L1: Nucleic Acids & Chemical Bonds Flashcards
(50 cards)
1
Q
what are the two broad areas of molecular biology
A
- Fundamental principles of the structure and function of DNA, RNA and protein
- Application of molecular techniques to interrogate problems in diverse fields
2
Q
Gregor Mendel
A
described genes as “hereditary determinants” but did not know what DNA was
3
Q
how did scientists answer “what are genes made of?”
A
- 2 key experiments
1. F. Griffith (1928): pneumonia-causing bacteria
2. Hershey and Chase (1952): bacteriophage T2
4
Q
what are genes made of? - F. Griffith
A
- looked at Streptococcus pneumonia
- that bacteria had two strains: rough colonies (non-pathogenic) and smooth colonies (pathogenic)
5
Q
what are genes made of? - F. Griffith experiments
A
- injected a mouse with the rough strain
- injected a mouth with the smooth strain
- heat-killed the smooth strain and injected it into a mouse
- mixed the rough strain and the heat-killed smooth strain into a mouse
6
Q
what are genes made of? - F. Griffith results
A
- rough strain: mouse was fine
- smooth strain: mouse died
- heat-killed smooth strain: mouse was fine
- mix of heat-killed smooth strain and rough strain: mouse died
7
Q
what are genes made of? - F. Griffith explanation for results
A
- in the experiment with the rough and heat-killed smooth strain, there is something at the protein level that made the rough strain turn pathogenic
- Griffith termed the cellular component responsible as “Transforming Principle”
- Griffith believed to be genetic information (found out to be DNA)
8
Q
what are genes made of?: F. Griffith - why did the rough strain become pathogenic
A
- the smooth strain has a capsule protecting it
- once heat-killed, the capsule gene is fragmented
- the rough strain then takes in the gene and gets the capsule to protect it
9
Q
what are genes made of? - Hershey-Chase experiment
A
- they determined whether genes were comprised of DNA or protein
- used bacterium E. coli and the infecting virus T2 (only has DNA and protein)
10
Q
what are genes made of?: Hershey-Chase experiment - how the experiment was conducted
A
- label viruses
- infect bacteria
- agitate cultures
- centrifuge results
11
Q
what are genes made of?: Hershey-Chase experiment - label viruses
A
- they grew the virus in the presence of one of two types of radioactive isotopes
- 32P labels DNA
- 35S labels protein
12
Q
what are genes made of?: Hershey-Chase experiment - agitate cultures
A
- they knew that the material that the virus injected into the cell was necessary for virus replication
- used agitation to get rid of anything that was not injected into the cells
13
Q
what are genes made of?: Hershey-Chase experiment - centrifuge solutions
A
- viral capsids (protein) in solution
- genes/DNA in pellet
14
Q
what are genes made of?: Hershey-Chase experiment - what does the centrifuge solution imply
A
- the viral DNA is important since its inside the cells
- the protein is not genetic material since it is not in the cell
15
Q
structure of DNA - explain what was known about the structure of DNA in the 1950s
A
- primary structure of DNA is known
- secondary structure is unknown
16
Q
structure of DNA - what is “Photograph 51”
A
- it is an x-ray diffraction pattern taken by Rosalind Franklin
- it showed that DNA structure was helical and composed of two strands
17
Q
structure of DNA - Watson and Crick
A
- established that
1. DNA is a double helix
2. DNA strands are antiparallel
3. purines (A and G, have 2 rings) pair with pyrimidines (C and U/T, have 1 ring)
18
Q
structure of DNA : Watson and Crick - what does it mean to be antiparallel
A
- hydrophilic sugar-phosphate backbone faces exterior
- nitrogenous bases face interior as pairs
- stabilized by hydrogen bonding and hydrophobic interactions
19
Q
structure of DNA: Watson and Crick - what did the secondary structure show
A
- a mechanism of DNA replication
- first strand dictates the precise
nucleotide sequence of the other (semiconservative replication)
20
Q
structure of DNA - what is Chargaff’s rules
A
- number of purines = number of pyrimidines
- total A = total T, total C = total G
21
Q
DNA replication - A. Kornberg
A
- identified DNA polymerase I
- it only works in the presence of a template
- it only synthesizes in the 5’-to-3’ direction
22
Q
mode of replication - three hypotheses
A
- semiconservative replication
- conservative replication
- dispersive replication
23
Q
mode of replication: three hypotheses - semiconservative replication
A
- parental strands separate and each used as template for the synthesis of a new strand
- result is double stranded molecule with one old (parental) and one new DNA strand
24
Q
mode of replication: three hypotheses - conservative replication
A
- parental strands serve as template for an entirely new double helix
- result is original double helix and an entirely newly synthesized double helix
25
mode of replication: three hypotheses - dispersive replication
- template double helix is broken down into small pieces, DNA replicates, then pieces are brought back together again
- result is two DNA double helices each with new and old segments mixed together
26
mode of replication - Meselson-Stahl experiment
- determined which hypothesis was correct
- they grew *E. coli* in the presence of "heavy" nitrogen (15N) to label bacterial DNA
- after many generations (bacterial cell divisions), they moved bacteria onto media with normal nitrogen (14N)
- isolated DNA from the cells after 1 or 2 new cell divisions and separated it based on density
27
mode of replication: Meselson-Stahl experiment - prediction for gen 0
only 15N band for all hypotheses
28
mode of replication: Meselson-Stahl experiment - prediction for gen 1
- semiconservative: two hybrid bands
- conservative: one 15N band and one 14N band
- dispersive: two hybrid bands
29
mode of replication: Meselson-Stahl experiment - prediction for gen 2
- semiconservative: one hybrid, one 14N
- conservative: one 15N, one 14N
- dispersive: both hybrid
30
mode of replication: Meselson-Stahl experiment - results for all gens
- gen 0: only 15N
- gen 1: hybrids (can rule out conservative)
- gen 2: hybrid and 14N (confirms semiconservative)
31
mode of replication: Meselson-Stahl experiment - prediction for gen 3
14N band becomes brighter and hybrid band becomes diluted out
32
DNA vs RNA
- DNA: (1) has a thymine, (2) double stranded, (3)no hydroxyl group at 2' position but has one at 3' position
- RNA: (1) has a uracil, (2) single stranded, (3) hydroxyl group at 2' position and 3'
33
Francis Crick
1. determined DNA secondary structure along with James Watson
2. proposed central dogma of biology: DNA -(transcription)-> DNA -(translation)-> protein
3. developed adaptor hypothesis
34
Francis Crick - adaptor hypothesis
- prediction that an intermediate molecule was needed between mRNA and protein synthesis
- bc chemical groups of DNA bases should interact w hydrophilic surfaces but many amino acids have hydrophobic side chains
- adaptor = tRNA
35
Translation
- read information from mRNA using tRNA to bring codons together to form a polypeptide
- ribosome is needed to catalyze this reaction
36
define chemical bond
attractive force that holds atoms together
37
example of chemical bonds
- covalent bonds
- hydrogen, hydrophobic, ionic bonds
38
chemical bonds - covalent bonds
- strong bond
- do not come apart at physiological temperatures
- electrons are shared between atoms
39
chemical bonds - hydrogen, hydrophobic, ionic bonds
- weak bonds
- exist transiently, but can be stabilized in large numbers
- based on attractions between electrical charges
40
weak chemical bonds - hydrogen bond
- forms between positively charged H atom and a negatively charged atom (usually O or N)
- between nitrogen bases so DNA can be pulled apart for replication
- meaningful if you create a ton of them
- Electrons not always shared equally in covalent bond - not full charges
41
weak chemical bonds: hydrogen bond - how are electrons not shared equally
- atoms with high electronegativity:
1. holds electrons more tightly and is partially negative (δ–)
2. the other atom will become partially positive (δ+)
42
weak chemical bonds - electronegativity
- O > N > C ~/= H
- oxygen is the most electronegative, followed by nitrogen, then carbon which is approximately equal to hydrogen
43
weak chemical bonds: electronegativity - polar covalent
electrons are asymmetrically shared
44
weak chemical bonds: electronegativity - non-polar covalent
- electrons are shared equally
- no partial charges
45
weak chemical bonds - hydrophobic interactions
- not a true “bond”
- nonpolar groups aggregate to prevent contact with water
46
weak chemical bonds: hydrophobic bonds - nonpolar vs polar molecules
- nonpolar molecules have no charge and are hydrophobic
- polar molecules have full or partial charges and are hydrophilic
47
weak chemical bonds - ionic bonds
electrostatic attraction between two oppositely charged groups (full charge)
48
chemical bonds - high energy bonds
- created through polymerization (a monomer turning into a polymer)
- it's facilitated by an enzyme and energy is released
49
chemical bonds: high energy bonds - facilitated by an enzyme
speed chemical reaction rates by lowering activation energies of molecular rearrangements
50
chemical bonds: high energy bonds - energy is released
- monomers are converted into high energy “activated” precursors prior to polymerization
- these precursors exhibit high energy bonds that yield energy when cleaved
