Proteins & Enzymes | Quizlet

Topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

Molecular Chaperones (examples?)

A protein that helps other proteins fold or refold from a partially denatured state

Examples: Bips

What are the advantages to having subunits for proteins?

- Repeated subunits require less genetic information

- Assembly/disassembly can be easily controlled reversible processes since subunits bond with relatively low energy

- Errors in the synthesis of of proteins are less likely as more correctional structures are in place for common subunits

What are the four types of bonds to aid proteins into their secondary structure?

- Hydrogen Bond

- Electrostatic Attractions

- Van Der Waals Attractions (an electric force that attract neutral molecules to each other)

- Hydrophobic Clustering Force

Nucleoporins

A type of protein that makes up a nuclear pore complex. Creates an inner mesh that aids in transmembrane transportation specificity.

On which side of a peptide are amino acids added?

C-Terminus

What's the difference between DNA Topoisomerases I & Topoisomerases II

DNA Topoisomerases I creates a single stranded break which allows the two strands to twist independently of each other to relieve tension during replication.

Topoisomerase II forms a covalent bond to both strands making a transient double-strand break. The strands reseal once the tension is relieved.

Origin Recognition Complex (ORC)

a complex of six proteins found in eukaryotes that is necessary to initiate DNA replication. It recognizes and recruits proteins to the origin sequence in DNA

DNA Gyrase

Unwinds DNA

DNA Helicase

Unzips the DNA by breaking hydrogen bonds between the two strands.

Single Stranded Binders (SSB)

Protective proteins that protect the single stranded DNA by preventing reannealing, straightening the DNA, & keeping bases available.

Primase

A protein that joins RNA molecules to the DNA in order to create a primer for DNA polymerase to begin & stop

DNA Polymerase III

Starts the RNA primer, attaches to the sliding clamp, & covalently joins nucleotides in a 5'-3' direction. It also proofreads the sequence by checking the affinity of the bases.

Exonuclease

Removes RNA primers

Polymerase I

Fills in any gaps (mainly caused by the removal of primers)

Ligase

Uses ATP to bind all nucleotides together and seal the new strand

Telomerase

Replenishes the repeated sequences at the end of a DNA strand. This is because DNA replication has no mechanism to synthesize DNA at the end of a lagging strand.

Telomeres gradually shorten which is thought to be a way of preventing the unlimited proliferation of adult tissue.

Histone Chaperone Proteins

bind the highly basic histones and release them for assembly only in the appropriate context

CapZ

Actin regulator that binds to the plus end to prevent any further growth on that side

Tropomodulin

Actin regulator that binds to the negative end to prevent further growth on that side

Tropomyosin

Actin regulators that binds to 6/7 monomers to stabilize/stiffen the filament. This also prevents interaction with other proteins (i.e. protective shield)

Profilin

Actin regulator that binds to the plus end and promotes adhesion of monomers using ATP (i.e. it increase plus-side growth)

Thymosin-β4

Actin regulator that competitively binds to ATP bound G-Actin to prevent it from binding to the plus end

Cofilin

Actin regulator that degrades ADP-loaded F-actin segments which promotes turnover/treadmilling. Done by making the filament twist more than usual causing the point to become brittle and easy to break using thermal motions.

Gelsolin

Actin filament that severs filaments and binds to the positive end

Formin

Actin filament stimulates nucleation and elongation of F-actin filaments that can be cross linked by other proteins to form parallel filaments. The formin protein stays associated with the filament allowing new subunits to attach

Cdc42-GTP

Activates WASP which brings in Arp2/3 to branch Actin

WASP

Activated by Cdc42-GTP to bring in Arp2/3 and branch Actin

Arp2/3

Branches Actin at a 70 degree angle

GTP-β-Tubulin caps

Regulates tubule dynamic stability. If the cap is on, plus-sided growth can occur. If the cap is lost, rapid dissociation occurs.

Kinesin-13

Removes ɑβ-Tubulin dimers

Stathmin

Binds to protofilaments to accelerate catastrophe & lower concentration of available protofilaments

TIP Proteins

Recognizes plus-end structures and bins the microtubule to the actin cordial endoskeleton.

Katanin

Severs microtubules to destabilize them (13 longitudinal bonds)

Kinase

An enzyme that transfers phosphate ions from one molecule to another

phosphatease

removes phosphate group

Guanosine triphosphate binding proteins (GTPases)

Inactive when bound to GDP but becomes activated when GDP is phosphorylated in GTP. Important for cytoskeletal reorganization, cell polarity, cell cycle progression, & gene expression.

Ras Protein

GTP-binding protein which, when activated, exchanges its GDP for a GTP molecule in response to extracellular signals (such as growth factors) to bind to the receptors in the plasma membrane

Histone

Protein molecule that tightly binds DNA to organize it

Histone subunits

H2A, H2B, H3, H4

Nucleosome

Histone + DNA

Writer Proteins

Gives histones a mark to signal for a modification (Acetylation or methylation)

Reader Proteins

Identifies writer's marks & binds to the newly modified nucleosome. The reader protein activates an attached writer enzyme which marks the adjacent nucleosome causing a cycle

Kinesins

Motor protein that moves in the anterograde direction (to positive end) of microtubules

Dyenines

Motor protein that moves in the retrograde direction (to the negative end) of microtubules

Hemidesmosomes

attach epithelial cells to basal membrane

Desmosomes

Anchors cells to their neighbors

Plakins

Family of proteins which link intermediate filaments to each other, and to the rest of the cytoskeleton

Plakin Septins

Assemble into nonpolar filaments to form rings & cage-like structures, which acts like a scaffold to compartmentalize membranes or recruit/organize the actin & microtubule cytoskeleton

Lamin

nuclear class of intermediate filament binds to chromatin & the cytoskeleton to protect DNA, regulate gene expression, and manipulate the position of the nucleus within the cell

Rho

Small GTPase

RAN

Small GTPase assists with transport route

GEF

Guanine exchange factor (switches Rho on)

GAP

GTPase activating protein (switches Rho off)

GDI

GDP-dissociation inhibitor (prevents activation & recruitment to the plasma membrane)

RNA polymerase

Unwinds the DNA & catalyzes phosphodiester bonds that link the ribonucleotides together.

Energy required comes from the hydrolysis of ATP, GTP, UTP, CTP (5' → 3' of nascent strand)

𝜎-factor

Protein that can recognize related sequences used in both terminator & initiator sites to compare sequences with basic functions

TFIID

Binds to short helical DNA sequence primary composed of A & T nucleotides (The TATA box)

M-Cyclin

Activates M-Cdk

M-Cdk

Protein complex that triggers the M phase of the cell cycle; consists of an M cyclin plus a mitotic cyclin-dependent protein kinase (Cdk).

Phosphatase Cdc25

dephosphorylates M-CDK/Cyclin B/CDK1 and thus activates it

Polo-like & Aurora Kinases

Aids in controlling early mitotic events

G1/S-cyclins

bind Cdks at the end of G1 and commits the cell to DNA replication.

S-cyclins

stimulates chromosome replication in S phase

Cdk inhibitor proteins (CKIs)

Inhibits cyclin-cdk complexes

Cyclin C (Aka APC)

Used in numerous cell processes to stimulate the proteolytic destruction of specific regulatory proteins. They also catalyze the destruction of securin (separates the sister chromatid pairs) as well as S- & M-cyclins. This inactivates most Cdks in the cell.

Skp, Cullin, F-box containing complex (SCF)

An important protein that ubiquitises proteins involved in the cell cycle which helps control activation of S-Cdks & DNA replication.

Caspases

A protease that triggers cell death & only becomes active during apoptosis.

Initiator Caspases

Begins the apoptotic process after the apoptotic signal triggers its assemblage

Death receptors

Triggers the extrinsic pathway of apoptosis

Fas ligand

Activates Fas on the surface of a target cell, which forms a death-inducing signaling complex (DISC)

Apaf1

transformers into an apoptosome, which recruits proteins, & catalyzes cell death

Executioner Caspases

the enzymes that hydrolyze diverse biological molecules

Laminin

Binds collagen IV, proteoglycans, other multi-adhesion proteins (nidogen), & integrins. Combination of α-, β-, & γ- subunits determines the interaction partners

Fibronectin

An extracellular glycoprotein secreted by animal cells that helps them attach to the extracellular matrix.

Elastin

A protein that is similar to collagen and is the chief constituent of elastic fibers.

Collagen

A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom.

Importins

transport proteins containing a NLS into nucleus

Exportins

Recognizes export signal sequences (NES) and mediates transportation out of the nucleus

Heat shock proteins (cytosolic HSP70)

keeps protein from folding to more efficiently pass through channels

Transporter of Outer Membrane (TOM)

ATP driven translocation channel in the outer membrane of the mitochondria. Receptors in this complex read & recognizes the signal sequence.

Transporter of Inner Membrane (TIM)

ATP driven translocation channel that is located in the inner membrane of the mitochondria

Signal Peptidase

Cleaves signal peptide

SAM Complex

A transposon used for proteins that need to be embedded within the outer membrane

TIM 23 complex

Transfers proteins across inner membrane of the mitochondria. Used in inner membrane protein anchoring.

OXA complex

Mitochondrial inner membrane translocator which mediates the insertion of mitochondrial encoded proteins and nuclear-encoded matrix proteins into the inner membrane.

TIM22

incorporates multipass integral proteins into mitochondrial inner membrane

Binding immunoglobulin proteins (BiP)

an ATP-dependent binding protein that allows protein time to fold as it enters the ER lumen. Binds to hydrophobic regions of the protein. Only needed for post-translational translocation

Sec61 complex

Three-subunit core of the protein translocator that transfers polypeptide chains across the endoplasmic reticulum membrane.

SecA

Protein that pushes protein through the translocon from the cytosol by hydrolysing ATP

SecB

Only in bacteria, this protein is needed to recognize signal sequences of secretory proteins

Cohesin

protein that holds sister chromatids together

Cdc6 & Cdt1

In late mitosis and early G1, these proteins collaborate with the ORC to load inactive DNA helicases near the replication origins to form pre-replicative complexes

Anaphase-promoting complex/cyclosome (APC/C)

A ubiquitin ligase that triggers progression from metaphase to anaphase by signaling the degradation of cyclin B and cohesins.

Geminin

Negative control of replication

Shugoshin Protein

protects cohesin from being degraded by separase

CKIs

cyclin kinase inhibitors

Synaptonemal complex

A zipper-like protein structure that causes replicated homologs to become physically connected during prophase of meiosis I; sets the stage for crossing over.

Condensin

proteins that help sister chromatids coil during prophase

SCF

Ubiquitin ligase, ubiquitylates certain CKI proteins in late G1, thereby helping to control the activation of S-Cdks and DNA replication