Bio 2 Flashcards
What 5 things can gluconeogenesis make glucose from?
pyruvate lactate Krebs cycle intermediates glycerol carbon skeleton of glycogenic amino acids
What is one cell respiration molecule that can NOT be used for gluconeogenesis?
acety-CoA
Where does gluconeogenesis occur in the body? Where does it occur in cells?
can start in the mitochondrial matrix, but its mostly in the cytoplasm
major organ is the liver, kidney can also do some
What is required for gluconeogenesis?
ATP
Does gluoconeogenesis use the same enzymes as glycolysis?
yes except for the 3 irreversible steps
What enzyme converts G6P to glucose in gluconeogenesis?
glucose-6-phosphatase
What enzyme converts F1,6P to F6P in gluconeogenesis?
F 1,6 biphosphatase
What does pyruvate carboxylase do? What does it use?
converts pyruvate to OAA requires ATP (one for each pyruvate)
What does PEP carboxy kinase do? What does it require?
converts OAA to PEP requires GTP (one for each OAA)
What does PFK2 do?
converts F6P to F26P (regulatory molecule)
What regulates PFK2?
decrease in blood sugar gives increase in glucagon gives increase in cAMP activates PKA PKA inhibits PFK2
insulin stimulates PFK2
What does F-2,6-bisphosphatase do?
coverts F-2,6-P to F6P
How is F-2,6-bisphosphatase regulated?
PKA stimulates it (low blood sugar>glucagon>cAMP>PKA)
insulin inhibits it
What does F-2,6-bisphosphate do?
stimulates PFK and inhibits F-1,6-bisphosphatase
What effects does citrate concentration have on metabolism?
high citrate concentration inhibits glycolysis and stimulates gluconeogenesis
What effects do AMP and ADP concentration have on metabolism?
high AMP and ATP stimulate glycolysis and inhibit gluconeogenesis
What effects does ATP concentration have on metabolism?
high ATP inhibits glycolysis (and PFK) and stimulates gluconeogenesis
Describe the regulation of phosphofructokinase
stimulated by F2,6P and AMP
inhibited by ATP
Describe the regulation of fructose-1,6-bisphosphatase
inhibited by F-2,6-P and AMP
Describe regulation of isocitrate dehydrogenase
stimulated by ADP
inhibited by ATP and NADH
Where is glycogen found?
muscle and liver cells
What kind of bonds does glycogen have?
alpha 1,4 bonds with alpha 1,6 branches
glucose polymer
When do glycogenesis and glycogenolysis occur?
glycogenesis occurs when blood sugar is high
glycogenolysis occurs when blood sugar is low
What is the key enzyme in glycogenesis? How is it regulated?
glycogen synthase
stimulated by insulin
inhibited by glucagon and epinephrine
What is the key enzyme in glycogenolysis? How is it regulated?
glycogen phosphorylase
stimulated by glucagon and epinephrine
inhibited by insulin
What are the steps in beta-oxidation? What is produced?
oxidation-FADH2 produced
hydration
oxidation-NADH produced
cleavage
Where does beta-oxidation occur?
in the mitochondrial matrix
Where does fatty acid activation occur for lipid catabolism?
at the outer mitochondrial membrane?
How are activated fatty acyl-CoA molecules transported into the mitochondrial matrix for beta-oxidation?
via the carnitine shuttle
Where does lipolysis occur? How do fatty acids move through the blood and into target cells?
lipolysis occurs in adipocytes
fatty acids move through the blood bound to carrier protein i.e. albumin and then diffuse into target cell
If an 18 carbon fatty acid chain went through bet-oxidation what would the resulting molecules be?
8 FADH2 8 NADH 9 acetyl-cow which would make (in Krebs cycle): 27 NADH 9 FADH2 9 GTP
What is produced in the final cleavage of a fatty acid undergoing beta-oxidation?
NADH
FADH2
2 acetyl-CoA
Describe how unsaturated fatty acids are dealt with in lipid catabolism
if there is more than one cis double bond it is reduced by reductase using NADPH (makes NADP+)
when there is only one cis bond left isomerase coverts it into a trans bond
molecule then enters step 2 of beta-oxidation (hydration)
Where does lipid anabolism occur?
cytoplasm
What is the “committed” step in lipid anabolism? What enzyme performs this step? What is the reaction?
activation is the committed step
acetyl-CoA carboxylase performs it
turns acetyl-CoA into malonyl-CoA
What does malonyl-CoA regulate?
carnitine shuttle, so that fatty acids can’t go into the mitochondrial matrix
What are the 4 steps in biosynthesis of fatty acids? What enzyme is used? What molecule are used/produced?
enzyme = fatty acid synthase
1) elongation
2) reduction- uses NADPH and makes NADP+
3) dehydration
4) reduction- uses NADPH and makes NADP+
How does an increase in blood glucose affect fatty acid synthesis?
increase in blood glucose causes insulin to be released
which increases transcription and translation of both acetyl-CoA carboxylase and fatty acid synthase
How does a decrease in blood glucose affect fatty acid synthesis?
decrease in blood glucose causes glucagon and epinephrine to be released
which causes an increase in cAMP
which activates PKA
which inhibits acetyl-CoA carboxylase and stimulates lipase (for catabolism)
Where does ketogenesis occur?
in the mitochondrial matrix in the liver
What organs use ketone bodies made by the liver? When do they use them?
heart and central nervous system
use them during starvation or when glucose can’t enter cells i.e. type 1 diabetes mellitus
Name 3 ketone bodies
aceton
acetoacetate
beta-hydroxybutyrate
What are ketone bodies made from in the liver?
acetyl-CoA
How are ketone bodies metabolized?
transported through the blood
go into the mitochondria
are oxidized back to acetyl-CoA
enter the Kreb’s cycle
Can amino acids be stored or excreted?
no not as is
What is another name for protein anabolism?
translation
Where does deamination occur? What are the products?
in the liver
produces alpha-keto acids and NH3
What happens to NH3 produced by the deamination of amino acids?
go into the urea cycle
produce urea
are then excreted in the urine
What can alpha-keto acids be turned into?
glucogenic amino acids or ketogenic amino acids
Describe what the body does with glycogenic amino acids that it produces
they are turned into pyruvate or Kreb’s cycle amino acids
they then can go into cell respiration or gluconeogenesis
Describe what happens to ketogenic amino acids that the body produces
they are turned into acetoacetate then acetyl-CoA or directly into acetyl-CoA
they then go into fatty acid biosynthesis, ketogenesis or the Kreb’s cycle
Can ketogenic amino acids ever be turned into glucose?
no
Where does the pentose phosphate pathway occur?
in the cytoplasm
What are the products of the pentose phosphate pathway?
ribose-5-phosphate, NADPH, CO2 and metabolic intermediates
What is G6P dehydrogenase?
enzyme that catalyzes the oxidation of G6P in the pentose phosphate pathway, using NADP+ and making NADPH
What is a nucleoside?
sugar and base
What is a nucleotide?
sugar and base and phosphate
What holds DNA strands together?
H-bonds between bases
intermolecular forces between bases
hydrophobic interactions between bases
What is Tm?
the temperature at which a solution of DNA molecules is 50% denatured/melted
What would attaching the phosphate oxygens along a DNA double helix to methyl groups do to its Tm?
it would increase Tm because the charged phosphates repel each other
Describe a telomere
6-8bp that are repeated 50-1000 times
need special replication
have ~300 nucleotides ss at the end which loop around or bind proteins
What are centromere made of? What surrounds them?
made of heterochromatin repeats
surrounded by kinetochores
Which arm of the chromosome is q? Which one is p?
q is the long arm
p is the short arm
Describe the shape of viruses, prokaryotes and eukaryotes genomes
viruses- linear or circular
prokaryotes- 1 circular chromosome
eukaryotes- many linear chromosomes
How do the sizes of genomes of viruses, prokaryotes and eukaryotes compare?
viruses- 3200 to 1.6 million bp
prokaryotes- 10^6 bp
eukaryotes- 10^9 bp
How does the density of viral, prokaryotic and eukaryotic genomes compare?
viruses- very high density
prokaryotes- high density
eukaryotes- low density
How are viral genomes packed?
they have minimal packing
How are prokaryotic genomes packed?
they are supercoiled using DNA gyrase which requires ATP
How are eukaryotic genomes packed?
they are wrapped around histones to form nucleosomes which are then packed into chromatin and then chromosomes
What are tandem repeats?
short regions go variable length that repeat 3-100 times
useful in DNA fingerprinting
can cause disease if they are too many etc
ie Huntington’s
What is metacentric centromere positioning?
in the middle, both arms are the same size
What is submetacentric centromere positioning?
centromere is a bit closer to one end than the other, one set of arms is slightly smaller
What is acrocentric centromere positioning?
centromere is a lot closer to one end, one set of arms are much smaller than the other
What is telocentric centromere positioning?
centromere is at one end, there is only one set of arms
What do the simplest transposons have? What can they do?
inverted repeats, encode a transposase in the middle
after transcription and translation of the transposase, it can cut the transposon out of the genome and paste in another spot
What does a complex transposon contain?
inverted repeats with a transposase and gene(s) in the middle
What is a composite transposon?
when there are 2 transposons with inverted repeats on either side of a “central region” (part of the genome)
What is the start codon?
AUG (codes for Met)
What are the stop codons?
UAA
UAG
UGA
What is a balanced translocation? Unbalanced?
balanced translocation is when no info is lost
unbalanced is when some genetic info is lost or degraded
What effects can transposons have on DNA?
insertion mutations
deletions or inversions during recombination if there are 2 beside each other
What type of viruses can cause mutations?
lysogenic because they insert into the genome
What is direct reversal?
some bacteria and plants can directly reverse mutations i.e. pyrimidine dimers via photoreactivation
What are the two types of homology-dependent DNA repair?
excision repair
mismatch repair
When does excision repair occur?
during replication
cut out defective nt and replace with the right one
When does mismatch repair occur?
during or after replication
identify new vs old strands
cut out defective nts on old strand and replace
What are the two types of double-stranded break repair?
homologous recombination and non-homologous
What is homologous recombination? When does it occur?
occurs while cells are growing and dividing
uses sister chromatids to make a joint molecule and repair double-stranded break
What is non homologous recombination? When does it occur?
occurs when cells are not dividing
stabilize and ligate nonspecific DNA fragments
