Biochem Quicksheets Flashcards
Most important Biochem concepts
Amino acids have what chirality
L
Amino acids have what configuration
S
What are the nonpolar, nonaromatic amino acids
GAVLIPM
What are the positively charged amino acids
HRK
What are the negatively charged amino acids
DE
What are the polar amino acids
STNCQ
What are the aromatic side chains
FWY
Peptide bond formation is what reaction
Condensation (dehydration) - Nucleophilic amino group attacks the carbonyl C
Primary structure
linear sequence of AAs
Secondary structure
local structure, stabilized by H bonds
a helices and b bleated sheets are an example of what degree of structure?
secondary
Tertiary structure
3D structure stabilized by hydrophobic interactions, H bonds, acid-base (salt bridges), and disulfide bonds
disulfide bonds are made of what AAs
cysteines
Quaternary structure
interactions b/w subunits
What can cause denaturation of structure?
heat and solutes
what do enzymes do?
lower activation energy and change rate at which equilibrium is reached
what do enzymes NOT do?
alter free energy (G) or enthalpy (H)
Ligase
joins 2 large biomolecules (usually same type)
Isomerase
catalyze interconversion of isomers (ex constitutional and stereoisomers)
Lyases
catalyze cleavage without the addition of water or transfer of e- (*synthesis is the reverses rxn and is more important)
Hydrolases
catalyze cleavage with the addition of water
Oxidoreductases
catalyze redox rxns that involve transfer of e-
Transferases
move FG from 1 molecule to another
Saturation kinetics
as [s] increases, rxn rate increases until reaches a max
At 1/2 Vmax, [s] =
Km
Michaelis-Mentin equation
Competitive inhibitor effects
- Binds to:
- Impact on Km?
- Impact on Vmax
- active site
- increases
- no change
Noncompetitive Inhibitor effects
- Binds to
- Impact on Km
- Impact on Vmax
- Allosteric site (E or ES)
- No change
- Decreases
Uncompetitive Inhibitor
- Binding site
- Impact on Km
- Impact on Vmax
- ES complex
- Decreases
- Decreases
5 structural proteins
collagen, elastin, keratin, actin, tubulin
Motor proteins (3)
capable of force generation through a conformation change
(myosin, kinesin, dynein)
Binding proteins
bind a specfic substrate, either to sequester it in the body or hold its concentration at steady state
CAM
cell adhesion molecule - binds cells to other cells or surfaces
(cadherins, integrins, selectins)
Antibodies (Ig)
Immunoglobulins - target a specific antigen on a pathogen or toxin
Ion channels
3 types
used for regulating ion flow into/out of cell
ungated, voltage-gated, ligand gated
Enzyme linked receptors
participate in cell signaling thru extracellular ligand binding and initiation of second messenger cascades
GPCR
G protein coupled receptor - membrane-bound protein associated with a trimeric G-protein (initiate 2nd messenger systems)
Cooperative Enzymes show what kind of curve
sigmoidal
trioses
tetroses
3-carbon sugars
4-carbon sugars
aldoses
ketoses
sugars with aldehydes as their most oxidizedgroup
sugars with ketones as their most oxidized group
D-sugars
-OH (highest # chiral carbon) on the right
L-sugars
-OH on the left
Diastereomers
differ at at least 1 but not all chiral carbons
2 kinds of diastereomers
epimers - differ at 1 chiral carbon
Anomer - differ at the anomeric carbon
anomeric carbon
new chiral center formed in ring closure, carbon containing the carbonyl in straight-chain form
alpha and beta anomers
alpha - trans to -CH2OH (below ring)
Beta - cis to CH2OH (above ring)
mutarotation
one anomeric form shifts to another, with the straight-chain form as an intermediate
4 monosaccharides
D-fructose, D-glucose, D-galactose, D-mannose
D-fructose
D-glucose
D-galactose
D-mannose
carbohydrates undergo what 3 types of rxns?
oxidation-reduction, esterification, glycoside formation
esterification
a reaction of an alcohol with an acid to produce an ester and water.
glycoside formation
basis for building complex carbs and requires anomeric carbon to link to another sugar
deoxy sugar
replace -H with -OH
Common disaccharides
- sucrose (glucose-a-1,2-fructose)
- lactose (galactose-b-1,4-glucose)
- maltose (glucose-a-1,4-glucose)
3 polysaccharides to know
cellulose - main structural component of plant cell walls, main source of fiber for human diet
starches (amylose and amylopectin) - main energy storage forms for plants
glycogen - a major energy storage form for animals
nucleoside
five carbon sugar + nitrogenous base
nucleotide
nucleoside + 1-3 phosphate groups (ex. ATP)
Nucleotides in DNA contain what sugar?
Nucleotides in RNA contain what sugar?
deoxyribose
ribose
DNA reads in what direction?
What is the polarity?
What is the structure?
5’-3’
antiparallel
double helix
In RNA, A pairs with ___ via # hydrogen bonds
U, 2
Nucleosomes are made of
(H2A, H2B, H3, H4)x2 histones with DNA wrapped around. stabilized by H1
Telomeres
ends of chromosomes, high G-C content to prevent DNA unraveling
Centromeres
hold sister chromatids together until they are separated during anaphase in mitosis, high G-C content
DNA replication in prokaryotes
- # origins of replication
- unwind of DNA helix with?
- Stabilization of unwound template strands with?
- Synthesis of RNA primers with?
- Synthesis of DNA with?
- Removal of RNA primers with?
- Replacement of RNA with DNA by?
- Joining of Okazaki fragments by?
- Removal of positive supercoils ahead of advancing replication forks by?
- Sythesis of telomeres
- one per chromosome
- Helicase
- ssDNA binding protein
- Primase
- DNA pol III
- DNA pol 1 (5’-3’ exonuclease)
- DNA pol I
- DNA ligase
- DNA topoisomerases (DNA gyrase)
- not applicable
DNA replication in eukaryotes
- # origins of replication
- unwind of DNA helix with?
- Stabilization of unwound template strands with?
- Synthesis of RNA primers with?
- Synthesis of DNA with?
- Removal of RNA primers with?
- Replacement of RNA with DNA by?
- Joining of Okazaki fragments by?
- Removal of positive supercoils ahead of advancing replication forks by?
- Sythesis of telomeres
- multiple per chromosome
- Helicase
- ssDNA-binding protein
- Primase
- DNA pol alpha, delta, epsilon
- RNase H (5’-3’ exonuclease)
- DNA pol delta
- DNA ligase
- DNA topoisomerases
- Telomerase
In what direction does DNA polymerase read? In what direction is DNA synthesized?
read 3’-5’, synthesized 5’-3’
leading strand
1 primer and can be synthesized continuously
lagging strand
many primers, synthesized in okazaki fragments
Recombinant DNA
dna composed of nucleotides from 2 diff sources
DNA cloning
introduces fragment of DNA into vector plasmid
restriction enzyme
restriction endonuclease - cuts both the plasmid and the fragment, leaving them with sticky ends, which can bind
DNA library
large collections of known DNA sequences
Genomic libraries
contain large fragments of DNA (coding and noncoding regions) CAN’T be used to make recombinant proteins or for gene therapy
cDNA libraries (expression libraries)
contain smaller fragments of DNA (only include exons of genes expressed) CAN be used to make recombinant proteins or for gene therapy
Hybridization
joining of complementary base pair sequences
PCR
polymerase chain reaction - automated process to make millions of copies of a DNA sequencefrom a small sample by hybridization
agarose gel electrophoresis
separate DNA molecules by size
Southern blotting
to detect presence and quantity of various DNA strands in a sample. After electrophoresis, sample is transferred to a membrane that can be probed with single-stranded DNA molecules to look for a sequence of interest
DNA sequencing
uses dideoxynucleotides to terminate DNA chain cuz they lack a 3’OH group
Central Dogma
DNA-RNA-proteins
Degenerate code
allows multiple codons to encode the same amino acid
Initiation codon
AUG (methionine)
Termination codons
UAA, UGA, UAG
wobble
3rd base in the codon can be different and won’t affect protein
4 types of point mutations
silent - no effect
nonsense (truncation) - premature stop codon
missense - codes for diff AA
Frameshift - nt add/deleted and changes reading frame
RNA differences from DNA (3)
ribose sugar, Uracil instead of Thymine, single-stranded
3 major types of RNA
mRNA, tRNA, rRNA
messenger RNA
carries message from DNA in the nucleus via transcription of the gene, travels into the cytoplasm to be translated
transfer RNA
brings in AA, recognizes the codon on the mRNA using its anticodon
ribosomal RNA
makes up much of the ribosome, enzymatically active
Describe the very basic steps of transcription
- helicase and topoisomerase unwind DNA double helix
- RNA pol II binds to TATA box in the promoter region
- hnRNA synthesized from DNA template (antisense strand)
Describe the basic post-transcriptional modifications
- 7-methylguanylate triphosphate cap added to 5’ end
- polyadenosyl tail added to 3’ end
- splicing done by spliceosome, introns removed and exons ligated together
alternative splicing
combines different exons to acquire different gene products
where does translation occur
at the ribosome
what are the 3 stages of translation
initiation - The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon
elongation - tRNA transfers an amino acid to the tRNA corresponding to the next codon. The ribosome then moves (translocates) to the next mRNA codon to continue the process, creating an amino acid chain.
termination - When a stop codon is reached, the ribosome folds the polypeptide into it’s final structure.
Describe the post-translation modifications
- folded by chaperones
- formation of quaternary structure
- cleavage of proteins or signal sequences
- covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
operons (what model)
Jacob-Monod model - inducible or repressible clusters of genes transcribed as a single mRNA
transcription factors
search for promoter and enhancer regions in the DNA
promoters and enhancers
promoter - within 25 bp of the transcription start site
enhancer - more than 25 bp away from the transcription start site
osmotic pressure (and equation)
pressure applied to a pure solvent to prevent osmosis, related to the conc of the solution
π = iMRT
i = Von’t Hoff factor - # ions in solution
M - conc in mol/L
R - 0.08206 L atm mol-1 K-1
T - temp in K
Passive transport
3 types
does not require ATP cuz the molecule is moving down its conc gradient from high to low
- simple diffusion - no transporter, small, nonpolar molecules move
- osmosis - diffusion of water across semipermeable membrane
- facilitated diffusion - use transport proteins
active transport (primary and secondary)
primary - requires energy ATP
secondary - use ion gradient (antiport or symport)
pinocytosis
phagocytosis
cell drinking
cell eating
Need to memorize glycolysis! But what are the 7 enzymes that are important?
glucokinase, hexokinase, PFK-1, PFK-2, Glyceraldehyde -3-phosphate dehydrogenase, 3-phosphoglycerate kinase and pyruvate kinase
glucokinase
present in the pancreatic beta-islet cells as a glucose sensor and is responsive to insulin in the liver
hexokinase
traps glucose
PFK-1
rate-limiting step of glycolysis
PFK-2
produces fructose-2,6-bisphosphate to activate PFK-1
glyceraldehyde-3-phosphate dehydrogenase
produces NADH
3-phosphoglycerate kinase and pyruvate kinase
substrate-level phosphorylation (add phosphate group to ADP or GDP to make ATP or GTP)
3 enzymes of irreversible rxns
glucokinase/hexokinase, PFK-1, pyruvate kinase
what happens to NADH produced in glycolysis aerobically and anaerobically
aero - oxidized by mitochondrial ETC
anaero-oxidized by lactate dehydrogenase
pyruvate dehydrogenase
converts pyruvate to acetyl-CoA. stimulated by insulin and inhibited by acetyl-CoA
Need to memorize Citric Acid Cycle! What is the main purpose of it? and where does it occur
oxidize acetyl-CoA to CO2 and generate NADH and FADH (electron carriers) and GTP
in mitochondrial matrix
Need to memorize ETC! Where does it take place?
matrix-facing surface of the inner mitochondrial membrane
ETC
NADH donates electrons and passed down complexes, reduction potentials INCREASE and end on Oxygen (highest reduction potential)
Can NADH get across mitochondrial membrane? Mechanisms?
HECK NO, uses shuttles
- glycerol 3-phosphate shuttle
- malate-aspartate shuttle
proton motive force
electrochemical gradient generated by the ETC across the inner mitochondrial membrane
inner mitochondrial membrane has higher proton conc than matrix
chemiosmotic coupling
form ATP as protons create gradient passing thru ETC
ATP synthase
enzyme responsible for generating ATP from ADP and an inorganic phosphate Pi
Energy yield of glycolysis
2 NADH and 2 ATP
energy yield of pyruvate dehydrogenase
1 NADH (2 NADH per molecule of glucose cuz 2 pyruvate formed)
energy yield of citric acid cycle
6 NADH, 2 FADH2, 2 GTP per glucose
1 NADH = ? ATP
2.5
1 FADH2 = ? ATP
1.5
Total energy yield from metabolism
30-32 ATP
glycogenesis
build glycogen using 2 enzymes (glycogen synthase and branching enzyme)
glycogen synthase
glycogen synthesis - creates alpha-1,4-glycosidic linkages b/w glucose molecules
activated by insulin in the liver and muscles
branching enzyme
moves a block of oligoglucose from one chain and connects it as a branch using an alpha-1,6 glycosidic link
glycogenolysis
breakdown of glycogen using 2 enzymes (glycogen phosphorylase and debranching enzyme)
glycogen phosphorylase
removes single glucose 1-phosphate molecules by breaking alpha-1,4 glycosidic links
- in liver, activated by glucagon to prevent low blood sugar
- in muscle, activated by epinephrine and AMP to provide glucose to muscle
debranching enzyme
moves a block of oligoglucose from one branch and connects it to the chain using an alpha-1,4 glycosidic link
gluconeogenesis
occurs in cytoplasm and mitochondria, mostly in liver tho
reverse 3 irreversible steps
- pyruvate carboxylase and PEP carboxykinase bypass pyruvate kinase
- Fructose 1,6 bisphosphatase bypass phosphofructokinase-1
- glucose-6-phosphatase bypasses hexokinase/glucokinase
pentose phosphate pathway
occurs in the cytoplasm of most cells - generates NADPH and sugars for biosynthesis.
rate limiting step of pentose phosphate pathway
glucose-6-phosphate dehydrogenase activated by NADP+ and insulin, inhibited by NADPH
postprandial metabolic state
well-fed (absorptive) - insulin secretion is high and anabolic metabolism prevails (building up molecules)
postabsorptive metabolic state
fasting - insulin secretion decreases while glucagon and catecholamine secretion increases
prolonged fasting metabolic state
starvation - dramatically increases glucagon and catecholamine secretion (most tissues relying on fatty acids)
liver metabolism
maintains blood glucose thru glycogenolysis and gluconeogenesis
processes lipids, cholesterol, bile, urea, and toxins
adipose metabolism
stores and releases lipids
resting muscle metabolism
conserves carbohydrates as glycogen and uses free fatty acids for fuel
active muscle metabolism
may use anaerobic metabolism, ox phosph, direct phosphorylation, fatty acid oxidation
Cardiac muscle metabolism
fatty acid oxidation
brain metabolism
uses glucose except in prolonged starvation (in which it will use ketolysis)
lipid transport
chylomicrons, VLDL, IDL, LDL, HDL
cholesterol metabolism
key enzyme?
obtained thru diet or synthesis in liver
HMG-CoA reductase
Palmitic acid
the only fatty acid that humans can synthesize - produced in the cytoplasm from acetyl-CoA transported out of the mitochondria
fatty acid oxidation
occurs in mitochondria after transport by the carnitine shuttle via beta-oxidation
shuttle - transfers long-chain fatty acids across the barrier of the inner mitochondrial membrane to gain access to the enzymes of beta-oxidation
beta oxidation
catabolic process by which fatty acid molecules are broken down in the mitochondria in eukaryotes to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in the electron transport
-the beta carbon of the fatty acid undergoes oxidation to a carbonylgroup
ketogenesis
ketone bodies form during prolonged starvation state due to excess acetyl-CoA in the liver
ketolysis
regenerates acetyl-CoA for use as an energy source in peripheral tissue
protein digestion
occurs in SI, AA carbon skeletons used for energy, amino groups fed into urea cycle to be excreted
