases
What is the zymogen for Carboxypeptidase, where is it synthesised and what activates it?
Procarboxypeptidase. Pancreas. Trypsin
What is the zymogen for Elastase, where is it synthesised and what activates it?
Proelastase. Pancreas. Trypsin
How does a deficiency of a1 antitrypsin cause emphysema?
The deficiency means less trypsin is broken down. This means elastase is produced in excess and breaks down the walls of the alveoli
Describe the extrinsic pathway of the clotting cascade
Membrane damages exposes the domain of factor 3. It’s activates factor 7 which in turn activates factor 10
Describe the intrinsic pathway of the clotting cascade
Factor XI is activated which in turn activates factor IX. This combines with the activated factor XIII and the extrinsic pathway to activate factor X. Factor IX and X are targeted to the damaged membrane by Gla domains. Ca2+ ions play a role.
Which factors are get feedback activation from thrombin in the clotting cascade?
Factor XI, VIII and V
Outline how a fibrin clot is formed from the fibrinogen
The thrombin cleaves fibrinopeptides A and B from the main fibrinogen (feet and stalks) the domains at the C terminal of the beta and gamma parts (claws) can attach to the cleaved chains
Haemophilia is the result of a defect in which factor of the clotting cascade?
VIII
How is the clotting process stopped?
Clotting factors are diluted and removed by the liver. Others are degraded by proteases such as protein C and finally some are factors are inhibited (antithrombin)
What are the 7 key control points in clotting?
Inactive zymogens present in low concentrations. Proteolytic activation. Amplification of signal by cascade. Clustering of clotting factors at damage site. Feedback activation by thrombin maintains clotting. Termination of clotting by multiple mechanisms. Clot breakdown controlled by proteolytic activation.
How many hydrogen bonds form between bases A and T?
2
Which bases are pyrimidines and which are purines?
Pyrimidines: C, T and U
Purines: A and G
What are the 4 stages of the cell cycle and what happens in each one?
G1 - cellular components except chromosomes are duplicated
S - all 46 chromosomes are duplicated
G2 - chromosomes are checked for errors
Mitosis
What enzyme unravels the DNA double helix?
Helicase
The new strand created by DNA polymerase grows in which direction? What end is the template strand therefore read in?
The chain grows 5’ to 3’. The DNA is read 3’ to 5’
What are the 3 steps of DNA replication?
Initiation, elongation and termination
What is required to initiate DNA replication?
Primers, primase and DNA polymerase
Outline the elongation part of DNA replication
Moving replication forks. Helicase unzips double strand. 3’ strand (lead) extends continuously and 5’ strand (lagging) grows in Okazaki fragments. DNA ligase joins the DNA joins the DNA strands together with phosphodiester bonds
How do the roles of DNA polymerase and ligase differ?
Polymerase adds free nucleotides to the 3’ end of the template strand. Ligase joins the strands together by forming phosphodiester bonds
Outline the termination stage of DNA replication
The replication forks meet and ligase joins them together. Chromosome number stays the same despite now being made up of 2 chromatids
What happens in prophase (mitosis)?
Nuclear envelope disappears. Chromosomes condense. Spindle starts to form
What happens in metaphase (mitosis)?
The chromosomes attach to the spindle at the metaphase plate
What happens in anaphase (mitosis)?
The chromatids are pulled apart to become 2 separate chromosomes.
What happens in telophase (mitosis)?
2 nuclear membranes form and chromosomes decondense.
What happens in cytokinesis?
At the same time as telophase the cell starts to split into 2
What causes variation in meiosis?
Crossing over, random segregation and mutations
How does meiosis differ from mitosis?
Produces 4 cells not 2. Cells aren’t genetically identical. Cells are haploid. 2 rounds of division.
Define heterozygous, homozygous and hemizygous
Homo-both alleles same. Hetero-both different. Hemi-in x sex linked as there’s only 1 allele
What is a dominant allele and what is a recessive allele?
The dominant allele will be expressed if present. The recessive requires both alleles to be there to be expressed
What would a pedigree of an autosomal recessive disease look like and give an example?
Disease can skip generations and appear to have come out of nowhere. Males and females are equally affected. Examples include cystic fibrosis and sickle cell disease
What would a pedigree of an autosomal dominant disease look like and give an example?
Disease can’t skip generations so every affected individual will have at least one affected parent. Males and females equally affected. E.g. Huntingtons disease
What would a pedigree of an x-linked recessive disease look like and give an example?
Affect males more than females. Every affected male has a carrier/affected mother. Every affected female has an affected father and carrier/affected mother. E.g. Haemophilia a
What is codominance and give an example?
Neither allele is dominant over the other so they are both expressed. Blood group
What is an example of complementation?
Albinism
What is stage G0 and why does it exist?
G0 is a stage where the cell is not dividing/preparing to divide. It could be to regulate growth or as the final destination
During DNA replication, why can’t both strands grow continuously?
During DNA replication a new DNA strand can only grow in a 5’-‐‑>3’ direction (using a 3’-‐‑>5’ template). As the two original DNA strands are antiparallel and are both used as a template, only one of the two templates (the 3’-‐‑>5’ template) can be replicated continuously while the replication fork ‘unzips’ and the other one is replicated in small sections
How many chromosomes does every human somatic cell contain in G2, just before mitosis?
46 - despite the chromosome being replicated they are still viewed as 1 chromosome
How is recombination frequency estimated?
Number of recombined progeny/number of informative progeny
Where does transcription occur and where does translation occur?
Transcription occurs in the nucleus. Translation occurs in the cytoplasm
What length does the chain grow in transcription?
5’ to 3’
What are the 3 types of post transcriptional modification that convert pre-mRNA to mature mRNA
Capping, tailing/polyadenylation and splicing
What are endonucleases and exonucleases and how do they differ?
Endonucleases break within the polynucleotide and are either specific or non specific. Exonucleases degrade from the 5’ end or the 3’ end
Briefly describe initiation in transcription
Initiation code is recognised (5’ TATA 3’) and transcription factors bind here which attracts RNA polymerase to start production upstream.
Briefly describe elongation
RNA polymerase travels along the mRNA picking up base pairs and copying them into a complementary RNA strand
Briefly describe termination in transcription
When the gene has been transcribed a methyl-guanine cap is added to the 5’ end. At the 3’ end the stop codon cleaves the mRNA and approximately 200 adenine nucleotides are added. Both of these protect against degradation.
What type of RNA polymerase make mRNA, what percentage of RNA is mRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase II, 2%, 100,000s of kinds, few copies
What does rRNA do?
Ribosomal RNA binds to the mRNA and provides the location for tRNA
Which RNA polymerase produces rRNA, how much of the RNA is rRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase 1, >80%, few kinds, many copies
Which RNA polymerase produces tRNA, how much of the RNA is tRNA, how many different kinds are there and how many copies of each kind?
RNA polymerase 3, 15%, 100 kinds, very many copies
Describe initiation in translation
The starting codon 5’AUG will bind to a corresponding anticodon 5’CAU on the tRNA. The 5’ cap binds to the 40s sub unit and then the 60s sub unit binds
What does the P site do and what does the A site do in a ribosome?
P site is for holding the Peptide chain
A site is for Accepting the tRNA
Describe elongation in translation
tRNA occupies P site and another aminoacyl tRNA occupies the A site. Peptide bond forms between them. tRNA leaves
Describe termination in translation
Stop codon is read on the mRNA (UAA, UGA, UAG) no corresponding anticodon so the peptide chain is hydrolysed and released.
Define a gene
A unit of heredity; a transcription unit, i.e. a length of DNA on a chromosome that contains the code for a protein (or RNA) as well as sequences necessary for its expression, such as promoter and terminator sequences and introns.
What are the implications of a degenerate code?
Substitutions can lead to a different primary sequence which affects the tertiary structure. If a stop codon is altered it affects the length of the polypeptide.
How would a mutation outside the gene coding area affect gene expression?
It may affect the promoter region where transcription factors bind.
How is bacterial gene expression different?
Bacteria have: simpler promoters, different transcription factors, smaller ribosomes (clinically useful as can target the 30s sub unit only found in bacteria), coupled transcription-translation, different translation factors and no post translational modification
Describe the key differences between transcription and translation in a human cell
Transcription: makes mRNA, occurs in the nucleus
Translation: makes a polypeptide, occurs in the cytoplasm
How are translation and transcription similar?
Both read a “code”, consist of 3 stages (initiation, elongation and termination) and both require energy and enzymes.
What is a polysome?
A length of mRNA covered in many actively translating ribosomes
What length is the mRNA read in translation?
5’ to 3’
What direction is the DNA read in transcription?
3’ to 5’
How does constitutive secretion differ from regulative secretion?
Constitutive secretion is a continuous process where the proteins are constantly packaged into vesicles and released by exocytosis. Regulative secretion puts proteins into vesicles but are not released until a signal is received
What is the difference between N-linked glycosylation and O-linked glycosylation?
N-linked: carbohydrate is added to the amide nitrogen of Asn in the ER
O-linked: carbohydrate is added to the hydroxyl of Ser or Thr in the Golgi
