Biology part 1 Molecules Flashcards
Consensus sequence
_ The most commonly found promoter nucleotide sequence recognized by a given species of RNA polymerase
_ variation from this sequence causes RNA polymerase to bond less tightly and less often to a given promoter
The template strand / antisense (-) strand
is the DNA stand that gets transcribed
_ the other stand is called the coding strand / sense (+) strand protecting its partner against degradation
Rho proteins (in transcription)
help to dissociate RNA polymerase from the DNA template at the termination sequence
Activators/repressors
_ bind to DNA close to the promoter and either activate or repress the activity of RNA polymerase
_ often allosterically regulated by small molecules such as cAMP
Enhancers
_ short, non-coding regions of DNA found only in eukaryotes
_ function similarly to activators but act at a much greater distance from the promoter
Jacob-Monod model of prokaryotic genetic regulation
the genetic unit consisting of the operator, promoter, and genes that contribute to a single prokaryotic mRNA is called the “operon”
ie. the lac operon in E.coli
Lac operon
is only activated if both of 2 conditions are met:
1: glucose is scarce
2: lactose is present
Low glucose => cAMP up and binds to CAP protein => CAP binds to CAP side adjacent to the promoter on the lac operon
For positive control: CAP binds to the promoter => transcription and translation of 3 proteins
For negative control: when lactose is not present, the lac repressor binds tother operator sites and prevents transcription. This inhibition is abolished when lactose is available and binds to the repressor.
Post transcriptional processing of RNA
Occurs both in eukaryotic and prokaryotic cells
In prokaryotes, rRNA and tRNA go through post transcriptional processing, but almost all mRNA is translated directly
Post transcriptional processing of RNA in eukaryotes
1/ helps the molecules that initiate translation recognize the mRNA
2/ protects the mRNA from degradation
3/ eliminates extraneous sequences of nucleotide
4/ provides a mechanism for variability in protein products produced from a single transcript
5’ cap
even before the mRNA is completely transcribed, the 5’ end is capped in a process using GTP
_ serves as an attachment site in protein synthesis during translation and protection against degradation
Ribozyme
an RNA molecule capable of catalyzing specific chemical reactions (snRNAs)
Start codon
AUG
Stop codons
UAA, UAG, and UGA
Prokaryotic ribosome
30S + 50S = 70S
Eukaryotic ribosome
40S + 60S = 80S
Nucleolus
A special organelle that makes the ribosomes
Prokaryotes dont have nucleolus but synthesis is similar to that of eukayotic ribosomes
Transition mutation
A base substitution exchanging one purine for another purine (A to G) or a pyrimidine to a pyrimidine (C to T)
Transverse mutation
A base substitution that includes a change from a purine to a pyrimidine or vice versa
Silent mutation
The type of neutral mutation in which the amino acid sequence is unchanged
Misssense mutation
When a base substitution changes a codon which results in the translation of a different amino acid
Could be neutral or detrimental
Nonsense mutation
A change in the nucleotide seq creates a stop codon where none previously existed
Frameshift mutation
When addition or deletion occurs in multiples other than 3
Chromosomal deletion
occur when a portion of the chromosome breaks off, or when a portion of the chromosome is lost during homologous recombination and/or crossing over events
Chromosomal duplication
occur when a DNA fragment breaks free of one chromosome and incorporates into a homologous chromosome
Chromosomal translocation
when a segment of DNA from one chromosome is exchanged for a segment of DNA on another chromosome
Chromosomal inversion
the orientation of a section of DNA is reversed on a chromosome
Synaptonemal complex
when crossing over occur, the 2 chromosomes are zipped along each other where nucleotides are exchanged
Chiasma
under the light microscope, a synaptonemal complex appears as a single point where 2 chromosome are attached, creating an X shape
Gene linkage
when genes on the same chromosome are located close together, they are more likely to cross over together, and are said to be linked
Single crossover
when crossing over occurs, the chromosomes may exchange sections of genetic information just once
Double crossover
when crossing over occurs, chromosomes may also trade a segment once and then trade back a sub-section of that segment so that each chromosome regains some of its own original genetic material
The first polar body
in the case of the female, one of the oocytes is much smaller and degenerates
This occurs in order to conserve the cytoplasm, which is only contributed to the zygote by the ovum
Nondisjunction
if during anaphase I or II the centromere of any chromosome does not split
one possible outcome of nondisjunction is having 3 copies of a single chromosome
Oogonia
Similar to the males, in the females the diploid oogonium undergoes mitosis to produce two primary oocytes. BUT unlike in males, this step in females primarily takes place before a female is born and the process does not proceed further until the female has reach puberty.
Primary oocytes remain arrested in prophase I of meiosis I until they receive the hormone signal to participate in the menstrual cycle
In meiosis 1 one daughter cell receives all of the cytoplasm and becomes a secondary oocyte, the other cell which receives no cytoplasm is the 1st polar body and discarded.
The resulting secondary oocyte, now haploid, begins the process of meiosis II but is arrested at metaphase II. In this arrested state, the secondary oocyte completes meiosis II only when penetrated by a sperm during fertilization.
The penetration initiates the completion of meiosis the completion of meiosis II, dividing the secondary oocyte into a second polar body, which is also discarded, and an ootid, which matures into an ovum
Spermatogonia
a spermatogonium (the diploid progenitor cell) undergoes mitosis to produce 2 diploid copies know as primary spermatocytes.
Each primary spermatocyte undergoes the reduction division of meiosis I to become 2 haploid secondary spermatocytes.
After the division of meiosis II, each secondary spermatocyte becomes 2 spermatids.
A spermatid undergoes a process of maturation in which it loses its cytoplasm and gains a tail to become a mature male gamete called “sperm”
Pentose Phosphate Pathway
Diverges from glycolysis and eventually merges back at glyceraldehyde-3-phosphate.
Its purpose is to create NADPH and some five carbon sugar, including ribose.
This pathway is constitutively active. While it occurs to some extent in all tissues, it occurs most commonly in tissues involved in lipid synthesis, such as in the liver and adipocytes.
This pathway is not regulated by an external hormone, but by NADPH, which inhibits the 1st step.
NADPH
used in various synthetic functions of the body, such as making cholesterol, and also acts as an antioxidant.
Glucoseneogenesis
liver cells have the unique property of being able to synthesize glucose from non-carbohydrate products, such as proteins and lactic acid.
Almost a reversed pathway of glycolysis. Only a few reactions with large delta G have enzymes that are distinct from those of glycolysis.
To be a substrate for gluconeogenesis, the substrate must have a 3-carbon backbone.
Thus, while glycerol can be used, fatty acids can not. Some, but not all, amino acids can be used. Lactic acid can be used.
Glycogen
a polymer of glucose molecules linked by a-1,4 glycosidic bonds.
Its primary substrate is glucose-6-phosphate
Glycogen synthesis uses 1 UTP, thus does not require ATP. Instead an inorganic phosphate is enzymatically added to each a-1,4 bound glucose.
Glycogen has an occasional a-1,6 glycosidic bonds that create side chains
Glucagon
promotes gluconeogenesis and glycogenolysis
Fatty acids
can be used in 2 different ways in the body
1/ used directly by the organ into which they diffuse. broken down into acetyl-CoA via beta-oxidation
2/ in the liver, converted into a new molecule, called a ketone body, which can be shared with other organs for energy, = Ketogenesis
Contain the greatest reducing potential per unit mass compared to carbohydrates and proteins
Fatty acids
can be used in 2 different ways in the body
1/ used directly by the organ into which they diffuse. broken down into acetyl-CoA via beta-oxidation
2/ in the liver, converted into a new molecule, called a ketone body, which can be shared with other organs for energy, = Ketogenesis
Beta oxidation
2 steps:
1/ fatty acids => acyl-CoA, costing 1 ATP along the outer membrane of the mitochondria
2/ Acyl-CoA => mitochondrial matrix, where it is cleaved two carbons at a time to make acetyl-CoA, producing FADH2 + NADH for every 2 carbons taken from the original fatty acid.
Acetyl-CoA then enters the TCA cycle. The glycerol backbone of the triglyceride is converted into an intermediate of glycolysis.
Beta oxidation works well for even chain fatty acids, BUT odd chain end with a 3 carbon fatty acid. These 3 carbon molecule and glycerol can be substrates for gluconeogenesis.
Ketogenesis
3 primary ketone bodies in humans: acetone, acetoacetic acid, and beta-hydroxybutyrate
Each of these is a small molecule with a carbonyl group, which allows them to dissolve in the blood stream via hydrogen bonding
The purpose of ketone bodies is to spare glucose for the brain and red blood cells by providing an alternative source of energy for the other organs.
HOWEVER, if needed the brain can use ketone bodies as an energy source as well.
Ketogenesis takes place in the mitochondria of liver cells. Fatty acids enters the liver and is processed into ketone body. Ketone bodies are not substrates for gluconeogenesis.
During starvation, energy for the livers come from fatty acids.
Lipoproteins
produced primarily in the liver, intestines, and adipcytes, and are expelled from these cells via exocytosis.
These are the primary transport molecules that carry lipids from the intestines to the liver.
The liver repackage chylomicrons as “very low density lipoproteins (VLDL) and high density lipoproteins (HDL).
Chylomicron
special type of lipoproteins produced by the intestines, contains higher ratio of lipid to protein
Very low density lipoproteins (VLDL)
transport lipids such as triglycerides, phospholipids, and cholesterol from the liver to the body, such as muscle and adipocytes
Lipase
an enzyme that hydrolyzes triglyceries and releases free fatty acids into the bloodstream.
Intestinal lipase tries to get triglycerides into cells.
Hormone sensitive lipase tries to get triglycerides out of cells (adipocytes)
Anabolism
= protein formation.
Occurs during the fed state and should be associated with glycolysis, glycogenesis, and lipid storage
Catabolism
= protein breakdown
Occurs during the fasting state and should be associated with gluconeogenesis, glycogenolysis, beta-oxidation, and ketone body synthesis.
Begins with the hydrolysis of amino acid chains in the small intestines.
Amino acids are connected by amide bonds, which can be hydrolyzed into an amine + carboxylic acid.
Amino acid break down
beings with the removal of the nitrogen group => producing ammonia + a carbon chain
Amonia is fed into the urea cycle to become urea, which is excreted in the urine
Blood glucose
ONLY can come from the intestines or the liver
Primarily regulated by insulin and glucagon, although epinephrine and cortisol are also involved.
Red blood cells and the brain
ALWAYS require glucose
Present a fixed and steady glucose demand
Glucose is one of the few molecules that can penetrate the blood-brain barrier
Red blood cells require glucose b/c they don’t have mitochondria => their metabolism is limited to fermentation in the cytosol.
All organs, except red blood cells, can also use ketone bodies for energy
What are the source of abundant glucose Immediately after a meal?
the intestines are a source of abundant glucose
When the supply of glucose coming from the intestines, metabolic pathways tends to use glucose and store excess glucose as glycogen and triglycerides = ALL organs will use blood glucose
What are the source of glucose a few hours after a meal?
The liver becomes the primary supplier of blood glucose
This is nowhere near as abundant as that which comes from the intestines during and immediately after a meal.
When glucose is being provided by the liver, metabolic pathways release glucose and fatty acids for use = Most organs will begin to use fatty acids from adipocytes
Muscles and their glucose
They have their own internal glycogen supply.
They keep glucose produced from their glycogen stores for internal use rather than releasing it.
They can use fatty acids as well.
Insulin
released from the pancreas in response to increased blood glucose levels and promotes glycolysis in all tissues, glycogenesis in the liver and muscle, fatty acid synthesis in the liver, and fatty acid storage in adipocytes.
Glucagon
released from the pancreas in response to decreased blood glucose levels and promotes glycogenolysis in the liver and muscle, gluconeogenesis in the liver, fatty acid release in adipocytes, and beta-oxidation in almost all tissues
What happens in late starvation?
the absence of insulin promotes ketogenesis
Epinephrine
is released in response to stress and, like glucagon, promotes glycogenolysis, the removal of glucose from storage.
Cortisol
is released in response to stress, but ONLY promotes gluconeogensis.
Hydrophilic hormones
such as insulin, epinephrine, and glucagon have receptors on the outside of the cell membrane
Hydrophobic hormones
such as cortisol, have receptors in the nucleus
Metabolic features of red blood cells
in fasting state, red blood cells rely upon liver gluconeogenesis for their glucose supply. They do not have the enzymes necessary to produce glucose themselves.
Red blood cells do not store glycogen, so they can’t have glycogenolytic pathways active.
They dont have mitochondria so they dont have the citric acid cycle.
The pentose phosphate pathway is used to generate NADPH, which will be used to reduce glutathione in red blood cells.
What happens to glycolysis when there is an abundant amount of ATP in the cells?
Glycolysis slows down b/c ATP phosphorylates fructose 6-phosphate, which allosterically regulates phosphofructokinase
ATP synthase
operates by brute force.
It forces the ADP and phosphate group to join by smashing them together
> positive delta G
Oxidative phosphorylation
occurs when oxidation reactions provide energy for phosphorylation
NAD+
consists of 2 nucleotides joined together by phosphate groups
NADH carries elections to the electron transport chain, acting as soluble electron carrier. The hydride ion serves as the source of electrons passed down the electron transport chain to oxygen, powering the movement of 3 x H+ into the intermembrane space of the mitochondria, empowering ATP synthase.
Most NADH comes from the TCA cycle
Acetyl-CoA
is a coenzyme that transfers 2 carbons (from pyruvate) to the 4-carbon oxaloacetic acid to begin the TCA cycle
TCA cycle
2 x carbons are lost as CO2, and oxaloacetic acid is regenerated
Each turn of the cycle produces 1 ATP, 3 NADH, and 1 FADH2, + 2 CO2
1 glucose molecule powers 2 turns of TCA cycle
Regulation is tied to the amount of NAD+ available
Electron transport chain
is a series of proteins that carries electrons from NADH to O2
These proteins include ubiquinone and cytochromes, which are intermediate electron carriers.
FADH2
works in a similar fashion to NADH, except that FADH2 reduces a protein further along in the ETC series, and thus only about 2ATP are produced for each FADH2, as compared to 2-3 ATP for each NADH, depending on whether an ATP was spent to transport NADH into the mitochondrial matrix
Net ATP of aerobic respiration including glycolysis
= 36 ATP
