Cell Exam 1
What relieve the tension in DNA in front of Helicase, caused by Helicase unwinding DNA
topoisomerases
What is a fat that is unsaturated by lays like a saturated fat?
trans fat
what is the process of making an RNA copy of the information originally stored in DNA?
transcription
what produces RNA that is complementary to one strand of DNA
transcription
What must assemble at each promoter, along with the polymerase, before transcription can begin (in eukary, these are a large group of accessory proteins that help recognize transcription)
transcription factors
what control the initiation of transcription in eukary and are much more elaborate than those that operate in prokary
transcription factors
What embedded in the plasma membrane control the passage of nutrients and other small molecules into and out of the cell
transporters and channels
T/F: atoms of more than 4 electron shells are rare in biological molecules
true
T/F: some covalent bonds involve more than one electron pair
true
G proteins have a natural ability to ______ ______ ____
turn themselves off
How many membranes does the mitochondria have?
two
how many strands does DNA have?
two (double helix)
When is the diameter of DNA more than it should be?
two purines together
When is the diameter of DNA less than it should be?
two pyrimidines together
Proteasomes act primarily on proteins that have been marked for destruction by the covalent attachment of a small protein called ________
ubiquitin
what is a little molecular marker that marks a protein for degradation by a proteasome?
ubiquitin
How can one rapidly adjust the structure of chromatin?
using ATP dependent chromatin-remodeling complexes
What amino acid is at location 147 in sickle cell?
valine
What are weak interactions that together create a bigger affect that help a protein hold its particular shape?
van der waals interactions
The antigen binding site is what holds the _________ region
variable
what ferries materials between one membrane-enclosed organelle to another?
vesicle
Which membrane-bound organelle are little packages that have to get passed around and released from the cell by fusing with the plasma membrane and then releasing its inner contents?
vesicles
how do proteins hold their shape?
via noncovalent interactions
how do mRNAs get into the cytoplasm?
via nuclear pores
Addition of _____ breaks polymer apart and the removal of _____ creates large polysaccharides
water
what does it mean to be hydrophobic
water fearing
what does it mean to be hydrophilic?
water loving
A large Km (Michaelis constant) means the substrate binds (tightly/weakly)
weakly
When can proteins bind to DNA?
when DNA gets distorted from its 2 nm width
What does DNA polymerase's exonuclease capability do?
when it is processing 5' to 3', and adds the wrong base, it can back up, cut it off, then keep synthesizing.
What is one way genes get turned on and off?
when proteins bind to the major groove of DNA, bending the DNA and changing the width
Detailed structure of an interphase chromosome can differ from one cell type to the next, helping to determine what?
which genes are switched on and which are shut down
Can DNA polymerase self-correct?
yes
Can eukaryotes be single celled?
yes
Do mitochondria contain their own DNA?
yes
does an acetyl group open up a histone to be modified? Like can the DNA be accessed
yes
can ionic bonds be formed in proteins?
yes (amino acids with different charges can associate)
Which model organism is transparent for the first two weeks of its life, providing the ideal system to observe how cells behave during development?
zebrafish
what match amino acids to codons in mRNA
tRNAs
the packing of fatty acid ______ facts the fluidity of the membrane
tails
5' capping occurs in eukary when...
takes place after RP2 has produced about 25 nucleotides of RNA
what replicates the ends of eukaryotic chromosomes?
telomerase
Why is it important to keep telomeres from shortening?
telomere shortening is associated with aging
What attract other telomere-binding proteins that physically protect chromosome ends and help maintain telomere length?
telomeres
what are ends of a chromosome
telomeres
what contains repeated nucleotide sequences that are required for the ends of chromosomes to be fully replicated
telomeres
what serve as a protective cap that keeps the chromosome tips from being mistaken by the cell as broken DNA in need of repair
telomeres
Does RNA polymerase read the coding strand or the template strand?
template strand
what is electronegativity?
tendency of an atom to attract electrons
As helicase moves forward, prying open the double helix, what problem does this cause?
tension in the DNA occurs and increased coiling further up makes the unwinding of the double helix increasingly difficult, ultimately impeding the forward movement of replication
Elongation of mRNA continues until the enzyme counters a second signal in the DNA, the _______, where the polymerase halts and releases both the DNA template and the newly made RNA transcript
terminator
what make up the majority of the chemicals in the body?
the 4 major biomolecules
What work together in a quaternary structure to function hemoglobin?
the 4 polypeptide chains
What allow mRNA to be transported through nuclear pore?
the addition of a cap binding protein and poly-A-binding protein
what shows that a distinctive type of chemistry operates in biological systems?
the fact that organisms are made up predominantly of C, H, O, and N
A copied DNA strand (newly synthesized) is identical to what strand
the former partner of the template strand
Why is cancer more prevalent in the elderly?
the longer we live, the more mutations build up and are not fixed.
Why can alpha helices cross the lipid bilayer
the outside of the helix may be hydrophobic but the inside could be hydrophilic, allowing water-loving things to enter the cell
Why can you not synthesize 3' to 5'?
the phosphate that you need to link are not in the right spot to take advantage of them.
If the ligand binds too tightly to the protein, what can happen?
the protein becomes inactivated
quarternary structure
the shape resulting from the association of two or more polypeptide subunits.
if you have 2 strands of DNA, one of them is the code for the RNA. The other strand is complimentary to the code. Which strand does the RNA read?
the strand complimentary to the code.
Why can there be genes on both strands of DNA (in the same location just on different strands)?
the strands run antiparallel, so they get read differently
Why is it so difficult to "wash away" skunk spray when your doggie get sprayed?
the thiol group in skunk spray binds to cysteines in dog hair/fur because the cysteines get oxidized when exposed to oxygen, causing disulfide bridges between skunk spray and dog hair (so, can't just wash away, must add hydrogens back in to break those bonds)
What causes DNA to be bidirectional?
the two forks moving away from the origin in opposite directions
what allows DNA polymerase to self-correct its mistakes?
their 3' to 5' exonuclease capabilities
Why are phosphate groups so high in energy?
their negative charges next to each other make them extremely unstable, unhappy, and reactive. So, they're looking for any reason to break
Why are the nitrogenous containing rings of DNA/RNA referred to as "bases"?
they act as a base in acidic conditions
When proteins bind to the major groove, what do they do to the DNA?
they bend the DNA (changing the width to more than 2nm)
Why are prions considered infections?
they can spread from an affected individual to a normal individual
why are oxygen radicals bad for a cell?
they have the potential to break apart other things because the radical will take an electron from whatever it can, often taking it from biomolecules that result in the breakdown of the biomolecule
What is the group called at the end of a cysteine side chain?
thiol
Which genes are transcribed and translated most often?
those that encode for proteins that continuously need replaced
How does an enzyme recognize its substrate?
through the formation of multiple noncovalent bonds
use of _____ rather than uracil further enhances DNA's stability by making it easier to repair
thymine
what occurs when adjacement thymines form a covalent bond in the presence of UV light, altering the diameter of DNA
thymine dimer
A small Km (Michaelis constant) means the substrate binds (tightly/weakly)
tightly
What add extra functions to proteins?
tightly bound molecules
Cells are _______ _______, deploying a wide variety of mechanisms to make sure that each of their chemical reactions occur at the right place, time, and rate
tightly regulated
Fibrous proteins have a lot of _______ strength, the strength that it takes to pull something apart and break it
tinsel
Dogma of Molecular Biology
The processes of DNA replication, transcription, and translation
What is a transcriptome
The transcripts actually encoded for by the genes within a genome
Why do proteins have a 3D shape?
Their 3D shape is their lowest energy conformation. They have a natural, lowest energy conformation. Hydrophobic interactions, ionic charges, noncovalent interactions, and more make a protein take on a certain 3D structure.
Why can not every protein begin with methionine?
Methionine gets cleaved as a post-transcriptional modification
How does splicing work?
There are some discrete characteristics of every intron. There will be a highly conserved (always in the same place) nucleotide. There will be an A in a very particular spot. There will be little proteins that can recognize intron/exon junctions. These proteins will interact with each other and line up over the conserved A, forming a little loop (lariat structure). These proteins that recognize the intron/exon junctions will interact with each other, form a lariat, then splice out. The two exons can not be brought together and reformed in their sugar-phosphate backbones.
Complex humans have (more/less) genes
More
How does an organism/DNA know WHICH strand is messed up?
Newly synthesized one is not methylated yet
Are all protazoans predators?
No
Are mRNAs the bulk of RNAs in a cell?
No
Are ribonucleic acids stable?
No
Are viruses alive?
No
Can DNA fold into a variety of sahpes?
No
Do prokaryotes have introns?
No
Do prokaryotes have organelles?
No
Does RNA polymerase need to have proofreading abilities?
No
Does RNA primer synthesize DNA?
No
Does RNA remain H bonded to the DNA template strand?
No
Does depurination break the DNA phosphodiester backbone?
No
Does primase proofread its work?
No
Does the RNA primer have to be complementary to the DNA?
No
Does the amount of DNA in cells correlate with the complexity of the organism?
No
Does the amount of genes correlate to the amount of DNA?
No
Does the newly formed RNA anneal with the DNA template?
No
If DNA polymerase were able to synthesize in the opposite direction, would it be able to proofread?
No
Is homologous recombination necessary to fix?
No
Is the replication fork symmetrical?
No
can RNA polymerase II (RP2) initiate transcription on its own?
No
Is cell division always exactly equal?
No (It is disproportionate of the cytoplasm and cell, but it is equal of one nucleus into two)
If one strand of DNA is damaged, is the information entirely lost?
No (due to the backup version of the altered strand remains in the complementary sequence of nucleotides on the other strand)
did watson and crick do any lab work?
No (just looked at data from other research(
Are Double stranded DNA breaks easy to repair?
No (they're extremely difficult)
Are bacteria and archaea closely related?
No, they differ from each other just as much as either does from eukaryotes
What occurs in many cell types and is carried out by a specialized group of enzymes that "clean" the broken ends and rejoin them by DNA ligation, but is a risky strategy for fixing broken chromosomes? (cleaning the break to make it ready for ligation, nucleotides are often loss at the site of repair, possibly disrupting the activity of a gene)
Nonhomologous end joining
What are the fragments on the lagging strand called?
Okazaki Fragments
Why is transport of mRNA from the nucleus to the cytosol highly selective?
Only correctly processed mRNAs are exported and therefore available to be translated
How do viruses replicate?
They parasitize the reproductive machinery of the cells they invade to make copies of themselves
Why does A always pair with T and C always pair with G?
This complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement along the interior of the double helix. So, In this arrangement, each base pair has the same width, thus holding the sugar-phosphate backbones an equal distance apart along the DNA molecule
How did mitochondria originate?
Thought to derive from bacteria that were engulfed by some ancestor of the present-day eukaryotic cells, this fostered a symbiotic relationship in which the host eukaryote and the engulfed bacterium helped each other survive and reproduce
How does one prep a slide for electron microscopy?
Tissue often has to be fixed (preserved by pickling in a reactive chemical solution, supported by embedding in a solid wax or resin, cut (sectioned), into thin slices, and stained before viewing
Which microscope transmits a beam of electrons rather than a beam of light through the sample?
Transmission electron microscope
What kind of nucleotides get brought in for DNA replication?
Triphosphate nucleotides
T/F ribosome is a ribozyme
True
T/F: All living cells have evolved from the same ancestral cell
True
T/F: Although the atoms buried in the interior of a protein have no direct contact with ligand, they provide an essential framework that gives the surface its contours and chemical properties
True
T/F: Although the precise order of their amino acids give proteins their shape and functional versatility, sometimes amino acids by themselves are not enough for a protein to do its job
True
T/F: Antibodies binds to a specific target molecule EXTREMELY tightly, either inactivating the target directly or marking it for destruction
True
T/F: Cells have similar basic chemistry
True
T/F: DNA must continuously be pried apart so that the incoming nucleoside triphosphates can form base pairs with each template strand
True
T/F: Enzymes can be used over and over again
True
T/F: Eukaryotic transcription initiation must deal with the packaging of DNA into nucleosomes and higher-order forms of chromatin structure
True
T/F: Every Okazaki fragment needs a primer
True
T/F: High fidelity with which DNA sequences are replicated and maintained is important for BOTH germ-line cells and somatic cells
True
T/F: If a DSB occurs in a double helix shortly after that stretch of DNA has been replicated, the undamaged copy can serve as a template to guide the repair of both broken strands of DNA
True
T/F: Just because the majority of the hydrophobic side chains are in the core of the protein, doesn't mean there could still be some hydrophobic side chains outside of the core
True
T/F: Most cell types express only about half of the genes that they contain, many only active at low levels
True
T/F: Most synthetic catalysts are nowhere near as effective as naturally occurring enzymes in terms of their ability to speed the rate of chemical reactions
True
T/F: One protein does not necessarily have just one function
True
T/F: Only when the match is correct between an incoming nucleotide and the template strand does DNA polymerase undergo a small structural rearrangement that allows it to catalyze the nucleotide-addition reaction
True
T/F: Prokaryotes can use oxygen to oxidize food
True
T/F: Protein kinases and phosphatases work together as a couple
True
T/F: RNA doesn't need to unwind DNA, it temporarily opens a small area of DNA (like a transcription bubble)
True
T/F: RNA polymerase will read the entire DNA strand, including introns
True
T/F: RNA polymerases can start an RNA chain without a primer and do not accurately proofread their work
True
T/F: RP2 must be released from the complex of general transcription factors to begin making the RNA molecule
True
T/F: Separating a short length of DNA a few base pairs at a time therefore does not require a large energy input and the proteins can unzip short regions of the double helix at normal temperatures
True
T/F: Since protons can be passed readily to many types of molecules in cells, which alters the molecules' character, the H+ concentration (pH) inside a cell must be closely controlled
True
T/F: There is a lot of DNA in an organism that is "non-coding," it doesn't necessarily have the instructions to encode a protein
True
T/F: Van der Waals forces occur in all types of molecules, even those that are nonpolar and cannot form ionic or hydrogen bonds
True
T/F: While RNAs are single stranded, they're capable of forming double stranded structures
True
T/F: almost every human gene has a counterpart in the mouse
True
T/F: at conception (once we are a zygote), we have all the information needed to make proteins, grow, divide, etc.
True
T/F: both strands of DNA are capable of being a template to copy
True
T/F: both strands of DNA must be copied at the same rate, despite one being continuous and one discontinuous
True
T/F: cells have a relatively narrow range of temperatures allowed for them to function optimally
True
T/F: cells have very distinctive, positional relationships of things
True
T/F: centromeres are specialized pieces of DNA
True
T/F: chloroplasts are not found in animal cells and fungi
True
T/F: chloroplasts are similar to mitochondria, just have a different function
True
T/F: chromatin can describe how tightly packed the DNA is
True
T/F: chromosomes contain both DNA and proteins
True
T/F: covalent modifications can also control the location and interactions of proteins
True
T/F: differences in branching for polysaccharides make a difference in the structure and function
True
T/F: different domains of a protein are often associated with different functions
True
T/F: double-stranded RNA is antiparallel
True
T/F: enzymes often work in sets
True
T/F: eukaryotic genomes have the capability to replicate a large genome much more rapidly
True
T/F: even bacteria contain proteins that are distantly related to those that form the cytoskeletal elements involved in eukaryotic division
True
T/F: every protein starts with an initiator tRNA with methionine
True
T/F: for a ribosome to function, both the large subunit and small subunit have to come together
True
T/F: genome organization does not define the complexity of an organism. It is where the genes are relative to other genes within the genome that influence the phenotypic manifestation of what we see
True
T/F: if we change the pH, a protein will change its confirmation. However, it IS possible to change the pH back and the protein will go back to its original conformation
True
T/F: in all cells the genetic material is constructed out of the same chemical building blocks, interpreted by similar chemical machinery, and replicated in the same way during reproduction
True
T/F: in prokaryotes, translation occurs simultaneously with transcription (directly after transcription)
True
T/F: in some organisms, there may be duplicate copies of a gene
True
T/F: increased length of a poly-A tail increases the lifespan of an RNA
True
T/F: individual chromosomes tend to occupy discrete locations within the nucleus
True
T/F: just because there are multiple copies of a gene in an organism, this doesn't mean that there will be twice as much RNA produced
True
T/F: lots of DNA in eukaryotes is junk DNA (doesnt encode for proteins)
True
T/F: most isotopes of all the elements occur naturally
True
T/F: most mutations do not affect the organism in a noticeable way
True
T/F: most require assistance of chaperone proteins, which steer them along productive folding pathways and prevent them from aggregating inside the cell
True
T/F: much of the DNA that is folded into heterochromatin does not contain genes
True
T/F: one gene makes one polypeptide chain
True
T/F: only living cells can perform the feats of self-replication
True
T/F: polysaccharides can be linear and/or highly branched
True
T/F: post-translational modifications are often needed for a newly synthesized protein to become fully functional
True
T/F: prokaryotic ribosome can readily bind directly to a start codon that lies in the interior of an mRNA, as long as a ribosome-binding site precedes it by several nucleotides
True
T/F: proofreading takes place at the same time as DNA synthesis
True
T/F: ribosomes are found in general locations
True
T/F: some chromosomal regions are physically attached to particular sites on the nuclear envelope or nuclear lamina
True
T/F: some plants depend on prokaryotes for photosynthesis
True
T/F: some prokaryotes die in the presence of oxygen
True
T/F: some proteins fold spontaneously, as they emerge from the ribosome
True
T/F: some proteins have to be transcriptionally modified to become activated while other proteins can naturally form into their lowest energy conformation tertiary structure
True
T/F: synthesis of the next RNA is usually started before the first RNA has been completed
True
T/F: the binding of a protein to other biological molecules always shows great specificity: each protein molecule can bind to just one or a few molecules out of the many thousands of different molecules it encounters
True
T/F: the biological functions of proteins, nucleic acids, and many polysaccharides are dependent on the particular sequence of the subunits within the chain
True
T/F: the bonds that hold together a polypeptide involve atoms in the polypeptide backbone AND atoms within the amino acid side chains
True
T/F: the catalytic activities of enzymes are often regulated by other molecules
True
T/F: the cell interior is in constant motion
True
T/F: the longer you live, the more methylation that occurs in DNA, which can influence which genes get expressed
True
T/F: the noncovalent bonds of macromolecules determine the chemistry and activity of the macromolecules and dictate their interactions with other molecules
True
T/F: the positions of a gene are also important relative to other positions of other genes
True
T/F: there are proteins that are accessory components to RNA
True
T/F: there is an antiparallel beta sheet
True
T/F: there was an RNA world before DNA
True
T/F: transport of mRNA from the nucleus to the cytosol is highly selective
True
T/F: various organelles are often times positioned related to other organelles because of the interactions between them
True
T/F: without the sliding clamp, DNA polymerase would only synthesize a short string of nucleotides before falling off the DNA template strand
True
T/F: you can have two separate polypeptide chains or one chain and two separate cysteines held together by a disulfide bridge
True
T/F: we can use some amino acids to make other amino acids
True (can use aspartic acid to make lysine)
Why can we not digest cellulose?
Our enzymes do not recognize the glycosidic bonds in cellulose.
Amino acid is then linked to the growing peptide chain, which is held in place by the tRNA in the neighboring _ site
P
In eukaryotes, initiator tRNA is charged with methionine and loaded into the _ site of the small ribosomal subunit, along with additional proteins called translation initiation factors ***this tRNA is different from the tRNA that normally carries methionine***
P
What causes the DNA to have a negative charge?
Phosphate groups in the backbone
How does DNA polymerase know when it has made a mistake?
Physical feature of DNA is distorted from the typical 2nm diameter.
How does a polar covalent bond occur?
Polar structure is one which the positive charge is concentrated toward one atom in the molecule and the negative charge is at the other atom in the molecule
What is an example of an RNA polymerase, an enzyme that synthesizes RNA using DNA as a template?
Primase
What is the RNA primer laid down by?
Primase
Why is deaminization easier to detect in DNA?
Product of deamination of cytosine is, by chance, uracil. Uracil already exists in RNA and could not be detected by repair enzymes in RNA
why does proline alter the integrity of the alpha helix?
Proline binds back to the amino acid backbone, causing kinks in the alpha helix
What is the width of DNA between each base pair?
0.34 nm
how many double bonds does a monounsaturated fatty acid contain?
1
How does heterochromatin spread?
1. heterochromatin histone tail modifications attract a set of heterochromatin-specific proteins, including histone-modifying enzymes 2. this then adds the same histone tail modifications on adjacent nucleosomes 3. This recruits more of the heterochromatin-specific proteins, causing a wave of condensed chromatin to propagate along the chromosome 4. Then, the extended region of heterochromatin will continue to spread until it encounters a barrier DNA sequence that stops the propagation
How does the cell fix a double stranded DNA break?
1. hurriedly stringing the broken ends back together before the DNA fragments drift apart and get lost --> nonhomologous end joining 2. homologous recombination
How has diversity arisen in cells if they came from the same ancestral cells?
1. replication is not always perfect, instructions are corrupted by mutations which change the nucleotide sequence 2. pattern of heredity may be complicated by sexual reproduction because the genetic cards are shuffled, re-dealt, and distributed in new combinations to the next generation to be tested again for their ability to promote survival and reproduction
DNA polymerase is so accurate it only makes about one error in every _____ million nucleotide pairs it copies
10
how many base pairs are there per helical turn?
10
heterochromatin typically makes up about __% of an interphase chromosome
10%
How many bases per second does a eukaryotic DNA polymerase synthesize?
100
How many bases per second does a bacteria DNA polymerase synthesize?
1000
how many nucleotides wrap two times around the histone core?
146
Which amino acid is changed in hemoglobin to produce sickle cell?
147
when were microscopes invented?
1600s
the fourth and fifth shell of an atom can contain how many electrons?
18
When were electron microscopes invented?
1930s
What year did Watson and Crick discover DNA?
1953
What catalyze the replication of DNA and the transcription of RNA while also participating in the translation of RNA into proteins
Proteins
(DNA/RNA) acts as a more transient carrier of molecular instructions
RNA
Info encoded in these DNA molecules is transcribed (read) into a related set of polynucleotides called ____
RNA
Ribosomes are predominantly made up of (DNA/RNA)
RNA
____ preceded DNA in evolution. DNA took over the primary storage of genetic information, and proteins became the major catalysts, while RNA remained the connection between the two
RNA
what enzyme works for transcription
RNA polymerase
which RNA polymerases transcribe genes encoding tRNA, rRNA, and various other RNAs that play a structural and catalytic role
RNA polymerase I and III
which RNA polymerase transcribes mRNA?
RNA polymerase II
what catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain
RNA polymerases
What is the process in eukaryotic cells in which segments of an RNA transcript are removed
RNA splicing (intron splicing)
Why is is permissible that RNA polymerase not read its work?
RNA strands are not the sole information holder, so mistakes have minor consequences
When you want to turn on a G protein, what must you do?
Remove the GDP and put back in a GTP
Why can't people with red-green colorblindness differentiate red and green?
Rhodopsin is mutated, its structure is a little off. This means that a photon from two different wavelengths (red or green) can both stimulate the same rhodopsin.
First shell of an atom can contain how many electrons?
2
How many molecules thick are the internal membranes that surround most organelles?
2
How many oxidation states does iron have?
2
how many amino acids does a ribosome add to a polypeptide chain each second?
2
how many electrons are in a single bond?
2
how many replication forks are at each replication origin
2
how many times does DNA wrap around a histone?
2
How many double bonds does a polyunsaturated fatty acid contain?
2 or more
Accurate and rapid translation of mRNA into protein requires a molecular machine that can latch onto an mRNA, capture and position the correct tRNA molecules, and then covalently link the amino acids that they carry to form a polypeptide chain. What is this molecular machine?
Ribosome
What is a large macromolecule complex in which RNAs are translated into proteins?
Ribosome
how many naturally occurring amino acids are there?
20
how many sites can a p53 protein, a protein that plays a central part in controlling how a cell responds to DNA damage and other stresses, be modified at?
20
how many genes are on the Y chromosome
256
How many tails does glycerol have?
3
In order to change a shape of a protein and restore it, how many conformations does a protein typically go through?
3
how many reading frames does a single mRNA have?
3
if 3 proteins can be made from the same prokary mRNA, how many start/stop signals are there on the mRNA?
3
How many carbons does glycerol head have?
3 carbons
Synthetase-catalyzed reaction that attaches the amino acid to the __ end of the tRNA is one of many reactions in cells that is coupled to the energy-releasing hydrolysis of ATP
3'
What end of DNA do nucleotides get added on?
3'
amino acid is linked to the __ end of a tRNA molecule
3'
What end do nucleotides get added on?
3' end
In what order are nucleotides added?
3' to 5'
Which direction does RNA polymerase read the template strand?
3' to 5'
Which way is the wrong way for DNA to be synthesized?
3' to 5'
polymerase can only synthesize RNa in the 5'-to-3' direction, so it must use the DNA strand that is oriented in the __-to-__ direction as a template
3' to 5'
How along ago did bacteria and archaea diverge?
3.5 billion years ago
How many genes are in our genome?
30,000
the ability of RNA to fold into a complex __ shape allows it to carry out various functions in cells (like structural, regulatory, or catalytic roles)
3D
What is the wobble effect?
3rd nucleotide of the codon can vary, due to degeneracy of the genetic code
All __ of the histones that make up the octamer are relatively small proteins with a high proportion of positively charged amino acids (hint: #)
4
How many DNA polymerases are involved in replication in a replication fork?
4
How many biomolecules are cells made up of?
4
How many bonds can carbon form?
4
How many polypeptide chains are in hemoglobin?
4
How many valence electrons does carbon have?
4
how many electrons are in a double bond?
4 (2 coming from each participating atom)
how many carbons are in the sugar of a nucleotide?
5
Monosaccharides are typically found in _ or _ carbon chains/rings
5 or 6
how many carbons are in a monosaccharide sugar
5 or 6
Small ribosomal subunit loaded with the initiator tRNA binds to the __ end of an mRNA molecule, which is marked by the 5' cap that is present on all eukaryotic mRNAs
5'
The ____ end of the mRNA code will correspond to the N terminal of the growing polypeptide chain
5'
RNA polymerase polymerizes in the __ to __ direction
5' to 3'
in what direction does DNA replication occur
5' to 3'
mRNA is pulled through the ribosome in what direction?
5' to 3'
what direction does DNA run in?
5' to 3'
how many nucleotides are between each histone?
50
Fatty acids can be used as a food reserve and broken down to produce about __ as much usable energy as glucose
6x
How many subunits is histone made of?
8
the second and third shell of an atom can contain how many elections?
8
how many naturally occurring elements are there?
90
what percent of genes are thought to undergo alternative splicing?
95%
How many cells does c. elegans have?
959
C, H, N, and O constitute what % of any organism's weight?
96%
To add an amino acid to a growing peptide chain, a charged tRNA enters the _ site by base-pairing with the complementary codon on the mRNA molecule
A
What is a fate map?
A map that follows cells as they divide and differentiate to their final cell form
What is the TATA box?
A sequence on DNA that signals the beginning of a gene for RNA polymerase
What is the promoter region?
A specific sequence of DNA bases at the start of a gene on the sense strand where RNA polymerase binds, typically made up of a series of T-A base pairs
What are the three sites of a tRNA molecule?
A, P, and E
If Deamination occurs to a cytosine, what will be the corresponding base pair
A-T
Origins of replication are made up of which base pairs?
A-T
regions of more (A-T/G-C) bonds is where the origin of replication begins
A-T
By staining chromosomes with dies that bind to certain types of DNA sequences, one can determine whether their DNA is rich in ____ nucleotide pairs of _____ nucleotides pairs
A-T, G-C
what is the basic chemical fuel that powers most of the cell's activities
ATP
What allows motor proteins to produce directed movements in cells?
ATP hydrolysis
protein machines use energy of ____ ________ to change the position of the DNA wrapped around nucleosomes
ATP hydrolysis
Translation of an mRNA begins with the codon ____, for which a special charged tRNA is required
AUG
When this ___ (start codon) is recognized by the initiator tRNA, several of the initiation factors dissociate from the small ribosomal subunit to make way for the large ribosomal subunit to bind and complete ribosomal assembly
AUG
To force a protein to proceed in a single direction, the conformational changes must be unidirection by making one of the step irreversible. How is this achieved?
Achieved by coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein—which is why motor proteins are also ATPases
What are the purines?
Adenine and Guanine
what are the nitrogenous bases in DNA?
Adenine, Thymine, Guanine, Cytosine
What are the nitrogenous bases in RNA?
Adenine, Uracil, Guanine, Cytosine
What is the genome?
All the DNA in one cell of an organism
What is the classic model organism for plants?
Arabidopsis
What latch onto the single-stranded base pairs and keep them in an elongated form so they can serve as efficient templates
Single-stranded DNA binding proteins
what is the anchor called that makes sure DNA polymerase stays on the right track?
Sliding clamp
What cells normally function as carefully regulated members of the complex community of cells in a multicellular organism
Somatic cells
Why would we want to know about the genome of plants?
Benefits us to know things about our food source
what are mixtures of weak acids and bases that will adjust proton concentrations around pH 7 by releasing protons (acids) or taking them up (bases) whenever pH changes
Buffers
What kind of bond is a nonpolar covalent bond?
C-H
What are the 4 thing we should not eat?
CRAP (caffeine, refined sugar, artificial colors, and processed foods)
(Strong/Weak) acids give up their hydrogen readily
Strong
what sequence of DNA does the sigma factor have an affinity for?
T-A-T-A
what initiates the addition of phosphate groups to the "tail" of RP2, which allows its removal from GTF
TF2H (a general TF that contains a protein kinase as one of its subunits)
Once ____ has bound to the TATA box, other factors assemble, along with RPII to form a complete transcription initiation complex
TFIID
what causes a dramatic local distortion in the DNA double helix of eukary?
TFIID
Monosaccharides are primarily made of what 3 elements?
Carbon, Hydrogen, and Oxygen
What is an example of different domains of a protein doing different functions?
Catabolite activator protein (CAP) has two domains , small domain binds to DNA and large domain binds to cAMP (When this binds to the cAMP, it causes a conformational change in the protein that enables the small domain to bind to a specific DNA sequence, promoting the expression of an adjacent gene)
What are small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and then dividing into two?
Cells
Who provided the key inside to cellular diversity, using his theory of evolution (1859), explaining how random variation and natural selection gives rise to diversity among organisms that share a common ancestry?
Charles Darwin
What build a scaffold off the end of a chromosome, allowing for DNA polymerase to anchor and copy (on the lagging strand at the end of a chromosome)
Telomerases
What is another DNA sequence that marks the end of each chromosome
Telomere
How does cholera interfere with GTPase activity?
Cholera interferes with GTPase activity (Chloride channel-protein) in the walls of intestine. The protein is a chloride pump, pumping chloride ions into lumen of intestines. If you have a large amount of salt going into intestines, water is going to go into intestines as well (by osmosis), causing diarrhea. Cholera toxin interferes with GTPase activity of chloride ion pump, now allowing it to turn off.
what is DNA that interacts with proteins
Chromatin
(DNA/RNA) acts as a long-term repository for hereditary information
DNA
The sequences of nucleotides in a molecule of _____ dictates the sequence of amino acids in a protein
DNA
What can program the growth, development, and reproduction of living cells and complex organisms?
DNA
What carries the genetic information of the cell and that the protein components of chromosomes function largely to package and control the enormously long?
DNA
What encodes the information that ultimately directs the assembly of proteins?
DNA
Which enzyme joins the 5'-phosphate end of one DNA fragment to the adjacent 3'-hydroxyl end of the next
DNA ligase
Movement of a replication fork is ultimately driven by...
DNA polymerase
What is used to synthesize new strands of DNA?
DNA polymerase
Which enzyme replaces the RNA primer with DNA?
DNA polymerase I (also called a repair polymerase)
Which DNA polymerase is the one that replicates DNA?
DNA polymerase III
Specialized ____ ________ are required for DNA replication and chromosome segregation
DNA sequences
Nucleus contains molecules of _____ which turn into _______ during cell division
DNA, chromosomes
What occurs when you take of an amino group (like from a cytosine) creating a uracil
Deamination
secondary structure
Either an alpha helix or beta pleated sheet.
The _______ ______ is enormously enlarged in cells that are specialized for the secretion of proteins
Endoplasmic reticulum
What organelle is an irregular maze of interconnected spaces enclosed by a membrane?
Endoplasmic reticulum (ER)
what are acetylations and methylations to DNA?
Epigenetic changes (or posttranslational modifications)
(Prokaryotes/Eukaryotes) DO have well-defined, portioned organelles
Eukaryotes
What is the process by which living species become gradually modified and adapted to their environment in. more and more sophisticated ways?
Evolution
T/F: 1 gene makes 1 protein
False
T/F: DNA polymerase adds nucleotides on and edits them in the same exact spot
False
T/F: DNA polymerase dissociates from the DNA each time it adds a new nucleotide to the growing strand
False
T/F: Protein kinases and phosphatases do not work together as a couple
False
T/F: RNA polymerase has proofreading capabilities
False
T/F: RNA polymerase needs the DNA to be unwound before it can synthesize
False
T/F: all living cells evolved from either a prokaryote or a eukaryote
False
T/F: amino acids are the only thing needed for a protein to do its job
False
T/F: cells can survive in a wide variety of temperatures
False
T/F: every gene undergoes transcription at the same rate
False
T/F: genes occur in the entire genome
False
T/F: one protein has a single function
False
T/F: synthetic catalysts are just as effective as biological catalysts
False
T/F: the cytosol is static
False
T/F: the more DNA one has, the more complex they are
False
T/F: the noncovalent bonds of macromolecules do not play a role in the chemistry and activity of the macromolecuels or dictate their interactions with other molecules
False
T/F: various organelles are often times positioned away from other organelles even when they interact nicely
False
T/F: the more complex and organism, the larger the genome
False (not always true)
Ferrous
Fe2+
Ferric
Fe3+
What does the body use to stop the production of a product if we have plenty of that product?
Feedback inhibition
___ ____ binds to a short segment of DNA double helix that contains the ___ box
GTF TFIID, TATA
G proteins are active when ______ is bound
GTP
Which membrane-bound organelle has lots of membranes and modifies proteins that have been made to help transport them?
Golgi
Which organelle is made up of stacks of flattened, membrane-enclosed sacs
Golgi
Which organelle modifies and packages molecules made in the ER that are destined to be either secreted from the cell or transported to another cell compartment
Golgi
What sits at the very front of the replication machine, where it uses the energy of ATP hydrolysis to propel itself forward, prying apart the double helix as it speeds along the DNA
Helicase
What takes the double strand of DNA and opens it up? (which enzyme)
Helicase
What uncoils the strand of DNA while primase lays down the primer?
Helicase
How is an alpha helix formed?
Hydrogen bond is made between every 4th amino acid, linking the C=O of one peptide bond to the N-H of another, giving rise to a right-handed helix with a complete turn every 3.6 amino acids
What can influence the optimal temperature and pH of proteins?
Hydrogen bonds
What seals the nicks in the backbone of DNA between okazaki fragments?
Ligase
What helps to fix mutated DNA?
Ligase (wrong nucleotide cut out, right one put in, then ligase seals the nick in the DNA)
who discovered electronegativity?
Linus Pauling
what causes sickle cell anemia?
When you change on amino acid in one particular spot in the primary sequence (147) should be glutamic acid (hydrophillic) to valine (hydrophobic), nonpolar side chains al want to cluster together. So, this changes the shape. So, this one substitution in the beta chains at 147, it changes the shape of the entire red blood cell from a round, donut shape to a sickle shape, causing sickle cell anemia
Why is the location of the bond relative to the plane, in a polysaccharide, important?
Whether the bond is above or below the plane of the ring is important because there are particular enzymes that aid in breaking the molecules apart and recognize whether the bond is above or below the plane of the ring.
which is particular dangerous because it can lead to the fragmentation of chromosomes and the subsequent loss of genes?
double strand DNA break
what occurs when there is a mishap at the replication fork, or radiation, or various chemical assault fractures the DNA
double-strand DNA break
Why can't the mRNA transcript be read by a ribosome when miRNA/siRNAs make the transcript double stranded?
double-stranded pieces cannot fit into the ribosomal complex
What can be used to determine the precise positioning of atoms within the 3-D structure of protein molecules and complexes?
X-ray crystallography or cryoelectron microscopy
what is the general shape of an antibody?
Y shape
Are both ATP-dependent chromatin-remodeling complexes and histone-modifying enzymes are tightly regulated?
Yes
Are cells diverse?
Yes
Are covalent bonds strong enough to survive the conditions inside cells?
Yes
Are the RNA primers removed from newly synthesized DNA?
Yes
Can RNA base pair with itself?
Yes
Can RNA fold into a variety of shapes?
Yes
Can an alpha helix be used to create a hydrophilic core and a hydrophobic outer layer and shoved in a membrane to create an channel?
Yes
Can bacteria form a series of chains?
Yes
Can drugs inhibit enzymes?
Yes
Can prokaryotes undergo photosynthesis?
Yes
Can prokaryotes use energy from the chemical reactivity of inorganic substances in the environment?
Yes
Can the sigma factor recognize the promoter sequence on DNA without having to unwind the DNA?
Yes
Could RNA molecules have been catalysts?
Yes
Do cells differ from one another?
Yes
Do cells have a variety in size and shape?
Yes
Do chloroplasts contain their own DNA?
Yes
Do mitochondria and chloroplasts interact with each other?
Yes
Do mutations occur randomly?
Yes
Does DNA polymerase I (repair polymerase that takes off the RNA primer) proofread as it synthesizs?
Yes
Does RNA bring in triphopshate nucleotides?
Yes
Does RNA have a sugar-phosphate backbone?
Yes
Is the terminator sequence of DNA transcribed?
Yes
can the leading strand be replicated all the way to the end of a chromosome?
Yes
does telomerase carry its own RNA template?
Yes (it uses it to add multiple copies of the same repetitive DNA sequence to the lagging strand template)
Are DNA molecules homologous?
Yes (they have identical or nearly identical nucleotide sequences outside the broken region)
CAN humans be used as a model organism?
Yes (we know the human genome)
Can feedback inhibition be reversed?
Yes (when product levels fall)
Can mutations benefit an organism? If so, what is an example
Yes, like bacteria with antibiotics
Does DNA have a charge?
Yes, negative
In order for DNA polymerase to work, what must it need?
a little bit of double strandedness using an RNA primer
what do nucleosomes consist of?
a nucleosome core particle plus one of its adjacent DNA linkers
What tells the RNA polymerase to stop transcription?
a stop signal at the end of a gene
which of the following RNAs work together to get the information stored in the mRNA chemically converted into a polypeptide chain? a. mRNA b. rRNA c. tRNA d. miRNA e. a, b, c f. all of the above
e
what is a protein family?
each family member has an amino acids sequence and a 3D conformation that closely resemble those of other family members
Deaminization, one of the most common detrimental chemical changes occurring in polynucleotides, is (easier/harder) to detect and repair in DNA
easier
what are model organisms?
easy to study organisms that reproduce rapidly and are convenient for genetic manipulations
the most abundant scaffold proteins in cells are (elastic/rigid)
elastic
what naturally have a particular lowest energy level confirmation that is curved, but can be stretched and held together by disulfide bridges (which maintain the polyeptide chains together). When unstretched, this protein returns back to its lowest energy level confirmation
elastic fiber
What protein is another example of a fibrous protein but is formed by relatively loose and unstructured polypeptide chains that are covalently cross-linked into a rubberlike elastic mesh work
elastin
What microscope allowed us to see organelles (not just nucleus and in finer detail)?
electron microscope
Which microscopes uses beams of electrons to illuminate cell interiors because they have short wavelengths, giving rise to fine details of cells?
electron microscopes
what allows us to predict the nature of the bonds that will form between atoms?
electronegativity
What type of protein purification is being described: 1. A mixture of proteins is loaded onto a polymer gel and subjected to an electric field 2. Polypeptides will then migrate through the gel at different speed depending on their size and net charge 3.Yield a number of bands or spots that can be visualized by staining 4. Each band or spot contains a different protein
electrophoresis
proteins can be separated by __________
electrophoresis
Why was studying cultured human cells important?
embryo cells can be stimulated to turn into other cells
What occurs when a portion of plasma membrane tuck in and pinch off to form vesicles that carry material captured from the external medium into the cell
endocytosis
Which membrane-bound organelle lies in close proximity to the nucleus?
endoplasmic reticulum
Which organelle is the site where most cell-membrane components, as well as materials destined for export from the cell, are made?
endoplasmic reticulum
What promote intracellular chemical reactions by providing intricate molecular surfaces contoured with particular bumps and crevices that can cradle or exclude specific molecules
enzymes
The affinities of enzymes for their substrates and the rates at which they convert bound substrate to product vary widely from one enzyme to another --> this can be determined experimentally by mixing purified ________ and _________ together in a test tube
enzymes and substrates
Most cancers are cancers of what kind of tissue?
epithelial
What kind of chromatin is transcriptionally active
euchromatin
what is the rest of interphase chromatin called? (other than heterochromatin)
euchromatin
What occurs when vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium
exocytosis
most of the hormones and signal molecules that allow cells to communicate with one another are secreted from cells via what process?
exocytosis
What are the coding regions of an mRNA strand?
exons
what chew away at the ends of nucleic acids?
exonucleases
genes that accidentally become packaged into heterochromatin usually fail to be __________
expressed
Regions of the chromosome containing genes that are being actively expressed are generally more (extended/condensed), whereas those that contain silent genes are more (extended/condensed)
extended, condensed
What cell components were seen with a light microscope?
extracellular matrix, plasma membrane, nucleus, and cytoplasm
Where do we find rhodopsins?
eyes
RNA synthesis and processing takes place in "_________" within the nucleus
factories
Do prokaryotes reproduce fast or slow?
fast
What is stored in the cytoplasm of many cells in the form of fat droplets composed of triacylglycerol molecules?
fatty acids
what are the building blocks of membranes?
fatty acids
What occurs when an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway (so the pathway can be slowed down or stopped when large quantities--more than needed--are made)
feedback inhibition
Molecules that have poorly matching surfaces have (many/few) noncovalent interactions. Therefore, the 2 molecules dissociate as rapidly as they come together. This prevents incorrect and unwanted associations from forming between mismatched molecules
few
What is a major cell type in connective tissue that secretes proteins that form the extracellular matrix?
fibroblasts
What protein structure is like a rope or fiber, intertwined with multiple threads (like a coil of coils).
fibrous
what type of protein is especially abundant outside the cell, forming extracellular matrix that's gel-like and helps bind cells together to form tissues?
fibrous proteins
Long polypeptide chains are very ______, as many of the covalent bonds that link the carbon atoms in the polypeptide backbone allow free rotation of the atoms they join
flexible
The packing of fatty acid tails affects what property of the membrane?
fluidity
Which microscopes use sophisticated methods of illumination and electronic image processing to see fluorescently labeled cell components in much finer detail?
fluorescence microscopes
Today, the predominant way to discover the precise ______ _______ of any protein is by using x-ray crystallography, nuclear magnetic resonance spectroscopy, or cryoelectron microscopy
folding pattern
Where do you get the energy to add a phosphate on to ADP or AMP?
food or the sun
fatty acids can be used as a ______ _______ in cells
food reserve
Ribose readily formed from _________ which is one of the principal products of experiments simulating conditions of primitive earth
formaldehyde
Which model organism provided the evidence that genes are carried on chromosomes?
fruit flies
Which model organism showed that genes for their development are similar in humans
fruit flies
Which model organism showed us how the genetic instructions encoded in DNA direct the development of a fertilized egg cell into an adult multicellular organism
fruit flies
Which model organism was the model for human development and genetic basis of human diseases?
fruit flies
Differences in size, shape, and chemical requirements often reflect differences in _________
function
Each cell has a specialized ____, integrated by an intricate system of cell-to-cell communication
function
Structure is related to ________
function
at the fundamental level, what controls the amount of each protein is made by controlling the expression of the gene that encodes that protein
fundamental level
reduction is
gain of electrons
What is a specific set of instructions used to make a specific protein?
gene
what is often defined as a segment of DNA that contains the instructions for making a particular protein or RNA molecules
gene
What refers to the process by which the information encoded in a DNA sequence is converted into a product that has some effect on a cell or organism
gene expression
what is the conversion from DNA to mRNA or translation of mRNA to proteins?
gene expression
what is the process by which the nucleotide sequence of a gene is transcribed into the nucleotide sequence of an RNA molecule which is then translated into the amino acid sequence of a protein
gene expression
What provide instructions for the form, function, and behavior of cells and organisms?
genes
Advances in _______ ___________ techniques now permit the production of large quantities of almost any desired protein
genetic engineering
All cells contain ________ ________ in the genes which is carried in the DNA molecules
genetic information
What contains a message from the distant past?
genome
What is the entire sequence of nucleotide in an organism's DNA?
genome
What provides the genetic program that instructs a cell on how to behave?
genome
Where is a record of the fidelity of DNA replication and repair is preserved?
genome sequences
which cells transmit genes to next generation?
germ-line cells
cells can use simple polysaccharides composed only of ______ units as long term stores to reserve for energy production
glucose
what carbohydrate is used as a energy source for cells?
glucose
What amino acid should be at location 147 in hemoglobin?
glutamic acid
A phospholipid is anchored in the ________ molecule
glycerol
Smaller ogliosaccharides (3-4 sugar polymer) can be covalently linked to proteins to form _________ or to lipids to form __________ (both found in cell membranes)
glycoproteins, glycolipids
what is the covalent bond that forms when monosaccharides are linked together to form larger carbohydrates?
glycosidic bonds
how does a histone, which gets made in the cytoplasm, get into the nucleus?
goes through nuclear transport through a nuclear pore
What does RNA produce when it base pairs with itself
hairpin loops
What double-stranded structures does RNA produce?
hairpin loops
which chains of the antibody have a ton of disulfide bridges (and is not real variable)
heavy chains
Antibodies consist of ______ chains and ______ chains
heavy chains and light chains
Each polypeptide chain in hemoglobin hold a ______ group, which binds and releases oxygen and CO2
heme
Most highly condensed form of interphase chromatin is called ___________
heterochromatin
What kind of chromatin is more tightly packed and transcriptionally silent
heterochromatin
Additional packing of nucleosomes into a chromatin fiber depends on a 5th histone called _______ ___, which is thought to pull adjacent nucleosomes together into a regular repeating array
histone H1
what serve as docking sites on the histone tails for a variety of regulatory proteins?
histone modifications
what convert the DNA molecules in an interphase nucleus into a chromatin fiber that is approximately 1/3 of the length of the initial DNA?
histone proteins
what are subject to several types of reversible, covalent chemical modifications that control many aspects of chromatin structure?
histone tails
Another way of altering chromatin structure relies on the reversible chemical modification of ________, catalyzed by a large number of different histone-modifying enzymes
histones
Complex task of packaging DNA is accomplished by specialized proteins that bind to and fold the DNA, called _________, generating a series of coils and loops that provide increasingly higher levels of organization and prevent the DNA from becoming a tangled, unmanageable mess
histones
What are responsible for the first and most fundamental level of chromatin packing: formation of the nucleosome?
histones
What are the proteins that DNA wrap around?
histones
what are the proteins that interact with DNA?
histones
what initiates repair via a recombination-specific nuclease which chews back the 5' ends of the two broken strands at the break?
homologous recombination
what is an error-free strategy for repairing double-strand breaks?
homologous recombination
what is the most handy DNA repair mechanism available to the cell, used to repair many other types of DNA damage (not just a double strand break)
homologous recombination
what occurs shortly after a cell's DNA has been replicated, when the duplicated helices are still physically close to each other?
homologous recombination
All purpose nature of __________ _________ repair probably explains why this mechanism and the proteins that carry it out have been conserved in virtually all cells on earth
homologous recombinational
what determines whether a primary structure will turn into an alpha helix or beta sheet?
how the amino acids interact and the hydrogen bonds that form
The linkage and binding of the ligand to the pocket is critical because...
how tightly the ligand binds influences the function
hemophilia blood doesn't clot, and this is associated with a mutation in what gene?
human factor 8
DNA is held together by
hydrogen bonds
Each chain, or strand, is composed of 4 types of nucleotide subunits held together via _______ ______ between the base portions of the nucleotides
hydrogen bonds
What holds the DNA together?
hydrogen bonds
Disaccharides undergo what kind of reaction to form monosaccharides?
hydrolysis
Reaction catalyzed by a lysozyme is a ______ reaction
hydrolysis
to break a disaccharide into monosaccharides, what reaction must be done?
hydrolysis
what kind of reaction occurs to break glycosidic bonds (turn polysaccharides into monosaccharides)?
hydrolysis
fatty acids are made up of a ______ end and a _____ end.
hydrophilic (polar) and hydrophobic (nonpolar)
What tend to be forced together to minimize their disruptive effect on the hydrogen-bonded network of the surrounding water molecules in an aqueous environment
hydrophobic forces
what is generated by a pushing of nonpolar surfaces out of the hydrogen bonded water network, where they would otherwise physically interfere with the highly favorable interactions between water molecules?
hydrophobic forces
what gives phospholipids their strength?
hydrophobic interactions between the tails
what drives a lot of structural components?
hydrophobicity
the _____ group of the carbohydrate ring will be above or below the plane of the ring, which is critical for recognition of cells
hydroxyl
When was the first time we were finally able to see cells?
in 1600s when microscopes were invented
how is DNA packaged?
in chromosomes
Where are chloroplasts found?
in eukaryotes that can undergo photosynthesis
Where do hydrophobic regions, of proteins, tend to cluster together? (inside or outside of the core)
inside
lipids are (soluble/insoluble) in water
insoluble
Which filament of the cytoskeleton is intermediate in thickness and strengthens most animal cells
intermediate filaments
What are the regions of the primary transcript that do not code for proteins?
introns
what kind of interactions are happening between histones and DNA?
ionic
what is formed when electrons are donated from one atom to another?
ionic bond
Interphase chromatin (is not/is) uniformly packed
is not
what are sets of molecules with the same chemical formula but different structures?
isomers
what have a different number of neutrons but the same number of protons
isotopes
Why can't DNA polymerase proofread if it synthesized DNA in the 3' to 5' direction?
it would create a chemical dead end—a strand that could no longer be elongated
Why do we use mice as model organisms?
it's more ethical to use than a person and they have the same genes as we do
Why can heterochromatin spread to neighboring regions of DNA?
its histone tail modifications attract a set of heterochromatin-specific proteins, including histone-modifying enzymes
What disease is caused by misfolded proteins called prions
jakob disease
Why is RNA single-stranded?
just behind where the ribonucleotides are being added, the RNA chain is displace and the DNA double helix reanneals
What can detect changes/alternations and even abnormalities that can be associated with disease in chromosomes
karotype
what is a structural protein with multiple alpha helices interacting with each other that forms coiled coils, making a really strong rope-like connection? (hint: found in connective tissues of the body)
keratin
Which strand has a problem replicating DNA all the way to the end of a chromosome?
lagging strand
Which strand of DNA is replicated in portions?
lagging strand
which subunit of the ribosome catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain
large subunit
Which strand of DNA is replicated continuously?
leading strand
How does the RNA polymerase know which DNA strand to read?
lies in the structure of the promoter
Ability of a protein to bind selectively and with high affinity to a ______ is due to the formation of a set of weak, noncovalent interactions—H-bonds, electrostatic attractions, and van der Waals attractions—as well as favorable hydrophobic forces
ligand
what is a molecule that binds to a binding pocket of a protein?
ligand
Which microscopes use visible light to illuminate specimens, allowing biologists to see for the first time the intricate structure that underpins all living things?
light microscopes
Eukaryotes have (circular/linear) chromosomes
linear
steroids are a _____
lipid
oxidation is
loss of electrons
(lower/higher) numbers of chromosomes are bigger and have more genes
lower
Proteins fold into a conformation of (highest/lowest) energy
lowest
which amino acids make up the majority of histones?
lysine and arginine
Which membrane-bound organelle is involved in digestion?
lysosomes
which organelle is a small, irregularly shaped organelle in which intracellular digestion occurs, releasing nutrients from ingested food particles into the cytosol and breaking down unwatned molecules for either recycling within the cell or excretion from the cell?
lysosomes
what was the first enzyme to have its structure worked out at the atomic level by x-ray crystallography?
lysozome
what protein breaks apart carbohydrates?
lysozyme
what is the RNA that codes for proteins?
mRNA
which RNA gets translated
mRNA
Where do transcription factors bind? (i.e., major or minor groove)
major groove of DNA
When proteins interact on the DNA, where do they typically bind? (to what grooves)
major grooves
How many replication origins do eukaryotic chromosomes contain?
many, to allow the long DNA molecules to be replicated rapidly
What process is being described: 1. Peptides derived from digestion with trypsin are blasted with a laser o Heats the peptides, causing them to become electrically charged (ionized) and ejected in the form of a gas 2. Accelerated by a powerful electric field, the peptide ions then fly toward a detector; the time it takes them to arrive is related to their mass and their charge 3. Set of very exact masses of the protein fragments produced by cleavage then serves as a "fingerprint" that can be used to identify the protein
mass spectrometry
what determines the exact mass of every peptide fragment in a purified protein, allowing the protein to be identified from a database that contains a list of every protein thought to be encoded by the genome of the relevant organism
mass spectrometry
what is the mRNA called when it has the 5' cap, the 3' poly-A tail, and the introns spliced?
mature mRNA
By moving ions across the _________ of the mitochondria, we get energy
membranes
Enzymes often work in sets, with the product of one enzyme becoming the substrate for the next, resulting in an elaborate network of _________ ___________
metabolic pathways
Initiator tRNA always carries the amino acid ________
methionine
what gets added onto the 5' end of a eukary mRNA?
methylated G cap
What is the prime reason replication machinery chooses the wrong base?
methylation of the DNA
what are small little pieces (like 22 nucleotides long) that form double stranded RNA structures over small regions of mRNA (help regulate gene expression)
miRNA
What can keep the mRNA transcript from being synthesized by ribosomes by making the transcript double-stranded in some parts
miRNA and siRNA
what serve as key regulators of eukaryotic gene expression?
miRNAs
Which filament of the cytoskeleton is rearranged into a spectacular array in dividing cells, helping to pull duplicated chromosomes apart and distribute them equally into the two daughter cells
microtubules
Which filament of the cytoskeleton is the thickest
microtubules
Final folded conformation of any polypeptide chain is determined by energetic considerations: a protein generally folds into the shape in which its free energy (G) is (minimized/maximized) and disorder is (increased/decreased)
minimized, increased
_________ repair plays an important role in preventing cancer in humans
mismatch
What corrects 99% of replication errors?
mismatch repair
humans who are more predisposed to cancer often inherit cells with one damaged ______ _______ gene
mismatch repair
what is a backup system that is dedicated to correcting errors of replication?
mismatch repair
What is the powerhouse of the cell?
mitochondria
Which organelle gets energy from food via cellular respiration?
mitochondria
Without ________, cells would be unable to use oxygen to extract the energy they need from food molecules that nourish them
mitochondria
what are organelles that generate energy in eukaryotes are thought to have evolved from aerobic bacteria that took to living inside the anaerobic ancestors of today's eukaryotic cells?
mitochondrion
Factories in the nucleus are made up of what?
molecular aggregates made up of RNA polymerases and RNA-processing proteins that help make the final mRNA molecule
what are the building blocks of polymers
monomers
What are the building blocks of polysaccharides?
monosaccharides
what are monomers of polysaccharides?
monosaccharides
_____ proteins generate the forces responsible for muscle contraction and most other eukaryotic cell movements
motor
What proteins power the intracellular movements of organelles and macromolecules?
motor proteins
What use energy stored in molecules of ATP to move track and cables that carry organelles throughout the cytoplasm?
motor proteins
What is the simplest vertebrate model organism?
mouse
Which model organism was used to study mammalian genetics, development, immunology, and cell biology?
mouse
how many origins of replication does eukaryotic DNA have
multiple
What allows for a larger eukaryotic genome to be synthesized rapidly?
multiple origins of replication
What must happen to cysteine in order to form a disulfide bridge?
must be oxidized
Can produce small variations that underlie the differences between individuals of the same species
mutations
Changes in DNA sequence can cause ________
mutations
what protein binds oxygen like hemoglobin, but it made up of 1 subunit (not 4)
myoglobin
mutations that negatively affect an organism typically gets eradicated via _____ ______
natural selection
What is the charge on a phosphate group?
negative
when the polar molecule becomes surrounded by water molecules, protons will be attracted to the partial (positive/negative) charge on the oxygen of water molecules
negative
Feedback inhibition is a form of _________ regulation
negative (prevents enzyme from acting)
What cell receives signals from other, similar, cells through a collection of shorter extensions that sprout through the body like a tree?
nerve cell
What kind of cell sends out its electical signals along a single, axon that is 10,000 times longer than it is thick?
nerve cell
are electrons in covalent bonds often shared equally?
no
It is the total number of the _________ _________ that causes the protein to take the shape that it likes
non-covalent interactions
the hydroxyl group of the carbohydrate ring will be _____ or ______ the plane of the ring, which is critical for recognition of cells
above or below
what give protons away?
acids
Which filament of the cytoskeleton is abundant in all eukaryotic cells, especially in muscle cells because it serves as a central part of the machinery responsible for muscle contractions
actin
Which filament of the cytoskeleton is the thinnest?
actin
what are the 3 major filaments of the cytoskeleton?
actin, microtubules, and intermediate filaments
what do neutrons do?
add mass and contribute to the stability of the nucleus
What are 3 ways histones can be modified?
addition of a methyl group, acetyl group, and a phosphate
What are other covalent modifications (other than phosphorylation) that can affect a protein's function
addition of an acetyl group to a lysine side change and attachment of ubiquitin which causes degradation
How is RP2 liberated from the transcription factors?
addition of phosphate groups to its "tail"
tails of all four of the core histones are particularly subject to these covalent modifications (name the 3 modifications)
addition or removal of acetyl groups, phosphates, or methyl groups
what is the most common nucleoside?
adenosine triphosphate
the most efficient forms of protein chromatography separate polypeptides on the basis of their ability to bind to a particular molecule--a process called ________ chromatography
affinity
when does RNA splicing occur?
after transcription and 5' and 3' modifications
What are large sub-compartments in cells?
aggregates formed by sets of proteins, RNAs, and protein machines can grow quite large, producing distinct biochemical compartments within the cell
Proteins can be controlled by a regulatory site called an ___________ site, here a hydroxyl group can be phosphorylated to induce a 3D conformational change of the protein
allosteric
Single bonds (allow/do not allow) rotation, so most polymer chains with single bonds have great flexibility
allow
How can you get multiple mRNAs from one gene?
alternative splicing
Amyloid structures are thought to contribute to a number of neurodegenerative disorders like ________ and _______.
alzheimer's and huntington's
Many enzymes participate intimately in the reaction by briefly forming a covalent bond between the substrate and an _________ _________ _____ ______ in the active site
amino acid side chain
Loopy regions outside the beta sheet has very specific ______ ______ that will bind with an individual antigen. Loopy regions are the specific regions.
amino acids
Protein molecules are built by
amino acids
what are the building blocks of proteins?
amino acids
many biologically important bases have what functional group?
amino group
recognition and attachment of the correct amino acid depends on enzymes called __________ __________
aminoacyl-tRNA synthetases
what covalently couple each amino acid to the appropriate set of tRNA molecules
aminoacyl-tRNA synthetases
phospholipids are ________
amphipathic
thanks to their __________ nature, pure phospholipids readily form membranes in water
amphipathic
Some sub-compartments of cells are based on ________ __________, reversible assemblies of stacked beta sheets that come together to produce a "hydrogel" that pulls other molecules into the condensate
amyloid structures
When proteins fold incorrectly, they sometimes form ________ __________ that can damage cells and even whole tissues
amyloid structures
________-________ ________ thus have functional roles in cells, but for a handful of these amyloid-forming proteins, mutation or perturbation can lead to neurological disease
amyloid-forming proteins
What is a Barr Body?
an inactivated X chromosome
what is a coenzyme?
an organic nonprotein helper for catalytic reactions.
negative ions are
anions
_________ are little medicinal molecules that "gum-up" the works and stop the function of ribosomes
antibiotics
inhibitors of prokaryotic protein synthesis are used as _________
antibiotics
what exploit the small structural and functional differences between bacterial and eukaryotic ribosomes, so they interfere with bacterial protein synthesis and not eukaryotic protein synthesis?
antibiotics
what are immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface of an invading microorganism
antibodies
what is a set of 3 consecutive nucleotides that bind, through base-pairing, to the complementary codon in an mRNA molecule
anticodon
What is an antibody's target molecule?
antigen
Catalase is an ________, helping to sequester the free radicals that form in a cell
antioxidant
Which model organism was important for us to study so that we knew what we were eating?
arabidopsis
Where is heterochromatin concentrated?
around the centromere region and in the telomeric DNA at the chromosome ends
How do ionic bonds form?
as a result of a gain or loss of electrons
how is glucose stored in animals?
as glycogen
how is glucose stored in plants?
as starch
where does DNA replication synthesis begin?
at origins of replication
Where does DNA replication begin?
at replication fork
what occurs when chromosome 12 gets a piece of chromosome 4
ataxia
smallest particle of an element that retains distinctive chemical properties is a(n) ______
atom
What is equal to the number of protons plus neutrons?
atomic weight
What is the mass relative to a hydrogen atom?
atomic weight (molecular weight)
Life requires ______, molecules possess the ability to catalyze reactions that lead--directly or indirectly--to the production of more molecules like themselves
autocatalysis
the first 22 pairs of chromosomes are
autosomes
What is a rod shaped bacteria called?
bacilli
for the strand being synthesized in the 3' to 5' direction, polymerase moves (forward/backward) with respect to the direction of the replication fork movement so that each new DNA fragment can be polymerized in the 5' to 3' direction
backward
_____ translation can be faster because its mRNA does not need to be processed and is physically accessible to ribosomes while it is being synthesized
bacterial
What enables DNA replication?
base pairing
what accept protons?
bases
Why is are replication forks asymmetrical?
because of the lagging strand having to synthesize in fragments
where are the hydroxyl groups in the sugar ring of a nucleotide?
below (2' and 3')
When you get a little closer to look at the antigen binding site, you start to see there can be a series of ______ _______ that are held together by disulfide bridges and in between the beta sheets there are loopy regions (still amino acid sequences, but are not going to form a beta sheet).
beta sheets
how does a neurotoxin work?
bind into a (sodium) channel, acting like a plug and now allowing ions to pass through (neurons function via the influx of ions)
Region of a protein that associates with a ligand, known as its ________ ____, usually consists of a cavity in the protein surface formed by a particular arrangement of amino acid side chains
binding site
Why is a lysozyme required for breaking apart polysaccharides?
breaking apart a polysaccharide molecule distorts the polysaccharide into a molecule into a particular shape--transition state--in which the atoms around the bond have an altered geometry and electron distribution
We have learned a lot about the cellular replication cycle by observing which model organism?
brewer's yeast
What is the simplest eukaryotic organism
budding yeast
Why must triphosphate nucleotides be brought in?
by breaking off 2 phosphates, give enough energy to create the desired bond
How was the mitochondria's function found?
by breaking open cells and spinning the soup of cell fragments in a centrifuge, separating the cells according to their size and density. mitochondria were then purfied and tested to see what chemical processes they could perform. this revealed that they generate chemical energy for he cell by harnessing energy from the oxidation of food molecules to produce ATP
How do chloroplasts carry out photosynthesis?
by trapping energy of sunlight in their chlorophyll molecules and using this energy to drive the manufacture of energy-rich sugar molecules and releasing oxygen as a by-product
how many phosphate groups does a nucleotide have?
can be anywhere from 1-3
what can histone modifications do for the chromosomes?
can promote condensation or expansion and access to the DNA
What protein identifies methylated 5' g-cap?
cap-binding protein
positive ions are
cations
What is the study of cells and their structure, function, and behavior?
cell biology
Sugars are also used to make mechanical supports. This, in plants, is _______ and also _______ in insects (makes up the exoskeletons and fungal cells walls)
cellose, chitin
All living things are built from _____
cells
Higher organisms are communities of ____ derived by growth and division from a single founder cell
cells
what are the simplest form of life?
cells
Why must free radicals be digested by peroxisomes?
cells are sensitive to oxidative stress and will break down in the presence of free radicals
What process does the mitochondria undergo to extract energy from food sources?
cellular respiration
Flow of information from DNA to RNA to protein is so fundamental to life it is referred to as the ________ _______ __ __________ ________
central dogma of molecular biology
what is a bend in a chromosome; a central, constricted region of a chromosome
centromere
What allows the mitotic spindle to attach to each duplicated chromosome in a way that directs one copy of each chromosome to be segregated to each of the 2 daughter cells
centromeres
what allows duplicated chromosomes to be separated in M phase?
centromeres
what allow access to DNA (for like replication or transcription)?
changes in nucleosome structure
What does histone H1 do?
changes the path the DNA takes as it exits the nucleosome core, allowing it to form a more condensed chromatin fiber
What does changing the pH do for the amino acid?
changes the protonation of its amino and/or carboxyl groups
Although it can fold into its correct conformation without outside help, protein folding in a living cell is generally assisted by a large set of special proteins called ____________ proteins
chaperone
What form isolation chambers in which single polypeptide chains can fold without the risk of forming aggregates in the crowded conditions of the cytoplasm
chaperone proteins
what bind to partially folded chains and help them to fold along an energetically favorable pathway?
chaperone proteins
When an amino acid is bound to a tRNA molecule using ATP, we say that this tRNA molecule is __________
charged
What allows plants to produce the food molecules and the oxygen that mitochondria use to generate chemical energy in the form of ATP?
chloroplasts
What capture energy from sunlight?
chloroplasts
Which is more recent: chloroplasts or mitochondria?
chloroplasts
What enables plants to get their energy directly from the sunlight?
chloroplasts (photosynthesis)
Which is more complex: chloroplasts or mitochondria?
chloroplasts (they contain internal stacks of membranes containing chlorophyll)
What is an example of a disease that interferes with GTPase activity?
cholera
Where did scientists get the word chromosomes from?
chroma = color, from their staining properties
what is a single, enormously long linear DNA molecule associated with protein s that fold and pack the fine thread of DNA into a more compact structure
chromatin
In ___________ (to separate proteins), use different materials to sparate the individual components of a complex mixture into portions or fractions based on the properties of proteins--like size, shape, and electrical chard
chromatography
what are threadlike structures in the nucleus of eukaryotic cells that become visible as the cells begin to divide
chromosomes
what are hairlike projections whose sinuous, coordinated beating sweeps the cell forward, rotating as it goes?
cilia
Assembly of the sliding clamp around DNA requires the activity of the _____ _____
clamp loader
What is an enzyme that hydrolyzes ATP each time it locks a sliding clamp around a newly formed DNA double helix?
clamp loader
What is a round bacteria called?
cocci
what is a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule.
codon
_____ in mRNA signal where to start and stop protein synthesis
codons
What protein has 3 chains that are coiled around each other?
collagen
what is an example of a coil of coil fibrous protein?
collagen
The RNA chain produced by transcription—the RNA transcript—therefore has a nucleotide sequence exactly (identical/complementary) to the strand of DNA used as the template
complementary
The replicated strand is (identical/complementary) to the template strand
complementary
Recognition of a codon by the anticodon on a tRNA molecule depends on ___________ __________ used in DNA replication and transcription
complementary base-pairing
RNA strand is _______ the template strand but _____ to the coding strand
complementary, identical (but with uracil)
How does a cell control protein activities?
confining the participating proteins to particular sub-cellular compartments (either enclosed by membranes or created by other proteins)
Phosphorylation can control protein activity by causing a ________ _______
conformational change
what is the word to describe proteins that are continuously used, degraded, and remade over and over and over?
constitutive
How does the mitochondria extract energy from food source? (specific)
control release of ions across a membrane to generate energy
Why can't the large ribosomal subunit align over the A site?
couldn't accept any more amino acids
Phosphodiester bonds are _________ bonds
covalent
what kind of bond is a disulfide bridge?
covalent
what is formed when atoms share electrons
covalent bond
a disulfide bond is an example of a covalent _____ ________ in proteins that tie together 2 amino acids in the same polypeptide chain or joins together many polypeptide chains in a large protein complex
cross-link
what often occurs after S phase but before M phase, occuring in regions of DNA that are similar (but do not have to be identical). This phenomenon also creates novel nucleotide sequences and is the key feature of genetic diversity of mitosis
crossing over (homologous recombination)
What does it mean to be a nitrogenous base?
cyclic aromatic structures that have nitrogen as well as carbon and hydrogen
What protein is a carrier in the mitochondria involved in shuttling electrons from the second subunit to the third subunit
cytochrome C
where are proteins made?
cytoplasm
What are the pyrimidines?
cytosine, thymine, uracil
What supports the cell and provides shape to the cell?
cytoskeleton
what is responsible for directed cell movements?
cytoskeleton
What is a concentrated aqueous gel of large and small molecules?
cytosol
What is the jelly-like material all organelles are suspended in?
cytosol
What is the part of the cytoplasm that is not contained within intracellular membranes?
cytosol
What is the site of many chemical reactions that are fundamental to the cell's existence? (also the place where early steps of metabolism occurs and where most proteins are made by ribosomes)
cytosol
Prokaryotes are either a. bacteria b. archaea c. amoeba d. a and b
d
Cells can also regulate the rate at which the protein is ________
degraded
Monosaccharides undergo what kind of reaction to form a disaccharide?
dehydration
glycosidic bonds form via what kind of reaction?
dehydration synthesis
how do peptide bonds form?
dehydration synthesis
what are fluctuations in the distribution of electrons in every atom, which can generate a transient attraction when the atoms are in very close proximity
Van der Waals attractions
How do cells become differentiated when all arise from a single, fertilized egg?
Varied cells stem from the way individual cells use their genetic instructions
What, in carrots, is good for our eyesight?
Vitamin A
Why is vitamin A good for our eyes?
Vitamin A's structure is similar to retinal, it's a source to get modified to retinal that can be combined with opsins to make rhodopsins.
What is a change in shape that stops the protein from functioning?
denature
What protein is a globular protein (enzyme) that specifically binds to DNA
deoxyribonuclease
nucleotides with deoxyribose are known as
deoxyribonucleotides
If the 2' carbon of a nucleotide does not have an oxygen, what kind of sugar is it?
deoxyribose
One the (phosphorylated/dephosphorylated form of RP2 can re-initiate RNA synthesis)
dephosphorylated
What occurs when a purine is cut off form its sugar-phosphate backbone, leaving the complementary strand completely open and a "wild card"
depurination
In general, are mutations more likely to be detrimental or beneficial
detrimental
What did we learn from fruit flies?
development
because genes typically have only one promoter, the orientation of its promoter determines in which ______ the gene is transcribed and therefore which strand is the template strand
direction
What is a 2 sugar molecule called?
disaccharide
what can result due to genes becoming unexpressed?
diseases and X inactivation (x-inactivation is an extreme example of a process that takes place in all eukaryotic cells)
Once transcription has begun, most of the general TF _________ from the DNA and then are available to initiate another round of transcription with a new RNA polymerase molecule
dissociate
a molecule with a highly polar covalent bond between a hydrogen and another atom (dissolves/precipitates)
dissolves
what is a covalent interaction that can hold some proteins together?
disulfide bond (disulfide bridges)
Two cysteines can get oxidized (remove H) and can form a ________ __________, a covalent bond
disulfide bridge
When you get a little closer to look at the antigen binding site, you start to see there can be a series of beta sheets that are held together by ______ ______ and in between the beta sheets there are loopy regions (still amino acid sequences, but are not going to form a beta sheet).
disulfide bridges
Telomeres will shrink until they essentially disappear. In the cells without telomeres, they will completely stop ______. This can be used as a safeguard against cancer
dividing
who discovered DNA's structure?
Watson and Crick
Why does CO interfere with oxygen and CO2 binding with hemoglobin?
When CO binds with iron, it binds tightly, tighter than CO2 and O2
Prokaryotic cells (do/do not) have a nucleus
do not
Prokaryotic cells (do/do not) have well-defined, segmented, portioned off organelles
do not
Which type of bonds affect rotation of atoms
double and triple
Shape of each of these folded chains of proteins is constrained by many sets of weak ______ ________ that form within proteins
noncovalent bonds
Shapes of most biological macromolecules are highly constrained because of the weaker, ________ _________ that form between different parts of the molecule
noncovalent bonds
Stability of the folded shape is determined by the combined strength of large numbers of ____________ ____
noncovalent bonds
What hold together RNA (nucleic acids) and proteins (amino acids) together to make the ribosome structure?
noncovalent bonds
What is weaker? noncovalent bonds or covalent bonds
noncovalent bonds
What specify the precise shape of a macromolecule?
noncovalent bonds
What hold together the ligand to the pocket of a protein?
noncovalent bonds (typically hydrogen)
what kind of bonds are hydrogen bonds?
noncovalent vonds
Proteins often employ small, ______ _______ to perform functions that would be difficult or impossible using amino acids alone (for example, rhodopsin uses retinal to help detect light)
nonprotein molecules
The nucleus is enclosed within two concentric membranes that form the ______ _______
nuclear envelope
What connect the nucleoplasm with the cytosol and act as gates that control which macromolecules can enter or leave the nucleus
nuclear pores
which enzyme degrades the RNA primer?
nuclease
what enzyme cut the DNA, by breaking the phosphodiester bonds, between nucleotides?
nucleases
what leave the covalent bonds that join the damage nucleotides to the rest of the DNA strand, leaving a small gap on one strand of the DNA double helix?
nucleases
What are the 4 basic biomolecules in all cells?
nucleic acids, amino acids, carbohydrates, and lipids
During interphase, parts of different chromosomes that carry genes encoding ribosomal RNAs come together to form the _____. In here, the ribosomal RNAs are synthesized and combine with proteins to form _______, the cell's protein-synthesizing machine.
nucleolus, ribosomes
What is the largest sub-compartment in the cell?
nucleolus, the nuclear compartment in which ribosomal RNAs are transcribed and ribosomal subunits are assembled
A base and its sugar (without a phosphate group) is called a _________
nucleoside
what is the bead-like structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins
nucleosome
chromatin-remodeling complexes can locally alter the arrangement of the ________, rendering the DNA more accessible to other proteins in the cell
nucleosomes
what are proteins that bind to DNA to from eukaryotic chromosomes are traditionally divided into 2 general classes: histones and the non-histone chromosomal proteins
nucleosomes
what are the basic units of eukaryotic chromosome structure?
nucleosomes
Eukary mRNA is for (one/multiple) polypeptide chain(s)
one
How many strands does RNA have?
one
how many origins of replication does a bacteria cell have
one
in prokaryotes, multiple proteins can be made from the same mRNA. This is called a(n) _______
operon
Forks move away from each other in (opposite/similar) directions
opposite
Electrons in an atom can exist only in certain discrete regions of movement—very roughly speaking, in distinct _______
orbits
where does DNA replication begin?
origin of replication
Two cysteines can get ___________ (remove H) and can form a disulfide bridge, a covalent bond
oxidized
The mitochondria consumes _______ and releases _______ ______
oxygen, carbon dioxide
which arm of the chromosome is the shorter arm?
p arm
What is the concentration of hydrogen ions?
pH
what kind of bonds to polypeptides have?
peptide bonds
Which model organism led to detailed molecular understanding of apoptosis?
roundworm
Which membrane-bound organelle modules, mediates, absorbs, and deactives free radicals?
peroxisomes
which organelle is a small, membrane-enclosed vesicle which provides an insulated environment for a variety of reactions in which hydrogen peroxide is used to inactive toxic molecules
peroxisomes
phosphates are linked by what kinds of bonds (in ATP)
phosphoanhydride bonds
What holds together the backbone of DNA?
phosphodiester bonds
Which model organism was important to observe the developmental and cell diversity?
roundworm
what is c. elegans?
roundworm
what are packed with additional proteins for form small nuclear ribonucleoproteins (snRNPs)
sRNAs
What is a fatty acid who's tail contains only single carbon-carbon bonds?
saturated fatty acid
what are large molecules that contain binding sites recognized by multiple proteins
scaffold proteins
many interacting proteins are brought together by _________
scaffolds
Generally speaking, a protein must be (dephosphorylated/phosphorylated) to be activated
phosphorylated
Enzymes responsible for RNA processing ride on the ______ ______ of RP2 as it synthesizes an RNA molecule
phosphorylated tail
What allows proteins to switch from one conformation to another, quickly?
phosphorylating and dephosphorylating proteins from a particular side chain, like a continuous cycle
_____________ can create docking sites where other proteins can bind, promoting the assembly of proteins into larger complexes
phosphorylation
Different rhodopsins are sensitive to different ________ ____ ________
photons/wavelengths of light
tertiary structure
physical 3D final shape of a protein
biological properties of a protein molecule depend on its ______ ________ with other molecules
physical interaction
A cell in the surface layer of a ______ is squat and immobile, surrounded by a rigid box of cellulose with an outer waterproof coating of wax
plant
which microscope scatters electrons off the surface of the sample and is used to look at the surface detail of cells and other structures?
scanning electron microscope
What kind of replication style does DNA have?
semiconservative
When synthesis of protein is finished, the two subunits of the ribosome (stay together/separate)
separate
Primary structure
sequence of amino acids
what determines the shape of the protein and, therefore, its function?
sequence of amino acids
what are the 3 amino acids that have a hydroxyl group?
serine, threonine, and tyrosine
the 23rd pair of chromosomes are
sex chromosomes
double bonds are (shorter/longer) than single bonds and (stronger/weaker)
shorter and stronger
what are prokaryotic chromosomes called
plasmids
each promoter has a specific _____; contains 2 different nucleotide sequences laid out in the 5'-to-3' order, upstream of the transcriptional start site
polarity
what gets added onto the 3' end of a eukary mRNA?
poly-A tail
what protect mRNA from exonucleases?
poly-A tails
what protein recognizes the poly-A tail on an mRNA?
poly-A-binding protein
________ of an RNA molecule into mRNA is used by the protein-synthesis machinery to make sure that both ends of the mRNA are present and that the message is complete before protein synthesis begins
polyadenylation
prokary ribosomes are ____, they encode several different proteins on the same mRNA molecule
polycistronic
what is the polymer of amino acids?
polypeptide
in hemoglobin, what is the ring called the holds the iron atom in the center?
polyphorin
Proteins are produced on ___________
polyribosomes
what is a 3 or more sugar molecule called?
polysaccharide
What, in monosaccharides, influence the reactivity and recognition of the sugar molecules?
position of carbons and oxygens
________ regulation occurs when an enzyme's activity is stimulated by a regulatory molecule rather than being suppressed
positive
what charge do histones have?
positive
what is mRNA called before its post-transcriptional modifications?
pre-mRNA
Why is feedback inhibition good for the body?
prevents the waste of energy, time, and resources of making products the body already has plenty of
in eukary, what is the initial RNA produced called?
primary transcript
what is a form of a protein that can convert the properly folded version to an abnormal conformation
prions
Subsequent steps restore the _____ _____ to its original state, so the enzyme remains unchanged after the reaction and can go on to catalyze many more reactions
side chain
what give each amino acid its unique properties?
side chains
what helps bring the RNA polymerase into the right spot on a strand of DNA? (prokary)
sigma factor
What relay information from plasma membrane to the nucleus
signal integrator proteins
if histones are methylated, it is transcriptionally (active/silent)
silent
RNA is single or double stranded?
single
What keeps DNA from reannealing?
single-stranded binding proteins
at the molecular level, evolutionary change has been relatively (fast/slow)
slow
Fill in the blanks for the process of protein synthesis: The _____ ______ _____ binds to the initiator tRNA (a charged tRNA that has methionine). The tRNA associates with the _____ _____ _____. Then, they locate the start codon (___) and position themselves over the start codon. Then the ____ ____ ____ comes in, containing EPA sites. The large ribosomal subunit will align over the ___ site.
small ribosomal subunit, AUG, large ribosomal subunit, P
what subunit matches the tRNAs to the codons of the mRNA?
small subunit
RNA splicing is carried out largely by RNA molecules called ______ rather than proteins
snRNPs
what form the core of the spliceosome, the large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus?
snRNPs
what identify the intron/exon junctions in mRNA and form the lariat to cut out the introns?
snRNPs
what recognize splice-site sequences through complementary base-pairing between their RNA components and the sequences in the pre-mRNA
snRNPs
what is an example of alpha helices coming together to form a channel in a cell membrane?
sodium pump
What is a spiral shaped bacteria called?
spirillum
what is the large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus
spliceosome
Deoxyribose in the sugar-phosphate backbone makes chains of DNA chemically much more _____ than chains of RNA
stable (can go greater lengths without breakage and makes DNA a better suitor as a permanent storage of genetic information)
in a beta sheet, where are the r groups?
stick out out above or below the plain of the sheet
In the alpha helix, where are the r groups?
sticking out on the outside of the helix
(prokaryotes/eukaryotes) are the most diverse and numerous cells on earth
prokaryotes
___________ have a tough protective coat (cell wall) surrounding the plasma membrane, encloses a single compartment containing the cytoplasm and DNA
prokaryotes
All cells are either _________ or ___________
prokaryotic or eukaryotic
Which amino acids bends the alpha helix?
proline
Where does the sigma factor bind?
promoter
What are found in untranslated regions of mRNA (3' and 5')
promoter and regulatory regions
Why are ribonucleic acids not stable?
prone to hydrolysis
in what phase do chromosomes become visible?
prophase
the proteasome is a ______ that cleaves all the ____ ____ between amino acids in a polypeptide chain
protease, peptide bonds
what also recognize and remove proteins that are damaged or misfolded?
proteases
what cut the peptide bond between amino acids
proteases
what break down proteins?
proteasomes
Activity of an individual protein can be rapidly adjusted at the level of the _______ itself
protein
what is any segment of a polypeptide chain that can fold independently into a compact, stable structure
protein domain
a protein kinase or protein phosphatase can stimulate protein activity or inhibit it, it all depends on the _______ _______
protein involved
Appearance and behavior of a cell are dictated largely by its _________ __________
protein molecules
What catalyze the many other chemical reactions that keep the self-replicating system running?
proteins
most filaments have _____ associated with them
proteins
the ER is enormously enlarged in cells that are specialized for the secretion of ________
proteins
what are by far the most structurally complex and functionally sophisticated macromolecule?
proteins
what are the main building blocks from which cells are assembled
proteins
what constitute the most of a cell's dry mass
proteins
what alter the activity of the peptidyl transferase in the ribosome
proteins known as release factors
when an enzyme forms an enzyme-substrate complex, what does it do to the substrate?
puts pressure on a critical part of the substrate, making the breakage of the molecule easy for something else (like water). **It facilitates the reaction to occur to break up the substrate**
which arm of the chromosome is the longer arm
q arm
Proteins that are coils of coils of polypeptide chains are some of the (strongest/weakest) types of fibrous proteins
strongest
Weak interactions between macromolecules can produce large biochemical ____________ in cells
sub-compartments
When the polysaccharide binds to the lysozyme enzyme, the enzyme changes the shape of the _______, bending bonds so as to drive the bound molecule toward a particular transition state
substrate
Enzymes bind to 1 or more ligands, called ___________, and convert them into chemically modified products, doing this over and over again without themselves being changed
substrates
what is the backbone of DNA?
sugar and phosphate
Which RNA is the most abundant RNA in a cell?
rRNA
tRNA binding sites are formed primarily from what kind of RNA?
rRNA
which RNA make up the essential components of a ribosome?
rRNA
what are responsible for the ribosome's overall structure and its ability to choreograph and catalyze protein synthesis
rRNAs
Cells that divide (rapidly/rarely) keep their telomerase fully active
rapidly
Cells that divide (rapidly/rarely) do not keep their telomerase fully active
rarely
by binding a specific set of interacting proteins, a scaffold can greatly enhance the _____ of a particular chemical reaction or cell process, while also confining this chemistry to a particular area of the cell
rate
what makes up a nucleotide?
sugar, phosphate, nitrogenous base
what kind of coiling do chromosomes have?
super coiling
the hydroxyl group of the carbohydrate ring will be above or below the plane of the ring, which is critical for what?
recognition of cells
what is the most common color-blindness?
red-green
the vast bulk of our DNA includes a mixture of sequences that do what for our gene activity?
regulates gene activity (and allows for complexity and sophistication)
What allows access to a particular gene
regulatory DNA
noncoding RNAs, like proteins, various roles. Typically, they serve as ______, _____, and ______ components of clels
regulatory, structural, and catalytic
When you get to a stop codon, a tRNA does not bind into an A site. Instead, there will be a protein that can bind there known as a ______ _______, which signals for dissociation of everything.
release factor
The 3 codons that do not code for an amino acid, represented by stop codons, signal for proteins called _____ _____.
release factors
what cause the the addition of a water molecule instead of an amino acid to the peptidyl-tRNA
release factors
what are DNA molecules in the process of being replicated that appear like Y-shaped junctions?
replication forks
Cells must _________ to make more cells
reproduce
Retinal plus opsin creates
rhodopsin
Our ability to see color is based on our ability to see different ___________ that are active
rhodopsins
nucleotides with ribose are known as
ribonucleotides
RNA has a _____ sugar
ribose
what is a 5 carbon sugar called?
ribose (pentose)
what help fold and stabilize the RNA core, while permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis
ribosomal proteins
What is a large complex made from dozens of small proteins and several RNA molecules called ribosomal RNAs (rRNA)
ribosome
What was seen with fluorescence microscopes?
ribosomes
which organelle in eukaryotes is not lined in membranes?
ribozomes
what are RNA molecules that catalyze the splicing reaction of snRNPs?
ribozymes
what are RNA molecules that possess catalytic activity?
ribozymes
5' capping in bacteria occurs...
right in the beginning (the 5' end of the mRNA molecule is the first nucleotide of the transcript)
An alpha helix can be either _________ or ______ handed
right or left
Are monosaccharides typically found in chains or rings?
rings (typically 6 membered)
It is the combined action of the ___________ and ______ that allows reach codon in the mRNA molecule to be correctly matched to its amino acid
synthetases and tRNAs
what act like an adapter/convertor because on one end they have the amino acids while the other end base pairs/is complementary to the mRNA
tRNA
what enzyme puts amino acid onto tRNA?
tRNA synthetase
what is measured by the amount of energy that must be applied to break a bond?
Bond strength
amphipathic
Bot hydrophilic and hydrophobic regions.
Large ribosomal subunit shifts forward, moving the spent tRNA to the _ site before ejecting it
E
Most of our knowledge of the fundamental mechanisms of life (including DNA replication and how cells decode these genetic instructions to make proteins) have come from the studies of which model organism?
E. Coli
What is a gut prokaryote found in vertebrates? (Hint: also a model organism)
E. coli
What protein structure is a tertiary structure that typically has a pocket involved in binding and transport?
Globular
Which fatty acid is easier to stack?
Saturated fatty acid
what's the difference between Uracil and Thymine?
H on a carbon instead of a methyl group
Who realized all living cells are formed by the growth and division of pre-existing cells?
Schleiden and Schwann
How does an enzyme work in reactions involving two or more substrates?
In reactions involving two or more substrates, the active site acts like a template or mold that brings the reactants together in the proper orientation for the reaction to occur
who documented results of a systematic investigation of plant and animal tissues with the light microscope, showing cells were the building blocks of tissues?
Schleiden and Schwann
Who gave the name "cells"
Robert Hooke
Who discovered the width of DNA by performing an x-ray diffraction on a crystal structure of DNA?
Rosalind Franklin and Maurice Wilkins
when, in interphase, is the DNA copied?
S phase
What carbon will nitrogenous bases be bound to in nucleotides
carbon 1
Which carbon differs between RNA and DNA?
carbon 2
Fatty acids are predominantly made up of which 2 elements?
carbon and hydrogen
What molecule interferes with the exchange of oxygen and carbon dioxide in hemoglobin?
carbon monoxide
what is the only attachment that holds the growing polypeptide to the ribosome
carboxyl end of the polypeptide chain (addition of water from release factors helps release the protein chain)
when binding an amino acid to the tRNA, we can form a covalent bond to the _____ end of the amino acid, performing a ______ _______ reaction by removing water from the hydroxyl group from the __ end of the tRNA by using ATP.
carboxyl, dehydration synthesis, 3'
What are epithelial cancers called?
carcinomas
What protein is a large enzyme involved in converting (sequestrating) hydrogen peroxide into water?
catalase
Living cells are self-replicating collections of ___________
catalysts
By their (catalytic/anabolic) action, enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next
catalytic
polymerization and proofreading are tightly coordinated in a DNA polymerase enzyme. They are carried out by different _____ _____ in the same polymerase molecule
catalytic domains
Long polymer chains of DNA are made from the same set of four monomers, called ___________________
nucleotides
what are the building blocks of nucleic acids?
nucleotides
what are the monomers of nucleic acids?
nucleotides
what is a big problem of nonhomologous end joining?
nucleotides are often lost at the site of repair, which could present a huge issue if this occurs in a gene region
In what organelle is DNA housed?
nucleus
What is the most prominent feature we see in a eukaryotic cell?
nucleus
What is the most prominent organelle in eukaryotes?
nucleus
eukary RNAs are transcribed and processed in the ______
nucleus
where are histones found
nucleus
where are mRNAs made?
nucleus
where are proteasomes located?
nucleus and cytoplasm
strength of binding depends on what?
number of covalent bonds formed
atomic number of an element is determined by what?
number of protons
How does homologous recombination work?
o Initiates repair via a recombination-specific nuclease which chews back the 5' ends of the two broken strands at the break § With the help of specialized enzymes, one of the broken 3' ends "invades" the unbroken homologous DNA duplex and searches for a complementary sequence through base-pairing · Once a match is made, the invading strand is elongated by a repair DNA polymerase o Uses the complementary undamaged strand as a template o After the repair polymerase passed the point where the break occurred, the newly elongated strand rejoins its original partner, forming base pairs that hold the two strands of broken double helix together § Repair completed by additional DNA synthesis at the 3' ends of both strands of the broken double helix § Followed by DNA ligation § Net result: 2 intact DNA helices, for which the genetic information from one was used as a template to repair the other
How can we change the structure of proteins and other polymers?
pH and temperature
what is a polar covalent bond?
unequal sharing of electrons
What is a fatty acid in which has one or more double bonds in its tails?
unsaturated fatty acids
What are histone tails made of?
unstructured n-terminal amino acid
the promoter region is (upstream/downstream) of the 5' end of the gene
upstream
what is the base in RNA that differs from DNA?
uracil