DNA (lectures 1-5) Flashcards
What are the 3 domains of organism classification?
- Bacteria
- Archaea
- Eukaryotes
What is the cell theory?
This suggests that all living organisms are made up off cells that are derived from pre-existing cells.
What are the 3 general characteristics of a cell?
- Can obtain energy (light or chemical)
- Able to use available chemicals (to grow & multiply)
- Contains hereditary information (stored & passed on)
What are the main physical characteristics of a cell?
- Enclosed by plasma membrane
- nucleus
- mitochondria
- the ER (endoplasmic reticulum)
- the Golgi
- lysosomes
- peroxisomes
- chloroplasts
- cytoskeletal structure
Where is all hereditary information stored in a cell?
DNA
Can human DNA transcribe human proteins in bacteria?
No
Describe the transition from DNA to protein
DNA - Transcription - RNA - Translation - Protein
What is the polymer of a nucleotide?
Polynucleotide
What is the polymer of an amino acid?
Protein
What is the polymer of a monosaccharide?
Polysaccharide
What is the polymer of Acetyl coA?
Fatty acid
What is a hormone?
Small proteins that travel in the blood stream & bind to specific receptors elsewhere in the body
What are antibodies?
Recognize foreign material, allowing the immune system to respond
What are DNA binding proteins?
Proteins that bind to specific DNA sequences & affect gene expression
What is the role of porin? (clue in the name)
On the outer layer of bacteria & allows diffusion of certain molecules in the cell
What is the role of ferritin?
- Stores, transports & releases ions.
What is the main structure in the cytoskeleton (protein)
Microtubules
What is a microtubule made up of?
Alpha & Beta tubulin subunits
Describe the role of microtubules
- Separation of chromosomes during mitosis
- Specific structures at base of cilia & flagella
- Strong yet dynamic
What are enzymes?
Proteins that accelerate the rate of chemical reactions by reducing the activation energy needed.
How does an enzyme-substrate complex form?
An enzyme has an active site that binds the substrate & yields a product.
What differences do proteins have?
- Shape
- Size
- Electrical charges
- Polarity (charge isn’t even ly distributed (no overall charge)
How many amino acids are there?
20
What tens to be the pH of proteins?
7.4
Describe the primary structure of a protein
Order of amino acids
What joins amino acids (residues) together?
Peptide bonds
Describe the formation of a peptide bond
Loss of a water molecule (condensation) causes the formation of a peptide bond between a carbon & nitrogen.
Which way do polypeptide chains read? (Think terminus)
N(Nitrogen) terminus to C (carbon) terminus
What is another word for an unfolded protein?
Denatured
What is another word for a folded protein?
Native
What is sometimes required for a protein to become folded (native)?
Chaperones
What is formed on the backbone of DNA & stabilizes DNA?
Hydrogen bonds
What type of charge is the oxygen end of water?
Negative
What type of charge is the hydrogen end of water?
Positive
What 2 types of secondary structure are there?
- Alpha helix
- Beta sheet
In a alpha helix, what 2 substances does the Hydrogen bond form between?
Nitrogen group (positive) & Carboxyl group (negative)
How many residues are there between the Nitrogen group & Carboxyl group in an alpha helix?
4 residues
What type of structure does an alpha helix have?
Helical (spiral) structure, with side chains on the outside
What is the difference between the H bonds on an alpha helix & a beta sheet?
Beta sheet has bonds with residues further away on the primary sequence (e.g. on different strands)
What determines tertiary structure?
- Non-covalent interactions between side chains
- Electric charges
- Size & shape of side chains also constrains
What are the 2 types of side chains?
- Hydrophilic side chains
- Hydrophobic side chains
What type of bonds can hydrophilic side chains form?
Hydrogen bonds/ionic interactions
What type of chains do hydrophobic side chains form?
Non polar bonds
On what part of the proteins do polar residues end up on?
Outside of the protein
What is the purpose of the polar residues being on the outside of the protein?
Can interact with polar water molecules
Where do the nonpolar residues end up in a protein?
Centre of the proteins
Between what residues do the sulfide bridges form in the tertiary structure?
Cysteine
What is the purpose of the disulfide bonds between the cysteine residues?
To strengthen the tertiary structure
What can control how compact protein domains are?
The flexible regions within proteins
What determines whether a polypeptide has quaternary structure?
The number of subunits it has - 2+ subunits = a complex with quaternary structure.
What is the names given to proteins with 2, 3, & 4 subunits?
Dimer (2), Trimer (3), Tetramer (4)
What are 2 examples of post-translational modification & targeting?
- removal of parts of the sequence
- addition of molecules
What are 3 specific types of post-translation modification?
- Methylation
- Glycosylation
- Ubiquitination
What is methylation?
Addition of methyl group (-CH3) to histones, which control which parts of the genome is expressed.
What is glycosylation?
Addition of various sugars - especially on the cell surface & secreted proteins.
What is ubiquitination?
Addition of 76-aa polypeptide. Ubiquitin polymers mark out a protein for degradation
What is phosphorylation?
Reversible addition of phosphate (PO3) groups
What types of enzymes are used to allow phosphorylation to occur?
Kinases
Why is phosphorylation’s function in post-translational modification?
It is an important way of regulating enzyme function
What are Gregor Mendel’s 3 laws of inheritance?
Segregation - genes come in pairs (individuals only pass on one to offspring.
Independent assortment - different genes are passed on separately.
Dominance - an individual with 2 alleles of a gene will express the dominant form.
What 4 features about DNA was known previously?
There was:
- replication of information
- storage of information
- expression of information
- variation by mutation
What did Sutton-Boveri theory look into?
Chromosomal inheritance
What animal did Sutton do research in to?
Grasshoppers
What animal did Boveri do research into?
Ascaris worms
Why did Sutton-Boveri use grasshoppers & worms?
Because they have chromosomes that are large and few in number.
As a result they noticed that destruction of chromosomes will lead to prevention of the development of an embryo.
What 3 conclusions were drawn about chromosomes from Sutton-Boveri’s experiment?
- chromosomes are required for embryonic development.
- chromosomes carry “factors” (genes)
- chromosomes are linear structures with genes along them
What microorganism can cause pneumonia in humans & in mice?
Streptococcus pneumoniae
What are the 2 strains of neumonia?
S strain & R strain
Describe the 2 differences in the 2 strains of Streptococcus pneumoniae
S strain (pathogenic) - smooth bacteria - polysaccharide coats
R strain (non-pathogenic) - rough bacteria - no polysaccharide coats
How does the polysaccharide coats on the S strain cause it to be virulent?
The polysaccharide coat forms a capsule that protects some strains from the host immune system.
Does dead S bacteria & live R bacteria establish an infection? (WHY)
Yes - as the R cells have undergone a ‘transformation’. The hereditary material has been passed down and the bacteria has changed the genotype.
What was Griffin’s principle?
The transformation principle
What did Avery, MacLeod & McCarthy research?
Research into what molecules caused the transformation seen in Griffin’s experiment
How did Avery & McCarthy find out what molecule was responsible for causing the transformation to occur?
- Systematically destroyed each component of the S strain using enzymes to specifically digest each type of molecule.
- They then recombined the S strain with live R bacteria and watched what happened.
- Whatever compnent led to the S strain not living, meant that it was responsible for it being passed on.
What were the result of Avery & McCarthy’s experiment?
DNA encoding was required to make the polysaccharide coat.
What is the host for bacteriophage T2?
E. coli
What is the life cycle of bacteriophage T2?
- Destruction of host cell’s chromosome.
- Transcription & translation of viral genes & replication
- Assembly of new virus particles
What is the outline of Hershey’s experiment?
- Label bacteriophage DNA or protein with a radioactive isotope.
- Infect unlabeled bacteria with radioactive phage.
- Separate phage ghosts from infected bacteria.
- Test bacteria & phage ghosts for radioactivity.
What molecule does DNA contain that Hershey tested for?
Phosphate
What molecule does protein contain that Hershey tested for?
Sulphur
How did Hershey label the bacteriophages?
Grew bacteriophages in 1 of 2 medias - either containing 32P or 35S.
32P - bacteriophage would contain radioactively labelled DNA.
32S - bacteriophage would contain radioactively labelled protein.
How did Hershey remove the “phage ghosts” from the infected cell?
Agitated them in a blender
What did Hershey do to separate the phage & bacteria?
Centrifuge to separate them. The bacteria was heavier (pellet) and the phage was lighter (supernatant).
Both was tested for radioactivity/
What results were found in Hershey’s experiment?
DNA is being injected which leads to the formation of a new phage.
32P (DNA):
Phage ghost - no label
Bacteria - labelled
35S (protein):
Phage ghost - Label
Bacteria - no label
What is DNA composed of?
- Nucleotides
- Base sugar (deoxyribose)
- Phosphate
What way is DNA read?
5’ to 3’
What carbon (3 or 5) is joined to phosphate?
Carbon 5
What are the 2 purines?
- Adenine
- Guanine
What are the 2 pyramidines?
- Cytosine
- Thymine
What joins the chain of nucleotides?
Covalent bonds - bond created is called phosphodiester bonds.
What was Chargaff’s experiment?
- Isolate the nucleobase components of DNA from a number of species (USING PAPER CHROMATOGRAPHY)
What are Chargaff’s rules?
% Purine = %pyrimidines
%AT = %GC
%A = % T
%G = %C
What is X-ray crystallography structure of DNA?
- X-ray put through a crystalline solid.
- X-ray interacts with the solid.
- They will either be blocked, bounce-off or refract from the solid.
- Because its crystal, shaped-patterns with be formed.
Why is X-ray crystallography useful?
It allows you to gain information about the structure of a molecule.
What does an X pattern in X-ray crystallography signify?
Helical structure
What does a regular pattern in X-ray crystallography signify?
Repeating, even structure
What does the distance between spots mean in X-ray crystallography?
Distance of one turn (3.5nm)
What were the main features of the Watson & Crick Model?
- AT & GC hydrogen bonded pairs
- Antiparallel strands
- Right-handed double helix
- One helical turn every 10.5bp
- Major & minor grooves
How many hydrogen bonds are there between T-A nucleotides?
2
How many hydrogen bonds are there between G-C nucleotides?
3
The presence of which 2 nucleotides makes DNA more stable?
A higher ratio of C-G = more stable DNA
What is the difference between purines & pyrimidines?
Purines (A & G) = 2 carbon rings
Pyrimidines (C & T) = 1 carbon ring
What type of strands does DNA have?
Antiparallel & complementary
What type of helical structure does DNA have?
Double, right-handed helices
How long is one complete turn including a major & minor groove?
10.5 base pairs
What is a chromosome?
A long DNA molecule with part of all the genetic material of an organism.
What are histones?
Packaging proteins involved in chromosomes
How many chromosomes do humans have?
46 (23 pairs)
What is a centromere?
The specialized chromosomal region where spindle microtubules assemble.
Are histones conserved?
Yes
What are telomeres?
Repetitive DNA at the end of linear chromosomes
Describe prokaryotic genomes
Singular, circular chromosome (usually a few million bp)
How can plasmids be passed between cells?
Conjugation
What is an example of an advantageous gene that a plasmid could have?
Antibiotic resistance
What is a difference between DNA-binding proteins?
- Some have a general affinity for DNA, whereas some are sequence-specific.
- Some prefer single-stranded, whereas some prefer double-stranded DNA.
What are the 3 roles of DNA-binding proteins?
- Regulate gene expression
- Cut DNA at specific sequences
- Protect DNA
What are transcriptional regulators?
Proteins that bind regulatory sequences near the promotors of genes, to either stimulate or block transcription. This can bend DNA into a favorable or unfavorable shape.
What is an example of a transcriptional regulator?
Lac operon - E.coli (contains enzymes for breaking down lactose sugar)
How does the Lac operon regulate transcription?
- Lac repressor binds to DNA & blocks transcription (when lactose is absent)
- Catabolic activator protein binds to DNA & increases transcription (when glucose is absent).
What are restriction endonucleases?
Enzymes that cut DNA at specific, normally palindromic sequences 6-10bp.
Where do restriction endonucleases originate?
In bacteria, to restrict the action of viruses.
What were the 3 possible models for DNA replication?
- conservative
- semi-conservative
- dispersive
What did Meselson aim to find out?
What mechanism is used for DNA replication:
- conservative
- semi-conservative
- dispersive
How Meselson research into how DNA replication occurs?
- Used isotopes of nitrogen in DNA.
- Centrifuged caesium chloride.
- Separated the DNA by molecular weight.
- E.coli is grown in 15N (nitrogen) then transferred to 14N medium.
- It is then separated by heavy & light molecules by ultracentrifugation.
What type of replication was discounted as a result of Meselson’s experiment?
Conservative
Describe what semi-conserved DNA looks like
- One original strand
- One new strand
What type of direction are replication forks?
BIdirectional
Describe the enzymatic activities neccesary for DNA replication
- Primase
- DNA polymerase
- DNA ligase (Okazaki fragments)
- Single-strand binding protein
- Helicase
- Topoisomerase
What is the role of primase?
Enzyme that synthesizes RNA sequences called primers
What is the role of DNA polymerase
- Add nucleotides on at a time, in a 5’ to 3’ direction
What is the role of DNA ligase?
Enzyme that facilitates the joining of DNA strands together by catalyzing the formation of phosphodiester bond
What is single-strand binding protein?
SSB binds to separated strands, separating them.
What is the role of DNA helicase?
Used to unwind DNA (break hydrogen bonds)
What is the role of topoisomerase
Relieves pressure from overwinding around the replication bubble, by making & revealing breaks in the DNA.
Describe the leading strand
5’ - 3’ DNA synthesis points towards the replication fork can process continuously.
Describe the lagging strand
5’ - 3’ DNA synthesis points away from the replication fork and therefore is discontinuous (primed numerous times).
What is Okazaki fragments
The pieces of DNA that are stuck together to make up the lagging strand of replication.
Describe semi-continuous replication
Continuous replication of the leading strand & discontinuous replication of the lagging strand
What is the problem with telomeres?
Primer removal at the end of chromosomes leave a gap that can’t be filled in. This means a piece is lost from the end of the chromosomes.
What enzyme can replenish telomeres from an RNA template in some cell types?
Telomerase
