bio final review

State the potential benefits of the presence of introns in eukaryotic genes

alternative splicing, novel proteins

Some cells express aquaporin proteins—they are channel proteins that facilitate the flow of water molecules through the plasma membrane. What regulates the rate and direction of water diffusion across the membrane? a. aquaporin conformation b. resting membrane potential c. solute concentrations on either side of the membrane d. availability of ATP

c. solute concentatoin on either side of the membrane

•Define "resting membrane potential

electrical potential difference across the plasma membrane when the cell is in a non-excited state.

Why is energy released as electrons are transferred from less electronegative atoms to more electronegative atoms during redox reactions?

electrons have potentail energy when bonded to less electronegative atoms (H or C) and energy is relawed when the electrons transfer to a more electronegative atom(like O)

Distinguish between promoters and regulatory DNA sequences in terms of the roles they play in gene expression and the proteins that bind to them

promoters bind to RNA polyermases and includes a trnascription initiation site where RNA synthesis begins

Illustrate how transcription regulators recognize and bind to regulatory DNA sequences in a DNA double helix

regulatory DNA sequences must be recognized by transcription regulators which act as a control to transcirption they bind to DNA helix region to recognize specific nucleotide sequenes. reacts with the moleculees around in teh major groove and makes a tight bond.

State the number of covalent bonds that can be formed by atoms of hydrogen, oxygen, nitrogen, and carbon and express how the electronic configuration of carbon, in particular, dictates the three-dimensional shape of organic molecules

Hydrogen = 1 covalent Oxygen = 2 covalent Nitrogen = 3 covalent Carbon = 4 covalent electron configuration dictates how many bonds a molecule can make

Which of the following statements about transcriptional regulators is FALSE? •Transcription regulators interact only with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix. •Transcription regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA. •The DNA-binding motifs of transcription regulators usually bind in the major groove of the DNA helix. •The binding of transcription regulators generally does not disrupt the hydrogen bonds that hold the double helix together.

a. transcriptional regulators interact onlywith the suga-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix

Each nucleotide in DNA and RNA has an aromatic, hydrophobic base. What is the principal force that keeps the bases in a polymer from interacting with water? Ionic interactions •Hydrogen bonds •Covalent bonds •Hydrophobic interactions

hydrophobic interactions

Describe the consequences of a failure to repair damaged DNA

it it's not repaired one strand will have a permanent mutation

Explain how cells can produce large quantities of one protein and tiny quantities of another

large amound of proteins means mRNA has a longer lijfespan

Assess the role that covalent and noncovalent bonds play in the three-dimensional conformation of macromolecules

macromolecules are linked by covalent bonds. noncovalent bonds influenced confirmation

List some functions of plasma membrane proteins

most of membrane proteins are proetin transporters, channels, receptors and enzymes

Explain how DNA polymerase contributes to the accuracy of DNA replication

proofreads

Articulate the steps at which gene expression can be regulated and identify the step that, for most genes, is the main point of control

1. control when and how often gene is transcribed 2. controlling RNA processing 3. selecting mRNA localization 4. mRNA lifespan 5. selecting whihc mRNA are going to be protein 6. regulate how rapidly proteins are destoyed

Express how the chemical and physical properties of methyl groups (−CH3), hydroxyl groups (−OH), carboxyl groups (−COOH), phosphate groups (−PO32-), and amino groups (−NH2) influence the behavior of molecules in which these groups typically occur

CH3: NON-polar, hydropobic OH: Can Form H-bonds Caboxyl: Becomes CO O- in water phosphate group: high energy bond. forms free hydroxyl group amino groups: amide+acid in water

Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have inherited •a cancer-causing gene that suffered a mutation in an ancestor's somatic cells.• a mutation in a gene required for DNA synthesis. •a mutation in a gene required for mismatch repair .•a mutation in a gene required for the synthesis of purine nucleotides.

a mutation in a gene required for mismatch repair

Contrast photosynthesis and cellular respiration and evaluate how the processes complement one another

cellular respiration: in mitochondria, breaks down molecules, releases energy (exergonic, catabolic) photosynthesis: requires energy, produces molecules,

•Explain how a DNA double helix provides a template for its own replication, and describe the resulting daughter helices in terms of their sequence and the distribution of parental and newly synthesized DNA strands

complementary base pairing

A molecule with the molecular formula C5H10 is composed of nonpolar covalent bonds between the carbon and hydrogen atoms. Given the lack of polarity, describe how it is possible that multiple molecules of C5H10 can stick together.

covalent bonds between cabons

Contrast hydrogen bonds, electrostatic attractions, van der Waal's attractions, and the hydrophobic force in terms of how and when they form and the role they play in cell biology.

electrostatic attractions: the attraction or repulsive forces between charges van der Waal's: intermolecular attractions between atoms hydrogen bonds: hydrogen bonded to an electronegative atom hydrophobic force: polar and nonpolare substances repel

Relate how the energy of ATP hydrolysis can be harnessed to drive an energetically unfavorable condensation reaction

energy from ATP is used to convert the alcohol into an intermediate that reacts with the acid to extract water. (intermediate example is ATP to B-OH to make B-O-PO3)

Articulate how enzymes increase the speed of a chemical reaction.

enzymes how activation energy. they can bind to two substrate molecules and orient the to encourage a reaction. they can bind to substrate and rearrange electons to creat partial charges that favor reactions. lastly, enzyme can strain the bound substrate into a favorable transition state

Summarize how a limited number of transcription regulators can direct the differentiation of specific cell types

eukaryotes diversify during embryonic development. those small number of regultors activates transcription codes for specific proteins that are specific to teh DNA sequences

List three sources of energy used by transmembrane pumps to actively transport a solute against its concentration gradient

graident driven, ATP driven, light driven

•List some of the causes of DNA damage

mismatched pairs radiation, errors in replication and carcinogens can cause double stranded breaks (at nonhomologous end joining) homologous recombination is when teh break is spread out and filled in accurately using the undamaged strand

Summarize six basic mechanisms that generate genetic change.

mutation, duplication, divergence, exon shuffling, transposition, horizontal gene transfer

Although ATP and NADH are both important activated carrier molecules, ATP hydrolysis provides the direct molecular energy for most biochemical reactions. Why do the mitochondria also need to generate high levels of NADH?

nadh can donate electrons to make ATP

Explain how and why different forms of feedback control might be used to regulate enzyme activity

negative feedback is more used one because it promotes equilibum and turns off a process. while positive feeback can lead to uncontrolled processes and instability

Distinguish between integral membrane proteins and peripheral membrane proteins.

peripheral proteins are in the inner or outer surface of phospholipliid bilayer while integral proein is embedded in teh whole bilayer

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 .•Replication, transcription, translation •Replication, translation, transcription •Translation, transcription, replication •Translation, replication, transcription

replication, transcription, translation

How does the right amino acid get put on the right tRNA? How does an aminacyl-tRNA synthetase achieve specificity?

the anticodon specifies for the amino acid on the tRNA

Describe how translation is terminated in eukaryotes and in bacteria

the mRNA has several stop codons encoded. release factor engage in teh A site of a riboosome which causes the addition of water to the tRNA to free to polypeptide

What would happen if DNA polymerase made many mistakes?

they are usually promptly corrected. Polymerase reads the newly added base before adding it so that a correction can be made

Summarize the effects that uncoupling agents such as dinitrophenol have on the proton motive force in intact mitochondria

this would inhibit ATP production becaue there's no gradient for ATP synthase to shuttle protons

Categorize membrane proteins based on the way they interact with the lipid bilayer

transmembrane: extends through lipid bilayer monolayer associated a helix: proteins are anchored on half liplid bilayer and half cytoloic lipid linked: linked to either side of teh bilayer solely by covalenelty attached lipid molecule protein attached: proteins are attached to teh membrane only by relatively weka, noncovalent interactions with other membrane proteins

•Explain why much "junk DNA" is thought to serve a biological function

works in chromosome foldong and regulating gene expression

Describe the structural differences between prokaryotes and eukaryotes

Eukaryotes: Nucelus, more complex (Examples: plants, animals, fungi Prokaryotes: No Nucleus, circular DNA, smaller (bacteria and algae)

Explain how the structure of DNA suggests a mechanism by which genetic information can be copied

every strand is a template

T/F: Any covalently bonded H atom can participate in a hydrogen bond if it comes in close proximity with an oxygen atom that forms part of a water molecule.

false. hydrogens that are bonded to a carbon have no partial charge so they cannot participate in hydrogen bondig

Relate how the free-energy change of a reaction determines its energetic favorability

favorable reactins have a negataive delta G. Energetic favorability is increasing disorder by deceasing the free energy of teh system to which they belong

What would happen if DNA polymerase NEVER made mistakes?

no mutations..

State what drives the production of ATP by ATP synthase during photosynthesis

H gradient

Identify what determines the polarity of a chemical bond and summarize the consequences of this property for the solubility and hydrophobicity of a molecule or salt, as well as its ability to act as an acid or base

Polarity is determined by the difference in electronegativity. This affects soubility so that polar molecules dissolve polar and nonpolar dissolves. Polarity relates to acidity directly; the more polar a bond, the stronger the acid

You fertilize egg cells from a healthy plant with pollen (which contains the male germ cells) that has been treated with DNA-damaging agents. You find that some of the offspring have defective chloroplasts, and that this characteristic can be passed on to future generations. This surprises you at first because you happen to know that the male germ cell in the pollen grain contributes no chloroplasts to the fertilized egg cell and thus to the offspring. What can you deduce from these results?

The mutation is found in nuclear DNA not just chloroplost DNA. and the information to make chloroplast DNA is encoded by nuclear DNA

In stage 1 of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast? a.thylakoid space b.stroma c.inner membraned. thylakoid membrane

d. thylakoid membrane

Match the type of phenotypic change below with the type of genetic change most likely to cause it. Each type of genetic change may be used more than once, or may not be used at all.• Types of genetic change: A. mutation within a gene B. gene duplication C. mutation in a regulatory region D. exon shuffling E. horizontal gene transfer •Phenotypic changes:1. A protein normally localized in the nucleus is now localized in the cytoplasm. _________ 2. A protein acquires a DNA-binding domain. 3. Tandem copies of a gene are found in the genome. _________ 4. A copy of a bacterial gene is now found integrated on a human chromosome. _________ 5. A protein becomes much more unstable. 6. A protein normally expressed only in the liver is now expressed in blood cells. ________

1.a 2. d 3. b 4. e 5.a 6.c

Explain how the relationship between DNA, RNA, and protein—as laid out in the central dogma—makes the self-replication of living cells possible.

DNA RNA to protein is the central dogma. DNA is changed to RNA by transcription and RNA is changed to protein by translation

Explain how noncovalent interactions—including electrostatic attractions, hydrogen bonds, van der Waals attractions, and hydrophobic forces—influence the shape of a folded protein and how the polypeptide backbone and amino acid side chains participate in these interactions

Electrostatic attractions: positive and negative charges on amino side chains interact hydrogen bonds: connects backbones of polypeptide chains. van der waals: the nonpolar sidechains group together on the inside side chain: polar sidechains can hydrogen bond to water. side chains interact via hydrogen bonds polypeptide backbone: hydrogen bonds between atoms creates bonds between backbones

Indicate whether the following statements are TRUE or FALSE. If a statement is false, explain why it is false. a. CO2 and O2 are water-soluble molecules that diffuse freely across cell membranes .b. Transporters are similar to channels, except that they are larger, allowing folded proteins as well as smaller organic molecules to pass through them. c. Cells expend energy in the form of ATP hydrolysis so as to maintain ion concentrations that differ from those found outside the cell.

a. true b. false. transporters change conformatoin while channel discriminate on size and charge c. true

Which of the following statements about "redox potential" is TRUE?a.Redox potential is a measure of a molecule's capacity to strip electrons from oxygen. b.For molecules that have a strong tendency to pass along their electrons, the standard redox potential is negative. c.The transfer of electrons from cytochrome c oxidase to oxygen has a negative redox potential. d.A molecule's redox potential is a measure of the molecule's capacity to pass along electrons to oxygen.

b. form molecules that have a strong tendency to pass along their electrons, the standard redox potential is negative