Exam 1: Ch 1,3,4,6

FSU cell structure and functi flash cards

What are the universal features of life?

1. All cells store hereditary information in the form of double-stranded DNA molecules
2. All cells replicate their hereditary information via template polymerization
3. All cells transcribe portions of their DNA into RNA molecules
4. All cells use proteins as catalysts
5. All cells translate RNA into protein in the same way
6. Each protein is encoded by a specific gene
7. Life requires a continual input of free energy

Transcription

segments of DNA used as template for mRNA synthesis

Translation

RNA used to synthesize proteins

Gene

Segment of DNA corresponding to specific protein, catalytic, regulatory, or structural RNA molecule

What differentiates eukaryotes from prokaryotes?

* DNA-containing membrane-enclosed nucleus
* Cytoplasm
* Cytoskeleton

What is the function of the endoplasmic reticulum?

Membrane synthesis, synthesis of materials for secretion

What is the function of the Golgi apparatus?

Receives, modifies, and packages ER molecules.

What is the function of lysosomes?

intracellular digestion (inside of cell)

What is the function of peroxisomes?

cell detoxification

What is cytosol?

everything within the cell membrane besides membrane-bounded organelles

How did the first eukaryotic cell rise?

Archaea absorbed a bacteria (proto-mitochondria), forming an endosymbiotic relationship where the bacteria produced ATP for the archaea

* evidence
* mitochondria share many similar traits with bacteria such as division, DNA, ribosomes.

Which of the following is not true of all cells?

a. They synthesize proteins on the ribosome

b. They replicate their genome via DNA polymerization

c. They transcribe their genetic information by RNA polymerization

d. They use RNA as a template for genomic DNA polymerization.

d. They use RNA as a template for genomic DNA polymerization.

What would you NOT expect to find in a bacterial cell?

A. Swimming using flagella

B. Having a cell wall around the plasma membrane

C. ATP production in mitochondria

D. Protein production on the ribosome

C. ATP production in mitochondria

What makes up every protein?

**long unbranched chain** of amino acids, each linked to its neighbor through a **covalent peptide bond**.

What makes an amino acid side chain basic?

Positively charged N terminal

* ex) NH3+, +H2N, NH+ at N-terminal

What makes an amino acid side chain acidic?

The amino acid has no charge

What makes an amino acid side chain uncharged polar?

The amino acid has a polar group attached to them but remain uncharged

* ex) OH or NH2 group attached but still uncharged

What is unique about cystenine?

disulfide bonds can form between two cysteine side chains

What is the primary structure of proteins?

The linear sequence of amino acids

* influences possible bonding angles → impacts overall shape of the protein

What is the secondary structure of proteins?

The two patterns that proteins can fold into as a result of hydrogen bonding b/w N-H and C=O groups in **polypeptide backbone**


1. Alpha helix


1. Beta sheet → parallel or antiparallel

What are the two forms of beta sheets?

Parallel and antiparallel

How do alpha helices form?

hydrogen bonding forming between **every fourth peptide bond**

How do coiled-coil structures form?

forms when a helices have most of their non-polar (hydrophobic) side chains on one side.

* ex) a-keratin, myosin

What are tertiary structures of proteins?

The full three-dimensional organization of a polypeptide chain -including its alpha helices, beta sheets

What are quaternary structures of proteins?

protein structures formed by **more than one polypeptide chain**

* ex) hemoglobin

What determines the pattern of folding for proteins?

Weak non-covalent bonds → strong when together


1. hydrogen bonds
2. electrostatic attractions
3. van der Waals attractions

What is the hydrophobic clustering force?

Nonpolar side chains of amino acid tends to be forced together when suspended in H2O

What are covalent cross-linkages and what is their function in protein structure?

* Usually occur on extracellular proteins


* link 2 amino acids of same protein together
* help stabilize the protein
* ex) S-S bond in cysteine

What are protein domains?

sections of one single linear strand that has its own 3D structure, NOT QUATERNARY

What is domain shuffling?

* Joining of preexisting domains in new combinations.
* Originated from the accidental joining of the DNA sequences that encode each domain, creating a new gene

How do protein assemblies form?

have binding site complementary to another region of the surface of the same molecule.

* can only form in a specific way
* ex) Actin forms long helical structure

What are the advantages of using smaller protein subunits to build larger structures?

1\. Large structure built from repeating subunits requires minimal genetic information.

2\. Both assembly and disassembly can be readily controlled reversible processes

3\. Errors in the synthesis of the structure can be more easily avoided

* ex) tomato bushy stunt virus (TBSV)

When can protein assemblies go wrong, example?

Amyloid Fibrosis

* beta sheets in brain misfold on top of each other creating giant stacks of proteins
* seen in neurological diseases like parkinson’s and alzheimer’s

What is a ligand?

The substance that is bound by a protein

How do ligands bind the the binding site of an enzyme?

Weak non-covalent bonds allow proteins selectively bind to a ligand with high affinity.

* Each bond is weak
* Enough bonds form when surface contact between protein and ligand fit very closely.
* “Hand and glove”

What is a binding site of an enzyme?

The region of a protein that associates with a ligand.

* particular arrangement of amino acids
* amino acids can belong to different portions of the polypeptide chain.

Why are the binding sites of antibodies especially variable?

* Binding site is located between variable domains of heavy and light chains.
* Changes of amino acid length at hypervariable regions leads to enormous diversity

How do enzymes speed up reactions?

* Cause the chemical transformations that make and break covalent bonds.
* selectively stabilizes transition states to lower activation energy

What are the 3 ways that enzymes speed up reactions?

A. binding two substrate molecules together to encourage them to RX with each other

B. rearranging electrons in substrate to create partial negative/positive charges that favor a RX

C. enzyme bends the substrate into a particular shape that forces it into the transition state faster, favoring a RX

How do enzymes Use Simultaneous Acid and Base Catalysis to speed up reactions?

performs both acid and base catalysis to get fastest RX, with on or the other it is still fast but not as fast as using both.

How does the lysozyme enzyme work, and what does it do?

* It catalyzes the cutting of polysaccharide chains in the cell walls of bacteria.
* acts as a natural antibiotic found in saliva, eggs, etc.

What are cofactors/coenzymes and whats an example of one?

Cofactors are small non-protein “sidekicks” for enzymes that help them do their function more effectively

* ex) Iron in hemoglobin allows the protein to bind O2 effectively to carry it in RBCs

What are different ways that enzyme activity is regulated?

1. enzyme production control
2. isolating enzymes in compartments
3. enzyme degradation control
4. controlling enzyme activity directly (2 ways)


1. allosteric activation/inactivation
2. covalent modification

What is feedback inhibition of enzymes?

Product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway.

* example of negative regulation

What is the structure of enzymes that implement feedback inhibition regulation?

Enzymes regulated by feedback regulation have two binding sites:

* Active site: binds to substrate
* Regulatory site: binds to regulatory molecule
* Regulatory molecules control the function of the enzyme by conformational change in the protein.

What is positive allosteric regulation of enzymes?

Binding of regulatory molecule **increases** the affinity of the protein to the substrate.

What is negative allosteric regulation of enzymes?

Binding of regulatory molecule **decreases** the affinity of the protein to the substrate.

how does protein phosphorylation (via kinase) impact protein function?

* can **bend protein** (conformational change)
* can **create binding sites** for other proteins
* can **disrupt** protein-protein interactions
* effect **can be reversed** by phosphatases
* can either **increase** or **decrease** protein activity

How is the Src protein regulated by phosphorylation?

* phosphorylated = off
* un-phosphorylated = on
* activating ligand binds to SH3 domain
* phosphorylation in new configuration allows Src to activate

how are GTP binding proteins regulated?

* inactive when phosphate removed = GDP dissociation
* active when phosphate present = GTP binding

How do motor proteins “walk”?

binding of ATP → ATP hydrolysis → “foot picks up” → release of ADP allows for movement forward

Which of the regulatory interactions 1 to 5 depicted in the following diagram is NOT an example of a negative feedback regulation?

A. 1

B. 2

C. 3

D. 4

E. 5

E. 5

Two ligands, A and B, bind to two different conformations of the enzyme X. The ligand A is the enzyme’s substrate, whereas ligand B binds to a remote allosteric site and act as the allosteric inhibitor. Which of the following is a consequence of this arrangement?

A. Binding of B to X does not affect the rate of reaction catalyzed by X.

B. Binding of A to X increases the affinity of X for B.

C. Binding of B to X decreases the affinity of X for A.

D. Binding of B to X has a large effect on the binding of A to X, but binding of A to X has a small effect on X–B binding.

C. Binding of B to X decreases the affinity of X for A.

What was the result of Frederick Griffith’s work on heritable material?

Molecules carrying heritable information are present in the S strain of bacteria.

What were the 4 major molecules that were suspected by Avery, MacLeod, and McCarty to contain heritable information?

1. lipids
2. protein
3. DNA → isolated as source of heritable info
4. RNA

How and who discovered the structure of DNA?

* Double helix initially discovered by **Rosalind Franklin** using X-Ray diffraction analysis
* Structure was later modeled by James Watson and Francis Crick

What is the basic structure of a DNA molecule

nitrogenous base bound to a sugar, which are bound together by phosphate groups

What type of bond links nucleotides together?

phosphodiester bond

What is the direction of the DNA structure?

antiparallel

Which bases are purine and pyrimidine?

purine = G and A

pyrimidine = C and T

how long is the genome stored in a single human cell?

2 meters long

What is a chromosome?

a DNA molecule condensed with proteins

How many chromosomes are in the human genome?

46, 23 from mom and 23 from dad

What is an exon?

segment of eukaryotic genes that codes for proteins

What is an intron?

noncoding region b/w exons

what is a regulatory sequence?

sequence that controls expression of the gene at the proper time, level, and type of cell

What is the basic unit of chromosome structure?

nucleosomes = the first level of compaction

* beads on a string model
* beads = core histones
* string = linker DNA

What are the 8 histone proteins (histone octamer) that make up a nucleosome?

1. 2 H2A histones
2. 2 H2B histones
3. 2 H3 histones


1. 2 H4 histones

How does histone H1 help nucleosomal DNA compaction?

* contacts both DNA and the histone octamer and changes path of DNA as it exits nucleosome
* change in exit path helps compaction

What is heterochromatin?

highly condensed form of chromatin, closed and inaccessible

* \~80% of the genome


* the “.zip” fie

What is euchromatin?

less condensed chromatin, open and readable

* \~20% of genome

What does nucleosome sliding do?

allows nucleosome to reveal inaccessible parts of DNA

Where do histone modifications occur, are they reversible?

* most modifications occur at N-terminal histone tails
* all types of these modifications are reversible

What do reader complexes do in the context of histone tails?

they sit on the histone tail to identify regions with changes (damage) and recruits machinery to repair

How do writer enzymes work with reader proteins along histones?

* reader protein recognizes and binds to newly changed nucleosome
* writer enzyme is allosterically activated and attached to the reader
* mechanism works to spread heterochromatin (condensing) message

Which feature of DNA underlies its simple replication procedure?

A. The fact that it is composed of only four different types of bases

B. The antiparallel arrangement of the double helix

C. The complementary relationship in the double helix

D. The fact that there is a major groove and a minor groove in the double helix

C. The complementary relationship in the double helix

Each chromosome in a human eukaryotic cell is composed of how many independent double strands of DNA?

A. 1

B. 2

C. 23

D. 46

E. Over 200

A. 1

What is transcription?

Process of copying DNA information into a RNA molecule.W

What is translation?

Process where mRNA is used to direct the synthesis of a protein.

What are the differences between DNA and RNA?

1. nucleotides in RNA are ribonucleotides
2. RNA has U instead of T
3. RNA is usually single-stranded
4. RNA molecules can fold into 3D shapes


1. allows for enzymatic function (ribosomes)

What are the 3 steps of transcription?

1. DNA is unwound and bases are exposed
2. one strand serves as template for RNA synthesis
3. RNA is synthesized

Which DNA strand is the template strand and which is the coding strand?

5’ - 3’ = coding strand

3’ - 5’ = template strand → used in transcription

What is the process of transcription like in prokaryotes?

1. RNA pol holoenzyme finds promoter (sigma factor)
2. RNA polymerase holoenzyme forms transcription bubble at promoter
3. abortive initiation
4. promoter is cleared and sigma factor is released
5. elongation
6. termination → formation of hairpin at terminal signal (AT rich region)

What are required in order for eukaryotes to initiate transcription?

general transcription factors = allow RNA pols to find promoters and begin transcription

What happens in initiation of transcription in eukaryotes?

TBP subunit of TFIID binds to TATA box 30 nucleotides before the promoter

* causing a distortion of DNA and acts as a marker for active promoter
* more general TFs assemble alongside RNA Pol II to form **transcription initiation complex**
* TFIIH separates two DNA strands, exposing template
* phosphorylates CTD of RNA pol II allowing it to be released from general TFs → begins elongation

What proteins are “also” needed for initiation of transcription?

* **Activator Protein** = binds to enhancer and interacts with transcription initiation complex via mediator protein complex
* **Chromatin-modifying enzymes**

Where is polycistronic mRNA found?

**Only** in bacteria

What are the steps of RNA processing in eukaryotes?

1. 5’ capping
2. intron splicing
3. 3’ polyadenylation

How does 5’ capping occur?

* phosphorylation of RNA Pol II CTD recruits proteins initiating RNA processing
* modified guanine nucleotide (7-methylguanosine) attached to 5’ end of RNA, contains new 5’ to 5’ linkage
* cap acts as a signal for packaging, protecting the 5’ end of the RNA

How are introns spliced during eukaryotic RNA processing?

* **spliceosome** carries out transesterification
* 5’ end snipped first, followed by 3’ end
* cut out intron = **lariat**

How is 3’ polyadenylation carried out during eukaryotic RNA processing?

* CstF and CPSF bind to phosphorylated CTD on RNA Pol II
* these 2 factors recognize and bind to signal sequence on 3’ end of mRNA
* CsF and CPSF recruit additional factors that cut downstream of sequence
* PAP binds to freshly cleaved end and adds \~200 As to the end

Due to their high transcription rate, active ribosomal RNA (rRNA) genes can be easily distinguished in electron micrographs of chromatin spreads. They have a characteristic “Christmas tree” appearance, where the DNA template is the “trunk” of the tree and the nascent RNA transcripts form closely packed “branches.” At the base of each branch is an RNA polymerase extending that branch, while RNA processing complexes at the tip of the branch form terminal “ornaments.” Would you expect the top of the tree to represent the beginning or end of the rRNA gene? Would the “ornaments” be at the 3′, 5′, or both ends of the nascent rRNA molecules?

a. End; 3′

b. End; 5′

c. Beginning; either 3′ or 5′

d. Beginning; 3′

e. Beginning; 5′

e. Beginning; 5’

This large and complex general transcription factor has a DNA helicase activity that exposes the template for RNA polymerase II transcription. It also has a kinase activity that phosphorylates the C-terminal domain of the polymerase on Ser5 leading to promoter clearance. What is it?

a. TFIIB

b. TFIID

c. TFIIE

d. TFIIF

e. TFIIH

e. TFIIH

what are transfer RNAs (tRNAs)?

adaptor molecules that can recognize and bind both to the codon and to the amino acid

What are anticodons?

set of thee consecutive nucleotides that pair with complementary codon in an mRNA molecule

What is the amino acid attachment site?

short single strand region on 3’ end allows for codon to attach

What is the “wobble” position between a codon and anticodon?

it is where the 3rd nucleotide would match up, weaker bond. Because first 2 nucleotides are usually same for most amino acids

What do aminoacyl-tRNA synthetases do?

covalently couple each amino acid to its appropriate set of tRNA molecules → makes it **charged** and primed for translation

Where are new amino acids added along a growing chain of amino acids of a protein?

along the C-terminal end

* goes from N → C

What are the 3 sites that tRNAs bind to within the ribosome?

1. A site: binds to charged tRNA
2. P site: holds tRNA with growing polypeptide chain
3. E site: exit site