MOD 1 Flashcards
What are the key characteristics of Life?
- Cell based
- Can reproduce
- Are complex and organised
- User energy for growth and reproduction * Tend towards homeostasis
- Change over time
- Adapt to environment
- Respond to stimuli
Classify these organisms as prokaryotic or eukaryotic: humans, mushrooms, fish, bacteria, algae, gum trees
- Prokaryotes:
Eubacteria
Bacteria
Archaea - Eukaryotes:
Protests
Algae (Plants)
Gum trees
Fungi (Mushroom)
Animals (Human, Fish) - Virus is neither prokaryotes nor eukaryotes.
What properties of carbon make it central to life as we know it(i.e.carbon-based
life)?
- Can bond with itself
- Can bond with other elements (4 bonds) in lots of different ways
- All major biopolymers have a substantially carbon backbone
- “sweet spot” of stability (stable but not too stable) for forming covalent bonds
- Carbon bonds often under kinetic control (good for enzymatic regulation)
What are the most common elements in living things,and are they each usually polar or hydrophobic?
Common
- Carbon - C - non-polar / hydrophobic (water hating)
- Hydrogen - H - heavily influenced by what its near - C/H neutral, O/H polar either polar or non-polar
- Nitrogen - N - polar / hydrophilic (water liking) - partly (dipoles) or fully charged
- Oxygen - O - polar / hydrophilic (water liking) - partly (dipoles) or fully charged *
Smaller amounts
Phosphorous - P - polar / hydrophilic (water liking) - partly (dipoles) or fully charged
* Sulfur - S - (sometimes) polar / hydrophilic (water liking) - partly (dipoles) or fully charged either polar to non-polar
True or false: Hydrophobic things like to be in aqueous (water-based) environments.
False: hydrophobic is water-hating - don’t like to be in aqueous environments
how do you know if an element is polar or nonpolar
Non polar molecules are symmetric with no unshared electrons. Polar molecules are asymmetric, either containing lone pairs of electrons on a central atom or having atoms with different electronegativities bonded.
polar (contains Os, Ns, OH)
non-polar/ hydrophobic (contains lots of Cs and Hs)
What are the five main types of molecules used in Biology and what are their uses?
- Water
- Carbohydrates / sugars / saccharides
- Lipids (fats and others)
- Amino acids
- Nucleotides
True or False: The only role of Sugars/Carbohydrates is as energy sources?
False
* Sugar polymers (long chains of monosaccharides)
* Starch - Storage
* Chitin- Protection
* Cellulose - Structure
* Bacterial cell walls / surrounding coats (complex polymers)
Name three functions of lipids.
- Energy stores (triaglycerols)
- Signalling molecules (steroids)
- Protection and waterproofing (waxes)
- Structure / barriers (phospholipids)
What are the differences between amino acids and nucleotides?
Main difference: amino make proteins, nucleotides make nucleic acids Detailed differences: 20 amino acids and 4 types of nucleotides
What chemical properties can different amino acids have (name at least 3)?
Think about the side-chains: 20 amino acids
Non-polar (hydrophobic), polar (unchanged), charged (acidic pr basic) flexibility, charge
Aromatic
Size
Match the end to the biopolymer type to indicate the direction.
Nucleic acid
* 5’ to 3’ (five prime to three prime)
Protein
* N-terminus (or amino terminus) to C-terminus (or carboxy terminus)
What type of sequence is each of the following (DNA/RNA/Protein)?
A. AATTCGCGCTCTAGCT
B. AAHWYLDDEEPNQGS
C. AAUUCGCGCUCUAGCU
- A: DNA (contains T) * B: Protein
- C: RNA (contains U)
Which nucleobases base pair with each other (A,C,G,T,U), which are considered to have stronger base pairing and why?
- A = T (U)
- A and T/U complement each other (2 hydrogen bonds so a bit weaker)
*C=G - Strong base-pairing: C and G complement each other (3 hydrogen bonds so
stronger binding)
What properties of RNA mean that it is less stable than DNA?
Single-stranded: Expose base into aqueous environment; easy break bonds
Ribose vs deoxyribose: The OH group on ribose make it more susceptible to hydrolysis; stop forming B- type double stranded structure
Cytosine deamniation: C>U - lose information
RNA polymerases lacks proofreading activity: Lose information
Match the type of information containing biopolymer to its main role in the central dogma of Molecular Biology:
- DNA
- RNA
- Protein
- DNA: Doing molecules
- RNA: GeneticStore
- Protein: Messenger
Considermusclecells,brain cells and skin cells from the same individual .In general terms describe the genome, transcriptome and proteome for each cell type
- Genome
- Same DNA in all of your cells
- = complete genetic information
- Transcriptome
- Different: micro RNA, small nuclear RNA, messenger RNA, ribosomal RNA, transfer RNA
- Proteome
- Different: depends on function given different shape
What are the main differences between genomes and chromosomes from bacteria and eukaryotes?
- Most prokaryotes (bacteria and archea) have circular chromosomes * Tend to be relatively small genomes
- Eukaryotic genomes have linear chromosomes * Tend to be big
What does semi-conservative replication mean?
- Semi-conservative replication
- DNA contains one older and one newly replicated strand
What are the main challenges in copying DNA from DNA and how are they overcome?
Stopping DNA degradation when ssDNA: ssDNA binding proteins
Pulling the strands apart causes supercoiling, tangling:
topoisomerase/gyrase
Need to pull strands apart: Helicase
Leading and lagging strand: Okazaki fragments Copy small parts and stick
together; copying from 5’ to 3’
How do we start: AT rich sites; fewer H bonds; ORI origins of replication
WhataretherolesofthefollowingproteinsinDNAreplication:DNApolymerase, gyrase, helicase, ligase, primase?
- DNA polymerase: enzyme - make a DNA copy (lots of small fragments) from a DNA template
- Gyrase: enzyme, that relieves (stops) supercoiling (overwinding DNA)
- Helicase: enzyme, unwinds DNA
- Ligase: enzyme, joins pieces of DNA
- Primase: RNA polymerase that make primers for replication
How are RNA polymerases different from DNA polymerases?
DNA polymerases
* Make a DNA copy from a DNA template
* Do need a primer to start
* Use deoxynucleotide triphosphates (dNTPs: dATP, dGTP, dTTP, dCTP) as substrate
* “Proof read” the last nucleotide added; often have 3’ to 5’ exonuclease activity to remove a mismatched nucleotide
RNA polymerases
* Make an RNA copy from a DNA template
* Don’t need a primer to start
* Use ribonucleotide triphosphates (NTPs: ATP, GTP, CTP, UTP) as substrate
* Limited proofreading, no 3’ to 5’ exonuclease activity (make more mistakes)
What are the signals for transcription initiation and termination?
- Transcription initiation * Promoter
- Transcription termination * Terminator
How can different genes be transcribed into RNA at different rates?
Promotor strength
* Strong promoter - more copies
* Weaker promoter - less copies
Repressors
* Makes it easier for binding at promoter
Accelerators
* Blocks the binding of the sigma factor / RNApol complex and therefore RNA polymerase will have no space to bind
How do tRNA and amino acylRNA synthetases work together to correctly translate an mRNA sequence translated into a protein/peptide sequence?
Aa-tRNA synthetases
* Catalyse the activation of amino acids
* Use ATP hydrolysis to get the energy to make a high energy bond * Attach the correct amino acid to its matched tRNA
* Recognise the anticodon and other parts of the tRNA
What roles does the ribosome have in protein synthesis initiation, elongation and termination?
Initiation: Binds to mRNA, start codon, recruitment/ binding met-tRNA
Elongation: A site - aa-RNA binding
P site - joins amino acids together - peptidyl transferase activity
Termination: Stop Condon is reached, no tRNA matches and protein release factor binds
Peptide transferase activity adds water
True or False: Release Factor is a tRNA that binds to the stop codon to terminate protein synthesis
False - not tRNA, it’s protein
What are the differences between primary, secondary, tertiary and quaternary structure of proteins?
- Primary: Amino acid sequence
- Secondary: Local structures, Alpha helix and beta sheet
*Tertiary: Overall 3D arrangement of a polypeptide chain overall fold
-Quaternary: Organisation of subunits
What types of bonds and forces hold protein structure held together?
Hydrophobic effect: Tertiary (quaternary)
Hydrogen bonds: Secondary and tertiary
Covalent bonds: Primary - bonds that holds the polypeptide together
Polar interactions: Tertiary quaternary
Ionic binds/electrostatic / salt bridges: Tertiary quaternary
Describe how an element of protein secondary structure can complement dsDNA structure to allow protein-DNA interactions.
- Sidechains must point the right way to recognize either the backbone for general/non- sequence specific binding, or the bases for sequence specific binding
- α-helixes are a perfect size to fit into the major groove of DNA
- Single strands of protein Can fit in the minor groove
If a reaction is at equilibrium which of the following statements is true?
Substrate molecules are probably exchanging with product molecules and vice versa
What does it mean if a reaction is under kinetic rather than thermodynamic
control?
- Thermodynamic contorl is about the energy of the reactants / products * Kinetic control is about overcoming activation barrier
- Kinetically controlled reaction rate can be influenced by enzymes
True or False? A reaction (Substrate <-> Product) can be driven to the right by adding more substrate or removing the product.
True
What are three properties of enzymes that are important for biology and/or medicine?
- Can be regulated
- Can be localised in certain organelles * Can be organised into pathways
How can the hydrolysis of pyrophosphate drive unfavourable interactions?
- Release of energy from ATP to AMP > PP > P + P
- Gives energy required for overcoming unfavourable thermodynamics * Removes product, driving reaction to the right
transcription and translation
The process by which DNA is copied to RNA is called transcription, and that by which RNA is used to produce proteins is called translation.
mutations: Deletion
A deletion changes the DNA sequence by removing at least one nucleotide in a gene.
Mutations: insertion
An insertion changes the DNA sequence by adding one or more nucleotides to the gene. As a result, the protein made from the gene may not function properly.
Frameshift mutation
the insertion or deletion of nucleotide bases in numbers that are not multiples of three. rameshift mutations can result in a premature stop codon somewhere in the sequence, truncating the protein
silent mutation
A silent mutation is a type of substitution mutation (one base is replaced with another). This results in no change to the resulting protein
nonsense mutation
A nonsense mutation occurs when the substitution results in the formation of a stop codon.
substitution mutation
Nonsense mutation
Substitution
Substitution
Substitution – when one or more bases in the sequence is replaced by the same number of bases (for example, a cytosine substituted for an adenine
missense mutation
a DNA change that results in different amino acids being encoded at a particular position in the resulting protein. Some missense mutations alter the function of the resulting protein.
point mutation
Substitution mutation is when a nucleotide is substituted
An example of a sugar polymer is:
Chitin
“Deoxyribose nucleotides are joined together via _________(i) bonds with the help of a _________(ii) resulting in the release of an H2O by-product.”
(i) phosphodiester (ii) polymerase
Which of the following statements about protein synthesis is most correct?
A nucleotide sequence is effectively converted into an amino-acid sequence
Which of the following does not occur in transcription
Transcription of the whole genome
Which of the following catalyses the formation of peptide bonds
Ribosomal RNA
Which of the following is not a property of enzymes?
They are used up in the reaction
Protein sequences are correctly:
Defined by the mRNA sequence and tRNAs onl
In his famous 1928 experiment, Griffith found that when the “smooth virulent (S strain)” (a deadly bacterial colony) was heat killed, the resulting by-product was mixed with a solution containing the rough non-virulent (R strain) bacteria (a non-pathogenic bacterial colony) and injected into a mouse, what happened to the mouse?
The mouse died because the R-strain bacteria was transformed by DNA provided by heat-shocked S-strain bacteria
The removal of the –OH group from carbon 2′ of ribose in DNA to make deoxyribose:
Prevents the cleavage of the backbone by OH- attack
You have two fragments of DNA, one from E. coli and one from mouse liver. They both have 5,000 base pairs and 40 % G+C content. Which of the following parameters is most likely to differ between the two DNA samples?
The sequence of the DNA
What is the purpose of primase in DNA replication?
It synthesises a small sequence of RNA that is used as the starting point of replication
What kind of bond is found between two amino acids in a protein?
Peptide bond
If a reaction has a high activation barrier:
The speed of the reaction will be slow
Which of the following is most responsible for regulating how often a DNA sequence is transcribed into RNA?
Promoter sequences
