week 1 Flashcards
define nucleotide
base + sugar + phosphate; monomeric units of nucleic acids
define nucleoside
sugar + base; essentially a nucleotide w/o inorganic phosphate
nucleotide naming identifies…
1) base
2) sugar
3) # of phosphates
name the purines
adenine
guanine
name the pyrimidines
cytosine
thymine
uracil
deoxyribose has ___ attached to 2’ carbon
-H
ribose has ___ attached to 2’ carbon
-OH
DNA backbone is composed of…
sugars + phosphates
what type of bond holds the backbone together
phosphodiester bonds
what type of bond connects a pyrimidine with a purine to form the “rungs of the ladder?”
H-bonds
What is the order in which a primary transcript is modified?
1) 5’ capping 2) poly A tail added 3) splicing
guanine pairs with…
cytosine
adenine pairs with…
thymine (or uracil)
advantage of twisted, stacked spiral staircase
adds strength
phosphate backbone’s charge
negative
orientation of complementary DNA strands
anti-parallel
most common conformation of DNA
B-DNA; right-handed
define genome
all of an organism’s DNA (nuclear + mitochondrial)
how many chromosomes does the genome of a haploid cell contain?
23
how many chromosomes does the genome of a diploid cell contain?
46
define karyotype
the display of the 46 human chromosomes
ways to distinguish chromosomes
size
staining patterns
FISH color
each DNA molecule that forms a linear chromosome must contain…
1) a centromere
2) two telomeres (ends)
3) replication origin
in a karyotype, chromosomes are number in order of…
size
which amino acids would bind well in the groove of a double helix
arginine
lysine
histidine (in acidic environments; neutral in blood)
define locus
a specific location on a chromosome
define allele
alternate gene versions
define heterozygous
a cell containing two alleles that are functionally different
define homozygous
a cell containing two alleles that are NOT functionally different
does total number of chromosomes correspond with species complexity?
NO
define hemizygous
having only one allele for a given gene
introns make up what percentage of genes?
99%
DNA in prokaryotes exists as…
a single circular chromosome; double-stranded
how much are DNA molecules condensed?
10,000 fold
what issue does condensation of eukaryotic DNA pose?
it must be decondensed for replication to occur
Where does DNA replication begin in prokaryotes and what does the DNA bind?
single point of origin known as OriC and the DNA coils around the protein DnaA (major initiator protein) at the OriC
What is the primosome composed of in prokaryotes?
DnaB (DNA helicase) and DnaG (DNA primase)
What is the activity of helicases?
separate the DNA strands and unwind parental duplex
What effect does inhibition of HATs and HDACs have?
Inhibition of HATs–>can’t acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs–>can’t deacetylate tails, chromatin stuck in euchromatin
What is the function of topoisomerases?
enzymes that break phosphodiester bonds and rejoin them to relieve supercoiling tension
What is the major topoisomerase in bacteria?
DNA gyrase
What direction does DNA pol move on the template strand?
3’-5’
define heterochromatin
highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation
What is the function of primase?
lays down RNA primers for both lagging strand and leading strand synthesis
What is the function of ligase?
it joins DNA fragments together, typically in lagging strand DNA synthesis
What is the function of RNAse H?
removes RNA primers from Okazaki fragments working together with Pol I
What is the function of Pol I in prokaryotic DNA synthesis?
Pol I fills in the gaps left by the removal of the primers
What prevents DNA polymerase from falling off the template strand during DNA synthesis?
clamp proteins
Nonpolar Amino Acids
Glycine, Alanine, Valine, Leucine, Isoleucine, Proline
What effect do HATs have on chromatin?
Histone Acetyltransferase:
Add acetyl groups to histone tail lysines. Acetylation decondenses chromatin->euchromatin expressed
What effect do HDACs have on chromatin?
Histone De-acyteltransferase:
De-acytelation of histone tail lysines. De-acytelation allows chromatin recondensation->forms heterochromatin (not expressed)
What effect does inhibition of HATs and HDACs have?
Inhibition of HATs–>can’t acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs–>can’t deacetylate tails, chromatin stuck in euchromatin
eukaryotic DNA packaging involves wrapping of DNA around ___
histone proteins
the histone-DNA complex is called…
chromatin
define microRNA (mRNA)
non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis; regulates mRNA degradation, translation, chromatin condensation
define solenoid
helical, tubular coils that allow for further compaction of chromatin
core histones are rich in which amino acids?
arginine & lysine (positive charge neutralizes negatively charged DNA backbone)
acetylation of histone tails leads to…
destabilization/loosening of the chromatin due to neutralization of the histone’s original positive charge –> more difficult to neutralize the negative charge of the DNA as it is compacted
define euchromatin
loose chromatin that is open for transcription and replication; associated with acetylation
define heterochromatin
highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation
What is an example of an HDAC?
Sirtuins (SIR) protein
Explain how HDAC inhibitors are used as anti-cancer drugs
HDACs often upregulated in cancer cells to silence tumor suppressor genes by locking them in heterochromatin. Inhibitors allow expression of the silenced tumor suppressor genes.
What are the DNA polymerases that are found in E. coli?
Pol I, Pol II, Pol III - Pol III is primarily responsible for replication
What phase in eukaryotic cell cycle allows for DNA replication?
S phase
How many origins of replication due prokaryotes and eukaryotes have for DNA synthesis?
prokaryotes - 1
eukaryotes - many
What removes RNA primers from Okazaki fragments in eukaryotic cells?
Flap endonuclease I (FEN I) and RNAse H
How do eukaryotic cells solve the “winding problem” that occurs in DNA replication?
topoisomerases
How does topoisomerase 1 work?
nicks DNA and reforms it to relieve tension through a reversible nicking rxn
How does topoisomerase 2 work?
it prevents DNA from getting tangled by breaking dsDNA to allow DNA to be pulled apart
Why is topoisomerase 2 a good target for cancer treatment?
topo II is usually confined to proliferating cells in eukaryotes
what is the role of HAT?
“histone acetyltransferase” –> acetylates a histone
what is the role of HDAC?
“histone de-acetyltransferase” deacetylates a histone
HDACs are often unregulated in which type of cells?
cancer cells, leading to silencing of tumor suppressor genes; HDAC inhibitors are used as anticancer drugs
how does RNA form base pairs?
it is single stranded, but it may loop back on itself
RNAs can also act as…
enzymes (ribozymes)
function of mRNA
code for proteins
mRNA processing involves…
1) 5’ cap
2) poly-A tail
3) splicing out of non-protein coding sequences
tRNA function
carry amino acids to ribosomes so they may be incorporated into the polypeptide chain
accuracy of amino acid incorporation into proteins occurs via…
anti-codon of tRNA pairing with codon of mRNA
all tRNAs form which type of structure?
cloverleaf
retrovirus process
1) releases RNA genome into cell cytoplasm
2) reverse transcription into DNA
3) carries with it proteins that get integrated into host genome
4) reproduces within host genome
define microRNA (mRNA)
non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis
In DNA synthesis, which DNA strand is close to the product strand?
The coding strand is close to the product strand (same sequence). The template strand is read and the opposite bases are put into the product strand.
Define protein primary structure
Amino Acid Sequence
Define protein secondary structure
H-bond interactions of adjacent aa’s to form alpha helices or beta sheets
Define protein tertiary structure
Interactions of alpha helices or beta sheets and R groups
Define protein quaternary structure
Interaction of multiple polypeptides
Aromatic Amino Acids
Polar: Tryptophan, Tyrosine
Nonpolar: Phenylalanine
Sulfur-Containing Amino Acids
Methionine, Cysteine
Polar, Uncharged Amino Acids
Serine, Threonine, Asparagine, Glutamine
Charged Amino Acids
Negative/Acidic: Aspartate, Glutamate
Positive/Basic: Arginine, Lysine, Histidine
Which amino acids would be found on the interior of a protein?
Nonpolars (glycine, alanine, valine, leucine, isoleucine, proline), Aromatics (tryptophan, tyrosine, phenylalanine)
What amino acid can form disulfide bonds?
Cysteine
What amino acids can form H-bonds?
Polar, Uncharged Group (Serine, Threonine, Asparagine, Glutamine)
Tyrosine and Cysteine
What amino acids can form electrostatic interactions?
Charged Amino Acids
Which stereoisomer of alanine is found in bacterial cell walls?
D-alanine (bacDeria)
L-alanine is in human proteins and cells
What is the name of a covalent bond between carboxyl and amino groups of amino acids?
Peptide bond
Exposed hydrophobic protein patches form:
Aggregates
Denaturation of proteins is caused by:
Heat, oxidative damage, solvents, changes in pH
Anti-cancer drugs target chaperone protein inhibition because:
Cancer cells have many misfolded proteins, so chaperones help them survive. Inhibiting chaperones causes excessive protein aggregation and cancer cells die.
Hemoglobin has a sigmoid curve because of:
Cooperativity between subunits in ligand binding. This means low affinity at low oxygen pressures (in tissues).
What does 2,3-BGP do?
Promotes the T-state (tense/anti-oxygen state) of Hb, making it release oxygen to cells better.
Increased 2,3-BPG levels shift the Hb affinity curve:
Right (lower affinity)
Which level of protein structure is most important for function?
Tertiary. Primary sequences may vary between 2 proteins but as long as their aa properties are conserved, they form the same tertiary interactions and have similar functions.
Sickle Cell anemia caused by pos. 6 beta chain glutamate change to:
valine
T/F: Maternal Hb has higher affinity for oxygen than fetal Hb.
False! Fetal Hb has higher affinity (curve is shifted left) so it can take oxygen from the mother’s Hb
T/F: Hb contains 2 alpha chains throughout life.
True!
Fetal Hb has 2 alpha/2 gamma.
Adult Hb has 2 alpha/2 beta
Why don’t sickle cell symptoms show until 4 months?
The mutation is in the beta chains, which are not in fetal Hb, only adult Hb.
T/F: Fetal Hb has a low affinity for 2,3-BPG
True. It would be bad to bind 2,3-BPG because then it would be stuck in T-state and harder to get oxygen from the maternal Hb.
2,3-BPG is what type of molecule?
Allosteric inhibitor
Which factors would shift the hemoglobin affinity curve to the right? (lower affinity)
- Drop in pH
- Increase in 2,3-BPG
- Increase in temp.
