Biology Flashcards
acidic amino acids
aspartate and glutamate
basic amino acids
lysine, arginine, and histidine
polar amino acids
serine, threonine, tyrosine, asparagine, and glutamine
hydrophobic vs. hydrophilic amino acids
the acidic/basic/polar amino acids are hydrophilic, all others are hydrophobic
cysteine and cystine
cystine is formed when cysteine is oxidized to form a disulfide bridge
peptide bone formation
reaction of carboxylic group with amino group with a loss of water
hydrolysis of protein
proteolysis, breaking of peptide chain using water
amino acid important in alpha helix
proline
solvation layer
shell around protein that interacts with solvent (water)
isoelectric point
the point at which a molecule has no net charge, for an amino acid this occurs at the mean of the pKa’s
isoelectric focusing
an amino acid will be very positive at very low pH and will migrate towards the isoelectric point, it will be negative at high pH and migrate towards isoelectric point
how enzymes work
lower activation energy by stabilizing the transition state
types of enzymes
hydrolyase - break chemical bonds with water
isomerase - moves bonds around
ligase - joins together
lyase - breaks bonds without water or oxidation
kinase - phophorylates from another molecule
oxidoreductase - redox
polymerase - addition of many molecules
phosphatase - removes phosphate
phosphorylase - transfers phosphate from inorganic
protease - breaks protein with hydrolysis
active site model
lock and key - substrate and active site are perfecty complementary
induced fit model
substrate and enzyme differ slightly and binding introduces conformation change in enzyme
cofactor vs. coenzyme
same but a coenzyme is organic
cooperativity
like sigmoidal hemoglobin curve, binding of additional substrates
competitive inhbitor
same Vmax, larger Km
non-competitive inhibitor
smaller Vmax, same Km
uncompetitive inhibitor
binds to enzyme substrate complex, lower Vmax and Km
absolute configuration at the alpha position
amino acids in humans are L, sugars are D
proline special
kinks the chain, so it never appears in alpha helix
semiconservative replication
one strand is used as a template and the other has new bases added to it
euchromatin vs hetereochromatin
hetero - more dense, less transcribed genes
eu- less dense, more transcribed genes
topoisomerase
prevents supercoiling of DNA downstream from helicase
primase
adds an RNA primer to the growing strand
DNA pol 1 and 3
both present in prokaryotes
DNA pol 1 - adds nucleotides at RNA primer 5’ to 3’, also has exonuclease capabilities
DNA pol 3 - fast and accurate, does most of transcription, also has proofreading
differences between prokaryotic and eukaryotic replication
eukaryotic - several replication bubbles
prokaryotic - one site of replication, circular chromosome
telomerase
adds telomeres to ends of chromosomes, usually only present in germ line, stem cells or white blood cells, also tumor cells
missense mutation
one AA replaced with another
loss of heterozygosity
loss of one allele result in hemizygocity, if other gene if affected, can lead to disease
haploinsufficiency
one good gene is not enough for normal funciton
methylation to distinguish strands
used in prokaryotes, parental is labeled with methylation, daughter strand is not, is able to distinguish the difference, eukaryotes differentiate using free 3’ end or Okazaki fragments
difference between DNA and RNA
DNA - no 2’ hydorxyl group, less reactive, more stable
monocistronic vs polycistronic
eukaryotes are mono, prokaryotes are poly, mono means one strand encodes for one gene, encodes for one protein
heterogeneous nuclear RNA
made in the nucleus, immature or presursor to mRNA
tRNA
has anticodon that binds to mRNA and adds to growing polypeptide chain
rRNA
major component of ribosome, catalytic RNAs are called ribozymes
fidelity of RNA/DNA
RNA pol makes more mistakes, no editing capabilities
spliceosome
cuts out the introns and keeps exons, only present in eukaryotes
RNA pol 1,2,3
1 - rRNA
2 - hnRNA
3 - tRNA
in eukaryotes
relationship between tRNA and amino acids
each tRNA corresponds to one amino acid but each amino acid may have many tRNAs
wobble hypothesis
third amino acid of anticodon has some flexibility, allows for smaller number of tRNAs to be possible
aminoacyl-tRNA synthetases
combines tRNA and amino acid, requires 2 ATP, allows for specific AA and tRNA to bind and activates AA for growing polypeptide chain
subunits of ribosomes
50/30 in pro, 5.8/5/40/60 in eu
degenerate code
there are repeats in the code for amino acids
initiation and stop codons
initiation - AUG
stop - UAA, UAG, UGA
snRNPs
involved in spliceosome in eukaryotes, occurs in the nucleus, removes the introns, also associated with snRNAs
chaperones
helps proteins fold into their correct shape
locus
where a gene is located on a chromosome
alleles
a copy of a gene, one allele on each homologous chromosome
incomplete dominance
neither dominant nor recessive, instead of white and red you have pink
codominance
both alleles are expressed, but not blended, like blood type
synaptonemal complex
forms in prophase I, connects the two homologous chromosomes
natural selection, phenotypes and genotypes
natural selection only acts on phenotypes, not genotypes
differential reproduction
individuals that reproduce more will be selected for, individuals who reproduce less will be selected against
linkages in glycogen
alpha 1,4 linkages and alpha 1,6 at branch points
nucleolus
ribosome factory in the nucleus and site of transcription
localization sequence vs signal sequence
localization = nucleus, mitochondria and peroxisomes
signal sequence = secreted, plasma membrane, lysosome, ER, golgi