Unit 1 Exam Flashcards
semiconservative replication
each daughter DNA molecule contains 1 strand from parent and 1 newly synthesized strand
DNA structure
sugar-phosphate backbone gives DNA molecule overall negative charge
A and G are purines that have 2 rings and C and T are pyrimidines that have 1 ring (most energetically favorable pairings)
DNA bonds
phosphodiester bonds: OH group on 3’ carbon forms covalent bond with phosphate group on 5’ carbon below it
hydrogen bonds: A and T (forms 2 H bonds), C and G (forms 3 H bonds), H bonds force sugar-phosphate backbone in anti-parallel directions
nucleosomes
DNA wrapped around core of histone proteins- histones have (+) charge and DNA is (-) so this attraction encourages non-specific wrapping, histones form an octamer (2 sets of 4- H2A, H2B, H3, H4)
histone tails
1 protein end projecting out from histone, play important role in regulating opening and closing/condensing of chromatin, rich in lysines which give it a (+)
chromatin
fibers made up of packed nucleosomes, 30 nm fiber-coiled helix of nucleosomal DNA, requires 5th histone (H1) a linker histone on the edge of nucleosome where DNA exits spool and changes path of DNA promoting a twisting structure
chromosomes
organized subunits of genome (1 molecule of DNA), separates genome into manageable units that are organized spatially, 23 pairs in human genome
condensed heterochromatin
fits into small spaces and provides protection from damage
decondensed euchromatin
“beads on a string”, easier to read and allows access for DNA replication or transcription machinery
HATs and HDACs
histone acetyl transferases add acetyl group to histone tails, removing the (+) charge of lysines loosening interaction between histone and DNA, opening chromatin and increasing gene expression
histone deacetylases remove the acetyl group, returning (+) strengthening interaction and “closing” chromatin
chromatin remodeling enzymes
HDACs and HATs that modify histone tails to impact chromatin packing, regulating access to DNA
methylation of histone tails
“closes” chromatin decreasing gene expression; methyl transferase adds methyl group to histone tails and methylated histone tails bind protein HP1 that oligomerizes bringing nucleosomes together
cytosine methylation
cytosines followed by a guanine in the 5’ to 3’ direction receive a methyl group that makes DNA less accessible because it serves as a binding site for other proteins such as HDACs, is heritable (epigenetics)
epigenetics
study of heritable changes in gene expression that do not involve changes to underlying DNA sequence (phenotype not genotype change)
active/open chromatin
transcription possible, unmethylated cytosines, acetylated histones, unmethylated histone tails
silent/condensed chromatin
transcription impeded, methylated cytosines, deacetylated histones, methylated histone tails
inheritance of traits
stability of DNA from covalent phosphodiester bonds of phosphate-sugar backbone, protected due to double helix structure with bases H bonded, easily reproducible due to complementary base pairs
evolution of traits
DNA sequence is modular (bases can be easily swapped) introducing mutations that provide diversity for evolution to act on
transcription
process of making RNA copies of DNA template (gene), 1 DNA molecule used to make many identical RNA copies, in same language of nucleotides
spatial organization of gene expression within cell
DNA stored in nucleus but protein synthesis happens in cytoplasm so RNA copies leave nucleus
temporal organization
when and how much a gene is being expressed, changes throughout cell’s life and allows cells to specialize
constitutive gene expression
always being transcribed at a constant rate, required for normal cell function (housekeeping genes)
conditional gene expression
transcribed at different rates depending on conditions (induced or repressed, upregulated or downregulated)
initiation of transcription
promoter sequence determines start site (which comes after), TATA box about 25 bp upstream of gene bound by TBP bending DNA and providing landing spot for pre-initation complex to bind promoter region and recruit RNAP opening transcription bubble at start site
pre-initiation complex
general transcription factors required for expression of all genes
elongation of transcription
rNTPs become exposed to noncoding DNA strand and form H bonds with their complementary base pairs, RNAP then catalyzes the phosphodiester bonds forming backbone of mRNA allowing it to leave, DNA strands reform H bonds and exits
non-template strand
has same sequence as RNA strand, “coding” strand, reverse complement of template strand
template strand
strand forming H bonds with RNA, strand being read, “non-coding”
termination of transcription
RNAP reaches terminator sequence (AAUAAA) RNAP falls off and can rebind
RNA polymerase
includes DNA entry channel, pin that physically separates DNA strands as it enters main cavity forming transcription bubble, rNTP entry channel, RNA exit channel
regulation of transcription initiation
specific transcription factors
specific transcription factors
required for expression of specific sets of genes, have to be used with GTFs, often affected by environmental signals, can bind at sites near promoter (proximal) or far away (distal), introns can encode enhancer or silencer regions
activators and enhancers
TFs that bind enhancer regions to upregulate transcription
repressors and silencers
TFs that bind silencer regions to downregulate transcription
mediator
protein that forms a physical link between GTF complex, specific TFs and chromatin remodeling proteins
1. assembly of GTFs with RNAP at promoter
2. specific proteins bind to DNA and bending/looping brings them in proximity to RNAP
3. mediator links RNAP, GTFs and STFs
activators grant RNAPII permission to proceed with transcription and leave promoter (triggers TFIIH)
“committee” of factors controlling gene expression
transcription regulators and chromatin remodeling proteins work together to control gene expression
mRNA processing
pre-mRNAs have to receive 5’ cap, 3’ poly-A tail and undergo splicing to be exported from nucleus for translation in cytosol, cap binding protein and poly-A binding protein are recruited and interact forcing mRNA into circular shape
splicing
pre-mRNA contains introns (non coding sequences) and exons (coding sequence) so spliceosome removes introns and joins exons
spliceosome
multi-unit machines made of proteins and folded RNAs, forms intron into lariat by cutting it off at 5’ end and attaching it to 3’ end, then cut off and discarded, exons joined together and labeled with exon junction complexes
alternative splicing
sometimes some exons are removed during splicing to create different mature mRNAs from same pre-mRNA sequence, order of exons must be maintained, improved efficiency and diversity
nuclear pore complex
mediates mRNA export, pores are big enough for mRNA but too small for chromatin, lined with proteins that check mRNAs for EJCs and cap and tail binding proteins- proof of processing
RNA
RNA has 2 OH groups, is usually single-stranded allowing for intramolecular base pairing- 3D folding
3 RNA polymerases
RNAPI and RNAPIII used for RNA genes while RNAPII is used for protein-coding genes
DABFEH
TFs forming pre-initiation complex
TFIID binds to promoter, includes TBP subunit that kinks DNA at 90 degrees
TFIIA stabilizes TFIID and TBP
TFIIB stabilizes TFIIA and TFIID
TFIIF carries RNAPII
TFIIE stabilizes RNAPII
TFIIH phosphorylates RNAPII tail adding (-) forcing RNAPII out of PIC- after transcription tails dephosphorylated so can be recruited to promoter
tRNA
have 3 base anti-codon one one end that pairs with codon on mRNA, have extensive intramolecular basepairing forming a cloverleaf structure
ribosomes
huge conglomerations of RNA and proteins that synthesize proteins, large subunit forms peptide bonds between amino acids and small subunit matches mRNA codons to proper tRNA
A site
amino-acyl-tRNA, for tRNAs carrying single amino acid
P site
peptidyl-tRNA, for tRNAs carrying chains of amino acids
E site
exit
translation steps
- ribosome assembles around mRNA 5’ end
- tRNA containing correct anti-codon and amino acid enters A site and binds to codon
- aa forms peptide bond with aa chain linked to tRNA in P site transferring aa chain to the tRNA in A site
- translocation- ribosome shifts forward by 1 codon while tRNAs stay base paired with codons (only 2 tRNAs can be in ribosome at once)
chromatin remodeling complexes
force unwrapping of nucleosome and move histone to adjacent region using ATP, chromatin needs to be decondensed first
histone code
different patterns of modifications recruit or activate different enzymes and having inherent meaning like DNA sequence
replication fork
where 2 halves of parent DNA strands are split and each strand is used as a template for a new strand
topoisomerase
unwinds double helix of DNA
helicase
separates DNA strands break hydrogen bonds between bases
single stranded binding proteins
allows fork to stay open by preventing base pairing
primase
starts new strand by synthesizing short RNA sequence (primer)
DNA polymerase
elongates from primer catalyzing covalent bonds of sugar-phosphate backbone
lagging strand
synthesized away from replication fork in short Okazaki fragments
1. new RNA primer synthesis by primase
2. DNA polymerase starts at primer
3. exonuclease removes RNA primer
4. DNAP fills in gaps left by removal of primers
5. DNA ligase catalyzes covalent bonds of backbone of Okazaki fragments
loops around to match up with direction of leading strand (bc protein complex synthesizes work together)
origen of replication
encoded in specific sequence of bases, rep forks are made creating rep bubble, in order to replicate entire genome multiple bubbles form and rep stops when bubbles join together- machinery falls off and DNA ligase connects backbone
PCR (polymerase chain reaction)
amplifies specific sequence of DNA by recreating replication, uses DNA sample, DNA primers (designed for specific portions of DNA), free nucleotides, Taq polymerase and buffer
1 PCR cycle
denaturation- 95 deg. C hot enough to break H bonds separating strands
annealing- 55 deg C allowing H bonds to form and primers to bind
extension- 72 deg C Taq polymerase adds nucleotides
each rounds doubles amount of DNA sequence
