Molecular Bio Flashcards by Adam Purviance

What are the requirements of a chromosome?

Origin of Replication, telomere, centromere

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DNA is basepairing is antiparallel because each strand’s sequence is complementary to partner. True or false?

true

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Digestion with ___ break down DNA by cutting between nucleosomes and degrading the exposed DNA between nucleosome core particles (linker DNA)

nucleases

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Each individual nucleosome core particle consists of __ histone proteins

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Define pseudogenes

duplicated gene that has become irreversibly inactivated by multiple mutations

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Describe what happens in gene duplication and divergence

both copies remain functional while diverging in sequence and pattern of expression

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Name this DNA-binding motif:
simplest; two alpha helices connected by short chain of amino acids that make the turn at a fixed angle; longer helix portion = recognition module

helix-turn-helix

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Name this DNA binding motif:

includes Zn atom; amino acid sequence drawn out looks like finger; binds to major groove

zinc finger domain

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Name this DNA binding motif:
two alpha helical DNA binding domain; dimerizes through leucine zipper region; interactions between hydrophobic amino acid side chains at every 7 amino acids down one side of alpha helix: forms zipper structure; grabs DNA like clothespin

leucine zipper motif

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Name this DNA binding motif:
consists of a short alpha chain connected by a loop to a second larger alpha chain; can occur as homodimers or heterodimers; three domains: DNA binding domain, dimerization domain, activation domain

helix-loop-helix

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Describe regulation by RNA stability (2 things)

1 - decapping: exposed mRNA degraded from 5’ end

2 - mRNA degraded from 3’ end through poly-A tail and into coding region

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____ ___ modifications are required by proteins to be functional

post translational

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An apparatus that deliberately destroys aberrant protein is called what?

proteasome

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In regards to specificity of protein degradation, there is one E1 ubiquitin activating enzyme and 1 proteasome but 30 E2 ubiquitin conjugating enzymes and hundreds of E3 accessory proteins. True or false?

true

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Explain methylation and genomic imprinting

what genes get expressed (or not) from mom and dad

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X-chromosome inactivation

even things out XX vs. XY - 2 X chromosomes vs 1 X chromosome

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What are the 3 major transition checkpoints of the cell cycle

start: G1 to S
G2 to M
In M phase: anaphase and cytokinesis

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True or false? activites of Cdks rise and fall during the cell cycle

true

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Cdks are dependent on what proteins

cyclins

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Without cyclin bound (inactive state) the active site of Cdk is blocked by a region of the protein called the __ ___

T loop

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Phosphorylation of Cdk at T-loop fully activates enzyme. T or F?

true

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What phosphorylates Cdk?

CAK

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Name the effects of Wee1 and Cdc25 on Cdk-cyclin activities

Wee1: inactivates Cdk-cyclin by phosphorylation

Cdc25: removes phosphorylation, thus activating Cdk-cyclin

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The 2 step process of chromosome condensation and resolution is brought about by what?

condensin

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M-Cdk activates ____ to complete mitosis

APC/C

Chromosomes are attached to microtubules at the ____

kinetochore

Name the three forces that move chromosomes to opposite pole

1: depolymerization: major force pulls the kinetochore and chromosome toward the spindle pole. depolymerization of the plus end of the microtubule drives the pulling of the kinetochore poleward 2. microtubule flux: microtubules are moved toward spindle poles while being dismantled at minus end. tubular added at plus end while being removed at minus end 3. polar ejection force: kinesin-4, 10 motors on chromosomes interact with microtubules and transport chromosome from poles. results in push-pull phenomenon

Describe the intrinsic pathway of apoptosis

when cytochrome c is released from mitochondria, it binds to a protein called Apaf1 and forms apoptosome

What is the role of BH123 in apoptosis?

BH 123 proteins become activated, form aggregation in mitochondrial outer membrane and induce release of cytochrome c - then apoptosome formed

Bcl2 proteins regulate intrinsic apoptosis. true or false?

true note: Bcl2 is an anti-apoptotic protein

What is the role of BH3-only protein in apoptosis?

apoptotic stimulus

LAPs block caspases. true or false?

true

Anti-IAPs neutralize the IAPs and liberate what?

the caspases; leads to apoptosis

In regards to cancer genes, ___ involves single mutation event and activation of gene causing proliferation (dominant)

oncogenes

Describe tumor supressor genes and how they affect cancer

loss of function mutation. recessive - both alleles must be mutated

Heriditary form of Rb

loss of function or deletion of ONE copy of Rb in every cell- because defect is inherited

Sporadic form of Rb

since there are two normal alleles to begin with, need two sporadic mutations to occur

Describe the Apc mutation and how it can cause cancer

loss of function - Apc is a tumor suppressor gene

Gated Ion channels are common in ___ tissue

nervous

GPCRs use ___ transmembrane proteins

7-pass

Receptor tyrosine kinases are enzyme coupled. true or false?

true

Describe how a receptor tyrosine kinase receptor works

1. RTK binds to SH2 of Grb2 2. Grb2 also has SH3 domain 3. SH3 of Grb2 binds to pralines of SOS which then binds to Ras 4. Ras binds Raf and then rapid activation

___ subunits are compact and globular and are flexible structures 5-9 nm in diameter

actin

In treadmilling, the plus end remains in __ formation and the minus end adopts ___ formation

T;D

Nucleotide hydrolysis leads to ____

treadmilling

Treadmilling predominates in ___ filaments

actin

The following characteristics describe what: | long hollow cylinder; are made of tubulin, outer diameter 25nm, have one end attached to centrosome

microtubule

If nucleotide hydrolysis proceeds more rapidly than subunit addition, the cap is lost and the microtubule begins to shrink. This is called what?

catastrophe

GTP-containing subunits may still add to the shrinking end, and if enough add to form a cap, then microtubule growth resumes. This is called what?

rescue

dynamic instability predominates in ____

microtubules

the following characteristics describe what: | rope-like fiber; 10 nm diameter; help with mechanical strength

intermediate filaments

Describe the construction of intermediate filaments

alpha helical in monomer; coiled-coil dimer; staggered tetramer of two coil-coiled dimers

True or false? in intermediate filaments, there is no nucleotide binding site and structural polarity

true

Keratins impart mechanical strength by anchoring intermediate filaments at site of cell-cell contacts called ____ and cell-matrix contacts called _____

desmosomes; hemidesmosomes

In regards to accessory proteins for actin filaments, what does the ARP complex do?

nucleates assembly to form a web and remains associated with minus end

In regards to accessory proteins for actin filaments, what does cofilin do?

binds ADP-actin filaments, accelerates disassembly

In regardss to accessory proteins for microtubules, what does gamma-TuRC do?

nucleates assembly and remains associated with the minus end

``` Rac/Cdc42 = ___ actin Rho = ___ actin ```

dynamic; rigid

Rac activation promotes polymerization at the cell periphery leading to the formation of ___ extensions

lamellipodia

Cdc42 activation triggers actin polymerization and bundling to form ____

filopodia

Rho activation promotes both the bundling of actin filaments with ___ __ filaments into stress fibers and the clustering of interns and associated proteins to form focal contacts

myosin II

Name the junction: | seals gap between epithelial cells

tight

Name the junction: | connects actin filament bundle in one cell with that in the next cell

adherens

Name the junction: | connects intermediate filaments in one cell to those in the next cell

desmosomes

Name the junction: | allows the passage of small water-soluble molecules from cell to cell

gap

Name the junction: | anchors intermediate filaments in a cell to extracellular matrix

hemidesmosome

In regards to adhesion proteins, ___ mediate cell-cell connection and ____ mediate attachment of cells to matrix

cadherin; integrin

Adherents junctions often form a continuous ___ ___ close beneath the apical face of the epithelium, encircling each of the interacting cells in the sheet

adhesion belt

Each sealing strand of tight junction is composed of a long row of ___ pass transmembrane adhesion proteins embedded in each of the two interacting plasma membranes

two main tight junction proteins are what?

claudin and occludin

Gap junction is spanned by channel forming protein called what?

connexin note: 6 connexin protein subunits

Gap junctions couple cells both electrically and metabolically. True or false?

true

Intracellular linkage of integrin to actin is mediated by ___

talin

What are FAK molecules and what do they do?

cytoplasmic protein tyrosine kinase; they autophosphorylate each other and make docking sites for Src-family kinases

Describe the structure of a proteoglycan

long polysaccharide/core complex linked to extensive hyaluronic acid chain

describe the triple helix of collagen

each chain twists to left; twist helically around each other to the right

Procollagen triple helix is formed where?

ER/Golgi Complex

Procollagen is then cleaved outside of cell where it self-assembles into a what?

collagen fibril aggregation of fibrils forms fiber

What is the defective enzyme in scurvy?

prolyl hydroxylase

What is the defective enzyme in ehlers-Danlos VI?

lysl hydroxylase

What is the purpose of doing an SDS-PAGE?

separating proteins by size

Why would you do Mass Spec?

identify unknown proteins

Why would you do a western blot?

to analyze specific proteins

Which ELISA is necessary for HIV test?

indirect

What is an example of a sandwich ELISA?

pregnancy test

Why would you use nuclear magnetic resonance?

to analyze protein structure

Plasmids are cloning vectors. true or false?

true

How do cDNA clones work?

DNA copy of mRNA; use reverse transcriptase

What is pcr used for?

to detect altered genes or foreign DNA

What does CSI utilize?

STRs

True or false? mitochondria are more dynamic in high energy cells

false, less dynamic. become more fixed in high energy cells where they are packed tightly between myofibrils

Do mitochondria retain their own DNA?

yes

Mitochondria transfer RNAs are highly variable. changes in mt tRNAs have been linked to over 200 disease states. true or false?

true

Accumulation of ___ generated by the respiratory chain can cause mito DNA damage

ROS note: ROS increase with age, and the brain is particularly susceptible

list the layers of the epidermis

granular, prickle, basal, basal lamina

Olfactory receptors are what type of receptor?

G protein coupled receptor

Describe the flow of action potential from olfactory receptor

relayed via axon to brain to glomeruli

Where are glomeruli found?

olfactory bulbs

Define totipotency

ability of a cell to give rise to all cells of an organism, including embryonic and extra embryonic tissues ex: zygote

Define pluriptoency

ability of a cell to give rise to all cells of the embryo and subsequently adult tissues ex: embryonic stem cells

define multipotency

ability of a cell to give rise to different cell types of a given lineage ex: adult stem cells

true or false? founder stem-cell populations stay small; transit amplifying divisions let them generate and renew a big adult structure

true

Explain the immortal strand hypothesis

to combat passing on mutation, stem cells divide asymmetrically, passing down a template parental strand

How are ES cells derived?

what for zygote to become blastocyst and then take inner cell mass and culture on plate

True or false? Adult stem cells are tissue specific

true

give the function of the following types of RNAs: | tRNA; snRNA; snoRNA; miRNA; siRNA

tRNA: adaptor between mRNA and AAs snRNA: splicing of pre-mRNA snoRNA: chemically modify rRNAs miRNA: regulate gene expression - block translation of specific mRNAs siRNA: turn off gene expression

Explain eukaryotic transcription initiation

TFIID binds to TATA box; recruitment of other TFs; formation of transcription initiation complex; Phosphorylation of CTD by TFIIH = elongation

The genetic code is degenerate. True or false?

True

What is the anticodon loop on a tRNA molecule?

a set of 3 consecutive nucleotides that pair with a complementary codon in an mRNA molecule

What is the 3'CCA terminal region of a tRNA molecule?

the region which binds the AA that matches the corresponding codon

Some tRNAs require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch at the third (wobble) position. This wobble base pairing explains why.....

so many of the alternative codons for an AA differ only in their third nucleotide

UAA, UAG and UGA are what type of codons

stop codons

Protein transfer/transport to various compartments is guided by ___ signals. Signal ___ remove signal after protein reaches final destination

sorting; peptidases

Nuclear transport is ___, ___, and ____

bidirectional, selective, and gated

Molecular Bio Flashcards

(114 cards)