week 7 nucleic acids and protein synthesis Flashcards
DNA
deoxyribonucleic acid
RNA
ribonucleic acid
Common nucleotide structure?
1-3 phosphate groups
pentose (5 carbon) sugar
nitrogenous base (pyrimidine or purine)
1 phosphate group
Monophosphate (AMP)
2 phosphate groups
Diphosphate (ADP)
3 phosphate groups
Triphosphate (ATP)
Ribose (pentose sugar)
RNA only
2’ carbon hydroxyl group (OH)
Deoxyribose (pentose sugar)
DNA only
2’ carbon (H)
Purines
Adenine (A)
Guanine (G)
Pyrimidines
Uracil (U) - in RNA only
Thymine (T) - in DNA only
Cytosine (C)
Nucleoside
Nucleotide structure excluding the phosphate groups
Nucleotide functions (as monomers)
-building blocks of nucleic acids (RNA and DNA)
-Energy carriers (cell energy currency), carrying high-energy bonds between phosphate groups
-Form coenzymes (essential for enzymatic activity)
-Intracellular signalling molecules
Nucleic acid strand / backbone
In RNA/DNA, nucleotides are covalently linked to form a polynucleotide strand (backbone)
Phosphodiester bonds
Linking 5’ phosphate of one nucleotide to the 3’ OH of the next, creating a 3’-to-5’ directionality
Human cells
Nucleic acids of human cells have 5’ end and a 3’ end e.g., 5’-TCG-3’
Prokaryotic cells
5’ and 3’ ends of DNA strands are linked to form circular DNA, which is also found in plasmids and mitochondrial DNA
Hydrogen bonding between nucleotides
Two DNA strands are held together by hydrogen bonds between complementary base pairs in double - stranded nucleic acids
Purine-pyrimidine pairing
A with T (DNA) -> 2 hydrogen bonds
A with U (RNA)
C with G -> 3 hydrogen bonds, more stable than AT pairs
DNA double helix
The complementary base pairing cause the two DNA strands to twist around each other in helical manner -> stable DNA double helix
-Antiparallel (hains run in opposite directions)
DNA in B-form
Has two helical grooves of different widths, providing binding sites for proteins/drugs
Major
Wider
Minor
Narrower
RNA
Usually single stranded ssRNA in human cells
dsRNA (double stranded) is possible in nature - many viruses contain dsRNA chromosomes.
Immune cells recognise dsRNA as a viral signature, triggering antiviral responses
DNA denaturation
Separation of the DNA double strands into single strands
DNA renaturation
Restores DNA double helices (nucleotide pairs re-formed) When conditions are reversed, H bonds can be reformed
Conditions for DNA denaturation
High temperatures (90-100 degrees C) break H bonds between complementary nucleotide pairs. Higher G-C content increases DNA stability and so more energy needed
Gemome
Contains the genetic instructions guiding a cell’s survival and function
- Human genome has approx. 25,000 genes
DNA provides biological messages through the precise sequence of nucleotides
Gene
-A DNA segment that encode specific, inheritable traits
-Nucleotide sequence in genes determine the specific amino acid sequence of certain
proteins through the genetic code (DNA > RNA > PROTEINS)
Pharmacogenomics
Variations in individuals’ genes can influence the response to drugs
Eukaryotic DNA
-Nuclear DNA (nucleus)
-Mitochondrial DNA (mitochondria)
Nuclear DNA
DNA molecules are packaged
with histones into chromatin
Nucleosomes
Chromatin units
Eukaryotic Chromosomes
Linear DNA stored in the nucleus, usually in the form of chromatin. In dividing cells (after DNA duplication) chromatin is further condensed to the X shaped chromosomes
Karyotype
Representation of an individuals set of chromosomes
Human Chromosomes
Number, size of chromosomes is species-specific
Somatic cells
Human (somatic) cells have 46 chromosomes, 23 pairs -> in 22 pairs of homologous autosomal and a pair of sex chromosomes (XX/XY )
Gametes
(sperm and egg cells) have one set of 23 chromosomes (haploid cells)
Red blood cells
No DNA
DNA replication
DNA replication is the process by which DNA makes a copy of itself, before cell divisions
-Each chromosome will result in 2 identical DNA
-Copied DNA is segregated into daughter cells
-Occurs in the nucleus during the S phase of interphase
Mutations in DNA replication
DNA replicates rapidly and precisely to avoid errors (mutations)
-minimises mutations that can lead to disease
-Mutations in microorganisms can lead drug resistance
SEMI-conservative process
DNA replication is a SEMI-conservative process, It produces two copies of DNA, each containing one original strand and one new one
4 steps of DNA replication
- Replication Fork Formation
- Initiation
- Polymerase elongation
- Termination
- Replication fork formation
-DNA replication starts at a sequences called
origin of replication (rich in A - T)
-At each, DNA is denatured by initiator proteins
-Helicase enzymes unwind/unzip the DNA double strands bidirectionally by breaking H-
bonds, creating two Y-shaped replication forks
- Initiation
-DNA polymerase requires an RNA primer, created
by primase enzyme, to initiate synthesis
-DNA polymerase attaches to the 3’ end of the primer
and synthesises a new DNA strand in the 5’->3’
direction, using the parental strand as a template
-DNA polymerase forms phosphodiester bonds
between nucleotides, extending the new DNA strands
-The process requires deoxynucleotide triphosphates
(dNTPs) to drive the reaction
- Polymerase elongation
-The replication fork is asymmetrical (antiparallel strands)
-Replication of leading strand is continuous, same direction as the growing replication fork
-Replication of the lagging strand is discontinuous
▪ It requires many RNA primers
▪ Synthesis in short DNA fragments (Okazaki
fragments), each initiated by a new RNA primer
- Termination
-A nuclease degrades RNA primers
-The gaps are filled by DNA polymerase
-The enzyme DNA ligase joins adjacent Okazaki
fragments -> DNA Replication is complete
Proofreading activity of DNA polymerase
DNA polymerase introduces approx. 1 error/1010 nucleotide copied
-DNA polymerase has proofreading activity to check &
correct base-pairing errors
▪ When a mismatch occurs, DNA polymerase removes the
incorrect nucleotide and replaces it with the correct one.
-Any uncorrected mistakes, can be fixed by many DNA
repair mechanisms available in human cells
▪ Inactivation of DNA repair pathways is common in tumours
DNA polymerase summary
-A complex of polymerases
-Incorporates nucleotides to the growing DNA strands by forming phosphodiester bonds
-One nucleotide at a time (triphosphate form)
Helicase summary
-Unwinds parental double helix
Ligase summary
-Joins Okazaki fragments and seals other breaks in sugar-phosphate backbone
Other important enzymes
Primase
-> Synthesise RNA primers for DNA polymerase to start the polymerisation process
DNA Topoisomerase
-> Unravel twists in DNA that occur as a result of DNA replication
