WEEK 2 (STUDY GROUP) Flashcards
How does glucose enter the cell?
Facilitated diffusion through membrane transporters for glucose (the GLUT family)
What are the substrates and products of glycolysis?
1 glucose –> 2 pyruvate, 2 ATP (4 ATP is made, but 2 ATP are used) , 4 e (as NADH)
What gets glucose to glucose-6-phosphate?
Hexokinase + ATP
Where does glycolysis occur?
Cytosol
What gets fructose 6 phosphate to F-1,6-BP?
Phosphofructokinase-1, (PFK-1), ATP
What does fructose 1,6 BP break into and how?
DHAP (3 carbon) and G3P (3 carbon) through aldolase
Between DHAP and GA3P, which way does equilibrium lean?
Towards DHAP
After DHAP and GA3P is produced, there is another phosphorylation and there is rearranging to PEP. How does PEP convert into Pyruvate?
Pyruvate Kinase (phosphorylation), ATP
What happens to pyruvate in anaerobic conditions?
Pyruvate is reduced to lactate, catalyzed by a dehydrogenase and NADH donates its electrons. It happens in the cytosol. This produces the NAD + we need to continue oxidizing glucose!
What happens to glycolysis in aerobic conditions? How is NAD+ made?
A shuttle moves the NADH/FAD2H to the mitochondria where it is reoxidized to NAD+, thus allowing, it to continue oxidizing glucose. Either a glycerol 3 phosphate shuttle or a malate aspartate shuttle is used.
How does hexokinase regulate glycolysis?
It is product inhibited by glucose 6-P. It will downregulate the pathway from glucose to glucose 6 P, when there is already enough G6P
How does PFK 1 regulated? (PFK 1 is the enzyme that phosphorylates F6P to F1,6-BP)
It is upregulated by AMP and F-2,6-BP. F-2,6,BP is high in a well fed state, when insulin is high. When the state is well fed, then glycolysis will be favored. PFK-1 is downregulated by ATP and citrate (when ATP is already high, more is not neeeded)
How is the step from PEP to Pyruvate regulated?
It is upregulated by F-1,6-P (a product from earlier in the glycolysis pathway that ensures glycolysis continues downstream). It is downregulated by increased amounts of ATP.
How is fructose oxidized? How does it enter glycolysis cycle to make ATP?
Fructose –> Fructose 1 P (through kinase) –> DHAP and GAP (through aldolase). Then GAP –> GA3P (kinase), now it can enter glycolysis at the GA3P stage or the DHAP stage.
How is galactose oxidized? How does it enter glycolysis? (First Step. Galactose –> _____?)
Galctose 1-P through GALK (kinase) and ATP
How is galactose oxidized? How does it enter glycolysis? (2nd Step. Galactose –> Galactose 1-P –> _____?)
G1P –> UDP Galactose through GALT (transferase)
How does UDP Galactose –> UDP Glucose?
GALE (epimerase)
How is galactose oxidized? How does it enter glycolysis? (Galactose –> Galactose 1-P –> UDP Galactose –> UDP Glucose –> _____?)
Glucose 1-P, then Glucose 6-P and enters glycolysis
What are some of the biosynthetic functions of glycolysis?
Can make 5 C Sugars, Amino acids, Fatty acids
What is glycation?
Non enzymatic addition of reducing sugars to proteins
What are the 2 functions of the pentose phosphate pathway?
Generate NADPH (by reducing NADP). And to protect against reactive oxygen
When and where does glucogenesis occur?
In the liver, during fasting/starvation/low carb diet. More glucose is needed
Glucogenesis is the opposite of glycolysis. Except for one step which can’t be easily reversed. Which step is that and how does it occur instead?
Pyruvate –> PEP! Pyruvate goes into Mitochondria instead where it is converted into OAA through Carboxylase, CO2 and ATP.
How does OAA taken out of cytoplasm?
Converted into malate through transporter; converted into Asp through transporter; Converted straight into PEP (through PEPCK)
What is glycogen?
Storage form of glucose
How is glucose synthesized? What enzymes are used?
Glycogen synthase is the addition of glucose through activated intermediate UDP-glucose, and transferase is used
How is glucose degraded? What enzymes are used?
Glycogen phosphorylase removes single glucose molecules, a debranching enzyme moves 3 piece glucoses to the end of the chain
variant
single specific difference between genetic sequence of 2 ppl
tandem duplication
copy next to it
interspersed duplication
copy elsewhere
copy number variant
multiple copies in a row, varies in length
silent/synonymous
AA (amino acid) does not change
nonsynomous
a single AA is changed
nonsense
early stop codon
splice variant
disrupts splicing motif, severe but variable effects, cuases various splice errors like exon skipping on intron retention
loss of function
partial or total reduction of protein levels
gain of function
allele causes protein to function in a new way instead of the normal way (eg. TF activates wrong gene, or a signalling protein is always on)
exome
the entire protein coding of the genome, aka all the exons, only 1% of the human genome
what is the classification for variants
benign, likely benign, uncertain significance, likely pathogenic, pathogenic
- Why are genotypes described using 2 letters (i.e. C/C or C/G)?
Genotypes are described always using 2 letters because humans have 2 copies of every chromosome, one maternal and one paternal (another word for this is ‘diploid’). The 2 genotype denotes whether a variant is homozygous (both alleles the same) or heterozygous (one of each allele).
- What kinds of variants are most likely to result in a Loss of Function?
Loss of Function means an allele that is not able to make any protein of any function. This is usually caused by deletions (whole gene or large segments are missing from genome), or variants that result in a premature stop codon (nonsense, frameshift, some splice variants). These variants are sometimes referred to as ‘truncating’ variants.
- How might a single missense variant cause disease?
A single missense variant might cause disease through a Gain of Function – for example, causing a protein to misfold, which distorts the structure of the cell, which causes disease (this is what happens in Sickle Cell Disease). A single missense variant could also cause disease through Loss of Function – for example, a variant in a critical protein region that prevents a protein from binding to any partner (this happens in some forms of Hereditary Breast/Ovarian Cancer
What types of work is ATP hydrolysis used to power, and what are examples of each?
Mechanical (ex: conformational changes in proteins), transport (ex: ion pumps), biochemical (ex: coupling favorable & unfavorable reactions; generating activated intermediates; protein modification)
What is an oxidation-reduction reaction?
Chemical reaction that involves a transfer of electrons between 2 species
What does positive vs negative delta G for a reaction mean?
negative = spontaneous reaction, positive = non-spontaneous
What does delta G depend on?
substrate and product concentrations
What is the major cell type affected in Gaucher disease?
macrophage
What are the 3 major organ systems affected in Gaucher disease?
liver, spleen, bone marrow
What is the treatment for Gaucher disease?
enzyme replacement therapy: administer glucocerebrosidase every 2 weeks
What is the pathophysiology of Gaucher disease?
deficiency of glucocerebrosidase (breaks down glucocerebroside into glucose and ceramide) –> results in accumulation of glucocerebroside in macrophages
What are the sources of acetyl-CoA?
fatty acids, ketone bodies, pyruvate, ethanol
