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Biochemistry Final
many biochem topics
136
Chemistry
Undergraduate 1
05/10/2006

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Term
Nucleosomes
DNA
Histones
Definition
DNA and histones, gene expression occurs
Negative Charge
Positive Charge..electrostatic bond
Term
DNA polymerase
Definition
makes 2nd DNA strand
Term
Topoisomerase
Definition
relieves supercoiling by breaking DNA
phosphodiester bonds
Term
Helicase
Definition
unwinds DNA (H bonds)
Term
A&T
Definition
Form 2 H bonds
Term
G&C
Definition
form 3 H bonds
Term
Primase
Definition
short RNA nucleotide, helps start synthesizing of daughter strands
Term
DNA polymerase
Definition
synthesize daughter strands,
Term
lagging
Definition
3-5 produces okazaki fragments
Term
leading
Definition
5-3
Term
DNA Repair
DNA glycosylase
Definition
recognizes and removes damaged base
Term
endonuclease
Definition
cuts backbone
Term
exonuclease
Definition
removes wrong nucleotide
Term
polymerase
Definition
adds right nucleotide
Term
Transcription
Definition
in nucleus
DNA - RNA
RNA polymeraseII
capping at 5'
introns removed
poly AAA at 3'
Term
translation
Definition
in cytosol on ribosomes
mRNA-protein
tRNA brings AA to mRNA template
Term
codon
Definition
mRNA
Term
anticodon
Definition
tRNA
Term
Activation
Definition
add AA to tRNA
Term
Initiation
Definition
40s+60s+tRNA (bonds to P site)
Term
Elongation
Definition
build peptide bond, AA in A site
Term
Termination
Definition
stop codon
Term
Regulation Levels
Definition
Modification of DNA
transcription-mRNA production
translation-protein
post translational-chameronins, proteasomes
Term
chaperonins
Definition
fold proteins
Term
proteosomes
Definition
degrate protein
Term
Mutations
Definition
mostly detrimental
during transcription-non hereditary
during replication-passed on!
Term
Reverse Transcription
Definition
RNA-DNA
not efficient, many mutations
EX. HIV (retrovirus) attacks CD4
RNA w/ virus replicates into DNA
Term
Reverse transcriptase
Definition
produces complementary DNA strand
Term
DNA polymerase (Reverse Transcription)
Definition
makes double stranded DNA then transfers into nucleus of lymphocyte
Term
Termination Signal
Definition
signals RNA polymerase to stop synthesizing mRNA strand
Term
Gyrase
Definition
enzyme that winds the original DNA into a dbl helix
Term
splicing mechanisms
Definition
exercises introns
Term
codon
Definition
codes for single aa, gene sequences in DNA and mRNA
Term
AUG
Definition
start codon, express Met residue
Term
UAA, UGA, UAG
Definition
stop codons
Term
open reading frame
Definition
order of codons that will be read to form protein
Term
Translation Steps
Definition
Activation-ribosome binds to mRNA
Initiation-ribosome matches tRNA anticodon w/ mRNA codon
Elongation-each tRNA AA gets added to the elongating polypeptide chain
Termination-ribosome continues until stop codon
Term
anticodon
Definition
region of 3 nucleotides that contains complementary bases to the ones on mRNA
Term
Aminoacyl-tRNA
Definition
tRNA covalently linked to it's AA
Term
tRNA
Definition
carry ribosomes @ precise moment specified by genetic code on mRNA
by covalent attachment
clover leaf structure
Term
Aminoacyl tRNA synthetase
Definition
activate AA to attach to tRNA
DURING ACTIVATION STEP
Term
Peptidyl transferase
Definition
tRNA base pairs with next codon on mRNA at the A site
Term
Translocation
Definition
moving of ribosomes downstream
peptide chain increases one AA at a time
Term
Termination
Definition
after stop codon is read, no more AA
chain is cleaved by releasing factors
folds and is functional protein
Term
Activators
Definition
enhance RNA polymerase
encourages gene expression
Term
Repressors
Definition
bind to noncoding sequence of DNA strand
stops RNA polymerase, stops transcription
Term
Constitutive Genes
Definition
on all the time, housekeeping
Term
Inducible Genes
Definition
expressed only during certain times
Term
Gene Regulation
Definition
process of turning on and off genes
gene expression- on
gene repression- off
Term
Post Translational
Definition
removal of N-term Met
chaperones assist in folding
proteasomes degrade misfolded proteins
Term
Types of Mutations
Definition
substitution of a base
insertion of a base
deletion of a base
-cause by chem/phys agents
Term
Integrase
Definition
puts DNA into host cell during reverse transcription
lots of mutations
aids in antibiotic resistance
Term
Genes
Definition
hereditary unit
sequence of DNA
Term
Mut proteins
Definition
recognize damages base then signal repair
Term
DNA glycololases
Definition
hydrolyze glycosidic bond of wrong base
Term
interons
Definition
stretches of noncoding sequences
no message
Term
promoter
Definition
conatins intitation signal
controls transcription
Term
chromosomes
Definition
structures in nucleus
contain very long DNA chains
consist of chromatin
DNA,histones,proteins, and enzymes
Term
Ribozyme
Definition
RNA with special enzymatic functions
Term
Exons
Definition
stretches of coding sequence
message
Term
mRNA
Definition
carries info from DNA to ribosome sites
nucleus to cytoplasm
Term
Structural Region of Genes
Definition
carries encoded message
interupted by noncoding sequences
Term
Gluconeogenesis
Definition
glucose from pyruvate(or other intermediate)
Term
Glycogenesis
Definition
glycogen from glucose
Term
Glycogenolysis
Definition
glucose from glycogen
Term
Glycolysis
Definition
breakdown of glucose
Term
Ketose Sugar
Definition
Fructose ( =O )
Term
Aldose Sugar
Definition
Glucose ( OH )
Term
Maltose
Definition
Glucose & Glucose, A 1,4
Term
Sucrose
Definition
Fructose & Glucose, A 1,2
Term
Lactose
Definition
Galactose & Glucose, B 1,4
Term
Hemiacetals
Definition
Alcohols & Ketones
Term
Cyclic Hemiacetals
Definition
alcohols and ketones on same molecule
Term
furanose
Definition
5 membered cyclic hemiacetal
Term
pyranose
Definition
6 membered cyclic hemiacetal
Term
D-Monosaccharide
L-Monosaccharide
Definition
OH right
OH left
Term
Isocitrate - Oxalosuccinate
Definition
isocitrate dehydrogenase
NADH produced
Term
Oxalosuccinate-ketogluterate
Definition
isocitrate dehydrogenase
Co2 produced
Term
ketogluterate-succinyl CoA
Definition
ketogluterate dehydrogenase
Co2, NADH produced
Term
Succinate-Fumarate
Definition
succinate dehydrogenase
FADH2 produced
Term
succinyl CoA-succinate
Definition
ketogluterate dehydrogenase
CoA, GTP produced
Term
Fumarate-Malate
Definition
Fumerase
Term
Malate-OAA
Definition
malate dehydrogenase
NADH produced
Term
Monosaccharide Reactions
Definition
alditol-glucose-glucitol
aldonic acid-glucose-gluconic acid
uronic acid-glucose-glucuronic acid
Term
Starch
Definition
energy storage for plants
amylose-linear
amylopectin-branched, A 1,6
Term
Glycogen
Definition
animal energy storage
Term
Hyaluronic acid
Definition
lubrication
Term
Heparin
Definition
prevents clotting
Term
AMP
ADP
ATP
Definition
C-O-P
P-O-P
P-O-P-P-O-P
Term
NAD,NADH
FAD,FADH2
Definition
NAD,FAD-Oxidized
NADH,FADH2-Reduced
Term
Omega-3
Definition
GOOD,fish oils..etc.
Term
HDL
Definition
good
Term
LDL
Definition
bad
Term
Glycerophospholipids
Definition
structural lipid- Phospate attached
Term
Sphingolipid
Definition
FA + Sphingosine, by amide bonds
Term
Sterols
Definition
3 cyclohexane, 1 cyclopentane
Term
Lipids
Definition
energy storage in animals as FA derivatives in adipose tissue
Term
Membrane
Definition
Lipids & Proteins
Term
Lipid Bilayer
Definition
phospholipids, sphingolipids
Term
Insulin
Definition
glucose from blood
diabetes
Term
Glucagon
Definition
glucose from liver
Term
FA catabolism(B oxidation)
Definition
Goal- to produce Acetyl CoA
Glycerol + FA = lipid
glycerol-glycolysis
FA-B oxidation
CoA turns into carnitine to cross membrane, then turns back into CoA
Term
FA CATABOLISM ATP COUNT
Definition
Cycles(5 ATP) = n/2-1

Acetyl CoA(12 ATP) = n/2

minus 2 ATP from total, due to activation
Term
KETONE BODIES
Definition
no OAA, TCA cycle slows down, Acetyl CoA builds up
Term
AA catabolism
Definition
urea and energy produced
transamination 1st step
Term
Parkinson's Disease
Definition
not enough dopamine in synapse
Term
Schizophrenia
Definition
too much dopamine in synapse
Term
Paracrine
Definition
localized
Term
Autocrine
Definition
more mobile, in same cell
Term
Neurotransmission
Definition
chemical messengers travel across synapse to inhibit target cell
Term
Neurotransmitter
Definition
chemical messenger
Term
neuron
Definition
basic unit of nerve tissue
Term
Acetylcholine transferase
Definition
Ach PRODUCED
Term
Acetycholine esterase
Definition
Ach REMOVED
Term
Glycine
Definition
inhibitory
Term
Aspartate
Definition
excitatory
Term
Glutamate
Definition
excitatory- most common
Term
GABA
Definition
inhibitory, major in the brain
Term
INNATE
Definition
nonspecific
external-skin
internal-NK,macrophages
Term
Acquired
Definition
Cellular-MHC-APC-lymphocytes-Tcell-Cd4-Cd8
Humoral-MHC-APC-lymphocytes-Bcell-plasma-memory-antibodies
Term
O-linked saccharide
Definition
Serine,Thr
Term
N-linked saccharide
Definition
Ash
Term
converge to TCA cycle
Definition
catabolism of lipids, proteins, carbs
Term
Phagocytosis
Definition
macrophages ingest m/o
Term
perforin
Definition
t cells
Term
Human synthesis occurs
Definition
in cytoplasm only
Term
Methionine
Definition
sulfur atom
Term
Nterm,Cterm
Definition
ASN-LYS-ARG-LEU-LYS
N C
Term
Tryptophan
Definition
indole ring for side chain
Term
Transferases
Definition
kinase- add phosphate
transaminase- add NH3
Term
Hydrolases
Definition
cut w/ water across dbl bond
lipases,proteases,nucleases,amylases
Term
Lyases
Definition
non-water removal/additon
dehydrase-remove water
decarboxylase-remove C02
Term
Ligase
Definition
joins molecules w/ ATP
synthetases,carboxylase
Term
proenzymes
Definition
inactive until cleaved
Term
ER
Definition
synthesis of proteins occur here
Term
cyclic form of a sugar
Definition
has one more chiral center than open chain form
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