MCAT biology Flashcards
What are the three physiological rooles of lipids?
- Triglycerides store energy
- Phospholipids constitute barrier between intra and extracellular environment
- Cholesterol is the building block for hydrophobic steroid hormones
Why are fats more efficient energy storage molecules than carbohydrates?
- Packing: Their hydrophobicity allows fats to pack together much more closely than carbohydrates
- Energy content: Fat molecules store much more energy than carbohydrates. More energy carbon-for-carbon than a carbohydrate
The lipid bilayer of phospholipids are stabilized by ___
van der Waals forces between the long tails
What are the structural determinants of lipid membrane fluidity?
- Degree of saturation
- Tail length
- amount of cholesterol
___is a triterpene and important in the synthesis and manufacturing of steroids, also a component of ear wax
Squalene, made of six isoprene units
What are the three reasons that phosphate anhydride bonds store so much energy?
- When phosphates link, their negative charegs repel each other strongly
- Orthophosphate has more resonance forms and thus a lower free energy than linked phosphates
- Orthophosphate has a more favorable interaction with water than linked phosphates
Two phosphates are linked by a high-energy bond called a ___
anhydride linkage forming pyrophosphate
What type of glycosidic linkages can mammals digest?
Mammals generally can difest alpha glycosidic linkages, but generally not B linkages
Nucleotides in the DNA chain are covalently linked by ___
phosphodiester bonds between the 3’ group of one deoxyribose and the 5’ phosphate group of the next deoxyribose
Centromeres are made of ____ and ___
heterochromatin and repetitive DNA sequences
___is a region of a chromosome that spindle fibers attach to during cell division
Centromeres
Spindle fibers attach to the centromere via ___ a multiprotein complex that acts as an anchor attachment site for spindle fibers
kinetochores
A single piece of double-stranded DNA; part of the genome of an organism. In prokaryotes it is circular and eukaryotes it is linear
chromosomes
What is the purpose of DNA gyrase?
DNA gyrase is used in prokaryotes to break and tist the two sides of the circular prokaryotic DNA, this aids in packing prokaryotic DNA and making it more sturdy
__are variations in a single nucleotide from one person’s DNA gene sequence to another’s. These minor mutations can produce changes in phenotype
Single nucleotide polymorphisms
___are regions of the genome where short sequences of nucleotides are repeated one after the other anywhere from 3 to 100 times
Tandem repeats
The enzymatic process of reading a strand of DNA to produce a complementary strand of RNA
Transcription
A structure made of two protein subunits, this is the site of protein synthesis (translation) in a cell
Ribosomes
What is the thermodynamic driving force for the polymerization and addition of nucleotides to new daughter DNA strands
The removal and hydrolysis of pyrophosphate (P2O7^4-)
___is repsonsible for super fast, super accurate elongation of the leading strand, NO KNOWN function in repair. Considered a replicative enzyme
DNA polymerase 3
___starts adding nucleotides at the RNA primer, it can only add 15-20 base pairs per second. It also removes the RNA primer and is very important in excision repair
DNA polymerase 1
During translation, the next codon to be translated is expose in the ___site
A site, since this is where the next amino acid to be added must bind
___is complementary to the pyrimidine-rich region on the samll subunit, helps position initiation machinery on the transcript for prokaryotes
Shile-Dalgarno sequence
What are differences between prokaryotic and eukaryotic translation?
- the ribosome is larger (80s) and has different components than the prokaryotic ribosome
- mRNA must be processed before it can be translated (spliced, with cap and tail added)
- N terminal amino acid is different (Met instead of fMet)
- mRNA must be transported from nucleus to cytoplasm to be translated, not simultaneous
Are the newly formed polypeptide chains emerging from a polyribosome in a eukaryote all the same?
UES, eukaryotic mRNA is monocistronic. In prokaryotes, different polypeptides may be translated from a single piece of mRNA
What two process may occur simultaneously on the same RNA molecule in a eukaryotic cell?
Transcription and splicing
___is the principle site of regulation of gene expression in both Eukaryotes and Prokaryotes
Transcripion
What are the two ways that DNA methylation turns off Eukaryotic gene expression?
- physically blocks the gene from transcriptional proteins
- Certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change the winding of DNA around histones
Silencing of a certain gene involves ___,___and___
- DNA methylation
- Histone modification
- binding of long ncRNA’s
In humans, X-inactivation occurs early in development, at the ___
blastocyst stage
What is the primary method of regulation of gene expression in Prokaryotes?
Regulation of transcription
The ___is an inducible
Lac operon
-Catabolic enzymes whose transcription can be stimulated by the abundance of a substrate are called inducible enzymes
The ___is repressible
trp operon is repressible
-Anabolic enzymes whose transcription is inhibited in the presence of excess amounts of products are repressible
What are the two components found in all operons
- coding sequence for enzymes
- upstream regulatory sequence or control site
What are the 4 regions of the lac operon?
- P site: the promoter site on DNA to which RNA polymerase binds to initiate transcription of Y,Z, and A genes
- O region: the operator site to which the Lac repressor binds
- Z genes: codes for the enzyme B-galactosidase
- Y gene: code for permease, a protein which transports lactose into the cell
- A gene: codes for transacetylase, an enzyme which transfers an acetyl group from acetyl-CoA to B-galactosides (not required for lactose metabolism)
What does the P region of the lac operon do?
P region is the promoter site on DNA to which RNA polyermase binds to initiate transcription of Y,Z, and A genes
What does the O region of the lac operon do?
The operator site to which the Lac repressor binds
What does the Z gene of the lac operon do?
The z gene codes for enzyme B-galactosidase, which cleaves lactose into glucose and galactose
What does the Y gene of the lac operon do?
Codes for permease, a protein which transports lactose into the cell
What are two genes that code for important proteins in the regulation of the lac operon?
- Crp gene: located at a distant site, this gene codes for a catabolic activator protein (CAP)
- I gene: located at a distant site, this gene codes for the Lac repressor protein
The ___gene codes for the lac repressor gene
I gene
The __lcodes for the catabolic activator protein (CAP) involved in the lac operon
Crp gene
If the operator is mutated so that the lac repressor can no longer bind, what effect will this have on transcription?
If the repressor cannot bind to the operator, RNA polymerase will transcribe all the genes on the operon continuously
___is a highly conserved DNA recognition sequence for the TBP, binding of TBP to this region initiates transcription complex assembly at the promoter in Eukaryotes
TATA box
TBP is tata box binding protein
IF a mutation in a eukaryotic fat cell reduces the level of several proteins related to fat metabolism, does this mean the proteins are encoded by the same mRNA?
No it does not. Eukaryotic mRNA is monocistronic. More likely number of genes located throughout the genome have regulatory sequences that bind the same specific transcription factors. This is the means used by eukaryotes to achieve coordinate expression of genes.
PRoteins that bind to enhancer sequences in eukaryotes to increase transcription
Activator proteins
A sequence of three nucleotides found in the antiocodon loop of tRNA, that is complementary to a specific codon in mRNA. The codon to which the anticodon is complementary specifies the amino acid that is carried by that tRNA
anticodon
Aminoacyl-tRNA site; the site on a ribosome where a new amino acid is added to a growing peptide
A site
A structure near the middle of eukaryotic chromosomes to which the fibers of the mitotic spindle attach during cell division
Centromere
A family of proteins that assists in the folding of other proteins
Chaperones
Structural variations in the genome that lead to different copies of certain sections of the DNA, due to duplication of those sections or deletions of those sections
copy-number variation
this is the enzyme that replicates DNA. Eukaryotes and prokaryotes have different versions of this enzyme
DNA polymerase
Stop codons and the poly-A-tail are found “__”
downstream toward the 3’ end
Proteins that assist with peptide bond formation during eukaryotic translation
Elongation factors
Changes in gene expression that are not due to mutations, but are long-term and heritable (DNA methylation, chromatin remodeling, and RNA interference)
Epigenetics
A nucleotide sequence in RNA that contains protein-coding information
Exon
A mutation casued by an insertion or deletion of base pairs in a gene sequence in DNA suh that the reading frame of the gene (and thus the amino acid seuqence of the protein) is altered
frameshift mutation
An enzyme that unwinds the double helix of DNA and separates the DNA strands in preparation for DNA replication
Helicase
A gene appearing in a single copy in diploid organisms (ex: X-linked genes in human males)
Hemizygous gene
Hetereogenous nuclear RNA; the primary transcript made in eukaryotes before splicing
hnRNA
Physical change to a gene on DNA, such as methylation or histone binding, that renders it inactive, so that only one allele of the gene is expressed
Imprinting
A system where the expression of those genes is stimulated by an abundance of substrate
Inducible system
Eukaryotic proteins that assemble in a complex to begin translation
Initiation factors
A nucleotide sequence that intervenes between protein-coding sequences. In DNA, these intervening sequences typically contain regulatory sequences, however in RNA they are simple spliced out to form the mature (translated) transcript
Introns
Multiprotein complexes that attach the spindle fibers to the centromere of a chromosome
Kinetochore
A set of genes for the enzymes necessary to import and digest lactose, under the control of a single promoter, whose expression is stimulated by lactose it is INDUCIBLE SYSTEM
lac operon
An enzyme that connects two fragments of DNA to make a single fragment. This enzyme is used during DNA replication and is also used in recombinant DNA research
ligase
A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid
Missense mutation
mRNA that codes for a single type of protein, such is found in eukaryotic cells
monocistronic mRNA
The monitoring of mRNA transcripts to eliminate those that are defective
mRNA surveillance
A structure composed of a ribose molecule linked to one of the aromatic bases.
nucleoside
A structure composed of two coils of DNA wrapped around an octet of histone proteins. It is the primary form of packaging of eukaryotic DNA
Nucleosome
Small fragments of DNA produced in the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand
Okazaki fragments
A specific DNA nucleotide sequence where transcriptional regulatory proteins can bind
Operator
A nucleotide sequence on DNA that contains three elements:
- coding sequence for one or more enzymes
- coding sequence for regulatory protein
- upstream regulatroy sequences where the regulator protein can bind
Operon
The speicifc location on a DNA strand where replication begins. Prokaryotes typically have a single origin of replication, while eukaryotes have several per chromosome
Origin of replication
The enzymatic activity of the ribosome that catalyzes the formation of a peptide bond between amino acids. It is thought that the rRNA of the ribosome possesses the peptidyl transferase activity
Peptidyl transferase
A type of mutation in DNA where a single base is substituted for another
Point mutation
A string of several hundred adenine nucleotides added to the 3’ end of Eukaryotic mRNA
Poly-A-tail
An RNA polymerase that creates a primer (made of RNA) to initiate DNA replication. DNA poly binds to the primer and elongates it
Primase
The sequence of nucleotides on a chromosome that activates RNA polymerase so that transcription can take place.
Promoter
Peptidyl-tRNA site, the site on a ribosome where the growing peptide (Attached to a tRNA) is found during translation
P site
A cytoplasmic protein that binds to a stop codon when it appears in the A_site of the ribosome. Release factors modify the peptidyl transferase activity of the ribosome, such that a water molecule is added to the end of the completed protein. This releases the finished protein from the final tRNA, and allows the ribosome subunits and mRNA to dossociate
Release factor
The site where the parental DNA double helix unwinds during replication
Replication fork
Multiple sites of replication found on large, linear eukaryotic chromosomes
Replication bubbles
A system (set of genes) where the expression of those genes is inhibited by the gene product (trp operon)
Repressible system
A regulatory protein that binds DNa at a specific nucleotide sequence to prevent transcription of downstream genes
Repressor
A structure made of two protein subunits and rRNA; this is the site of protein synthesis (translation) in a cell.
Ribosome
Small noncoding RNA’s that bind to mRNAs these double stranded RNAs are then degraded and gene expression is reduced
RNA interference (RNAi)
An enzyme that transcribes RNA. Prokaryotes have a single one while eukaryotes have 3
RNA polymerase
What are the functions of RNA polymerase 1 in EUaryotes
Transcribes rRNA
What is the function of RNA polymerase 2 in Eukaryotes
transcribes mRNA
The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5’ to the start codon
Shine Dalgarno sequence
A group of three nucleotides that does not specify a particular amino acid, but instead serves to notify the ribosome that the protein being translated is complete. The codons are UAA, UGA, and UAG, also known as NONSENSE CODONS
stop codon
Regions of the genome where short sequences of nucleotides are repeated one after another, anywhere from three to 100 times
Tandem repeats
An enzyme that cuts one or both strands of DNA to relieve the excess tension caused by the unwinding of the helix by helicase during replication
Topoisomerase
A point mutation in which a pyrimidine is substituted for a purine or vice versa
Transversion mutation
The type of RNA that carries amino acids from the cytoplasm to the ribosome for incorporation into a growing protein
tRNA
The attachment of an amino acid to a tRNA requires TWO HIGH ENERGY PHOSPHATE BONDS
tRNA loading
A set of genes for the enzymes necessary to synthesize tryptophan under the control of a single promoter, the expression of which is inhibited by the presence of tryptophan
trp operon
Enzymes that degrade various macromolecules and that require an acidic pH to function properly, these enzymes are found inside of lysosomes of cells
Acid hydrolases
A contractile protein. In skeletal and cardia muscle it polymerizes to form the thin filaments. IT is involved in many contractile activites, such as cytokinesis, pseudopod formation, and muscle contraction.
Actin
A carrier protein that transports two molecules across the plasma membrane in opposite directions.
Antiport
An integral membrane protein that undergoes a conformational change to move a molecule from one side of the membrane to another.
Carrier protein
A family of proteases that carry out the events of apoptosis
Caspases
The primary enzyme in peroxisomes
Catalase
This enzyme catalyzes the hydrolysis of hydrogen peroxide into water and oxygen
Catalase
An integral membran protein that binds extracellular signaling molecules, such as hormones and peptides
Cell surface receptor
A structure composed of a ring of nine microtubule triplets, found in pairs at the microtubule organizing center
Centriole
The__duplicates during cell division and serves as the organizing center for the mitotic spindle
Centriole
A fibrous protein found on the intracellular side of the plasma membrane that helps to invaginate the membrane.
Clathrin
Properties that depend on the number of solute particles in a solution rather than on the type of particles
Colligative properties
What are some colligative properties?
- boiling point elevation
- freezing point depression
- vapor pressure depression
A general cell junction used primarily for adhesion
Desmosome
A contractile protein connecting microtubules in the “9+2” arrangement of cilia and eukaryotic flagella
Dynein
A junction formed between cells, consisting of a protein channel called a connexon on each of the two cells, that connect to form a single channel between the cytoplasms of both cells.
Gap junctions
__allow small molecules to flow between the cell and are important in cell-to-cell communication
Gap junctions
A membrane lipid consisting of a glycerol molecule esterified to two fatty acid chains and a sugar molecule
Glycolipid
A stack of membranes found near the rough ER in eukaryotic cells that is involved in the secretory pathway.
Golgi apparatus
The__is involved in protein glycosylation (and other protein modifications) as well as sorting and packaging proteins
Golgi apparatus
A protein embedded in the lipid bilayer a cell. These are typically cell surface receptors, channels, or pumps
Integral membrane protein
Cytoskeletal filaments with a diameter in between that of the microtubule and the microfilament. __are composed of many different proteins and tend to play structural roles in cells
Intermediate filaments
A protein channel in a cell plasma membrane that is specific for a particular ion, such as Na+ or K+.
Ion channel
The double lipid bilayer that surrounds the DNA in eukaryotic cells
Nuclear envelope
A protein channel in the nuclear envelope that allows the free passage of molecules smaller than 60 kD
Nuclear pore
Small organelles that contain hydrogen peroxide produced as a byproduct of lipid metabolism. __convert hydrogen peroxide to water and oxygen by way of the enzyme catalase
Peroxisomes
__consists of a glycerol molecule esterified to two fatty acid chains and a phosphate group
Phospholipids
A pathway through a plasma membrane that restricts passage based only on the size of the molecule
Pore
A highly specific cellular uptake mechanism. The molecule to be taken up must bind to a cell surface receptor found in a clathrin-coated pit
Receptor-mediated endocytosis
The resting membrane potential is approximately __
-70 mV with respect to the otuside of the cell
A large system of folded membranes within a eukaryotic cell that has ribosomes bound to it, giving it a rough appearance. These ribosomes synthesize proteins that will ultimately be secreted from the cell, incorporated into the plasma membrane, or transportd to the golgi apparatus or lysosome
Rough endoplasmic reticulum
Active transport that relies on an established concentration gradient, typically set up by a primary active transporter. relies on ATP indirectly
Secondary active transport
A network of membranes inside the eukaryotic cells involved in lipid synthesis (steroids in gonads), detoxification (in liver cells), and/or Ca2+ storage (muscle cells)
Smooth endoplasmic reticulum
