THE CELL TIM Flashcards
What are the four building blocks of life? How can these transition to disease?
lipids, carbs, proteins, nucleic acids
atherosclerosis
diabetes mellitus
sickle cell anemia
genetic disorders
What are the 8 broad causes for conversion from health to disease?
physical agents biological agents chemical agents lack of oxygen immunologic reactions nutritional imbalance genetic disorders endocrine imbalance
what are the three jobs of the cell?
survive
sense
respond
most abundant element on earth’s crust?
oxygen
what are the major elements of life? most abundant?
carbon
oxygen
hydrogen
nitrogen
carbon
after combining the 4 most abundant elements, which molecule of life is most plentiful?
water (60%) protein (20%) lipid (12%) minerals (6%) carbs (1.5%) RNA/DNA (0.5%)
what is the total body water percent intracellularly and extracellular?
60% intracellular fluid (28L)
40% extracellular fluid (14L)
how is the extracellular fluid broken down?
interstitial fluid (10.5L) 75% plasma (3L) 25%, note 93% H2O, 7% Protein and lipids transcellular fluid (1L) variable
T/F, non polar gases, such as oxygen and CO2, are poorly soluble in water, yet we depend on them getting into solution in order to get to or from cells?
T
this type of bond is most important in stabilizing the hydrophobic core of lipid bilayers and in stabilizing tertiary protein structure?
van der Waals bonds
what are the examples of saturated fatty acids discussed in class?
palmitate 16:0
stearate 18:0
what are the examples of monounsaturated fatty acids discussed in class?
oleate 18:1
what are the examples of poly unsaturated fatty acids discussed in class?
linoleate 18:2
linolenate 18:3
arachidonate 20:4
why do fatty acids exist in their salt form?
because the carboxyl group has a pKa of less than ambient pH so
palmitic acid=palmitate +H+
linoleic acid=linoleate +H+
so the polyunsaturated fatty acids cannot be produced by the body so they have to be consumed, what are they important in the synthesis of?
prostaglandins
leukotrienes
thromboxanes
what is the recipe for triglyceride (triacylglycerol (TAG) or neutral fat)?
three fatty acids and one glycerol
what is the recipe for a phosphatidate (the simplest phosphoglyceride but uncommon)? what is this the starting point for?
2 FFA, add a glycerol, one phosphate, an alcohol can be added if desired
glycerol based phospholipids in membranes
T/F, all cells including RBCs can synthesize phospholipids?
T
what are the most abundant lipids in the membranes?
phosphoglycerides
what are the different types of phospholipids?
phosphatidylcholine phosphatidyserine phosphatidyethanolamine phosphatidylinositol phosphatidylglycerol plasmalogen
phosphatidylcholine is also known as?
lecithin
phosphatidylglycerol is also known as?
cardiolipin (inner mito membrane and bacterial cell membrane)
this phosphglyceride is found primarily in heart membrane?
plasmalogen
what is a ceramide made of?
FFA and sphingosine
ceramide + phosphorylcholine produces?
sphingomyelin
sphingomyelins structure is very similar to what phospholipid?
phosphatidylcholine
where is sphingomyelin found abundant?
the glial cell membranes that insulate some neuronal axons, called the myelin sheath
what is a glycolipid comprised of? if a single sugar is added what is the structure called? sugar polymer?
ceramide and sugar
cerebroside (glucosylcerebroside and galactocerebroside)
ganglioside
how do gangliosides carry a negative charge?
they carry a N-Acetylneuraminic acid giving the polar head a negative charge
what are the three diseases due to abnormal glycolipid metabolism?
Tay-Sachs
Gaucher
Niemann-Pick
this type of molecule can insert in gaps in the lipid bilayer produced by the presence of c=c bonds
cholesterol
why are membranes important?
they define the limit of the cell
compartmentation of processes
allow adaptation because their composition can change
what properties of membranes enhance the chance of survival?
membranes are flexible
-fluid mosaic model
-movement of cell
-allow for growth of cell
self-sealing
-barrier remains intact after a minor tear
-cell division
-exocytosis
-increase intracellular calcium, SNARE/SNAP proteins,
hydrolysis of ATP
-endocytosis
selectively permeablewhat is the composition of membranes?
lipids (passive function)
proteins (active function)
sugars (recognition)
membrane turnover
what are some functions that take place at membranes?
transport
receptors
pumps
other (immunological functions, ECM attachment, interface with world)
what types of transport exhibit saturable kinetics?
active transport and facilitated diffusion
what is the most common type of active transport?
secondary active transport
what does not exhibit selectable kinetics?
facilitated transporters
HCO3/Cl
GLUT I glucose transporter (found in RBCs)
GLUTI
ubiquitous
GLUTII
liver, pancreatic islets, intestines
GLUTIII
brain/neurons
GLUTIV
muscle, fat, heart
which of the glut transporters is insulin-dependent?
glutIV
Na/K ATPase is what type of active transporter? secondary or primary active transport?
electrogenic antiporter, primary active transport
SERCA pump is what type of active transporter? secondary or primary active transport?
electrogenic uniporter, primary active transport
what are the factors hat increase membrane fluidity?
shorter length fatty acid chain
increased presence of unsaturated fatty acids
decreased cholesterol content of the membrane
what are the three primary types of lipids found in membranes?
phospholipids
glycolipids
cholesterol
name two disaccharides?
sucrose, lactose, maltose
name two oligosaccharides?
glycolipids and glycoproteins
name two polysaccharides?
glycogen, dextran, GAGs, cellulose
changing carbon #6 on glucose from -CH2OH to -COOH yields?
glucuronate
shifting the -COOH on glucuronate from above to below the pyranose ring converts it from glucuronate yields?
iduronate
amine groups can be added to hexoses to form?
hexosamines like glucosamine or galactosamine
what are the important components of GAGs?
glucuronate, iduronate, glucosamine, galactosamine
name the examples of GAGs?
Hyaluronan Chondroitan Sulfate Heparan Sulfate Heparin Keratan Sulfate Dermatan Sulfate
active functions of proteins?
enzymatic catalysis transport and storage movement support receptors and signaling immune system blood clotting control of growth/differentiation
amino acids in proteins are in what configuration?
L-configuration
what types of amino acids do not participate in hydrogen bonding? what else does this mean? where are they prevalent?
- non polar amino acids
- they are hydrophobic so the non polar R groups clump together
- core of globular proteins and in the transmembrane portion of membranous proteins
T/F, uncharged polar R groups are uncharged at physiological pH?
T (but cysteine and tyrosine do have pKs)
this also means they participate in H-bonding
what type of reactions are uncharged polar R groups involved in?
reactions that modify initial amino acid structures like post translational processing
in proteins, the -SH groups of the cysteines can form a dimer:cystine
what amino acids can be used as sites for attaching phosphate?
serine, threonine, tyrosine
when R groups are phosphorylated on a protein, what is the protein called?
phosphoprotein
what is the effect on protein configuration from protein phosphorylation? what amino acid is important to the enzymes that catalyze these reactions?
it adds a negative charge and changes protein configuration
serine
phosphorylating a catabolic enzyme does what to its activity? what does this do to an anabolic enzyme’s activity?
increases
decreases
what amino acids can be used to attach sugars?
asparagine
serine
threonine
what is produced when we add sugars to proteins?
glycoproteins, used for cell recognition
mucin
usually branched
what two amino acids can be used as condensation point for hydroxyapatite in calcified tissue?
proline(non polar) and lysine(basic), these are hydroxylated and then serve as condensation points for hydroxyapatite
this amino acid cross-links with another lysine, similar to how cysteine could form cystine?
lysine
by convention from left to right, what is the organization of the amino acid?
amine terminal to carboxyl terminal
the stiffness of hair is dependent on the number of what?
disulfide bridges between alpha helices creates cross linking of keratins
these types of proteins are fibrous proteins with a high% of B pleated sheets?
amyloid proteins
seen deposited in the brains of Alzheimers patients
what amino acids are involved in the B-turns?
proline and glycine
this is a 2ndry protein structure that refers to how neighboring alpha helices, beta sheets and beta turns are oriented to each other?
super secondary structures like greek key and B meander
motie
what do disulfide bonds give rise too?
tertiary structure
what is replication?
making a new set of DNA, reading DNA to write DNA
what is transcription?
making RNA from segments of DNA, read DNA to write RNA
what is translation?
making protein from an RNA code, reading RNA to write protein
A-T base pairs can form how many hydrogen bonds?
C-G base pairs can form how many hydrogen bonds?
2 hydrogen bonds
3 hydrogen bonds
what enzymes perform supercoiling and uncoiling?
DNA Gyrase
Topoisomerase
what are the five types of histones? what is the overall charge?
H1 H2A H2B H3 H4
positive charge
how can the charges on histones be altered post translationally?
methylation
ADP-ribosylation
phosphorylation
T/F, stem cells and cancer cell telomeres shorten?
false, they do not shorten
what do reverse transcriptase read and write?
they read RNA, but write DNA
how is prokaryotic replication accomplished?
semiconservative replication
what serves as the template for DNA polymerase?
ssDNA
what prevents and stabilizes the ssDNA?
single stranded DNA binding protein for prokaryotes and RPA for eukaryotes
what type of supercoils, negative or positive, are used to compact DNA while also making it easier to separate the strands for transcription?
negative supercoils
what type of topoisomerase is DNA Gyrase?
Type II, this enzyme produces negative supercoils for compacting DNA
what anticancer agents act by inhibiting human topoisomerase?
campothecins
Etoposides
what inhibits bacterial DNA Gyrase?
Flouroquinolones like ciprofloxacin, this produces an antibiotic effect
T/F, DNA polymerase can read in one direction and write in one direction?
T
this is the strand in which the DNA polymerase can just keep running right behind the fork, thus replication is completed?
leading strand
this is the lower strand that must wait until a primer can be produced before the DNA polymerase can begin? what are the short lengths of the new DNA that characterize called?
lagging strand
okazaki fragments
What is significant about DNA polymerase activity in prokaryotic replication?
DNA polymerases add 1 base at a time to the free 3’end of the new strand of DNA and write from 5’-3’
which polymerase does most of the work in prokaryotes?
DPIII
what are the three important activities of DPI in prokaryotic replication ?
DNA polymerase reads and writes DNA
5’-3’ exonuclease
3’-5’ exonuclease
what is exonuclease activity?
it removes a base and the polymerase then adds a new base
what is the effect of exonucleases in prokaryotic replication?
exonucleases allow DPI to correct mistakes and remove primers to be replaced with appropriate DNA
this enzyme is known as the ‘backspace’ in prokaryotic replication?
3’-5’ exonuclease
this enzyme is known as the ‘typeover’ in prokaryotic replication?
5’-3’ exonuclease
what is the KLENOW fragment in prokaryotic replication?
like DPIII which has no 5’-3’ exonuclease because it doesn’t remove the primer, found in the lagging strand
this DNA polymerase type, found in prokaryotic replication, is part of DNA repair?
DPII, it lacks 5’-3’ exonucleases and so there is proofreading between replications
t/f, all mitochondrial DNA is inherited from the mother? how can this be useful in clinical diagnosis?
T
we can use maternal lineage to track mitochondrial DNA
what are the different types of mutations that can occur in replication?
substitutions
transition
transversions
deletions
insertions
chemical
analogs
chemical reactions
interference
UVwhat are the significant differences from replication?
RNA is single stranded
only a portion of DNA is transcribed at a given time
transcription occurs throughout the cell cycle
because transcription is used to direct protein synthesis regulation of transcription is complex
what are the three major forms of RNA present in the cytosol?
mRNA
tRNA
rRNA
this type of RNA is the most diverse and least abundant?
mRNA
this type of RNA is more abundant than mRNA and represents 15% of the cytosolic RNA. This is the shortest of the RNAs and is from 75-95 bases in length?
tRNA
this type of RNA is the most abundant and least diverse?
rRNA
in order to perform transcription, what will we need?
double stranded DNA
ATP, GTP, CTP, UTP
RNA polyermase
signals to allow transcription to begin
is a primer required for transcription?
no primer is required
for transcription, what bond is formed when we add bases to the RNA strand?
phosphodiester bond (3’5’) on the free 3’ end of RNA
what direction does RNA polymerase read and write?
reads 3’-5’ (DNA)
writes 5’-3’ (RNA)
T/F, unlike the DNA polymerases, RNA polyermases have no exonuclease
T
why is there no exonuclease activity?
either because the RNA polymerase makes no mistakes or mistakes are not as critical for DNA
remember that a mistake in DNA sequence is handed down to all generations to come while RNA has a short life span
what are the types of mutations that can result from a point mutation?
silent mutation
missense mutation
nonsense mutation
what is the wobble hypothesis?
the first and second bases primarily determine the AA which is encoded for and there is significant wobbling allowed for the third
T/F, errors in RNA are not nearly as bad as DNA errors because the faulty RNA can be replaced?
T
for prokaryotes, how many RNA polymerase are there and what does this make?
what is it made of?
one
rRNA, tRNA, mRNA
2 alpha units, 2 beta units, and 1 sigma unit.
what is significant of the sigma unit in RNA polymerase for prokaryotes?
the sigma unit is used to recognize where to initiate transcription (the promoter site on DNA) and drops off when transcription begins (leaving behind the core enzyme)
what are the 3 distinct group of RNA polymerase in eukaryotes?
RNA polymerase I (rRNA),II (mRNA),III (tRNA)
where is the RNA polymerase I located in Eukaryotes?
nucleolus, and so this contains multiple copies of the rRNA that have to be clipped out using RNAase III
what are the three main stages of transcription?
initiation
elongation
termination
this subunit of the RNA polymerase is used to recognize the promoter site and so initiate transcription?
sigma subunit
how many genes does a promoter site control in eukaryotes and prokaryotes?
1 gene in Eukaryotes
multiple genes in prokaryotes
gene+control DNA results in?
operon
what are some mechanisms affecting initiation?
promoter site -transcription factors operator site -repressor protein regulator site -upstream, downstream, TF
what is an example of a repressor removed by binding with an inducer?
steroid hormone
for transcription, do we use the sense or antisense strand when coding for the protein?
antisense strand
what is the end point of transcription?
it is signaled by the DNA code, the palindromic sequence which is a poly-A sequence. The palindromic sequence allows RNA to base pair with itself and not with the antisense strand, destabilizing it
this protein terminates transcription?
the rho protein which is an RNA dependent ATPase which hydrolyzes ATP and uses the released energy to tug the RNA off the antisense strand
T/F, there is not one strand of DNA which is the sense strand with the other being the antisense strand?
T
how do we yield the final mRNA code for a protein?
we remove portions of the hnRNA to yield the final product
what RNA polymerase makes hnRNA?
RNA polymerase II
in post transcriptional processing, as the 5’ end of the RNA begins to emerge from RPII, what is added to that end?
a methylated G is added to the 5’ end and protects the hnRNA from rapid digestion and also is important for initiating protein synthesis
these enzymes clip out introns and splice exons?
snRNPs
what portion of the tRNA is the site of attachment of the specific amino acid?
3’ end
this part of the tRNA base pairs with the codon and is called this too?
anticodon
“decoder”
why is the DNA code said to be degenerate?
because 1 codon codes for only 1 amino acid, but 1 amino acid can have several different codons
so we know that the bacterial cell has 20,000 ribosomes, which make up 25% of the cell mass, what does this mean?
it indicates that protein synthesis is very active and important (adapting to new conditions)
in order for translation to occur, where must the ribosome assemble?
it assembles near the 5’ end of the mRNA
T/F, multiple ribosomes can be active on one strand of mRNA simultaneously and this called what?
T
polysome
what is the term used for the code for several proteins on mRNA translated by prokaryotes?
polycistronic
translation begins with what codon? to the left of this is what sequence?
AUG
shine delgarno sequence
the S-D sequence can base pair with a portion of which part of the rRNA?
16s, small subunit of the ribosome
what are the three initiation factors bound to the 30s subunit promoting its attachment to mRNA for prokaryotes?
how many eukaryotic initiation factors are there?
IFI
IFII
IFIII
9
which of the initiation factors (IF, eIF) is important for recognition of AUG by initiator tRNA?
IF2 or eIF2
what amino acid does the initiator tRNA bind with in eukaryotes? prokaryotes? (for the prokaryotes, what enzyme carries out this reaction?
methionine
formylmethionine by transformylase
what is the effect of the binding of met-tRNA?
release of IF1, IF2. IF3
hydrolysis of GTP
attachment of the large (50s) subunit
what site does the initiator tRNA project?
the P site
what is the third site to the left of the P site?
E site
this type of enzyme in prokaryotic translation breaks up the 3’ bond to the amino acid on the aminoacyl tRNA at the _____ site and forms a peptide bond between the freed amino acid and the AA of the aminoacyl tRNA at the A site?
peptidyl transferase
this enzyme in prokaryotic translation prompts hydrolysis of GTP to GDP+Pi and the energy is used to slide the ribosome 3 nucleotides in the 3’ direction? another name for this in eukaryotes and prokaryotes
translocase
EF-G in prokaryotes
eEF2 in eukaryotes
how much ATP is required per amino acid added?
4 ATP
2 ATP to attach AA to tRNA
1 GTP for EF-Tu
1 GTP for EF-G
note how GTP is a prime energy donor
what are the three stop codons and what signifies the end of elongate for translation?
UAA
UGA
UAG
when the anyone of the stop codons reaches the A site
how many prokaryotic releasing factors are there? what is the effect?
3 RFs, RF-1, RF-2 and a third RF-3 which binds to GTP and stimulates RF-1 and RF-2
the activated releasing factors cause the polypeptide to be released from the P site but not allowed to attach at the A site
each nucleated cell type in our body contains what kind of a set for the genetic code?
complete set
cells that selectively express some genes and not others result in what effect on the tissues of the body?
differentiation
differentiation results from the expression of what type of proteins in each cell?
unique proteins
T/F, we can get very different cells from very small variations in gene expression and regulation of which proteins are expressed determines differentiation?
T
in terms of regulating transcription, what are steroid receptors?
GRPs
how many unique cell types can be produced from the combination of 25 GRPs?
10,000 unique cell types
what are the gene regulatory proteins called? how?
master gene regulatory proteins (MGRPs)
controlling the expression of certain genes whose combinations result in cell types
how does gene regulation respond to changes in environment? how does protein kinase affect gene expression?
`some GRPs are bound to DNA but are only activated when they are phosphorylated
protein kinase can alter gene expression in some cases
how can we prevent early termination? )what must bind)
A regulatory protein must bind and stabilize the hnRNA to prevent the early palindrome from forming the loop
what happen in the absence of the stabilizing protein?
mRNA will not be produced
what is the average length of hnRNA? how much is made?
10 times longer than the mRNA produced from it, yet 1/20 is made
where is untransported mRNA catabolized?
nucleus
in translation, these proteins bind to mRNA and block translation? name an example too
what is the name of the proteins which promote translation of some mRNAs?
translation repressor protein (TRP); ferritin
translation enhancer proteins
shorter half life mRNAs encode for what?
regulatory proteins
how can mRNA stability be changed or regulated by signals?
these signals regulate the extent of response at the level of mRNA degradation, ie steroid signals increase transcription and inhibit mRNA catabolism to increase duration and effect of hormone
