biotech 5

metabolism

breakdown and synthesis of macromolecules in living cells

catabolism

the degradative process of metabolism that releases energy, pathways converge

anabolism

the building phase of metabolism that requires energy, pathways diverge

adenosine triphosphate (ATP)

energy cash, last 2 phosphates have high energy bond broken to produce energy, usually for heat

Bioenergy

comes from transfer of electrons

Electron donor

being oxidized

Electron receiver

being reduced

GLUT4

only glucose transporter responsive to insulin, present in muscle and fat peripheral cells

preparatory phase

1-5

payoff phase

6-10

glycolysis

oxidation and cleavage of glucose that occurs with all carbs in cytosol

2 pyruvate, 2 NADH, 2 ATP

net products

lactose intolerance

lactase deficiency

lactate

pyruvate in anaerobic conditions becomes _____ and transported to liver, where it is used for glucose production

Cori Cycle

facilitates muscle exertion, prevents lactate acidosis, source of gluconeogenesis during fasting

fermentation

pyruvate to acetaldehyde to ethanol process in yeast

thiamin pyrophosphate (TPP)

vitamin b1 cofactor for pyruvate decarboxylase

GLUT2

glucose transporter in hepatocytes

glucagon

hormone stimulating hepatocytes during fasting, producing glucose with G6Pase

insulin

hormone during fed state that increases glucose uptake, where it is converted into glycogen from normal form and lipids from pyruvate

rapidly contracting state

high levels of glycolysis and glycogen being used in muscle cells

resting state

low glycolysis and glycogen production in muscle cells, high ATP and low AMP levels

oxidative decarboxylation

catalyzed by pyruvate dehydrogenase complex converting pyruvate into Acetyl CoA, NADH, and CO2

TPP coenzyme

inhibited by arsenic

occurs in mitochondria

Kreb’s Cycle

oxygen is not directly involved, but is still required, so process is aerobic

produces 3 NADH, 1 FADH2, 1 GTP, and 2 CO2

stimulated by Ca2+ at low energy

anaplerotic

intermediates of TCA cycle are ______ because they participate in both catabolic and anabolic reactions

anaplerosis

replenishing intermediates that have been extracted for biosynthesis

redox potential

measure of the affinity for a compound to accept electrons, 02 is most likely and highest

proton-motive force

using H+ gradient as energy

24 ATP

Acetyl CoA to TCA Cycle

6 ATP

each NADH

micelles

smaller particles of fat globules that are made by bile salts

Pancreatic lipases

hydrolyze ester bonds of triglycerides in micelles

alpha end

Carboxylic acid end of fatty acid

short chain

less than 8 carbonsme

medium chain

8-12 carbons

large chain

more than 12 carbons

linoleic acid

essential proinflammatory fatty acid

18:2 (9,12)

linolenic acid

essential antiinflammatory fatty acid

18:3 (9,12,15)

arachidonate

synthesized from linoleic acid

a prostaglandin precursor

fatty acyl CoA synthetase (FACS)

occurs on mitochondrial membrane

cleaves C2 and C3 fatty acid bonds to produce FADH2, NADH, and Acetyl CoA without ATP

Fatty acid synthesis (FAS)

occurs in cytosol to make palmitate (16C), starting with 2C and goes through 7 cycles to add 2C each time

requires ATP

Ketone body synthesis

formed principally in liver mitochondria

diabetic ketoacidosis

absence of insulin means Acetyl CoA is unprocessed and builds up, high amounts of ketone bodies in blood reduces pH and disturbs nervous system

glutamate

central player of transamination reactions, created by a transaminase catalyzing a reaction between an amino acid and its alpha-ketoglutarate

glucogenic

TCA cycle intermediates or pyruvate

ketogenic

acetyl CoA, acetoacetyl CoA, acetoacetate

uncouplers

allow protons to reenter without oxidative phosphorylation, releasing energy as heat and using oxygen without producing ATP

mobile protein carrier

lipid soluble proteins that transport H+ (ex. DNP)

2,4-dinitrophenol

weight loss drug with high toxicity that was banned, caused high heat loss

shivering

muscle contraction produces heat using ATP, then leads to increased oxidative phosphorylation that increases heat and ATP

Non-shivering thermogenesis

thermogenin in brown fat used by babies because they can’t shiver well, uncoupling reactions to produce heat

Warburg effect

aerobic glycolysis in cancer cells even in presence of oxygen

Pasteur Effect

inhibition of oxidative phosphorylation in absence of oxygen, normal cell exhibit

Positron emission tomography

used for scanning tumors because of high rate of glucose metabolism

cyclophosphamide

prodrug activated by CYP450 that targets highly proliferative cells

PARP

repair double strand breaks in DNA, and can be targetted in cancer cells to cause apoptosis

BH3 only proteins

respond to stress to inhibit antiapoptotic Bcl-2 proteins

capsase 1,2,8,9,10

initiator capsases, activated by proximity

zymogens

form that inactive capsases are in

phosphatidylserine

usually on cytoplasm side of membrane, but flips to outside during apoptosis, annexin v binds to it

autophagy

the process by which cells recycle cytoplasm and dispose of excess or defective organelles

chaperone-mediated autophagy

chaperone proteins bring materials inside lysosome

macroautophagy

autophagosome fuses with lysosome, most important type of autophagy

Christian de Duve

1974 Nobel Prize for work in autophagy

Atg genes

autophagy-related genes in yeast that can be linked to some in humans, upregulation during starvation

LC3

essential for formation of lysosome, 1 is cytosolic form, 2 is membrane bound

2-deoxyglucose

cannot be metabolized by mammal cells

PI3K

lipid kinases that phosphorylate the 3’-hydroxyl group of phosphatidynolinositol and phosphoinositides

Vps34

leads to enlarged fatty liver

Atg5 knockout

neonates do not survive during lack of resources

hydroxychloroquine

treats malaria, reprotonated in lysosome

alkaline phosphatase

marker of liver and kidney function

340 nm

wavelength indicating high NADH, meaning high AST/ALT levels

specific activity

the ratio of enzyme activity to the amount of protein in the mixture

supernatant

cytoplasm area of centrifuged sample

velocity sedimentation

subcellular componenents sediment at different speeds based on size and shape, collected by puncturing plastic tube

equilibrium sedimentation

particles move until they match surrounding density

salting out

proteins are less soluble at high salt concentrations

UniProt

freely accessible database of protein sequence and functional information

X-ray crystallography

diffracted x rays hit crystallizable proteins to show electron density and determine structure

NMR spectroscopy

reveals structure based on proton density

Cryo-electron microscopy

elucidates structures

Knowledge-based methods

unknown primary structure is examined for compatibility with known structures

Ab initio predictions

without prior knowledge attempts to produce structure with lowest free energy

homology modeling

predicting structure based on known homologous proteins

Protein-ligand docking

predict and analyze binding between ligands and proteins

AlphaFold

AI program that predicts shape of protein

cannot predict mutations or how it interacts with ligands

Protein data bank

structures are published and can be accessed for visualization

Proteome

the whole set of proteins expressed in a cell at a particular time, not a fixed characteristic of the cell

Matrix-assisted laser desorption/ionization

produces ions using a laser energy absorbing matrix

usually combined with a time-of-flight detector

Quantitative proteomics

The measurement of the abundance of proteins across multiple diseases/states, reveals small molecule dynamics

sequencing

determining the exact order of the bases in a strand of DNA

Sanger sequencing

dideoxyribonucleoside triphosphates are used to prematurely terminate strands, which are then sorted by length and colored, producing a computerized visual of the base order

Illumina (next generation sequencing)

millions of short fragments are amplified on a solid surface

Principal component analysis

reduces data to 2 or 3 principal components

Volcano Plot

type of scatterplot that identifies events that differ significantly

Heatmap

data is represented by color

alignment

locating equivalent region of 2 or more sequences to maximize their similarity

sequence similarity

how alike two sequences are as a percentage

Homologous genes

derived from the same ancestor