Metabolism Flashcards
Difference between glucose and glycogen?
glucose - sugar in blood stream, glycogen - store glucose
Glucose is the sugar in our bloodstream that our body uses for energy. Glycogen is a stored form of energy. After eating, when there is too much glucose to be used, the extra glucose is converted to glycogen to be stored.
How does glucose become glycogen?
Glycogenesis
Glycogenesis is the formation of glycogen from glucose. Glycogen is synthesized depending on the demand for glucose and ATP (energy). If both are present in relatively high amounts, then the excess of insulin promotes the glucose conversion into glycogen for storage in liver and muscle cells.
What happens to glycogen if not used?
When the level begins to decline—either because you have not eaten or are burning glucose during exercise—insulin levels will also drop. When this happens, an enzyme called glycogen phosphorylase starts breaking glycogen down to supply the body with glucose.
Where is glycogen stored?
The two major sites of glycogen storage are the liver and skeletal muscle. The concentration of glycogen is higher in the liver than in muscle (10% versus 2% by weight), but more glycogen is stored in skeletal muscle overall because of its much greater mass.
Where does glycose come from?
Glucose or sugar comes from the food we eat. Carbohydrates such as fruit, bread pasta and cereals are common sources of glucose. These foods are broken down into sugar in our stomachs, and then absorbed into the bloodstream
how does insulin work on glucose
Insulin helps your body turn blood sugar (glucose) into energy. It also helps your body store it in your muscles, fat cells, and liver to use later, when your body needs it. After you eat, your blood sugar (glucose) rises. This rise in glucose triggers your pancreas to release insulin into the bloodstream.
How store lipids in body?
triglycerides - TAG
Lipolysis?
TAG- > glycerol + FA
Lipogenesis?
glycerol +FA -> TAG
Beta oxidation?
Fatty acids to Acetyl-Coa
Kreb cycle?
glucose and other molecules are broken down in the presence of oxygen into carbon dioxide and water to release chemical energy in the form of ATP.
If eating too much sugar and can’t use -
Lipogenesis
If breaking down Fats for energy?
Lipolysis (Glycerol + Fatty Acids) -
Glycerol -> DHAP
FA -> Acetylcoa (16c -> 8 x 2 c)
3 pathways (4) of gluconeogenesis?
AA, Lactic Acid, glycerol + Odd chain FA (17 on the chain so one space 3c to use)
Why do we need pentose phosphate pathway?
The pentose phosphate pathway is primarily catabolic and serves as an alternative glucose oxidizing pathway for the generation of NADPH that is required for reductive biosynthetic reactions such as those of cholesterol biosynthesis, bile acid synthesis, steroid hormone biosynthesis, and fatty acid synthesis.
glycolysis vs gluconeogenesis?
glycolysis makes ATP . Gluconeogenesis makes glucose
what do ribosomes do?
make proteins
endothelial cells?
The endothelium is a thin layer of single flat (squamous) cells that line the interior surface of blood vessels and lymphatic vessels. Endothelium is of mesodermal origin. Both blood and lymphatic capillaries are composed of a single layer of endothelial cells called a monolayer.
ependymal cells ?
are simple cuboidal cells that line the ventricles in the brain and the central canal in the spinal cord.
trophic center ?
Any part of the central nervous system whose proper functioning is thought to be necessary for the nutrition, growth, or maintenance of a peripheral part of the body; such as, the parietal lobe for the development of the muscles of an extremity.
What affects membrane capacitance?
The membrane capacitance is proportional to the cell surface area and, together with the membrane resistance, determines the membrane time constant which dictates how fast the cell membrane potential responds to the flow of ion channel currents.
Guillain-Barre syndrome
is a rare disorder in which your body’s immune system attacks your nerves. Weakness and tingling in your extremities are usually the first symptoms. These sensations can quickly spread, eventually paralyzing your whole body.
peroximsomes - refsum disease, Zellweger, adrenoleukodystrophy
synthesize cholesterol, bile acids and plasmalogenes (important membrane phosopholipid - esp white brain matter)
A major function of the peroxisome is the breakdown of very long chain fatty acids through beta oxidation. In animal cells, the long fatty acids are converted to medium chain fatty acids, which are subsequently shuttled to mitochondria where they eventually are broken down to carbon dioxide and water.
peroxisome vs lysosome?
They differ from lysosomes in the type of enzyme they hold. Peroxisomes hold on to enzymes that require oxygen (oxidative enzymes). Lysosomes have enzymes that work in oxygen-poor areas and lower pH. Peroxisomes absorb nutrients that the cell has acquired.
Protein catabolism,
done by peroxisomes, as well as ethanol catabolism
the breakdown of macromolecules, is essentially a digestion process. … The amino acids produced by catabolism may be directly recycled to form new proteins, converted into different amino acids, or can undergo amino acid catabolism to be converted to other compounds via the Krebs cycle.
kartagener’s syndrome - restaurant - take out only, there’s no Dynein
immotile cilia - dynin arm defect - auto recess
Charcot-Marie-Tooth disease (CMT)
is a group of inherited conditions that damage the peripheral nerves. It’s also known as hereditary motor and sensory neuropathy (HMSN) or peroneal muscular atrophy (PMA)
Diabetic neuropathy
is a type of nerve damage that can occur if you have diabetes. High blood sugar (glucose) can injure nerves throughout your body. Diabetic neuropathy most often damages nerves in your legs and feet
a connexon
also known as a connexin hemichannel, is an assembly of six proteins called connexins that form the pore for a gap junction between the cytoplasm of two adjacent cells. This channel allows for bidirectional flow of ions and signaling molecules.
labile cells - most affected by chemotherapy
hair follicles, skin, bone marrow, gut epitheleum, germ cells
are cells that multiply constantly throughout life. The cells are alive for only a short period of time. Due to this, they can end up reproducing new stem cells and replace functional cells.
amino acid residue
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
procollagen. - exocytosed step 4
Collagen is the main structural protein in the extracellular matrix in the various connective … This is not yet collagen but its precursor, procollagen.
What is phosphorylation in biology?
the addition of phosphate to an organic compound. Examples include the addition of phosphate to glucose to produce glucose monophosphate and the addition of phosphate to adenosine diphosphate (ADP) to form adenosine triphosphate (ATP).
Alport syndrome - Type 4 collagen, targeted by autoantibodies in Goodpastures
is a genetic condition characterized by kidney disease, hearing loss, and eye abnormalities. People with Alport syndrome experience progressive loss of kidney function. Almost all affected individuals have blood in their urine (hematuria), which indicates abnormal functioning of the kidneys.
type 2 cartilage?
vitreous body, nucleus pulposas, cartwolage, including hyaline
mannose 6 phosphate and ubiquitan
both have to do with destroying cells
SER
steroid synthesis and detox of drugs and poisons
location of glucose 6 phosphatase (last step in glycogenolysis)
Sterically inaccessible or accessible –>
follows TRANSCRIPTIONALLY inactive or active:
mitochondria and DNA?
circular, has it’s own, no histones
DNA - loops how many times around a histone? what’s the charge of a histone, and why
twice - w/ H1 histone linker H1 not part of nucleosome
histone + charge - from lysine and arganine
DNA - negative from Phosphate groups
cation- cathode vs anion, anode
molecule with positive charge, the positively charged electrode of an electrical device
anion - negative
Barr Bodies
inactive X chromosomes
DNA methylation
process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts to repress gene transcription
involved with aging, carcinogenesis, genomic imprinting, transposable element repression and inactivation of X chromosome
histone acetylation?
Acetylation makes DNA ACTIVE
removed histone’s + charge, relaxes coils therefore, transcription
NucleoSide v nucleoTide
Side - Sugar
Tide - phosphaTe
Tide has the PhosphaTe - only can make DNA, RNA - 5 arm links w 3 arm of prior nucleotide in chain - ONLY place to add on
Energy source for bond? in PhosphaTe
phosphodiester bond?
In DNA and RNA, the phosphodiester bond is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.
How is Thymine made?
Uracil is methylated - THYmine, meTHYlation
Deamination
Cytosine -> Uracil
Adenine -> Hypoxanthine
Guanine -> Xanthine
5-methylcytosine -> thymine
is the removal of an amino group from a molecule. Enzymes that catalyse this reaction are called deaminases. In the human body, deamination takes place primarily in the liver, however it can also occur in the kidney.
C-G bonds? 3
like Crazy Glue
Cats PURR until they GAG
purine synthesis - Glycine, Aspartate, Glutamine
Where are nucleotides found?
Nucleotides are the building blocks that constitute the RNA biopolymers found within living cells, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long and small noncoding RNAs.
helicase? ENZYME
unwinds strand, clips - uses ATP
single strand stabilization?
single stranded binding proteins - endonucleases would normally destroy the unzipped DNA _
RNA primers?
Primase - start the DNA replication process
Synthesis of DNA
DNA polymerase III (prokary); DNA polymerase alpha and delta (eukary)
removal of RNA primers (5’ - 3’ exonuclease
DNA polymerase I (prokary) - Rnase H (eukary
DNA gap fillers
DNA polyerase (prokary), Dna polymerase gamma - (eukary
Joining fragments
DNA ligase - first DNA polymerase I comes in and does some things - and then LIgase comes in at the end and snaps them together
supercoil hinge?
DNA gyrase (prokary) - topoisomerase (eukary)
telomeres
none (prokary), telomerase (eukary)
proofreading?
exonuclease - at end of strand - can cut off only last one - endonuclease can be in middle
ozaki fragments
lagging strand - A lagging strand is one of two strands of DNA found at the replication fork, or junction, in the double helix; the other strand is called the leading strand. A lagging strand requires a slight delay before undergoing replication, and it must undergo replication discontinuously in small fragments.
reannealing
zipping back up
gyrase (prokary) and topoisomerase (eukary)?
race ahead and nick DNA to deal with supercoils
wound healing?
needs ZINC and vitamin C - Zinc is cofactor - type 3 collagen 3 days onward - Type 1 collagen leaves a scar
wound healing
granulation tissue - type 3 collagen - MMPs - metal?
myofibroblasts help with would contraction
Capillaries provide nutrtion
Fibroblasts provide collagen
problems with wound healing?
can delay healing - also if uncontrolled diabetic (too much sugar)
Zinc, copper, Vit C, Foreign bodies , ischemia (bandage too tight, older people atherosclerosis), diabetes
Sclerodermia - autoimmunite, excessive?
excessive collagen - skin becomes stiff, hardened - other organs affected also like kidney
Collagenase?
degrades collagen - CT remodeling - wound healing, scarring
number of types of collagen?
29
What guides folding of proteins?
chaperones
how many levels of protein structures are there?
4 - primary formed during translation - others post translationally - - collagen not a primary structure
Kinases?
add phosphates
how to calculate BMI?
weight/height squared
50 kilos, 1.6 meters tall = 19.5
<18.5 underweight,
>25 - 30 preobesity
>30 Class I obesity
>35 Class II obesity
calories in carbs, proteins, fats?
4, 4, 9
BMR calculation DEE (how much you have to eat a day)
BMR - weight x 24 (50kilos x 24) = 1200 plus 30% of BMR if sedentary - ~~ 1600
two major buffers of blood?
bicarbonate and hemoglobin - phosphate also
buffers act in conjunction with what to maintain PH?
respiration - exhaling CO2 - and kidney’s excretion of protons
amino-acid residue?
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
two structural exceptions to amino acids?
glycine (no side chain) and proline (nitrogen is part of the ring)
L vs D configuration?
all are L in humans except glycine - that is neither - it is not “optically active”. It is the only one not an Asymmetric Carbon
D work for antibiotics
aliphatic
carbon atoms form open chains (as in the alkanes), not aromatic rings.
titration curves
are helpful in the identification of amino acids: The number of pKa values differentiates polar and nonpolar amino acids from charged amino acids. The position of the pKa values for charged amino acids allows one to identify positively charged from negatively charged amino acids.
polar vs non-polar AAs?
hydrophillic vs hydrophobic
If the R group is repelled by water, then it is hydrophobic (nonpolar), eg, valine; whereas hydrophilic (polar) amino acids are attracted to water, eg, arginine.
What do peptide bonds hold together?
The bond that holds together the two amino acids is a peptide bond, or a covalent chemical bond between two compounds (in this case, two amino acids). It occurs when the carboxylic group of one molecule reacts with the amino group of the other molecule, linking the two molecules and releasing a water molecule.
four different protein structures
primary, secondary (a-helices, B sheets); three dimension; fourth sub units
Covalent bond,
also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding.
denaturing
heat and urea - doesn’t affect primary structure
can undergo renaturation
is a disulfide bond covalent?
yes
When can ketone bodies enter the BBB?
when elevated in the blood - after 3 - 5 days of fasting - (skeletal muscles oxidize ketone bodies - from fatty acids from adipose, as fast continues, skeletal muscles will switch to oxidizing fatty acides, allowing ketone body levels to rise in blood) - blood still needs glucose as well - RBCs only use glucose
Can RBCs use fatty acids?
No, because RBCs have no mitochondria - needed for fatty acid oxidation
Does brain allow fatty acids to cross BBB?
Not usually, brain synthesizes its own fatty acids - and will use those
by convention - where are the N and C terminals located?
N on left - C on right
sickle cell anemia - is it more negatively charged than normal blood?
HbA (normal) HbS (sickle)
DRUG - hydroexurea treatment - increases levels of HbF in red blood cells which helps people - decreases HbS levels - note that this happens in adults for treatment - so HbF is not just in fetal situation
HbS has two fewer negative charges than HbA - mutation is E6V of both B chains rather than glutamate
Valine has hydrophobic side chain, Glutamate has acidic side chain - in deoxygenated state there is increased hydrophobic interaction - so if exercising or lack of oxygen - cell forms rigid rod within RBC
what binds at active sites?
substrates molecules and competitive inhibitors - allosteric and non-competitive do not (which reduce Vmax w/o affecting Kmax) ??
Michaelis-Menton equation
v=(Vmax x {S}/(Km + {S})
high altitude- trouble breathing, what can someone do to try to get hemoglobin to release oxygen more readily?
med: acetazolamide (carbonic anhydrase inhibitor) - which at high altitudes stabilizes deoxygenated form of hemoglobin - decreases pH via increased loss of bicarb in urine by inhibition of carbonic anhydrase w/in kidney - change in pH increases oxygen delivery - however if type 1 diabetic begins to produce ketone bodies to compensate - acidosis becomes more severe
deoxygenated blood needs to be stabilized, can occur by:
- decreasing PH
- Increasing CO2 concentration
- increasing concentration of BPG
2,3-Bisphosphoglycerate (BPG), also known as 2,3-Disphosphoglycerate (2,3-DPG), promotes hemoglobin transition from a high-oxygen-affinity state to a low-oxygen-affinity state.
does HbF have a greater or lesser affinity of HbA?
greater
scurvy, collagen problem marked by?
bleeding gums, teeth falling out, red spots on body -
Mutationsin fibrullin?
Marfans
lack of insulin?
diabetes
iron works with what?
iron is involved in heme synthesis - which regulates globin synthesis, absorption of iron in intestine stimulated by Vit C
ingestion of antifreeze leads to alkalosis or acidosis?
metabolic acidosis
Does folic acid increase Haemoglobin?
Folate is a B vitamin that your body uses to produce heme, the part of your red blood cells that contains hemoglobin. Without enough folate, your red blood cells can’t mature. This can lead to folate deficiency anemia and low hemoglobin levels.
carbonic anhydrase?
the enzyme carbonic anhydrase is used to balance the blood pH levels, and also to allow humans to breathe out CO2. It catalyzes the reaction to convert CO2 to carbonic acid, which breaks down into bicarbonate ions and protons.
panic attacked - hyperventilation - does pH go up or down?
UP! Acute respiratory alkalosis - usually less severe than metabolic alkalosis
antibiotics to be effective must be in what configuration?
D
malathion poisoning - farmer?
Exposure to high amounts of malathion in the air, water, or food may cause difficulty breathing, chest tightness, vomiting, cramps, diarrhea, watery eyes, blurred vision, salivation, sweating, headaches, dizziness, loss of consciousness, and death.
one of most common poisonings world wise - forms irreversible covalent bond between inhibitor and active site serine side chain inhibits acetylcholinesterASE in neuromuscular junction - without the ASE - acetylcoa accumulates in neuromuscular junction and causes these Sx
irreversible inhibitors?
bind tightly to enzyme and INACTIVATE it
non-competitive inhibitors
bind not at active site - decrease activity of enzyme (decreasing Vmax)
drugs used to inhibit enzymes?
cancer - 5FU
aspirin - pain - inhibits cyclooxygenase
Allopurinol - gout - (xanthine oxydase)
alcoholism - acetaldehyde leads to hangover symptons - inhibits aldehyde dehydrogenase
Baby dies when has heart attack, but lives 3 months first w/ no problems - why?
HbF has higher affinity for oxygen - lower affinity for BPG - as child matures and starts producing hbA - not enough oxygen
Mad cow disease? Cruesfeld Jacob Syndrome
prion disorder, misfolding second and tertiary structures -
gastric reflux?
drug omeprazoele - contains free sulgydryl group - forms disulfide bond with cysteine on gastric proton pump - inhibits gastric proton pump increasing pH of stomach
additional propane heater in apt - next day someone very hard to wake up, splitting headache, very tired, mucous membrane cherry red?
decreased oxygen delivery to tissue -
CO (carbonmonoxide) poisoning - CO bind to hemoglobin - has higher affinity than oxygen - in addition causes shifts oxygen binding to left, makes it more difficult for oxygen to be released ?? in presense of CO - oxygen affinity is increased
smoking, emphysema?
in a1-antitrypsin is absent - emphysema develops
decreased a1-antitrypsin activity in lung - lungs being destroyed by protease elastase - neutrophils in lung accidentally release elastase as destroy bacteria, etc - normally antitrypsin would bind to elastase and inhibit - but essential methionine side chain has been rendered inactive by smoking -
16 year old basketball player dies on court - shows increased intraventricular septum and left ventricular wall - what has mutated?
The MYH7 gene provides instructions for making a protein known as the beta (β)-myosin heavy chain. This protein is found in heart (cardiac) muscle and in type I skeletal muscle fibers. … The head region, called the motor domain, interacts with a protein called actin, which is important for cell movement and shape.
Beta-myosin heavy chain - died of FHC - cause of mutation in variety of sarcomeric proteins still unknown
Familial hypertrophic cardiomyopathy (FHC) is a disorder characterized by marked clinical and genetic heterogeneity. Patients with FHC can present with diverse clinical symptoms that range from mild dyspnea and chest pain to recurrent syncope, heart failure, and, most tragically, sudden death.
MYH7 is a gene encoding a myosin heavy chain beta (MHC-β) isoform (slow twitch) expressed primarily in the heart, but also in skeletal muscles (type I fibers)
lack of fibrillin - which can present with defective valves and aorta?
marfans - but doesn’t show heart greatly increasing in size
Alport’s syndrome
collage type 4 problem - kidney - basement membrane -
hearing loss, misshaped lens, , blood and protein in urine
type 4 collagen forms a meshlike structure - found in inner ear and eye also
mutation in spectrin?
hereditary spherocitosis
Why does pco2 decrease during hyperventilation?
Hyperventilation, sustained abnormal increase in breathing. During hyperventilation the rate of removal of carbon dioxide from the blood is increased. As the partial pressure of carbon dioxide in the blood decreases, respiratory alkalosis, characterized by decreased acidity or increased alkalinity of the blood, ensues.
most common type of RNA?
ribosomal
how do micrornas regulate gene expression
miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3’-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing
Charge of the amino acid side chains
At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
polar vs non-polar amino acids
What is the difference between polar and nonpolar amino acids?
Properties of amino acids are grouped based on the functional side chains (R), and one such property is hydrophobicity. If the R group is repelled by water, then it is hydrophobic (nonpolar), eg, valine; whereas hydrophilic (polar) amino acids are attracted to water, eg, arginine.
Amino acids can also be characterised as polar or non-polar and these dictate the amino acid function. There are 10 non-polar amino acids found in protein core, and there are 10 polar amino acids.
structure of DNA - stabilized by?
van der Waals forces, hydrogen bonds between complementary organic bases (a base pair), and hydrophobic interactions between the nitrogenous bases and the surrounding sheath of water.
What is pK value?
A measure of the strength of an acid on a logarithmic scale. The pK value is given by log10(1/Ka), where Ka is the acid dissociation constant. pK values are often used to compare the strengths of different acids
Why does pco2 decrease during hyperventilation?
During hyperventilation the rate of removal of carbon dioxide from the blood is increased. As the partial pressure of carbon dioxide in the blood decreases, respiratory alkalosis, characterized by decreased acidity or increased alkalinity of the blood, ensues.
tpn solution - needs all essential amino acids included
What type of solution is TPN?
Parenteral nutrition is by definition given IV. Partial parenteral nutrition supplies only part of daily nutritional requirements, supplementing oral intake. Many hospitalized patients are given dextrose or amino acid solutions by this method
Which of the following amino acids have polar uncharged side chains?
There are five amino acids that are polar but uncharged. These include serine, threonine, asparagine, glutamine and cysteine. Cysteine contains a thiol group that is responsible for creating disulfide bridges.
What are the four types of side chains found in the standard amino acids?
There are basically four different classes of amino acids determined by different side chains: (1) non-polar and neutral, (2) polar and neutral, (3) acidic and polar, (4) basic and polar.
Tryptophan
Tryptophan, an essential amino acid, is the largest of the amino acids. It is also a derivative of alanine, having an indole substituent on the β carbon. The indole functional group absorbs strongly in the near ultraviolet part of the spectrum.
Does hyperventilation cause acidosis or alkalosis?
Therefore, hyperventilation may be a cause of respiratory alkalosis or a compensatory mechanism for metabolic acidosis. Deep sighing respiration (Kussmaul breathing) is a common feature of acidosis (hyperventilation in an attempt to remove carbon dioxide) but may take some hours to appear.
What happens to blood pH during respiratory alkalosis?
During hyperventilation, serum pCO, decreases, serum pH increases, and serum bicarbonate concentration decreases. Hyperventilation causes a decrease in serum pCO2, as the lungs exhale more CO2 than in normal ventilation. According to Le Chatelier’s principle, the decreased serum CO2 level will drive the bicarbonate buffering system equilibrium (see the figure below) toward the left in an attempt to replace the lost CO2 and re-establish equilibrium.
Normally, the respiratory system keeps these two gases in balance. Respiratory alkalosis occurs when you breathe too fast or too deep and carbon dioxide levels drop too low. This causes the pH of the blood to rise and become too alkaline. When the blood becomes too acidic, respiratory acidosis occurs.
Why does
Hyperpolarizing the membrane potential cause an immediate reduction in the amount of potassium leaking out of a cell?
Hyperpolarizing the membrane makes the inside of the cell more
negative and therefore makes it more difficult for potassium to flow out of the cell.
