Unit 7: Nucleic Acids Flashcards
what is DNA
genetic material of all living organisms
(deoxyribose nucleic acid)
polymer made of monomers called nucleotides
Some viruses use RNA as their genetic material but viruses are not considered to be living.
what are the components of a nucleotide?
pentose sugar, phosphate group and nitrogenous base
see A1.2.2 on iPad
sugar-phosphate bonding and the sugar-phosphate backbone of DNA and RNA
see A1.2.3 on iPad for structure
Covalent bonds can be specified = phosphodiester bonds
this forms a strong sugar/phosphate backbone
nitrogenous bases within dna and rna
DNA:
adenine, thymine, cytosine, guanine
RNA:
adenine, uracil, cytosine, guanine
Purines: Adenine and Guanine
Pyrimidines: Cytosine, Uracil, Thymine
what is RNA
single strand of nucleotides, formed by condensation (removal of water to create a bond) of nucleotide monomers
see A1.2.5 on iPad for structure
what is DNA
a double helix made of two antiparallel strands of nucleotides with two strands linked by hydrogen bonding between complementary base pairs
antiparallel = parallel in opposite directions
see A1.2.6 on iPad for structure
differences between DNA and RNA
similarities:
polymer of nucleotide
cytosine + guanine
differences:
DNA: double stranded, deoxyribose sugar, adenine + thymine
RNA: single stranded, ribose sugar, adenine + uracil
what is the role of complementary base pairing in allowing genetic info to be replicated and expressed
DNA replication is semi conservative (each resulting copy is made of one parent strand and one new strand.
Parent strands are used as templates to make the new strands
see A1.2.8 on iPad for structure
gene expression: using codes in DNA to synthesise protein
why is there so much diversity of possible DNA base sequences?
DNA molecules vary in length
many possibilities for unique sequences
DNA is only 2nm in diameter, so cells can store long lengths of DNA
limitless capacity of DNA for storing information
what is the evidence of universal common ancestry
same codons on RNA code for the same amino acids in almost every organism = universal genetic code
directionality of RNA and DNA
carbons are numbered
(see A1.2.11)
New nucleotides can only be added to the 3’ end
purine to pyrimidine bonding as a component of DNA helix stability
each complementary pair has 1 purine and 1 pyrimidine
all pairs are equal length, increasing stability
structure of a nucleosome
DNA wrapped twice around a core of 8 histone proteins (see A1.2.13)
additional h1 histone stabilises the nucleosome and helps condense DNA
eukaryotes have nucleosomes, prokaryotes have naked DNA
hershey chase experiment for DNA as genetic material
which was responsible for transmitting hereditary info: DNA or proteins?
Viruses are made of DNA and protein
Viruses inject their host with their genetic material
grew 2 types of bacteriophage to identify genetic material, with different radioactive cultures.
1. ^35S (sulfur) adheres to proteins
2. ^32P (phosphorus) adheres to DNA
then allowed them to infect cells
Spun the cells in a centrifuge
cells will fall to the bottom, virus particles will remain outside
cells contained 32P –> DNA
chargaff’s experiment
would expect all 4 nucleotides to have equal amounts = tetranucleotide hypothesis (that DNA consists of a repeating sequence of 4 nucleotides in equal amounts and proteins were the genetic material)
but actually, there were different amounts
there is variation across all life forms (falsification of the tetranucleotide hypothesis)
complementary base pairings = A&T are equal, C&G are equal
what is dna replication
production of exact copies of DNA with identical base sequences
reproduction: passing hereditary info to offspring
growth and repair: cell division to create new cells (requires replication of DNA
semi-conservative replication and role of complimentary base pairing
semi-conservative = one strand is original, one new strand
this is to prevent errors
role of helicase and DNA polymerase in DNA replication
helicase: enzyme that breaks the hydrogen bonds between bases to separate the parent strands and unwind the double helix
(unzipping the genes lol)
DNA polymerase: adds free nucleotides to the new strand, creating a bond between the phosphate of the free nucleotide and the sugar of the last nucleotide on the strand
how to amplify and separate DNA?
PCR (polymerase chain reaction)
- amplifies DNA
- heat breaks the hydrogen bonds of DNA template and separates into single strands
- add in primer (to signal where to start copying)
- add in Taq polymerase (heat-tolerant) (to insert nucleotides and extend the new strand)
gel electrophoresis
- separates DNA molecules by length
- put DNA fragments into one end of porous gel
- apply electricity (neg. electrode at DNA end)
- DNA is also negative, so repelling force moves DNA through the gel
- shorter fragments go farther
what are some applications of PCR and gel electrophoresis
paternity testing (gel electrophoresis), forensic investigations, coronavirus testing
replication fork, leading and lagging strand
replication fork = site of separation when helicase separates DNA strands
leading strand:
- original strand starts at 3’, so new strand goes from 5’ to 3’ towards the fork
lagging strand:
- original strand starts at 5’, so short segments of nucleotides are added in the 5’3’ away from the fork (Okazaki fragments)
functions of DNA primase, DNA polymerase I, DNA polymerase III, and DNA ligase in replication
DNA primase: lays down RNA primer
DNA polymerase I: removes RNA primers and replaces with correct DNA nucleotides
DNA polymerase III: adds new nucleotides in the 5’ to 3’ direction and attaches the nucleotides together & proof-reading
DNA ligase: connects Okazaki fragments
explain DNA proof-reading
using DNA polymerase III
errors result in mutations
replaces incorrect nucleotide with correct one
how does transcription work?
using a strand of DNA as a template to synthesise a strand of RNA
RNA polymerase: enzyme that separates the strands, adds RNA nucleotides and creates the sugar phosphate bonds to create a continuous strand
RNA has uracil instead of thymine
role of hydrogen bonding and complementary base pairing in transcription
sense strand: contains the genetic information to be copied
antisense strand: the strand used as a template for transcription
complementary base pairing rules means that the RNA produced is an exact copy of the gene
hydrogen bonds can only form between complementary bases, ensuring that correct sequence of bases is maintained
stability of DNA templates
stable when strands are together, preventing changes in bases
when strands are temporarily separated, mutations can occur
transcription as a process required for the expression of genes
gene expression: protein production using the sequence of bases in a gene
only the genes that need to be expressed will be transcribed
what is translation
mRNA goes from DNA to polypeptide in the cytoplasm on a ribosome
roles of mRNA, ribosomes and tRNA in translation
codon: groups of 3 bases on the mRNA
there is a start codon and a stop codon on each strand of mRNA
tRNA - transfer RNA (transfers amino acids to ribosomes)
- has an anticodon and a specific amino acid
- anticodon that is complimentary to a specific mRNA codon
bottom, smaller subunit binds to the mRNA
large subunit binds to tRNA and also is a catalytic site to create peptide bonds
see D1.2.6 for structure
process of translation
- mRNA attaches to ribosome
- tRNA with anticodon complementary to the start codon attaches
- the ribosome slides to the next codon and the next tRNA attaches
- amino acids from tRNA are joined together (peptide bonds)
- continues until a stop codon is reached
- disassembly (small subunit of ribosome will detach, mRNA detach, polypeptide chain will detach)
complementary base pairing between tRNA and mRNA
codon = 3 bases
anti codon = complimentary to codon, also 3 bases
features of genetic code
code is read in triplets, allowing for 64 combos of the four bases
- the code is universal. the same codons make the same amino acids in all organisms and viruses (GOOD)
- degenerate: different codons can code for the same amino acid (GOOD)
Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide bonding to the growing polypeptide chain
- A site (right side of large subunit of ribosome): initial binding site for tRNA, peptide bond is formed between the amino acid on the tRNA and the polypeptide chain
- P site (middle of large subunit of ribosome): “empty” TRNA moves here as the ribosome slides down mRNA and the peptide chain is passed to the next tRNA that has entered A site
- E site (left of large subunit of ribosome): exit site
this occurs repeatedly, leading to the elongation of the polypeptide chain
mutations that change protein structure
mutation = change to the base sequence of a gene
base substitution: change to one base in a gene
- might change the amino acid
- might change the overall protein structure
directionality of transcription and translation
both in a 5’ to 3’ direction
transcription = new RNA nucleotides can only be added to 3’ end
translation = ribosome moves down the mRNA starting from its 5’ end and towards the 3’ end
initiation of transcription at the promoter
promoter = section of DNA that serves as a binding sit for RNA polymerase or other proteins that control transcription
transcription factors = molecules that regulate gene expression by promoting/inhibiting transcription
compare promoters and start codons
both nucleotide sequences important for gene expression
promoters on DNA, start codons on RNA
promoters for transcription, start codons for translation
non-coding sequences in DNA
base sequences that do not code for polypeptides, so are not genes
i.e.
- base sequences that produce tRNA or rRNA
- promoters
- structural DNA at the end of chromosomes (telomeres)
- introns (edited out after transcription
post transcriptional modification in eukaryotic cells
modification occurs in nucleus (hence only eukaryotes, prokaryotes have no true nucleus)
allows for many diff versions of a protein to be made using 1 gene
by eliminating different sections of the mRNA, can make different versions of the mRNA which will be translated into different amino acid sequences, even though they were all transcribed from the same gene
production of mature mRNA
1. introns are removed and exons are spliced together (because the mRNA has to EXIT the nucleus, but only the EXons can)
2. addition of a 5’ cap on the 5’ carbon side, and a poly-A tail on the 3’ end (a very long stream of nucleotides that all have adenine as their nitrogenous base)
alternative splicing of exons to produce variants of a protein from a single gene
removing diff introns to produce diff versions of protein from a single gene
initiation of translation
- tRNA activation
tRNA activating enzyme: an enzyme attaches the correct amino acid to the tRNA
–> aka aminoacyl-tRNA synthetase
diff enzymes for each tRNA and amino acid (requires ATP)
tRNA has 5’ and 3’ end, amino acid will attach to 3’ end using the enzyme + ATP - tRNA carrying methionine attaches to the small subunit of the ribosome
- small subunit slides down mRNA (5’ to 3’) until the tRNA anticodon binds with the complementary start codon on mRNA.
- large subunit binds with the small subunit with the tRNA in the p site
https://www.youtube.com/watch?v=qIwrhUrvX-k
modification of polypeptides into their functional state
polypeptides become proteins when they are modified into their functional shapes
- removal of methionine or whole sections
- modification of R groups on some amino acids
- folding into tertiary structures
- combining with other polypeptides (quarternary structure)
- adding non-polypeptide components
pre-proinsulin to insulin (110 amino acids)
- rough ER removes 24 amino acids (proinsulin)
- proinsulin is folded into tertiary structure using disulfide bonds
- some amino acids are removed from the middle, leaving 2 linked chains
- mature insulin has 2 chains help togheter by disulfide bridges, with a total of 51 amino acids
recycling of amino acids by proteasomes
proteasome = enzyme complex that breaks down proteins into short polypeptides, which can be broken down into amino acids later on
how are new cells generated and what are they needed for?
needed for growth, repair and reproduction
new cells come from existing cells
–> continuity of life
what is cytokinesis
division of the cytoplasm of a cell to form 2 daughter cells
animal
1. cleavage furrow (bit in between the 2 daughter cells)
2. contractile rings made of actin and myosin
3. then pinch apart
plant
1. vesicles form in the center to create new membranes
2. microtubule scaffold
3. each new cell builds a cell wall
equal and unequal cytokinesis
equal = parent cell equally divides into 2 daughter cells
unequal = can be possible, as long as the new cell has a nucleus, at least 1 mitochondrion, and any other organelle that cannot be synthesised by the cell
example = budding in yeast
oogenesis: meiosis has 2 cell divisions, produces one viable oocyte and 3 polar bodies
Roles of mitosis and meiosis in eukaryotes
cells MUST replicate nucleus before division to prevent the formation of anucleate cells
–> cannot synthesise proteins, limited lifespan (i.e. red blood cells)
Mitosis = diploid, produces 2 genetically identical daughter cells (asexual repro)
–> maintains chromosome number and genome of cells
Meiosis = haploid (sexual repro) halves the chromosome number and generates genetic diversity
what is a prerequisite for both mitosis and meiosis?
before cell division, DNA is elongated, replicated and condensed into chromosomes
before replication, 1 chromatid
After replication, each chromosome consists of 2 sister chromatids held together using cohesin loops until anaphase
after anaphase, 2 chromatids pulled apart
condensation of chromosomes
condensation of chromosomes helps move DNA safely and efficiently
supercoiling: DNA wraps around histones (always is to form nucleosome) but then the histones link together again and again until they form the chromosome
cytoskeleton microtubules are disassembled to form the spindle (used to move chromosomes during mitosis)
the spindle microtubules link with a structure called the kinetochore on the centromere (the middle of the chromatid). this acts like a microtubule motor (think chores, kineto = movement), remove microtubules to shorten the spindle, which pulls the chromatids apart
what are the phases of mitosis?
prophase, metaphase, anaphase and telophase
explain interphase
DNA is in the form of chromatin (not yet chromosomes)
growth, normal cell function, DNA replication
explain prophase
chromatids condense to chromosomes
spindle microtubules are starting to assemble
nuclear membrane breaks down
explain metaphase
microtubules attach to the centromeres
chromosomes align on the equator
explain anaphase
cohesin loops are cut
tension from the spindle pulls sister chromatids apart
chromosomes are moving towards the poles
explain telophase
new nuclear membranes form
chromosomes decondense back into chromatin
happen simulaneously with cytokinesis
what is meiosis
a reduction division –> creates genetically different haploid cells (usually gametes)
ensures zygote has 46 chromosomes
DNA is replicated once, but there are 2 cell divisions
explain anaphase 1 and anaphase 2
anaphase 1 separation of chromoSOME pairs
anaphase 2 separation of chromaTID pairs
what is nondisjunction
failure of the chromosomes to separate
results in gametes with too many or too few chromosomes, usually resulting in cell death
if 21st chromosome experiences nondisjunction, then Down syndrome
(trisomy 21)
–> highly correlated with maternal age
how important is meiosis as a source of variation
in prophase 1:
bivalent is the structure (pair of homologous chromosomes), synapsis is the formation of a bivalent
chiasma is the point of crossing over
CROSSING OVER = exchange of alleles on non sister chromatids of homologous chromosomes
number of chiasma and amount of genetic exchange seems to be random
RANDOM ORIENTATION
alignment of chromosomes is random = therefore there will be 2^n combos of alleles when chromosomes/chromatids are separated
phases:
1. DNA replication
2. Meiosis I
3. Cytokinesis
4. Meiosis II
5. Cytokinesis
under meiosis I, you have the same steps as mitosis
Prophase I - crossing over
metaphase I - homologous pairs align on the equator
anaphase I - separation of homologous pairs
telophase I - ends w/ 2 haploid cells
under meiosis II:
metaphase II - chromosomes align in center
anaphase II - sister chromatids separate
telophase II - ends w/ 4 haploid cells
What is cell proliferation and its function
cell proliferation = rapid increase in the number of cells
for growth (apical meristems), repair (wound healing) and cell replacement (skin cells)
what are the phases of the cell cycle
- interphase: G1 (growth), S (synthesising DNA), G2 phase (prep for mitosis)
- mitosis: prophase, metaphase, anaphase, telophase
- cytokinesis
explain cell growth during interphase
chromatin is relaxed, making it possible for it to be transcribed and translated. the membrane will increase in size, more organelles, high level of metabolism
how do cyclins control the cell cycle
cyclin = protein that controls cell cycle
cell must produce enough of each cyclin to progress to the next stage
what are the consequences of mutations in genes that control the cell cycle
cells have genes that ensure mitosis only happens when new cells are needed
-> proto-oncogenes (good)
—–> genes that control the cell cycle
—–> if mutate — oncogenes (BAD)
-> tumour-suppressor genes
—–> correct errors due to DNA damage
—–> most of these tumours are benign (harmless)
tumour = uncontrolled cell division due to the mutation in division-controlling genes
random mutation
heritable mutation
mutagens (chemical/radiation)
types of tumours
primary tumour = tumour cells that stick together
secondary tumour = tumour cells migrate and/or invade neighbouring tissue
metastasis = spreading of tumour cells to different parts of the body
malignant tumours = capable of metastasising (cancer)
–> more common in areas with more cell mutation
mitotic index =
(number of cells in mitosis)/total number of cells
higher mitotic index = more aggro
what are the functional benefits of the double membrane of the nucleus
