Biology 221 Final Review

In their 1953 paper on the double-helical structure of DNA, Watson and Crick famously wrote: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." What did they mean?

Each strand in a DNA double helix contains all the information needed to produce a complementary partner strand.

T/F: adenine and guanine are pyrimidines

False, adenine and guanine are purines while uracil, thymine, and cytosine are pyrimidines.

T/F: condensation is energetically favorable

False, hydrolysis is energetically favorable, condensation is energetically unfavorable

T/F: kinases remove PO4 from a protein

False. Kinases add PO4 from a protein, while phosphatase removes PO4

T/F: mature membranes are perfectly symmetrical

False. Mature membranes are asymmetric, which is why the cell has a rounded shape

T/F: rna is transcribed into protein

False. RNA is translated into protein. dna is transcribed into rna

T/F: longer hydrocarbon tails create a more fluid phospholipid

False. Shorter = more fluid

T/F: mutations in somatic cells are passed down to progeny

False. Somatic cells are only present in the life of the individual, mutations in germ line cells are passed on to progeny and can last generations

T/F: transmembrane proteins only pass through the bilayer once

False. Transmembrane proteins can be either single pass or multi pass.

T/F: both ends of a DNA molecule are chemically identical

False. one of of the molecule is chemically different from the other end

Nicotine (the addictive chemical in cigarettes) administration in mice has been shown to lead to increased acetylation of both histone H3 and histone H4 near a "master regulator" gene for addiction behavior (deltaFosB). How does nicotine affect the activity of deltaFosB? How could nicotine lead to H3 and H4 hyperacetylation

It increases it by leading to hyperacetylation which loosens the histone wrapping and making the DNA more available Multiple answers possible (recruitment of appropriate enzymes/cofactors), but research shows nicotine inhibits HDACs, leading to less deacetylation (meaning more acetylation)

What feature of DNA polymerase causes the end replication problem solved by telomerase?

Its requirement for an RNA primer to begin polymerization

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking DNA ligase were used to make the cell extracts and why?

Lagging strand completion

Which strand grows in the direction of the fork and consists of a singluar cohesive strand? The leading or lagging strand?

Leading

what causes the polypeptide chain's folding into a 3D conformation?

Non-covalent interactions (this includes hydrophobic interactions)

Which is a "rapid response" to a double stranded DNA break? Homologous recombination or non-homologous end joining

Non-homologous end joining

What is a hydroxyl group? Is it polar?

O-H, polar

What is a carbonyl group? Is it polar?

O=C, polar

What is a carboxyl group? Is it polar?

O=C-OH, acidic

What is a phosphate group? Is it polar?

OH | O=P-OH , acidic | O

What is the term for the series of short DNA pieces present on the lagging strand?

Okazaki Fragments

what are the parts of a nucleotide?

Phosphate, Sugar (5 carbon ribose), base (N containing ring)

Select all the cell types in which the listed structure or molecule can be found. Note that the structure or molecule can be found in more than one type of cell. Cell wall: Mitochondria: DNA: Lysosome: Plasma Membrane: Nucleus: Golgi apparatus:

Plant and bacteria animal and plant animal, plant, and bacteria animal and plant animal, plant, and bacteria animal and plant animal and plant

what are the 3 domains of life? which are prokaryotic?

Prokaryotes: Bacteria + Archaea, Eukaryotes

How many replication forks are formed when an origin of replication is opened?

2

how many hydrogen bonds are present between A and T nucleotides

2

how many hydrogen bonds are present between C and G nucleotides

3

How can you differentiate between the 3' an 5' ends of DNA?

3' has an OH group, which is necessary for the addition of new nucleotides. 5' has a phosphate group

what does the tertiary level of protein structure look like?

3D folding pattern of a protein due to side chain interactions (hydrophobic forces)

in which direction is DNA polymerized?

5' -> 3'

What is a methyl group? Is it polar?

CH3, nonpolar

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________.

CO2; photosynthesis.

What is one advantage that channels exhibit for transport of substances across a membrane that transporters do not exhibit?

Channels let many molecules of a substance cross the membrane with one conformational change, but transporters typically do not

Enhancers can act over long stretches of DNA, but are specific about which genes they affect. How do eukaryotic cells prevent these transcription regulatory sequences from looping in the wrong direction and inappropriately turning on the transcription of a neighboring gene?

Chromosome loop-forming proteins arrange the DNA into topological associated domains such that individual genes and their associated enhancer binding regions are in proximity.

What is the name of the enzyme that synthesizes new strands of DNA?

DNA polymerase III

what are the byproducts of photosynthesis?

Sugars and O2

What occurs when a cell epairs a double-strand DNA break by the process of nonhomologous end joining (NHEJ)?

The DNA sequence at the site of repair is altered by a short deletion

Which statement is true about the removal of a terminal phosphate from ATP?

The reaction is energetically favorable

Why are α helices and β sheets common folding patterns in polypeptides?

Side chains are not involved in forming the hydrogen bonds, allowing many different amino acid sequences to adopt these folding patterns

Where are membrane lipids made?

Smooth ER

What is typically true of ion channels?

They are gated

What is the function of single-strand binding proteins in DNA replication?

They bind to single-stranded DNA and prevent the single-strands from re-forming base pairs.

What is one way changes in histone modifications lead to changes in chromatin structure?

They help recruit other proteins to the chromatin.

T/F: The cytoskeleton is used as a transportation grid for the efficient, directional movement of cytosolic components

True

T/F: cholesterol makes a phospholipid less fluid, because it's rigid structure packs empty spaces

True

T/F: the nuclear envelope has an inner and outer membrane

True

T/F: unsaturated hydrocarbon tails create a more fluid phospholipid

True

T/F: all cell membranes in animals maintain a distinct inside and outside phospholipid monolayer

True. The cytosolic monolayer always faces the cytosol and the non-cytosolic monolayer always faces teh extracellular space.

what is a thymine dimer

UV light causes adjacent thymines to bond

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require __________ to selectively speed up reactions and meet the demands of the cell. a. enzymes b. atp c. heat d. ions

a

Complete the sentence with the best option provided below. The primary structure of a protein is the a. amino acid sequence b. average size of amino acid side chains c. lowest energy conformation d. amino acid composition

a

How does an allosteric inhibitor work? a. It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate. b. It binds to a site other than the active site, causing a conformational change in the enzyme that forces the product to leave the active site. c. It interacts covalently with the substrate, preventing it from fitting into the enzyme's active site. d. It outcompetes the substrate molecule and binds to the active site, preventing substrate molecules from binding there.

a

In water, hydrogen bonds can form between which of the following? a. A hydrogen atom of one water molecule and an oxygen atom of another b. The oxygen atom of one water molecule and the oxygen atom of another c. The hydrogen atom of one water molecule and the hydrogen atom of another d. The one oxygen atom and two hydrogen atoms of one water molecule

a

Proteins are important architectural and catalytic components within the cell, helping to determine its chemistry, its shape, and its ability to respond to changes in the environment. Remarkably, all of the different proteins in a cell are made from the same 20 __________. By linking them in different sequences, the cell can make protein molecules with different conformations and surface chemistries, and therefore different functions. a. amino acids b. sugars c. fatty acids d. nucleotides

a

Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? a. hydrogen bonds along the protein backbone b. specific amino acid sequences c. the hydrophobic-core interactions d. side-chain interactions

a

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation that you would observe after this segment has undergone two rounds of DNA replication? a. TCT b. TCGT c. TGTT d. TAT

a

The cell components that move materials from one organelle to another are called a. transport vesicles. b. endoplasmic reticulum. c. Golgi apparatus. d. cytosol.

a

The core histones are small, basic proteins that have a globular domain at the C-terminus and a long, extended conformation at the N-terminus. Which of the following is NOT true of the N-terminal "tail" of these histones? a. It binds to DNA in a sequence-specific manner. b. It helps DNA pack tightly. c. It extends out of the nucleosome core. d. It is subject to covalent modifications.

a

The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of a. chemical bonds b. brownian motion c. light waves d. heat

a

Two or three α helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by __________ interactions. a. hydrophobic b. ionic c. hydrophilic d. van der waals

a

__________ play an important role in organizing lipid molecules with long hydrocarbon tails into biological membranes. a. hydrophobic forces b. ionic bonds c. van der waals attractions d. hydrogen bonds

a

the main function of the nucleus is to a. house the DNA in a separate cell compartment. b. provide energy for the cell. c. allow cells to segregate enzymes. d. make proteins using the genetic material.

a

what is an ionic bond?

a type of non-covalent bond that involves the TRANSFER of electrons

Match the type of phenotypic change below with the type of genetic change most likely to cause it. a. A protein becomes much more unstable. b. Tandem copies of a gene are found in the genome c. A protein normally expressed only in the liver is now expressed in blood cells d. A copy of a bacterial gene is now found in a bacterial cell of a different species e. A protein acquires a DNA-binding domain.

a. mutation within a gene b. gene duplication c. mutation in a regulatory region d. horizontal gene transfer e. exon shuffling

A protein chain folds into its stable and unique three-dimensional structure, or conformation, by making many noncovalent bonds between different parts of the chain. Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules. From the list provided, choose the class of amino acids that are most important for the interactions detailed below. a. Tightly packing the hydrophobic interior core of a globular protein b. Localizing a membrane protein that spans a lipid bilayer c. Forming ionic bonds with negatively charged DNA d. Forming hydrogen bonds to aid solubility in water

a. nonpolar b. nonpolar c. positively charged d. uncharged polar

are carboxyl groups acidic or basic?

acidic

are phosphate groups acidic or basic?

acidic

In the cytoskeleton, rank the following filaments from shortest to longest: actin, microtubules, intermediate

actin, intermediate, microtubules

The movement of an ion against its concentration gradient is called what?

active transport

An single base pair genetic change found in the conserved sequence of the regulatory region of a gene is likely to

affect when and where the gene is expressed.

Proteins are formed from _______ Lipids are formed from _______ Nucleic acids are formed from _______ Carbohydrates are formed from _______

amino acids, fatty acids, nucleotides, monosaccharides

Which parts of amino acids are involved in a peptide bond?

amino group of one amino acid and carboxyl group of the other

if a molecule is both hydrophobic and hydrophillic, what is it termed?

amphipathic

The ribose sugar distinguishes DNA from RNA. What is DNA missing that RNA has?

an -OH group at C2'

where can you find cholesterol?

animal cells ONLY

negatively charged atoms are ____, positively charged atoms are ____

anions, cations

Carbon atoms can form double bonds with other carbon atoms, nitrogen atoms, and oxygen atoms. Double bonds can have important consequences for biological molecules because they are __________ compared to single covalent bonds. a. weak b. rigid with respect to rotation c. long d. unstable

b

How does phosphorylation control protein activity? a. The phosphate group serves as an added source of energy for a protein. b. The phosphate group induces a change in the protein's conformation. c. The phosphate group, with its positive charges, temporarily relieves feedback inhibition. d. The phosphate group, with its negative charges, prevents other negatively charged molecules from interacting with the protein. e. The phosphate group alters the primary structure of the protein.

b

In a DNA double helix, a. purines pair with purines b. the two DNA strands run antiparallel. c. thymine pairs with cytosine. d. the two DNA strands are identical.

b

In a DNA double helix, a. thymine pairs with cytosine. b. the two DNA strands run antiparallel. c. purines pair with purines. d. the two DNA strands are identical.

b

Muscle cells, which must use large amounts of energy very quickly to do work, contain more_____ than most other cells in the human body. a. vacuoles b. mitochondria c. chloroplasts d. lysosomes

b

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of a. a carbon atom b. a water molecule c. a carboxylic acid group d. an amino group

b

The best way to know if an organic molecule has been reduced is to see if there was an increase in the number of __________ bonds. a. C-N b. C-H c. C-O d. H-H

b

The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of __________ in a process called __________. a. ATP; phosphorylation b. water; hydrolysis c. hydroxide; hydration d. acetate; acetylation

b

Unlike what occurs when fuel is burned to make a fire, all living systems use the energy from heat-generating reactions to create and maintain a. movement b. order c. light d. electricity

b

Which of the following situations would facilitate the process of exon shuffling? a. a haploid genome b. introns that contain regions of similarity to one another c. shorter introns d. exons that code for more than one protein domain

b

Which of the following statements about sequence proofreading during DNA replication is FALSE? a. If an incorrect base is added, it is "unpaired" before removal. b. The exonuclease activity removes nucleotides from the 5' end of a growing DNA strand c. The DNA proofreading activity occurs nearly simultaneously with strand elongation. d. The exonuclease activity is in a different domain of the DNA polymerase.

b

Which of the following are components of the eukaryotic plasma membrane? (check all that apply) a. nucleic acids b. lipids c. carbohydrates d. proteins

b,c,d

Which of the following are ways cells can differ (check all that apply): a. method of interpreting genetic information b. method of obtaining energy c. size d. shape e. chemical composition

b,c,d

How do bacterial and eukaryotic chromosomes differ?

bacterial: single chromosome, circular, no nucleus, different proteins and packaging strategies eukaryotic: multiple chromosomes, linear, contained in nucleus, higher order packaging into chromatin, histones

are amino groups acidic or basic?

basic

How is it possible that a change in a single amino acid in a protein of 1,000 amino acids can destroy protein function, even when that amino acid is far away from any ligand-binding site?

because the amino acid sequence determines protein shape and protein shape determines function.

what is the down side to NHEJ?

blunt ends are required, and nucleotides are sometimes deleted, and the process is therefore less accurate

What is the function of the lysosomes and peroxisomes

break down molecules with enzymes, pH, and hydrogen peroxide

Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells harvest some of the potential energy in the chemical bonds of foodstuffs to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in __________ reactions. a. dehydrogenation b. hydrolysis c. condensation d. oxidation

c

Enzymes increase the speed of a chemical reaction because they a. make the reaction more energetically favorable b. increase the temperature to provide the necessary boost of energy. c. lower the activation energy needed to start the reaction d. make the reaction spontaneous

c

If a reaction is energetically favorable (exergonic), then it must produce a(n) a. decrease in heat b. decrease in reaction time c. increase in entropy d. increase in activation energy

c

Select the option that correctly finishes the following statement: A cell's genome a. is defined as all the genes being used to make protein. b. is altered during embryonic development. c. contains all of a cell's DNA. d. constantly changes, depending upon the cell's environment.

c

Which of the following is NOT a general mechanism that cells use to maintain stable patterns of gene expression as cells divide? a. faithful propagation of condensed chromatin structures as cells divide b. a positive feedback loop, mediated by a transcriptional regulator that activates transcription of its own gene in addition to other cell-type-specific genes c. proper segregation of housekeeping proteins when cells divide d. inheritance of DNA methylation patterns when cells divide

c

Which of the following statements is TRUE? a. Disulfide bonds are formed mainly in proteins that are retained within the cytosol. b. Disulfide bonds are formed by the cross-linking of methionine residues. c. Disulfide bonds stabilize but do not change a protein's final conformation. d. Disulfide bonds are more common for intracellular proteins, compared to extracellular proteins.

c

You have developed a promising anti-cancer agent, but it has poor solubility in water. Which of the following changes should improve water solubility? Please choose all correct answers. a. increasing the size of the drug b. adding a methyl group c. adding a carboxyl group d. adding a hydroxyl group

c,d

What is the function of the mitrochondria?

uses food molecules to generate ATP with a double membrane structure

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by

using the energy of ATP hydrolysis to move nucleosomes.

Viruses reproduce inside a host cell because

viruses use host-cell ribosomes to produce viral coat proteins.

What happens when a molecule is reduced? Oxidized?

when a molecule is reduced, it gains electrons (GER). when a molecule is oxidized, it loses elections (LEO). Alternatively, when a molecule is reduced, it gains a hydrogen. When a molecule is oxidized, it gains an oxygen

In a lipid bilayer, where do lipids rapidly diffuse?

within the plane of their own monolayer

Do DNA strands have polarity?

yes, courtesy of the phosphodiester backbone.

Viral genomes

can be either double stranded or single stranded and can be made of DNA or RNA

What can happen if DNA damage occurs and the cell fails to repair it?

cancer

in a fatty acid molecule, what kind of functional group makes up the head?

carboxyl group

Plasma membrane proteins that move ions in and out of cells using passive transport are called

channels

differentiate between transporters and channels

channels: discriminate molecules based on size and charge, passive transport based on concentration gradient transporters: highly selective, usually require energy; active transport, pumps.

Which of the following choices BEST describes the role of the lysosome?

clean-up, recycling, and disposal of macromolecules

in the mitotic phase, what do the chromosomes look like?

compacted

what is the difference between competitive and noncompetitive inhibitors?

competitive inhibitors block the binding site, whereas noncompetitive inhibitors bind to the enzyme at another site, allowing substrate binding, but blocking the reaction.

what are electrochemical gradients based off of?

concentration and voltage

what process produces glycosidic bonds?

condensation (water expulsion)

synthesis requires energy = _______ (_____ H2O)

condensation, release

the consistent diameter of the dna double helix arises because of which property?

constant base pairing of pyrimidines with purines

what kind of bonds involve the sharing of electrons?

covalent

Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below donates a chemical group rather than electrons? a. FADH2 b. NADH c. NADPH d. ATP

d

Cells that are specialized for the secretion of proteins are likely to have which of the following features? a. small volume of cytoplasm b. large population of mitochondria c. long bundles of actin/myosin proteins d. enlarged endoplasmic reticulum

d

Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that break down nutrients in food can be described as a. metabolic b. anabolic c. biosynthetic d. catabolic

d

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration? a. CO2; O2 b. CH3; H2O c. CH2OH; O2 d. CO2; H2O

d

How do protein, nucleic acid, and polysaccharide molecules polymerize (grow in length)? a. none of these b. oxidation reactions c. hydrolysis reactions d. condensation reactions

d

Telomeres serve as caps protecting the ends of linear chromosomes. Which of the following is FALSE regarding the replication of telomeric sequences? a. Additional repeated sequences are added to the template strand. b. The lagging-strand telomeres are not completely replicated by DNA polymerase. c. Telomeres are made of repeating sequences. d. The leading strand doubles back on itself to form a primer for the lagging strand.

d

The central dogma provides a framework for thinking about how genetic information is copied and used to produce structural and catalytic components of the cell. From the choices below, select the order of biochemical processes that best correlates with the tenets of the central dogma. a. replication, translation, transcription b. translation, replication, transcription c. translation, transcription, replication d. replication, transcription, translation

d

Which is NOT one of the central tenants of Cell Theory: a. All living things are comprised of one or more cells b. All cells come from pre-existing cells c. The cell is the basic organizational unit in all organisms d. all cells contain dna

d

Which of the following choices BEST describes the role of the lysosome? a. transport of material to the Golgi apparatus b. sorting of transport vesicles c. the storage of excess macromolecules d. clean-up, recycling, and disposal of macromolecules

d

Which of the following descriptions is consistent with the behavior of a cell that lacks a protein required for a checkpoint mechanism that operates in G2? a. The cell would pass through M phase more slowly than normal cells. b. The cell would be unable to enter M phase. c. The cell would be unable to enter G2. d. The cell would enter M phase under conditions when normal cells would not.

d

Which of the following examples does NOT describe a mechanism of post-transcriptional control of gene expression? a. the alternative splicing of a gene, leading to the production of a muscle-specific protein b. the degradation of an mRNA by miRNA binding and RISC activity c. translational inhibition of an mRNA by the binding of a protein at the 5´ untranslated region of the message. d. the action of the RNA component of telomerase

d

Which of the following statements about the newly synthesized strand of a human chromosome is TRUE? a. It was synthesized from multiple origins solely by discontinuous DNA synthesis. b. It was synthesized from a single origin by a mixture of continuous and discontinuous DNA synthesis. c. It was synthesized from a single origin solely by continuous DNA synthesis. d. It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.

d

Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds, respectively)? a. 20 carbons with two double bonds b. 16 carbons with no double bonds c. 24 carbons with one double bond d. 15 carbons with two double bonds

d

The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation?

decrease in gene expression

what is the purpose of nuclease?

degrades primer

what substance is most commonly used to help purify a membrane protein?

detergent

what do van der waals attractions depend on?

distance between molecules and fluctuating location of the electrons

miRNAs, tRNAs, and rRNAs all

do not code for proteins.

Which term correctly describes the entire phospholipid molecule? a. hydropathic b. apathetic c. hydrophobic d. hydrophilic e. amphipathic

e

DNA replication is considered semiconservative because

each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand.

if you wanted to see organelles, which kind of microscope would you use?

electron

What is the evolutionary origin of mitrochondira and chloroplasts, considering they have their own dna?

endosymbiosis; they began as bacteria that were engulfed by another cell

Cells that are specialized for the secretion of proteins are likely to have which of the following features?

enlarged endoplamic reticulum

The type of chromatin that participates in the active transcription of DNA to RNA is

euchromatin

T/F: DNA synthesis takes places in mitotic phase

false

T/F: Eukaryotic genes are distributed across multiple DNA molecules, which can be packaged into linear or circular chromosomes

false

T/F: ionic bonds are stronger than covalent bonds

false =

T/F: facilitated diffusion is another term for active transport

false . facilitated diffusion is a synonym for passive transport

T/F: a positive delta g means the reaction is favorable

false, a positive delta g means the reaction is unfavorable

T/F: amino acids are linked through non-covalent bonds

false, amino acids are covalently linked together

T/F: enzyme active sites aren't entirely picky regarding ligands

false; enzyme active sites show great specificity for ligands

T/F: mutations in a mother's somatic cell can cause disease in her daughter

false; mutations in a germ line cell can cause disease in progeny

what enzyme in the golgi transports specific phospholipids to the cytosolic monolayer?

flippase

what is a catabolic reaction?

fuels are broken down to produce energy

________ makes up _________ makes up __________ (polymers, functional groups, monomers)

functional groups, monomers, polymers

The complete set of information in an organism's DNA is called its

genome

What is the function of the cytoskeleton

give the cell structure and facilitates cell transport (train tracks for vesicles)

What is the bond called that connects two mono-saccharides by -OH groups

glycosidic bond

Where are membrane lipids rearranged?

golgi apparatus

Which enzyme opens the replication fork?

helicase

differentiate between heterochromatin and euchromatin

heterochromatin is silenced genetic material, whereas euchromatin is open for expression

what makes up a nucleosome?

histone protein octamer and DNA

which process is flawless? non-homologous recombination or homologous recombination?

homologous recombination. non-homologous recombination results in errors.

how do NADH and NADPH carry energy

hydrides (hydrogen with 2 high energy electrons)

what kind of bond connects base pairs

hydrogen

what does the secondary level of protein structure look like?

hydrogen bonding of peptide backbone causes the amino acids to fold into a repeating pattern (alpha helix or beta sheet)

What type of reaction is the reverse of a condensation reaction?

hydrolysis

breakdown releases energy = ________ (_____ H2O)

hydrolysis, use

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking helicase were used to make the cell extracts and why?

initiation of DNA synthesis

What part of the DNA replication process would be most directly affected if a strain of bacteria lacking primase were used to make the cell extracts and why?

initiation of DNA synthesis

what is mismatch

introduction of a wrong base

Combinatorial control of gene expression involves what

involves groups of transcription regulators working together to determine the expression of a gene.

Lipid bilayers are highly impermeable to which molecule(s)?

ions, such as NA+ and Cl-

RNA in cells differs from DNA in that

it is single-stranded and can fold up into a variety of structures.

What is the purpose of ligase?

joins the gap between nucleotides on the lagging strand

Define fluidity

molecules can move within the monolayer

what are hydrogen bonds?

non-covalent bond that involves attraction between partial charges (weak interaction between polar molecule and H atom in polar bond)

What type of bond occurs between antibody and antigen?

noncovalent

how does a ligand bond to an active site? noncovalent or covalent bonds?

noncovalent

How do peripheral membrane proteins associate with the membrane-embedded proteins?

noncovalent interactions

Are polar or nonpolar molecules more likely to naturally diffuse into a cell?

nonpolar

are methyl groups polar or nonpolar?

nonpolar

Rank the following in terms of diffusion likelihood through the lipid bilayer. Ions, small uncharged polar, large uncharged polar, nonpolar

nonpolar > small uncharged polar > large uncharged polar > ions

Transcription is similar to DNA replication in that

nucleotide polymerization occurs only in the 5´-to-3´ direction.

The chromosomes we typically see in images are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and

occupy discrete territories in the nucleus

what contain a cluster of genes transcribed as a single mRNA.

operons

what kind of bonds link amino acids to form polypeptide chains?

peptide bonds

What is the function of the chloroplasts?

perform photosynthesis

Proteins that are associated with the membrane by noncovalent interactions with other membrane proteins are called ___________ proteins.

peripheral membrane

how does ATP carry energy?

phosphate bonds

what kind of bond holds together neighboring subunits in a single strand of DNA

phosphodiester bond

what links together nucleotides?

phosphodiester bonds

are carbonyl groups polar or nonpolar?

polar

are hydroxyl groups polar or nonpolar?

polar

what leads to partial charges on atoms?

polar covalent bonds

In an aqueous environment, would polar or nonpolar side chains form hydrogen bonds with water?

polar. nonpolar side chains would be packed into the hydrophobic core region.

What are the two catalytic activities of DNA polymerase?

polymerizing and editing

macromolecules are ______ of many ______ covalently bonded together

polymers, monomers

What determines the specificity an antibody has for its antigen?

polypeptide loops in its variable domains

Proteins are _____ built from amino acids, which each have an amino group and a _____ group attached to the central _____ . There are 20 possible _____ that differ in structure and are generally referred to as "R." When a protein is made, amino acids are linked together through _____ , which are formed by condensation reactions between the carboxyl end of the last amino acid and the amino end of the next _____ acid to be added to the growing chain. WORD BANK: ionized, amino, length, peptide bonds, carbon, hydroxide, side chains, noncovalent, carboxyl, protein, popypeptides

polypeptides, carboxyl, carbon, side chains, peptide bonds, amino

It is now a routine task to determine the exact order in which individual subunits have been linked together in polynucleotides (DNA) and polypeptides (proteins). However, it remains difficult to determine the arrangement of monomers in a polysaccharide. Explain why this is the case.

polysaccharides can have branched formations of compiled monosaccharides, making the macromolecule difficult to read directionally. basically, monosaccharides can be added to many points of a polysaccharide, creating branches on the structure.

What kind of cell is the following: Cell wall, uni-cellular organism, with no membrane bound organelles

prokaryote

what does the quaternary level of protein structure look like?

protein consisting of more than one amino acid chain

what does the rough ER do?

protein synthesis

What type of macromolecule helps package DNA in eukaryotic chromosomes?

proteins

What type of macromolecule helps package DNA in eukaryotic chromosomes?

proteins (histones, specificially)

what differentiates purines and pyrimidines?

purines are a double ring, while pyrimidines are single ring.

which nucleotides are purines? pyrimidines?

purines: AG, phyrimidines: TC

what is the difference between pyrimidines and purines?

pyrimidines have only one ring, while purines have 2

1) By definition, catalysis allows a reaction to occur more _____ . 2) Chemical reactions occur only when there is a loss of _____ energy. 3) Enzymes act more _____ than other catalysts. 4) A catalyst decreases the _____ energy of a reaction. WORD BANK: completely, favorable, slowly, rapidly, selectively, unfavorable, free, kinetic, activation, chemical bond

rapidly, free, selectively, activation

what is an anabolic reacion?

requires energy to build higher degree molecules

building polymers ______ energy, while breaking them down ______ energy

requires, releases

does butter have more saturated or unsaturated bonds compared to oil?

saturated

What enzyme redistributes new phospholipids to other monolayer?

scramblase

what does the primary level of protein structure look like?

sequence of a chain of amino acids

A base substitution mutation in a gene sometimes has no effect on the protein the gene codes for. Why?

some amino acids have more than one codon; the genetic code is redundant

Transporters, in contrast to channels, work by ______

specific recognition of transport substrates.

Where does an incoming amino acid bind on another amino acid?

the carboxyl group (-OH)

how do enzymes decrease activation energy?

the enzyme brings substrates in close proximity and puts strain on the bonds

A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infection. This is because

the neuron expresses some mRNAs that the white blood cell does not.

In the α helices of single-pass transmembrane proteins, the hydrophobic side chains face which direction?

the outside of the membrane-spanning helix

what is the purpose of disulfide cross-links?

they provide structural stability

How do peripheral membrane proteins associate with the plasma membrane?

through noncovalent bonding with an integral membrane protein

What is the function of telomerase?

to extend telomeres at the end of template strand.

what is the purpose of the mitochondrial double membrane?

to increase surface area and make a gradient of hydrogen ions

Select the option that best completes the following statement: Nonhomologous end joining (NHEJ) is a process by which a double-stranded DNA end is joined

to the nearest available double-stranded DNA end.

what are the 3 types of integral membrane proteins?

transmembrane, monolayer-associated, lipid linked

T/F A thermodynamically unfavorable reaction can become favorable when coupled to a highly favorable reaction.

true

T/F: DNA polymerase can correct errors in synthesis by proofreading

true

T/F: In eukaryotic cells, DNA is wound around protein complexes called histones, which can be covalently modified to regulate the expression of genes

true

T/F: Membrane fluidity decreases when phospholipid chain lengths increase and fatty acids are fully saturated

true

T/F: Mitochondria and Chloroplasts have their own DNA

true

T/F: The lipid bilayer is made up of phospholipids that have an amphipathic chemical structure.

true

T/F: bacterial mrnas are transcribed and translated simultaneously

true

T/F: cellular respiration is a redox reactoin

true

T/F: exergonic = energetically favorable

true

T/F: homologous recombination requires a normal copy of the chromosome nearby

true

T/F: hydrogen bonds play a role in protein and DNA structure

true

T/F: hydrophobic is a synonym for non-polar

true

T/F: if electrons are shared unequally, it's a polar bond

true

T/F: single pass alpha helices require nonpolar amino acids while multiple pass alpha helices require a mixture of polar and nonpolar amino acids

true

T/F: the genetic code is redundant

true

how can you tell if a fatty acid is saturated or unsaturated?

unsaturated molecules have one or more double bonds in the hydrocarbon tail and therefore appear kinked. saturated molecules do not have any double bonds in the hydrocarbon tail.

Is the bond between A and T stronger than that between C and G?

No, DNA with a higher number of G-C base pairs will be stronger

Explain the process of DNA synthesis on the leading strand

1. Helicase opens fork 2. SSB proteins prevent reannealing 3. Primer (RNA) laid down by primase 4. DNA synthesis - DNA polymerase III

Explain the process of DNA synthesis on the lagging strand

1. Helicase opens fork 2. SSB proteins prevent reannealing 3. Primer (RNA) laid down by primase 4. DNA synthesis - DNA polymerase III 5. Primer laid down at new site 6. DNA pol III grows strand (repeated) 7. Nuclease degrades RNA primer 8. DNA pol I adds DNA 9. Ligase joins gaps between nucleotides and catalyzes phosphodiester bonds

What are the steps of single strand DNA repair?

1. segment of damaged strand is excised 2. repair dna polymerase fills in missing nucleotide in top strand by using bottom strand as a template. 3. nick in dna backbone is sealed by dna ligase

Which statement best represents the cell theory?

All cells are formed by the growth and division of existing cell.

Compared to adding heat to the system, what is the advantage of using an enzyme to overcome an energy barrier?

An enzyme is specific for one desired pathway and end product

Why does flip-flop of a phospholipid from one monolayer to another rarely occur?

Because that would require a nonpolar portion of the phospholipid to interact with an aqueous environment, which isn't energetically favorable.

What is the function of the nucleus?

Contains DNA, regulates entry and exit through pore usage, and has two concentric membranes that make up the nuclear envelope.

How do lipid linked proteins associate with the lipid bilayer?

Covalent attachments to the lipids within the bilayer

put these terms into the correct order: protein, dna, transcription, translation, replication, rna

Dna, replication, transcription, rna, translation, protein

T/F: Electrons are always shared equally between covalently bonded atoms

False

T/F: Enzymes lower the free energy released by the reaction that they facilitate

False

T/F: For a gene to function properly, every exon must be removed from the pre-mRNA in the same fashion on every mRNA molecule produced from the same gene

False

T/F: Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain

False

T/F: Short pieces termed primers are removed by primase that degrades RNA

False

T/F: The cytosol is fairly empty, containing a limited number of organelles, which allows room for rapid movement and diffusion of molecules

False

T/F: The methyl (CH3) groups on monosaccharides are reaction hot spots and can be replaced by other functional groups to produce derivatives of the original sugar

False

T/F: The presence of double bonds in the hydrocarbon tail of a fatty acid does not greatly influence its structure

False

What is the general formula of an amino acid

H | H2N - C - COOH | R

What is an amino group? Is it polar?

H-N-H, basic

Enzymes called HATs (histone acetyltransferases) and HDACs (histone deacetylases) regulate histone acetylation. Explain how each type of enzyme could change the expression of a gene.

HATs add acetyl groups to proteins, which relaxes the histone tails, and loosens dna, making it more accessible for expression. HDACs remove acetyl groups from proteins, tightening the histone tails and making it less accessible, silencing the genetic expression.

In a fatty acid molecule, which part is hydrophobic? hydrophillic?

Head=hydrophillic, tail=hydrophobic

Gene A, which is normally expressed, has been moved by DNA recombination near an area of heterochromatin. None of the daughter cells produced by cell division after this recombination event express gene A, even though its DNA sequence is unchanged. Explain this observation.

Heterochromatin = more tightly coiled, less accessible Euchromatin = uncoiled, "E" expressed Histone modifying complexes will modify the genes to which it was recruited to AND regulate neighboring genes (nucleosomes) causing repression/activation to propagate along the chromosome

differentiate between NHEJ and homologous recombination

NHEJ: rapid response to seal break, blunt ends are required, nucleotides are sometimes deleted, less accurate HR: precise, requires normal copy of chromosome nearby

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why?

Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus.

What is special about lipid molecules, which allows self-sealing of membranes?

Lipid molecules are amphipathic, and the nonpolar portions of the molecule can't interact with H2O, causing spontaneous assemble into bilayers.

At which temperature, hot or cold, would a more fluid structure be encouraged? More rigid?

More fluid: cold to prevent freezing More rigid: hot to prevent melting

Some applications in biology, such as PCR, require melting the DNA double helix into single strands of DNA. This can be accomplished by heating the DNA. As DNA is heated, why does the double helix structure denature into single strands of DNA but not into individual nucleotides? In other words, why do the single strands remain intact even though the double helix does not?

The double helix is held together with hydrogen bonds, while the single strands are linked by phosphodiester bonds.

Fats like lard and butter are solid at room temperature. What is it about the structures of their fatty acids that would support this trend?

The fatty acids are fully saturated, allowing them to pack tightly together.

What is likely to happen after the lipid bilayer is pierced?

The membrane reseals.

What does it mean for DNA replication to be bidirectional

The replication forks formed at the origin move in opposite directions.

Which of the following statements correctly explains what it means for DNA replication to be bidirectional?

The replication forks formed at the origin move in opposite directions.

Which of the following statements about how enzymes work is FALSE?

The shape of the active site is constantly changing, allowing the enzyme to bind many different substrates, catalyzing many different chemical reactions

T/F: Prokayotes and eukaryotes both have ribosomes, cell membranes, and DNA

True

The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length. The separation of the DNA strands for replication causes the strands to be "overwound" in front of the replication fork. How does the cell relieve the torsional stress created along the DNA duplex during replication?

Topoisomerases break the covalent bonds of the backbone, allowing the local unwinding of DNA ahead of the replication fork.

T/F: Eukaryotic cells have membrane-bound organelles

True

T/F: GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation, in which they're bound to GDP

True

T/F: Prokaryotic chromosomes have a single site of initiation of DNA replication

True

What is the function of the golgi apparatus

modifies molecules made in ER

If molecule a has 2 oxygens and molecule b has 1, which is most reduced?

molecule b

aAny substance that will bind to a protein is known as its ______ . The human immune system produces billions of different immunoglobulins, also called ______ , which enable the immune system to recognize and fight germs by specifically binding one or a few related ______ . These proteins have their _____ structure stabilized by _____ between heavy chain and light chain subunits. Enzymes bind their ______ at the _____ . Enzymes catalyze a chemical reaction by lowering the _____ , because they provide conditions favorable for the formation of a high-energy intermediate called the _____ . Once the reaction is completed, the enzyme releases the _____ of the reaction. WORD BANK: low-energy, ligand, antigens, active site, antibodies, substrates, free energy, quaternary, secondary, disulfide bonds, ionic bonds, transition state, products, activation energy

ligand, antibodies, antigens, quaternary, disulfide bonds, substrates, active site, activation energy, transition state, products

what does the smooth ER do?

lipid synthesis

in interphase, what do the chromosomes look like?

loose, unraveled

what is depurination?

loss of a nitrogenous base from the nucleotide

what is deamination?

loss of an amino group on cytosine, produces uracil

What is the function of the endoplasmic reticulum

making lipids and proteins

does phosphorylation loosen or tighten DNA around histones? acetylation? methylation?

methylation tightens, while phosphorylation and acetylation loosens

Which of the following organelles has both an outer and an inner membrane?

mitochondria and nucleus

Order these terms correctly pertaining to the assembly of macromolecules. (Subunits, macromolecules, noncovalent bonds, macromolecular assembly, covalent bonds)

subunits -> covalent bonds -> macromolecules -> noncovalent bonds -> macromolecular assembly

what is the main difference between symports and antiports?

symports transport two different ions the same direction while antiports transport one ion into the cell and the other out.

which part of the phospholipid molecule is non-polar?

tails

What is the function of the endosomes

takes material from outside the plasma membrane and brings it into the cell