BIOL 4100 Mehari Exam 1

Explain in at least three sentences, not more than 6 sentences, the relationship between cells, chromosomes, DNA, RNA, and proteins.

1. The central dogma states that the transfer of information flows from DNA to RNA to proteins.

2. Chromosomes are comprised of DNA (genetic material)

3. DNA, through the process of transcription, creates a complementary RNA strand.

4. The RNA strand, through the process of translation, creates proteins.

5. Proteins are responsible for the majority of the cell's functions, structures, and movement capabilities, providing the link between chromosomes and the greater mass of the cell.

The cytoskeleton of eukaryotic cells are responsible for directed cell movements. Which of the following make up the cytoskeleton?

Intermediate filaments

Actin filaments

Microtubules

Which of the following statements are TRUE of chloroplasts?

Chloroplasts absorb light and generate oxygen and electrons

Chloroplasts are thought to have originated from bacteria

Chloroplasts contain their own DNA

There are all the reasons why arabidopsis has been chosen as a model plant EXCEPT

Has one of the largest genome in plant kingdom

Mitochondria are thought to have evolved from engulfed aerobic bacteria. Which of the following are evidences that supported the theory of endosymbioisis in eukaryotic cells?

Mitochondria possess ribosomes similar in size to bacterial ribosomes

Mitochondria contains double membranes resembling that of a bacterial double membrane

Mitochondria contains DNA arranged in circular chromosomes

Mitochondria are essentially the same in all eukaryotes, including plants, animals, and fungi.

True

Eukaryotic cells engage in continual endocytosis and exocytosis across their plasma membrane. Why do cells engage in endocytosis?

To import extracellular materials

Within a developed multicellular organism, NOT all cells have the ability to divide

True

All of the following are advantages of using electron microscope when compared to light microscope EXCEPT

They are used to study live cells

In the electron micrograph below, identify the bacterial cell features labeled A to D respectively.

Cell wall, inner membrane, cytoplasm, outer membrane

The delta G of a reaction is -350 kCal/mol. Which of the following can be deduced about this reaction?

The reaction will proceed spontaneously under standard conditions

What can be said about the molecule presented below?

It belongs to RNA

It is a nucleotide

Which of the following are types of interactions that help bring molecules together in cells?

Covalent bond

van der Waals attraction

Hydrogen bond

Ionic bond

Which of the following is NOT a characteristic of yeast that make them useful model organisms?

Unlike other eukaryotes, yeast do not have membrane bound nucleus

Peptide bond formation between the amino group of one amino acid and the carboxyl group of another results in

Release of water molecules

When comparing liver cells and kidney cells within the same organism, which of the following is the same between the two cells?

DNA

You feed 2 glucose molecules to a yeast. Saccharamyces cervisae. How many total number of ATP will you expect to recover if the cell decided to ferment the sugars?

4

Which of the following is NOT correct with respect to the redox pair NAD+/NADH?

NADH can accept electrons from an electron transport system

Which of the following statements about NADPH and/or NADH is NOT true?

NADPH is used primarily by plants

Which of the following is NOT true of chemiosmosis?

It requires oxygen

ATP synthesis by chemiosmosis is similar in bacteria, mitochondria, and chloroplasts?

True

The TCA cycle is capable of generating all the following products from oxidation of each acetyl-CoA molecule EXCEPT

2 water molecules

The enzyme pyruvate kinase catalyzes the conversion of PEP to pyruvate. The phosphate group is transferred to ADP to form ATP. This reaction is an example of

ATP synthesis through substrate level phosphorylation

In brown fat of bears, the following transmembrane proteins are used to produce heat during cold season

Uncoupling proteins (UCPs)

Photosynthesis utilizes an electron transport system while fermentation does not utilize an electron transport system.

True

Fermentation produces more energy than anaerobic respiration

False

Production of ATP by ATP synthase directly depends on which of the following factors?

Proton motive force

What is the main purpose of malate-aspartate shuttle to cells

Transfer of electrons from cytosolic NADH across the inner mitochondrial membrane

Which of the following statements is TRUE to both FADH2 and NADH?

Both are electron carriers that power the electron transport system

Both have the ability to produce similar amount of ATP

Both are products of TCA

Which of the following allows the one way movement of electrons from one complex to the next in ETS?

Increase in reduction potential from NADH to O2

Oxygen is always required for the regeneration of NAD from NADH

False

Which of the following is NOT a method for controlling protein activity

Proteolysis

Which of the following does NOT represent covalent interactions?

Hydrogen-bonding between peptide bonds in adjacent strands in a beta sheet

Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?

Tyrosine to Tryptophan

Which of the following is NOT TRUE about the enzyme lysozyme?

It involves removal of water molecules

Which of the following is NOT a characteristic of a hemoglobin molecule

It is made of one large protein subunit

Which of the following determines how a protein will fold?

Amino acid sequence

A competitive inhibitor bound to an enzyme can be overcome by increasing the substrate concentration

True

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

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

Beta sheets of proteins

Are strands of poylpeptide chains that are held together by hydrogen bonding between peptide bonds in adjacent strands

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

The reaction is associated with a negative change in deltaG

Which of the following is NOT a function of an enzyme

Speed up reactions by increasing the activation energy

What determines the specificity an antibody has for its antigen?

Polypeptide loops in its variable domains

Which of the following technique would you use to separate two proteins with the same size but different isoelectric point

Two-dimensional PAGE

You purified a protein complex with multiple subunits bound together by a disulfide bond. Which of the following chemicals would you use to separate the subunits before loading it to polyacrylamide gel electrophoresis?

Mercaptoethanol

Which of the following can be used for separating different proteins within a sample?

Liquid chromatography

SDS-PAGE

You are running an experiment to mutate an enzyme in order to increase the enzyme's ability to bind its substrate. Using the graph as a comparison, what affect would the mutant version of the enzyme likely have on the Km?

The Km would move to the left (decrease)

Rate the following events in chronological order based on the figure below

A. eukaryotes and archaea diverged

B. Eukaryotes acquired chloroplasts

C. Bacteria and archaea diverged

D. Eukaryotes acquired mitochondria

C A D B

Explain, in at least 3 sentences but not more than 6, how regulatory GTP-binding proteins can be responsible for human cancer.

List your explanation by number or bullet points

Mention at least one example of a protein regulated by GTP binding

1. Regulatory GTP-binding proteins (like Ras) act as molecular "on/off switches" for cell signaling pathways that control cell growth and division.

2. When they bind GTP, they become active and send signals that promote proliferation; when they hydrolyze GTP to GDP, they normally switch off.

3. Mutations can lock these proteins in the GTP-bound active state, causing continuous signaling even without growth factors.

4. This constant "grow" signal can lead to uncontrolled cell division, a key feature of cancer.

Fundamentals of cells

Cells vary enormously in appearance and function

Living cells all have a similar basic chemistry

Living cells are self-replicating collections of catalysts

Living cells have apparently evolved from the same ancestral cell

Instructions for the form, function, and behavior of cells are organisms are stored in genes

In all living cells, genetic information flows from

DNA to RNA to protein

Light microscopes

Led to the discovery of cells

Reveal some of a cell's components

Electron microscopy

Reveals the fine structures of a cell

Prokaryotes

Most diverse and numerous cells on earth

Divided into two domains: bacteria and archaea

Some bacteria are photosynthetic

Eukaryotes

Possess nucleus and organelles

Mitochondria, chloroplasts, cytoskeleton

Mitochondria

Generate usable energy from food molecules

Thought to have evolved from engulfed bacteria

Chloroplasts

Capture energy from sunlight

Almost certainly evolved from engulfed photosynthetic bacteria

Cytoskeleton

Responsible for directed cell movements

Made of actin filaments, microtubules, and intermediate filaments

Network of protein filaments that can be seen crisscrossing the cytoplasm of eukaryotic cells

Rank the following events in chronological order.

a) eukaryote and archaea diverged

b) bacteria and archaea diverged

c) eukaryotes acquired chloroplasts

d) eukaryotes acquired mitochondria

B -> A -> D -> C

Internal membranes

Create intracellular compartments with different functions

Continual endocytosis and exocytosis

Eukaryotic cells use this- importing extracellular materials by endocytosis and secreting intracellular materials by exocytosis

Endocytosed material is first delivered to membrane-enclosed organelles called endosomes

Endosomes

Membrane-enclosed organelles that receives endocytosed material

Cytosol

Contained by cell membrane

Concentrated aqueous gel of large and small molecules

Intermediate filaments

Not found in cytoplasm of cells with cell walls, such as plant cells

Microtubules

Help segregate the chromosomes in a dividing animal cell

Chromosomes are pulled apart into separate daughter cells by the spindle microtubules

Eukaryotic cells may have originated as

predators

Eukaryotes have genomes that are _____ of DNA that was transferred horizontally across domain boundaries

chimeric mixes

E. coli

Molecular biologists have focused on this

Easy to grow and grows fast (G= 20 min)

Contains most of bacterial structures

Easy to manipulate, can accept foreign DNA

Single circular chromosome, may have some plasmids

Pathogenic, non-pathogenic or a commensal

Growth with oxygen or without oxygen

Saccharomyces cerevisiae

Brewer's yeast is a simple eukaryote

Model organism for studying activities of all eukaryotic cells, especially the cell cycle and secretion

Exists as both diploid and haploid

Can reproduce sexually or asexually

They share many of the more than 6000 proteins with most eukaryotic cells

Cell cycle, protein secretion

Mutations in yeast

Led to the identification of key cell cycle proteins

Most of these yeast cell cycle genes are found in human cells as well, and they encoded proteins have similar amino acid sequences

Subsequent studies showed that mutations in many yeast cell cycle proteins that allow uncontrolled cell growth also frequently occur in human cancers

Cell division cycle proteins

Very similar amino acid sequences in yeasts and humans

Cdc2

Human cell that is a cell cycle-regulated protein kinase that induces entry into mitosis

Drosophila melanogaster

Provided a key to the understanding of how all animals develop

Four stages: embryo, larva, pupa, adult

Rapid generation time, around 10 days

Used to discover chromosome theory of heredity

Caenorhabditis elegans

C. elegans is a small nematode worm that normally lives in the soil

C. elegans was the first multicellular organism to have its complete genome sequences

C. elegans mode of inbreeding by the self-fertilizing hermaphrodite combined with the ability to cross hermaphrodites with males

"C. elegans provides the researcher with the ideal compromise between complexity and tractability"

Zebrafish

Popular models for studies of vertebrate development

Small, hardy, tropical fish are easy and cheap to breed and maintain

Ideal for developmental studies, as their transparent embryos develop outside the mother; making it easy to observe cells moving and changing their characters in the living organism as it develops

Mouse model

Both have defects in the same gene (called Kit), which is required for the normal development, migration, and maintenance of some skin pigment cells

Useful because they share mammalian features with humans

Hela cells

The first immortal human cell

Moore v. Regents of the University of California

One of the judges "he had no property rights to his cells"

Cal Supreme court "hospital patient's discarded blood and tissue samples are not his personal property and that individuals.."

Common Rule

label given to the federal policy for the protection of human subjects

Arabidopsis

Model plant

Short generation time and ability to self-fertilize (selfing)

Small genome ~114.5 Mb

Genetically well characterized due to the volume of work being focused on this plant

Comparing genome sequences

Reveals life's common heritage

Covalent bonds

Two atoms share a pair of electrons in a molecular orbital

Strong enough to survive the conditions inside cells

Sharing of electrons most generally occurs in the outermost orbitals of atoms

Chemical bonds that hold together amino acids in proteins

Ionic bonds

Form by the gain and loss of electrons

Interaction between the two occurs because opposite charges attract one another

Hydrogen bonds

Important noncovalent bonds for many biological molecules

Commonly form between molecules that contain an Oxygen or Nitrogen

Hydrogen bonds between base pairs form the double helical structure of DNA

In proteins, B sheets and a helices are held together by hydrogen bonds

van der Waals

Noncovalent attraction bonds

Maintain membrane fluidity

The longer the hydrocarbon tail, the greater the strength of van der Waals forces

Cells are made of

relatively few types of atoms

Nucleus

Dense, positively charged and contains nearly all of atom's mass

Electrons occupy space around the nucleus

Isotopes

Proton number stays the same, but neutron number is different

Valence electrons

Electrons found in outermost orbitals of an atom

Hydrophobic force

Tendency of nonpolar substances to aggregate in an aqueous solution

Crucial for structure of cell membranes

Hydrocarbon chains in fatty acids

Have non-polar covalent bonds

Electrons are still moving around the atoms in the fatty acids, creating short-lived regions with slight negative charges

These are attracted to slight positive regions in another atom

The kinks in the fatty acids caused by double bonds reduces tightness between the molecules, causing a lower melting point

A cell is formed from

Carbon compounds

Contain four major families of small organic molecules

Sugars

Both energy sources and subunits of polysaccharides

Can form polysaccharides, glycogen, and starch (in plants)

Fatty acid chains

Primary components of cell membranes

Fats and membrane lipids

amino acids

Subunits of proteins

Held together by peptide bonds

C1 of one amno acid and N2 of another

Nucleotides

Subunits of DNA and RNA

Form nucleic acids

A chain of DNA molecule is formed by linking nucleotides with a phosphodiester bonds

5' end free phosphate group with the 3' free hydroxyl group

Energy is gained by hydrolysis of phosphate group

Disaccharide

Two monosaccharides linked by a covalent glycosidic bond

Condensation reaction

Two molecules join as a result of loss of water molecule

Requires an input of energy

Hydrolysis reaction

Water is added and separate the two molecules apart

Release of energy

Lipid bilayer

Made of amphipathic phospholipids

Hydrophilic heads of the phospholipid molecules are on the outside, facing the aqueous environment

Hydrophobic tails are on the inside, where water is excluded

Formed by fatty acids linked to G3P via ester bonds