Cell Biology Exam 2

What is the A Site?

(Aminoacyl-tRNA site) Receives charged tRNA Holds it until peptide bond is formed with the carboxyl end of growing (nascent) polypeptide (assuming an anticodon, codon match) Message read 5' to 3' end Growing peptide chain spooled one amino acid at a time (N terminal first)

What is the E Site?

(exit site) the site from which tRNAs leave the ribosome after they have discharged their amino acids

What is the P Site?

(peptidyl tRNA site) Holds the tRNA that is carrying the growing (nascent) polypeptide chain

What are some of the important covalent modifications that proteins undergo?

Addition or subtraction Phosphorylation (addition of a phosphoryl group), methylation (addition of methyl groups), acetylation (introduces an acetyl functional group), glycosylation (covalent addition of sugar moieties to specific amino acids)

How is Brownian motion involved in substrate binding, activation, and catalysis?

Substrate Binding: The random motion brings random collisions between enzymes and substrates. They randomly find one another and if they are a good conformational match enough weak bonds form to withstand thermal jolting Activation: Reactants find each other in proper orientation Catalysis: Substrate positioning determines predisposition to catalysis

Which loop of tRNA is Ribothymidine found in and what does it do?

T loop: Specialized region on the tRNA molecule which acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during protein biosynthesis or translation Helps with stability

What kinds of interactions stabilize intracellular and extracellular proteins?

Hydrogen bonds, electrostatic attractions, van der Waals attractions, Hydrophobic interaction (bury into core) Only extracellular proteins have disulfide bonds, and have covalent interactions. Intracellular have covalent and non-covalent.

What is a proteasome?

Protein destruction complex Degrades unwanted and misfolded proteins in the cytosol Hydrolyze peptide bonds in a process called proteolysis Abundant ATP-dependent protease complex , constitutes nearly 1% of a cell protein

How do temperature and pH affect enzyme function?

Temperature: enzyme activity is optimal at specific temperatures pH: enzymes sensitive to pH, charged amino acids at the active site usually result in pH dependence (ex: lysosome works at a pH of 5 created by proton pumps, while cytoplasm is pH 6)

Steps of Translation

Step 1: Charged tRNA enters the A-site by base-pairing with complementary codon on mRNA Step 2: Its amino acid is then linked to peptide chain held by the tRNA in the neighboring P-site Step 3: The ribosome shifts, and the spent tRNA is moved to E-site before being ejected Step 4: Small subunit moves three nucleotides along mRNA bringing it back to original position, creating an empty A-site for next tRNA

In general what are enzymes (ribozymes) and what do they do?

Substance that acts as a catalyst to bring about a specific biochemical reaction Bind to one or more ligands (substrates) and convert them into chemically modified products Binding site in an enzyme is called an active site Mediate virtually all cellular reactions

Define specificity.

The ability of a protein to bind to just one or a few molecules out of many thousands of different molecules it encounters

Understand the structures and functions of the small and large subunits of a ribosome.

The small subunit binds to the message first, then the large subunit binds when there is a conformational change to the small subunit. Small subunit matches the tRNAs to the codons of the mRNA and binds to the mRNA Large subunit catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain

What is the specific term used to describe the cellular process that synthesizes proteins from mRNA?

Translation-messenger RNA (mRNA) is decoded by a ribosome to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell.

What role do ribosomes (rRNA) play in in translation?

mRNA is decoded on ribosomes in the cytoplasm Ribosome moves along the mRNA: 1) 'Captures' charged tRNA molecules that complement the message codon 2) Holds charged tRNA in position 3) Covalently links the amino acids they carry to form a polypeptide chain

Important to understand about transport of mRNA out of the nucleus:

mRNA is modified in order to leave the nucleus. Proteins bind to specific modifications of the mRNA to signal that the mRNa is "export-ready" and may leave through the nuclear pore complex

What is required for an mRNA to be considered export ready?

mRNA must be bound to specific signal proteins to be correctly processed for export Poly-A-binding protein Cap-binding protein Exon junction complex

Understand the basic way that GTP and ATP binding, hydrolysis and exchange can regulate protein activity and function.

The protein is activated when bound to ATP or GTP, with hydrolysis removing a phosphate and changing to ADP or GDP the protein becomes inactive. The GDP or ADP is removed and the protein remains inactive until GTP or ATP is added again to make an active protein.

Define binding site.

The region of the protein which associates with a ligand

How does the structure of a protein dictate its function?

The shape of a protein is critical to its function because it determines whether the protein can interact with other molecules (binding ability). Structure/Shape is determined by amion acid sequences and their chemical properties (determined by R group).

How many consecutive nucleotides in an mRNA make up a codon?

3

How many codons specify one amino acid?

? Each codon specifies one amino acid

What can a dysfunction of the centromere lead to?

Chromosomes do not align and separate properly, resulting in aneuploidy-wrong number of chromosomes (Down syndrome)

Understand DNA packing and be able to describe the importance and functions of: Nucleosomes

Composed of 8 histone proteins, non-histone proteins, and associated DNA First and most basic level of DNA organization/packing Beads on a string (beads are nucleosomes)

How do aminoacyl-tRNA synthetases couple tRNAs to the correct amino acid?

Covalent bonds Once the correct amino acid is joined to its tRNA (the tRNA recognizes the codon on the mRNa, NOT the amino acid) The energy of the amino acid/tRNa bond is used in protein synthesis to link an amino acid covalently to the growing polypeptide chain

What is a protein machine?

Large complex, where each protein subunit of the machine works in a highly coordinated manner DNA replication, gene transcription, protein synthesis, vessicle budding transmembrane signaling Hydrolysis of bound GTP or ATP drives the ordered series of conformational changes, giving rise to coordinated motion

What are nuclear pore complexes (NPCs) and what do they do?

Large protein complex in nuclear envelope. Channels in the membrane connecting nucleoplasm and cytosol. The NPCs work ass gates to control what enters or exits the cell

Understand and be able to describe the importance and functions of: Telomeres

Located at the ends of chromosomes Enable the ends of chromosomes to be efficiently replicated Protect/cap the chromosomal ends from being recognized as "broken ends" by nuclear enzymes involved in chromosome repair and prevent DNA from forming a circle (fusing with itself)

Understand DNA packing and be able to describe the importance and functions of: Euchromatin

Loosely packed, transcriptionally active DNA However, there is variability in the degree of packing/condensation in euchromatin

How quickly can a Nuclear Pore Complex (NPC) transfer macromolecules and can macromolecules go in both directions at the same time?

NPCs can transfer up to 500 macromolecules pers secod in both directions at the same time

Understand DNA packing and be able to describe the importance and functions of: Histones

Packing proteins for DNA Histones have a positive charge, while DNA has a negative charge Due to charge, histones rarely disassociate completely from DNA; BUT there is a regulated unwrapping and rewrapping of DNA around histones

Post-translational processes that proteins might go through:

Protein Folding Protein Destruction Protein Modification: Addition or subtraction to primary sequence

Understand and be able to describe the importance and functions of: Centromeres

*DNA region required for orderly segregation (separation of chromosome), holds sister chromatids together, form kinetochore, pairs homologous chromosomes *Contain special DNA - super condensed *Has increased packing of chromatin: CENTRIC HETEROCHROMATIN

Understand and be able to describe the importance and functions of: Replication origins

*Have many origins in order to ensure chromosome is replicated rapidly during S phase *Replication origins are rich in A=T (adenine and thymine which is easier to break due to 2 H bonds, not 3) *Short sequences that attract initiator proteins

Understand DNA packing and be able to describe the importance and functions of: Heterochromatin

*Highly compact regions of transcriptionally quiescent (silenced) interphase chromatin *Found throughout the chromosome but most concentrated near centromeres and telomeres

Describe RNA processing, including: The three primary purposes of 5' capping and 3' polyadenylation of pre-mRNA.

*Involves either REMOVING portions of the primary transcript or ADDITION of or CHEMICAL MODIFICATION of specific nucleotides *Steps take place as the RNA is being transcribed rRNA, tRNA, and mRNA are all transcribed and processed in the nucleus Collectively the 5' cap and poly-A tail: *INCREASE STABILITY OF mRNA *AID IN ITS TRANSPORT OUT OF THE NUCLEUS *IDENTIFY THE RNA MOLECULE AS AN mRNA Three mRNA processing steps: *mRNA CAPPING (chemical modification) OF THE 5' END: 1) Addition of the guanosine nucleotide with a methyl group attached to the 5' cap 2) Occurs only on transcripts destined to become mRNA 3) Other forms of modifications occur for tRNA (e.g., pseudouridine) Polyadenylation of the 3' end: 1) Polyadenylation tail (poly-A tail) is the addition of a specific nucleotide (adenosine monophosphate) to 3' end of eukaryotic mRNA molecules 2) Ranging from 50-250 nucleotides in length 3) Occurs only on transcripts destined to become mRNA

Explain some different ways that enzymes can be regulated?

*Protein phosphorylation/dephosphorylation (COVALENT MODIFICATION); the activity of enzymes is affected by the addition or removal of specific chemical groups (functional groups) *Allosteric Regulation

Who is Linus Pauling and why is he important?

*Published on protein secondary structure without exact knowledge of atomic coordinates *Determined structures of both alpha helix and beta sheets *Discovered sickle cell anemia was a molecular disease

Who are James Watson, Francis Crick and Wilkins and why are they important?

*Put pieces together from sources to build correct DNA structure *Received Nobel Prize "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material"

What are RNA genes [genes that produce non-coding RNA (RNA that is not mRNA)] and what are their primary functions?

*non-coding RNA is an RNA molecule that is not translated into a protein *DNA sequences that codes for non-coding RNA are RNA genes *Play key parts in translating the genetic message into protein *Most non-coding RNAs self assemble/fold into helices, loops and other complex 3D conformations through extensive base pairing *Their highly structured nature reflects various cellular functions with secondary and tertiary structure (reminiscent of proteins)

Be able identify the locations and/or organelles within the cell where replication, transcription, the different kinds of RNA processing, and translation all occur within the cell.

...

Describe RNA processing, including: mRNA splicing - and the role of splicesosomes and introns, and the different ways that genes can be spliced.

1) Most RNAs are not functional/mature until the primary RNA transcript is radically modified by splicing 2) in eukaryotic cells the precursors for mRNAs contain introns=intervening sequences (sequences within the primary transcript that do not appear in the mature functional RNA). Exons=expressed (functional) sequences 3) introns are common and removed by splicing 4) How are introns recognized? Each intron contains a few short nucleotide sequences located at the intron/exon boudary that act as cues for its removal 5) RNA splicing performed largely by other RNA containing molecules (ribozymes) Splicesomes remove introns from pre-mRNA *splicesomes are assembled from small nuclear RNA and proteins (ribozyme) Function of introns: *In some cases, intron RNAs are not degraded but are processed to yield other kinds of functional RNA *introns may facilitate evolution A gene can be spliced in different ways: RNA splicing enables eukaryotes to increase the already enormous coding potential of their genomes

Explain the three basic ways in which a substrate can be activated.

1) enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them 2) Binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction 3) Enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction ) ALLOSTERIC-make multiple shapes and force a conformational change predisposed to reaction

What is an anticodon?

A set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule

Understand and be able to describe the importance and functions of: Kinetochores

A transient protein structure formed on surface of the centromeres, attachment of spindle microtubules, proper separation and movement of chromosomes during nuclear division

What are two common folding patterns found in the secondary level of protein structure?

Alpha Helices Beta Sheets

Explain the structure and organization of these two common folding patterns and explain how they commonly function in protein structures.

Alpha Helix: Abundant in proteins located in cell membranes, composed largely of amino acids with apolar R groups, common in hair, finger nails, and horns. May enter cell membrane due to hydrophobic nature of protein. Two helices may coil together and form a COILED COIL. Beta Sheet: Sheets of chains that are folded into accordion-like pleats, may be parallel or anti-parallel, very rigid, strong, form the core of many proteins, composed primarily of apolar amino acids. Common in silk, and amyloid fibers. GFP is a beta barrel.

What is the primary level of protein structure?

Amino acid sequence

What is a catalyst?

An enzyme that helps to speed up chemical reaction by lowering the energy needed to start a chemical reaction Not permanently changed/consumed Provides suitable surface and environment to facilitate reactions Form transition complex

Define ligand (ex.: antigen or substrate).

Any substance that can bind to a protein (another protein, ion, small molecule or other macromoleculees)

Understand where the fibrils and the nuclear basket are located relative the nuclear envelop and the cytosol.

Attached to the ring is a structure called the nuclear basket that extends into the nucleoplasm, and a series of filamentous extensions that reach into the cytoplasm. Both structures serve to mediate binding to nuclear transport proteins

What type of bonds are involved in binding a protein to its ligand?

Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces.

How are cofactors and associated proteins involved?

Binding of small molecular cofactors and association with other proteins to the synthesized protein

Where do covalent bonds occur in proteins and what different kinds of covalent bonds contribute to protein structure? (What areas of the proteins bind together?)

Covalent bonds help with stability Peptide bonds- Link amino acids together Disulfide bonds- Form between Cysteines to make an interchain disulfide bond (for extracellular proteins- going outside cell, disulfide isomerase) Backbone binds to backbone: Between atoms of two peptide bonds Amino acid to amino acid: Peptide bonds form polypeptide backbone Cysteine to cysteine (Thiol groups)- disulfide bonds

What kind of microscopy was used to determine the structure of ribosomes?

Cyro-electron microscopy done by Joachim Frank

Who is Rosalind Franklin and why is she important?

Discovered: *the sugar-phosphate backbone is on the outside of the molecule *the helical structure of DNA has two strands (not three as Pauling thought) *quantitative details about the shape and size of the double helix (just lacked data on how the bases paired on inside of helix)

During what phase of the cell cycle does the level of DNA packing vary?

During Interphase

What are some of the most important functions of proteins?

Enzymes Pumps, channels, transporters Molecular motors Cell Signaling Structure (Cytoskeleton, EM) Antibodies, Toxins, Hormones, Antifreeze, etc

What are the major functional classes of enzymes and what do each of them do, (including ligases)?

Enzymes are grouped into functional classes based on the chemical reactions they catalyze Ligases-catalyze the joining together of two molecules coupled with the breakdown of a pyrophosphate bond in ATP or a similar triphosphate. Hydrolase-catalyze a hydrolytic cleavage reaction Protease- Break down proteins by hydrolyzing peptide bonds between amino acids Nuclease- Break down nucleic acids by hydrolyzing bonds between nucleotides Synthase- synthesize molecules in anabolic reactions by condensing two molecules together Kinase- Catalyze the addition of phosphate groups to proteins and other molecules Phosphatase- catalyze the removal of a phosphate group from a molecule Polymerase- catalyze polymerization reactions such as the synthesis of DNA amd RNA ATPase- Hydrolyze ATP

Explain how enzyme active sites (binding sites) work.

Enzymes contain a domain that forms the active site Active site is the region that binds the substrate and provides a 3D configurations of the amino acid residues that participate in making or breaking bonds Active sites take up small part of total enzyme (5-6aa) Clefts or crevices that aid in creating the correct environment for reaction to occur 3D configuration of active site determines specificity of enzyme

Define and explain a Protein Domain.

First regions to form independently between secondary and tertiary folding. Different domains have different functions. Sites of interactions (loops are binding sites). Segment of polypeptide chain that can fold independently into a compact, stable structure. Functionality Conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded.

What is the quaternary level of protein structure and what is responsible for it?

Formed as a complex of more than one polypeptide chain Concerned with subunit interactions and assembly and applies only to multimeric proteins (i.e. hemoglobin) An example of such a protein is myosin, the motor protein found in muscle that allows contraction.

Explain free and bound ribosomes.

Free ribosomes are those not attached to an organelle (in cytoplasm), while bound ribosomes are attached to membrane surfaces (rER, nuclear and mitochondrial surfaces)

What is the tertiary level of protein structure and what is responsible for it?

Full three-dimensional structure formed by the entire polypeptide chain, which includes alpha helices, beta sheets and tertiary loops Loops are where binding sites occur Formed by interactions between various R groups and reflects the non-repetitive aspect of a polypeptide because it depends on the R group

Where do the four major non-covalent bonds occur in proteins that contribute to protein structure? (What areas of the proteins bind together?)

Hydrophobic Forces: Determining shape of protein- hydrophobic portion is inside and hydrophillic is outside Ionic Bonds: Between oppositely charged R groups (salt linkage, salt bridge, electrostatic bond) Hydrogen Bonds: Between backbones (and side chains) to stabilize folded shape (between two electron-attracting atoms) van der Waals Attractions: Weak forces between electron clouds of atoms close together (important when many together)

Can RNA copy itself?

In principle, RNA can copy itself

Why is the formation of a peptide bond energetically favorable?

In the formation of a peptide bond involves what is known as a condensation reaction. A condensation reaction has two molecules that are joined together and a molecule of water is released The growing C-terminus has been activated by the high-energy covalent linkage to a tRNA molecule. This so called peptidyl-tRNA linkage activates the growing end and is broken in the course of each addition, but immediately replaced by an identical linkage on the last added amino acid. Thus, the covalent linkage between the end of the polypeptide chain and the tRNA is regenerated during each addition

What are the primary functions of the 5' cap and 3' poly A tail?

Increase stability of mRNA (as RNA is not very stable) Aid in mRNA transport out of nucleus (destined to become protein, as proteins help it out) Identify the RNA molecule as an mRNA so the cell recognizes it as a message

Explain the structure and function of a polyribosome.

Many ribosomes read the same message (mRNA) at the same time, following closely behind each other to translate protein Increases the number of proteins synthesized When the ribosome reaches the stop codon the protein is released mRNA takes on a curled/circular formation

Why are misfolded proteins undesirable and what are some diseases that can be caused by misfolded proteins?

Misfolded proteins results in errors in conformation and can form aggregates that can damage cells, tissues, and lead to disease. A prion may bond to a normal protein and cause it to misfold. "sticky conformations" stick together and form amyloid fibrils. Alzheimer's disease Huntington's disease Type 2 Diabetes Prion disease etc

What are heat shock proteins and what do they do?

Molecular chaperones Couple to proteins where heat may effect folding Stabilizing new proteins to ensure correct folding when heat stress is present

How is the genetic code redundant but not ambiguous?

Multiple codons code for the same amino acid, but each individual codon only codes for one amino acid

Explain how matching surfaces are involved with protein function.

Need structural fit for multiple weak, non-covalent bonds to form and an interaction to occur. The effective interaction between the protein and its ligand is possible only if the surface of the ligand fits closely to the binding surface of the protein The ability of a protein to bind securely is due to the structural 'fit' AND formation of a set of weak, noncovalent interactions that form simultaneously

What are two of the important post-transcriptional modifications that are made to tRNA?

OCCURS IN NUCLEUS Pseudouridine (an isomer) is added to stabilize the local RNA structure- thought to play a role in binding aminoacyl tRNA synthases; found in all t and rRNA, but not in mRNA Dihydrouridine (with two additional hydrogen atoms in pyrimidine ring which destabilizes the RNA structure and makes it more fexible (found in psycrophiles that thrive in low temps)

Explain how directly phosphorylating/dephosphorylating an enzyme allows for regulating its activity (an example of covalent modification)

Occurs by the transfer/removal of a phosphate group from ATP to the protein. Alters conformation to activate or inactivate enzyme. Phosphorylation can either stimulate or inhibit protein activity. Energy comes from ATP to ADP EX: The inactive form of an enzyme can be converted to the active form by the transfer of a PO4 group from ATP to a particular amino acid (serine) on the protein; the phosphorylation is catalyzed by specific kinase and dephosphorylation by specific phospatase

Where is Pseudouridine found and what does it do?

On T loop (Specialized region on the tRNA molecule which acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during protein biosynthesis or translation), next to Ribothymidine It is the isomer of uridine, and stabilizes the local RNA structure and helps with binding aminoacyl tRNA synthases

Which loop of tRNA is Dihydrouridine found in and what does it do?

On the D loop Uridine with two additional hydrogen atoms DESTABILIZES the RNa structure, makes it more flexible Found in high levels in psychrophiles (thrive in low temps)

What happens to misfolded and unwanted proteins?

Protein destruction Dysfunctional proteins are broken down in a protein destruction complex called the proteosome Check proteins for misfolding (such as hydrophobic region exposed)

How are ribozymes representative of the ancient role of RNA in the evolution of life?

Provide the essential core of macromolecule synthesis in all life forms today Posses catalytic activity Ribozymes represent the ancestral role of RNA: preceded DNA Life evolved using RNA Ribozymes act on other nucleic acids RNA molecules catalyze their own replication and perform various cell functions

Describe RNA:

RNA stands for ribonucleic acid. It is an important molecule with long chains of nucleotides. A nucleotide contains a nitrogenous base, a ribose sugar, and a phosphate.

What is a ribozyme?

RNA that can act as an enzyme

Describe allosteric regulation and how the two different conformations of the enzyme affect its activity.

Rates of enzyme-catalyzed reactions are adjusted to meet cellular needs is allosteric regulation Allosteric regulation involves the binding of a regulatory molecule at one site that may induce conformational change in the protein which affects its catalytic site (the allosteric enzyme exist in two different forms). One form of the enzyme is active and one where the enzyme has greatly reduced or no activity.

How do tRNAs function as adaptor molecules?

Recognize and bind the codon at one site and to the amino acid on the other site Match amino acids with codons

What is the secondary level of protein structure?

Stable due to H-bonds of backbones between N-H and C=O Patterns of hydrogen bonds formed between amine hydrogen and carbonyl oxygen atoms contained in the backbone peptide bonds of the protein Alpha helices and Beta sheets

What are the three different regions of the chromosome described in lecture?

Replication Origins Telomeres Centromeres

What do these two folding patterns result from?

Result from hydrogen bonds that form between the N-H and C=O groups in the polypeptide backbone (see Figure 4-6). Because the amino acid side chains are not involved in forming these hydrogen bonds, α helices and β sheets can be generated by many different amino acid sequences. In each case, the protein chain adopts a regular, repeating form.

What are the three amino acids most commonly phosphorylated by kinases?

Serine, Threonine, Tyrosine

What size of molecule can pass through a NPC?

Small molecules (<50,000-60,000 daltons) can diffuse through NPCs, most macromolecules are too large to diffuse and need to use Gated Transport

What type of transport do NPCs use?

Small molecules use diffusion, however, active transport is required for macromolecules

Where are ribosomes located within the cell?

Some are free in the cytosol, others are attached to membrane surfaces of the ER (rough ER) and to a lesser degree the nuclear and mitochondrial surfaces

How does protein folding occur?

Some proteins, growing polypeptide chain aquires secondary and tertiary structure Amino (N terminal) domain folds first as the carboxyl terminal is still being synthesized The amino-acid sequence of a protein determines its native conformation.

What are some important examples of ribozymes?

Splicesome Ribosome

What end of the growing polypeptide chain are amino acids added to?

The first amino acid makes the N terminal and the following amino acids are added to the C terminal

What is the mRNA-binding site?

The message always binds to the subunit first, then the large subunit binds

What role do transfer RNAs (tRNAs) play in translation?

The tRNA carries a amino acid on its stem and a 3 nucleotide sequence specific to the amino acid in its loop. this is the anticodon which complements the sequence known as codon present in the DNA. Successive tRNAs bind to the DNA, the polypeptide chain is transferred to the newest tRNA that binds to the DNA and when translation is complete, the protein is synthesized and the tRNA becomes uncharged after the removal of protein from it.

Why is translation not a direct one to one correspondence between a single nucleotide on the mRNA and a single amino acid in a protein?

There are only four nucleotides, BUT 20 different types of amino acids

What is special about the DNA packing in the centromeres and what is the specific name given to the packed DNA there?

There is increased packing Centric heterochromatin

What is the specific term used to describe the cellular process that synthesizes RNA?

Transcription- Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase

What is proteolysis?

When proteases hydrolyze peptide bonds Pathway begins with the recognition of an abnormal patch on a protein's surface, ends with the delivery of entire protein to proteasome

Identify three methods that allow us to determine the three-dimensional structure of proteins and understand what size proteins can be used with each method.

X-ray Crystallography Need a lot of protein, forms crystal, exposed to high energy electron beam of Xray, scatter (defracted beams), resolution=.1nm NMR (Nuclear Magnetic Resonance) Need smaller protein, magnetic-molecules vibrate at certain frwequencies, patterns created with spots representing interactions of H bonds Cyro-Electron Microscopy-TEM .4-.5nm resolution, uses proteins that can not be crystalized, or are too large for NMR

Do ribozymes possess catalytic activity?

Yes, ribozymes posses catalytic activity

What role does ubiquitin (polyubiquitin) play in this process?

a small protein added to a dysfunctional protein to signal proteasome (amplify target protein)

What activated carrier is involved in the conformational change that causes the ratcheting movement between the large and small subunits of a ribosome?

hydrolysis of GTP to GDP

Understand and be able to describe the functions of the different types of RNA (See table 7-1 in lecture slides).

mRNAs: Codes for proteins rRNAs: Form part of the structure of the ribosome and participate in protein synthesis tRNAs: Used in protein synthesis aas adaptors between mRNA and amino acids small RNAs: Antisense RNA (aRNA)-Gene regulation, all organisms MicroRNA (miRNA)- gene regulation, most eukaryotes Small nuclear RNA (snRNA)- various functions (e.g., RNA splicing, maintenance of telomere), eukaryotes and archaea

What is the difference between charged vs. uncharged tRNAs?

tRNAs that are charged (aminoacyl) have an amino acid coupled to the 3' end, while uncharged tRNAs have no amino acid attached (Those that have transferred their amino acid to the growing polypeptide chain)