Biochemistry Flashcards
AA structure includes
basic amino group, acidic carbonyl group, R group, H atom
L-AA are used to
synthesize proteins
AA under low pH conditions =
protonated
AA under high pH conditions
deprotonated
_ AAs can destabilize or break down alpha helical 2 structures
glycine and proline
proline does NOT contain an
aromatic ring
_ AAs are the target of phosphorylation b/c they contain a hydroxyl functional group
serine, threonine, and tyrosine
_ AAs can form salt bridges
basic & acidic
_ can be used to break disulfide bonds in a western blot
BME
peptide bond
dehydration reaction in which the amino group of 1 AA acts as a nucleophile and attacks the carboxyl group of another AA, releasing a water molecule
amino and carboxyl functional group form a
amide group
formation of a peptide bond is a _ reaction
endergonic (E from ATP)
_ bonds stabilize secondary structure
H
_ structure forms optimal conformation of a protein
tertiary
what are the different forces stabilizing peptide bonds?
H bonds, ionic bonding/salt bridges, D-D interactions, LDF, and disulfide linkages
proteins fold into a state that _ the entropy of the system
maximizes, but minimizes their own energy
causes of protein denaturation
temperature, salinity, pH
solvation layer
water molecules that surround a protein
isoelectric focusing
each protein migrates until its reaches its pI
pH < pI =
+ charged
pH > pI =
- charged
native PAGE
separates proteins in their native tertiary state based on size and charge
SDS PAGE
separates proteins only based on their molecular mass NOT charge
western blot
proteins are visualized on a gel to see if a particular protein is present
formation of ES complex _ activation energy
lowers
oxidoreductase
transfer of electrons which result in change in oxidation state
transferase
transfer of a functional group from 1 molecular to another
hydrolase
breakdown of a covalent bond using water
lyase
breakdown of a covalent bond without water or electron transfer (oxidation)
isomerase
rearrangement of bonds within a molecule
ligase
formation of a covalent bond between 2 large molecules
enzyme approximation
enzyme catalyzes the reaction by bringing reactants in close proximity
covalent catalysis
enzyme catalyzes the reaction by forming a temporary covalent bond with the reactant
acid-base catalysis
enzyme catalyzes the reaction by acting as a n acid/base
metal ion catalysis
enzyme catalyses the reaction by assisting in electrophilic or nucleophilic interactions/binds to substrate
cofactors
inorganic ions (like iron or magnesium) that aids in activity
coenzymes
organic helpers and vitamins that aid in activity
2 ways to affect enzyme kinetics
increasing substrate concentration, increasing enzyme concentration
increasing substrate concentration beyond vmax effect:
none since the enzyme’s AS is already saturated
competitive inhibition
bind to AS, Km increased Vmax no change
non-competitive inhibition
bind to enzyme at allosteric site, no change in Km, decrease in Vmax`
mixed inhibition
bind to enzyme or allosteric site, decrease in Vmax, increase/decrease in Km
uncompetitive inhibition
bind to ES complex, both Vmax and Km decrease
3 components of nucleotides
nitrogenous base, pentose sugar, and phosphate group
4 nitrogenous bases
adenine, guanine, cytosine, thymine
phosphodiester linkages
formed between the 3’ carbon of 1 sugar and the 5’ carbon of another
nucleoside
pentose sugar attached to a nitrogenous base
watson-crick & DNA
DNA is a double helix and strands lie anti-parallel to one another
chargaff’s rule
total number of purines = total number of pyrimidines
G-C have a higher melting point b/c
they have more H bonds
hybridization of DNA
ssDNA can bind to another ssDNA of different origin if they have sufficient complementarity or base pairing
role of water
capable of H bonding (F, O, N) = elevated BP
lipid solubility
low solubility in water, high solubility in nonpolar organic solves (NP & hydrophobic)
role of lipids
energy storage, cellular organization and structure, precursor molecule for vitamins and hormones
fatty acids
building blocks of complex lipids which have a long C chain and carboxylic acid (most energy stroage)
triacylglycerols (triglycerides)
3c backbone (glycerol) and 3 FA chains, store E and provide insulation
phospholipids
have phosphate that replaces 1 of the FA, amphiphatic
glycolipids
carbohydrate replaces the phosphate in phospholipids, found in myelinated membranes
sphingolipids
have amino acid backbone` rather than glycerol found in triglycerides, have phosphate head and FA chain
steroids
4-ringed structure which contains cholesterol, important for membrane fluidity and precursor to steroid hormones
terpenes
pigments in the body (ex. vitamin A)
waxes
formed by ester linkage between alcohol chain and long-chain FA
eicosanoids
include prostaglandins, thromoxanes, etc Help to regulate BP, body temp, and muscle contraction
what allows lipids to be transported into the blood?
lipoprotein!
carbohydrates
have C-H bonds and alcohol chains, less E storage than lipids. join together via dehydration reactions
topoisomerase
works at the region ahead o the replication fork to prevent supercoiling by introducing breaks in the DNA and then resealing them
DNApol3
extends the primers, adds nucleotides in the 5’ to 3’ direction
DNApol1
replaces the primers with new DNA
DNApolII
has DNA proofreading ability and serves a repair fucntion
telomerase
not usually active in somatic cells, but is active in germ cells
mismatch repair
correct small insertions and deletions as well as correcting errors that occur right after replication is completed
glycosylases
detects and removes a specific kind of damaged base
2 pathways involved in double-stranded break repair
- Non-homologous end joining: two broken ends of the chromosomes are glued back together
Introduces a small mutation - Homologous recombination: information from the homologous chromosomes that matches the damaged one is used to repair the break
amber codon
mutation occurs and causes an early stop codon in an mRNA sequence
degenerate genetic code means
many AA are encoded by a few different codons
missense codons
encode an incorrect AA
nonsense coons
encode a premature stop codon
Aminoacyl tRNA synthetases:
enzymes that load individual amino acids onto the tRNA
eukaryotic transcription occurs in the
nucleus
prokaryotic. transcription occurs in the
cytoplasm
eukaryotes require _ to first bind to the promoter region
transcription facotrs
RNA pol1
synthesizes rRNA
RNApol2
located in the nucleus and syntehsizes all protein coding nucleuar premRNAs
RNApol3
in nucleus, transcribes a variety of structural RNAs
prokaryotes have 2 types of termination signals
Rho-dependent termination (protein dependent) and Rho-independent termination which is controlled by specific DNA sequences)
small ribosome subunit
binding of the mRNA template
large ribosome subunit
binds tRNAs (have A, P, and E sites)
most post-translational mods happen in the
ER and Golgi
-ex: glycosylation, lipidation, ubiquitination, phosphorylation
only AA that can undergo phosphorylation are
serine, tyrosine, and threonine
euchromatic
part of coding regions
heterochromatic
highly condensed, no coding, have regions that are silenced or suppressed by DNA mehtylation
monocistrionic expression
a single DNA promoter directs the synthesis of an mRNA containing 1 gene (seen in eukaryotic mRNA)
repressible operons
as long as the product of the pathway continues to be required by the cell, a repressible operon will continue to be expressed
inducible operons
expression of this (lac) is typically induced only in the presence of the substrate
lac operon
subject to activation in the absence of glucose, lactose must be present
CAP
protein that binds to the promoters of operons that control in the processing of alternative sugars
corepressor
protein that decreases gene expression by binding to a transcription factor that contains a DNA-binding domain
-Needs to recruit histone deacetylase which catalyzes the removal of acetal groups from lysine residues which makes the DNA less accessible to transcription
oncogenes
cause cancer
tumor suppressor genes
active in normal cells to prevent uncontrolled cell growth
Ex: p53: functions as a tsg and transcription factor
proto-oncogenes
positive cell-cycle regulators, when mutated can become oncogenes and cause cancer
acetylation
increases gene epxression
Cpg islands
stretches of DNA with a high frequency of C and G pairs found in the promoter regions of genes, can be methylated
what are the non-coding RNA
mi-RNA, snRNA, rRNA, tRNA
mi-RNA
involved in post-transcriptional regulation of gene expression and silencing of RNA, suppress translation
