Macromolecules (nucleic acid) Flashcards
1
Q
Structure of nucleotide
A
- phosphate grp, 5-carbon sugar and nitrogenous base
- P grp and sugar bonded via phosphoester bond
- sugar and base bonded via glycosidic bond
2
Q
different types of nitrogenous base
A
- Purine (BIGGER): Adenine, Guanine
- Pyrimidine (SMALLER): Thymine/Uracil, Cytosine
3
Q
Difference between sugar in DNA and RNA
A
- 2’ C in RNA is OH, as compared to DNA which has H as 2’ C
- partial (-) charge in OH repels partial (-) charge of P
- thus preventing RNA chain from coiling in as tight a helix as in DNA
- thus RNA is more susceptible to chemical and enzyme degradation
4
Q
How nucleotides are joined tgt to form polynucleotide
A
via condensation reaction
between 5’-phosphate grp of one nucleotide
and 3’-OH grp of another
to form phosphodiester bond
5
Q
Structure of DNA
A
- consists of 2 polynucleotide strands/chains
(- each strand forms a right-handed helix) - which coil around each other to form a double helix
- one full DNA helix turn comprises 10 base pairs
- there is presence of major and minor groves along the length of DNA
6
Q
Reasons DNA is a device for stable storage of genetic information (resistant to mutations)
A
- extensive H bonds between base pairs
- hydrophobic interactions between stacked base pairs
=> stabilise the structure of the double helix - hydrophobic nitrogenous bases safely tucked inside double helix (while hydrophilic phosphate grps are projected outside)
/ exposure to outside influences of only sugar-phosphate bb
=> protection of nitrogenous bases from degradation - complementary base pairs between 2 strands
=> each strand serves a template to repair any DNA damage - (Eukaryotes) double helix tightly wound around histones to form nucleosome
-> folded into highly compact chromosome
=> DNA protected from thermal and physical damage
7
Q
reasons for complementary base pairing between DNA strands
A
- steric restrictions
- dna has regular helical structure
-> double helix has uniform diameter of 2nm
-> must always pair 1 purine to 1 pyrimidine - H bond factors
- each nitrogenous base has side grps that can form H bonds with its appropriate partners
- A with T (2 bonds),
C with G (3 bonds)
8
Q
significance of complementary base pairing between DNA strands
A
- maintains integrity of DNA
- since base seq on 1 strand dictates base seq of other strand,
- thus making genetic info redundant - DNA rep
- where both parental DNA strands separate and act as templates for synthesis of daughter DNA strands
9
Q
gen 1 means after 1st replication
evidence for semi-conservative dna rep
A
- via density-gradient centrifugation
- gen 1: 100% of DNA mol are hybrid, resulting in only 1 band
- gen 2: 50% of DNA mol are hybrid and 50% are light, resulting in 2 separate bands
10
Q
gen 1 means after 1st replication
evidence for conservative rep
A
- via density-gradient dna centrifugation
- gen 1: both light and heavy DNA molecules, resulting in 2 separate bands
11
Q
gen 1 means after 1st replication
evidence for dispersive dna rep
A
- via density-gradient dna centrifugation
- gen 2: only hybrid DNA molecules present, resulting in only 1 band
12
Q
1st level of condensation of packaging of DNA in cell
A
- DNA is coiled around histone proteins, forming nucleosome core
- histones have (+)-charged residues, which form ionic bonds with (-)-charged sugar-phosphate bb of DNA
- nucleosome cores, together with linker DNA, forms 10nm chromatin fibre
13
Q
2nd level of condensation of packaging of DNA in cell
A
- DNA is further coiled to produce 30-nm solenoid
- histone H1 and linker DNA are involved in coiling
14
Q
3rd level of condensation of packaging of DNA in cell
A
- scaffold proteins are involved
- in condensing the 30-nm solenoid to form looped domains
- which further coil to produce the 1400-nm condensed chromosome
15
Q
Advantages of chromatin being dynamic molecule
A
- When condensed …
- more compact to fit into the nucleus
- has ability to save space
- helps to maintain the integrity of DNA - regulation of gene accessibility
- ability to regulate gene accessibility
- leading to differential gene expression
- e.g. when chromatin is organised as euchromatin (diffused form), available for transcription
- e.g. when chromatin is organised as heterochromatin (highly condensed form), transcriptionally inactive - regulation of cell cycle
- condensation of chromatin to discret chromosomes so that DNA does not get entangles and break during separation at anaphase
- uncondensed chromatin allows for ease of DNA rep during S-phase of interphase
16
Q
DNA methylation (control of transcription at chromatin level)
A
- addition of methyl grps to cytosine nucleotides in CpG dinucleotides in promoter region of genes
- catalysed by DNA methyltransferases
- thus changing 3D conformation of DNA
- and preventing the binding of transcription factors to the promoter
- thus preventing the formation of TIC
-> preventing transcription initiation - methylated DNA also serves as recognition signals to recruit histone deacetylases (HDACs)
17
Q
Histone deacetylation (control of transcription at chromatin level)
A
- removal of acetyl grps of lysine residues in in histone tails
- catalysed by histone deacetylases (HDACs)
- thus lysine residues regain their (+) charges, resulting in an increase in the affinity of the histone complex for DNA
- resulting in chromatin becoming more compact
- and preventing the binding of transcription factors to promoter
-> preventing formation of TIC
-> preventing transcription initiation
18
Q
silencer control element (control of transcription at transcription level)
A
- specific transcription factors known as repressor binds to it
- elaboration 1 (may or may not be needed):
- EITHER competitive binding with activator
- where binding of repressor to silencer region prevents binding of activator to enhancer region as repressor and activator competes for binding at the same DNA regulatory seq
- OR interaction with activation domain of bound activator
- where repressor binds to activator and prevents it from interaction with GTFs
- OR interaction with GTFs
- where repressor interacts with GTFs to prevent assembly of TIC
- results in decreased affinity of general transcription factors and RNA pol for promoter
-> prevention of formation of TIC
-> thus decreasing rate of transcription
- EITHER competitive binding with activator
- elaboration 2 (may or may not be needed):
- repressor recruits histone decacetylase which removes acetyl groups from lysine R grps of histones
OR recruits histone methyltransferases which add methyl groups to histones - thus promoting chromatin condensation
- repressor recruits histone decacetylase which removes acetyl groups from lysine R grps of histones
19
Q
why different people have different phenotypes
A
- even if genes (i.e. DNA seq) are the same, different gene expression
-> different genes being switched on
-> different gens being expressed
-> different proteins being produced at diff stages
-> leading to diff phenotypes - different environmental factors
- like diet, where consumption of different quality diets may result in differences in weight and height
- or lifestyle, where exposure to mutagens may lead to increase in gene mutations / risk for cancer
- or exposure to sunlight, where difference in production of melanin leads to difference in skin colour
20
Q
Reason it is necessary for 2 DNA pol enzymes to work together in a protein complex during DNA rep
A
- DNA pol is only able to synthesise from 5’ -> 3’ direction
- antiparallel nature of DNA strands, hence requiring 2 DNA pol to synthesise in the same direction
- 2 strands of DNA, thus require 2 DNA pol to increase efficiency
21
Q
significance of specific combinations of control elements and transcription factors in regulating gene expression
A
- allows for regulation of gene expression at a precise timing of development
(temporal control) - allows for regulation of gene expression in a specific cell type
(spatial control) - allows for correct amt of proteins/gene pdts produced
22
Q
secondary structure of tRNA
A
- 3 loops, held by complementary base pairing within the single-stranded molecule
- where 1 loop is the anticodon
- which consists of 3 bases
- and binds to specific mRNA codon via complementary base pairing
- also consists of the 3’ CCA stem (the part that is sticking out, opp the anticodon loop)
- which is the attachment site for a specific amino acid
23
Q
how tRNA acts as an adaptor molecule for translation
A
- translates base/nucleotide seq in mRNA into amino acid seq in polypeptide by …
- 3’ CCA stem binds via ester bond to specific amino acid
- decided by the anticodon on tRNA
- anticodon on tRNA then forms complementary bases pairs with codon on mRNA
- tRNA then binds to the A and P site to bring the amino acid in close proximity to the growing polypeptide
24
Q
function of aminoacyl-tRNA synthetase
A
- catalyses formation of ester linkage between 3’ CCA stem and amino acid
- which requires the hydrolysis of ATP
- does so by having an active site that is
complementary to the specific anticodon seq of tRNA
and complementary to the specific 3d conformation of specific amino acid
25
reason each amino acid can be carried by more than 1 tRNA
active site of aminoacyl-tRNA synthetase being complementary to the same amino acid but complementary to different anticodons
26
enhancer control element (control of transcription at transcriptional level)
- specific transcription factors known as **activators** bind to it
- thus recruiting **DNA-bending proteins** causes looping of DNA, (thus bringing activator closer to promoter)
- activator then interact with mediator protein, resulting in
a. **increased affinity of TFIID and RNA pol for promoter** to form** stable TIC**
b. facilitation of proper positioning of TIC
=> **rate of transcription increases**
- may also recruit **histone acetylase** which add acetyl groups to lysine R groups of histone
OR recruit chromatin-remodeling complexes
- thus resulting in **looser packing of chromatin **
27
role of promoter and how it influences transcription
- serves as recognition site for binding of general transcription factors and RNA pol
- has critical element TATA box, to which general transcription factors bind to,
and thus mediate binding of RNA pol to promoter to form TIC
- initiate transcription
28
differences between chromosome and chromatin
- chromosome: highly condensed form of DNA
chromatin: loosely-coiled and decondensed form of DNA
- chromosome: transcriptionally inactive
chromatin: transcriptionally active
- chromosome: has 2 sister chromatids that are visible
chromatin: do not have visible sister chromatids
