Cell Exam 1

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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

How does an organism/DNA know WHICH strand is messed up?

Newly synthesized one is not methylated yet

Are all protazoans predators?

Are mRNAs the bulk of RNAs in a cell?

Are ribonucleic acids stable?

Are viruses alive?

Can DNA fold into a variety of sahpes?

Do prokaryotes have introns?

Do prokaryotes have organelles?

Does RNA polymerase need to have proofreading abilities?

Does RNA primer synthesize DNA?

Does RNA remain H bonded to the DNA template strand?

Does depurination break the DNA phosphodiester backbone?

Does primase proofread its work?

Does the RNA primer have to be complementary to the DNA?

Does the amount of DNA in cells correlate with the complexity of the organism?

Does the amount of genes correlate to the amount of DNA?

Does the newly formed RNA anneal with the DNA template?

If DNA polymerase were able to synthesize in the opposite direction, would it be able to proofread?

Is homologous recombination necessary to fix?

Is the replication fork symmetrical?

can RNA polymerase II (RP2) initiate transcription on its own?

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

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***

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?

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

how many base pairs are there per helical turn?

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?

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?

How many molecules thick are the internal membranes that surround most organelles?

How many oxidation states does iron have?

how many amino acids does a ribosome add to a polypeptide chain each second?

how many electrons are in a single bond?

how many replication forks are at each replication origin

how many times does DNA wrap around a histone?

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?

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?

how many genes are on the Y chromosome

256

How many tails does glycerol have?

In order to change a shape of a protein and restore it, how many conformations does a protein typically go through?

how many reading frames does a single mRNA have?

if 3 proteins can be made from the same prokary mRNA, how many start/stop signals are there on the mRNA?

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

What end of DNA do nucleotides get added on?

amino acid is linked to the __ end of a tRNA molecule

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)

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: #)

How many DNA polymerases are involved in replication in a replication fork?

How many biomolecules are cells made up of?

How many bonds can carbon form?

How many polypeptide chains are in hemoglobin?

How many valence electrons does carbon have?

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?

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

The ____ end of the mRNA code will correspond to the N terminal of the growing polypeptide chain

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?

Fatty acids can be used as a food reserve and broken down to produce about __ as much usable energy as glucose

How many subunits is histone made of?

the second and third shell of an atom can contain how many elections?

how many naturally occurring elements are there?

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

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

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?

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

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?

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

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

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