Bio exam 4

What is cell communication

The process of cells detecting and responding to signals in the extracellular environment

What are the 2 types of cell communication

intercellular and intracellular signaling

What is intercellular signaling

communication between cells; signaling cells release ligands which interact with receptors

what are ligand molecules

signal molecules

what are receptors

proteins on target cells that accept signals

what is intracellular signaling

communication within cells

What are the 4 types of signaling

autocrine, direct across gap junctions, paracrine, and endocrine

What is autocrine signaling

signaling cells and target cells can be the same- a cell targets itself

What is “direct across gap junction” signaling

channels that connect plasma membranes; allows signaling molecules to pass from one cell to another

a cell targets a cell connected by gap junctions

what is paracrine signaling

signals that act locally between cells- a cell targets a nearby cell

what is endocrine signaling

signals, hormones, that travel long distances between cells- a cell targets a distant cell through the bloodstream

What are the 2 types of receptors

intracellular receptors and cell-surface receptors

what is intracellular receptors

receptors found in the cytoplasm of the cell

what is cell-surface receptors

receptors found on the cell surface and are integral proteins that bind to external ligand molecules

what are the 3 types of cell-surface receptors

enzyme-linked receptors, g-protein-coupled-receptors (GPCR), and ligand-gated ion channels

what is an enzyme-linked receptor

extracellular domain binds the signal and intracellular domain becomes a catalyst that promotes a reaction

what is a GPCR

a receptor made of 7 transmembrane segments and activates receptors binds to a G protein

what are ligand-gated ion channels

ligand binding causes ion channels to open and ions flow through the membrane

what are the 2 types of signaling molecules

small hydrophobic ligands and water-soluble ligands

what are small hydrophobic ligands

ligands that can directly diffuse through the plasma membranes and interact with intracellular receptors

what are water-soluble ligands

polar ligands, so they need help getting across the plasma membrane and they mostly bind to cell-surface receptors

what are the 3 stages of cell signaling

receptor activation, signal transduction, and cellular response

what does receptor activation do

binds a signaling molecule causes a conformational change in a receptor that activates its function

what does signal transduction do

once the ligand binds to the receptor, the signal is transmitted through the membrane into the cytoplasm, signals binding to the cell surface are the “first messengers”

what does signal transduction lead to

signal transduction pathways lead to the production of second messengers, which relay signals inside cells

what is the advantage of second messengers

signal amplification- the binding of signal to one receptor can cause the synthesis of many molecules that activates other proteins

speed- some signaling can spread through the body in less than 20 seconds

what is a signaling pathway

a chain of events set off by the activated receptor

what does cellular response do

different responses are possible and could include; changes in enzyme activity, altered function of structural proteins, changes in gene expression, cell growth, and cell death

what is apoptosis

programmed cell death, happens when a cell is damaged or potentially dangerous to the organism

what happens during apoptosis

the cell shrinks as nucleus and cytoskeleton are destroyed; the plasma membrane forms blebs

what is a bleb

an irregular extension that then break

What is the DNA structure

monomers of DNA are nucleotides and the basic structure of a nucleotide consist of a pentose sugar, phosphate, and a base

What is the basic pair rule

adenine-thymine and guanine-cytosine

what is the characteristic of the basic pair rule

is double-stranded, have antiparallel strands (sugar phosphate backbone on the outside, bases on the inside) and phosphodiester bonds (a phosphate group that links 2 sugars)

How is DNA typically started

5’ to 3’ (5’ - TAGC 3’) with a complementary strand (5’ - ATGC - 3’)

What is DNA replication

how cells make identical copies of their DNA

What are the 3 proposed models of DNA replication

Conservative, semi-conservative, and dispersive

What is semi-conservative DNA

each parental strand acts as a template for new DNA to be made, each double strand includes one parental and one daughter DNA

What is DNA polymerase

it adds nucleotides 1-by-2 to the growing DNA chain; this complementary to template strand; only works in the 5’ to 3’ direction. Requires energy -ATP- and other NTPs (high energy molecules)

What is the origin of replication

specific nucleotides sequence that signals where proteins should bind and begin replication

• prokaryotes have a stable origin while eukaryotes have multiple origins

What are the four types of DNA replication proteins

helicase, DNA topoisomerase, single-stranded binding, and primase

What us helicase

an enzyme that binds to the origin of replication and unwinds the DNA by breaking hydrogen bonds between base pairs; towards 5’ to 3’

what is DNA topoisomerase

protein that rewinds additional coiling pressure ahead of replication fork

what is the replication fork

a y-shaped structure that forms as DNA opens

what is single-stranded binding (SSB)

proteins that coat the single strands of DNA near the replication fork to prevent s-s DNA from unwinding into a double helix

what does primase do

it creates an RNA segment (primer) complementary to the template DNA

what is DNA replication and the 2 strands involved with it

DNA polymerase that can only work in the 5’ to 3’ direction

• leading and lagging strand

what is a leading strand

DNA created as 1 long molecule, primase makes a single RNA primer, and DNA polymerase adds nucleotides in the 5’ to 3’ direction

what does the lagging strand do

DNA is made as Okazaki fragments; fragments are made of RNA primers and DNA, joined together by DNA ligase

What are the 10 steps of DNA replication

DNA unwinds at origin of replication, helicase opens up the replication fork, SSB proteins coat the DNA to prevent rewinding, topoisomerase prevents recoiling, primase creates RNA primers, DNA pol II adds nucleotides in 5’ to 3’ direction, elongation of both lagging & leading strands continue, RNA primers are removed, gaps are filled by DNA pol I, DNA ligase seals gaps between Okazaki fragments

What enzymes are involved in DNA replication

DNA pol I & II, helicase, ligase, primase, sliding clamp, topoisomerase, and SSB

what does DNA pol I and II do

Pol I: removes RNA primer and replaces it with newly synthesized DNA

Pol II: main enzyme that adds nucleotides in the 5’ to 3’ direction

what does helicase do

opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases

what does ligase do

seals the gaps between Okazaki fragments to create one continuous DNA strand

what does primase do

synthesizes RNA primers needed to start replication

what does the sliding clamp do

helps to hold the DNA polymerase in place when nucleotides are being added

what does topoisomerase do

helps relieve the strain on DNA when unwinding causing breaks, then reseals the DNA

what does SSB do

binds to single-stranded DNA to prevent DNA from rewinding back

what are the enzymes in prokaryotes

the origin is simple, 1000 nucleotides added per second, 5 DNA polymerase types, telomerase isn’t present, DNA pol I is the RNA primer removal, DNA pol II is the strand elongation, sliding clamp is the sliding clamp

what are the enzymes in eukaryotes

origin is multiple spots, 50-100 nucleotides added per second, 14 DNA polymerase types, telomerase is present, RNase H is the RNA primer, pol a, b, and c is the strand nucleotides, and PCNA is the sliding clamp

what does telomere replication look like

prokaryotic chromosomes are circular, while eukaryotic chromosomes are linear

what is telomere replication

DNA pol that can only add nucleotides in the 5’ to 3’ direction, leading-strand synthesis continues until the end of the template is reached, lagging strand helps each Okazaki fragments is started by a separate primer, when the replication fork reaches the end of the linear chromosomes; there’s no way to replace the primer on the end of the lagging strand (telomere and telomerase)

what is telomere

is the end of the chromosomes that remain unpaired; made up of repetitive sequences that code for no specific gene

what is telomerase

an enzyme that adds telomeres to the ends of chromosomes

what does transcription do

generates messenger RNA (mRNA) then translated by ribosomes to make proteins; RNA uses the following base pairs (GC and AU)

what does the central dogma tell us

DNA turns into RNA which then turns into proteins

what are the 3 components of central dogma

transcription, translation, and genetic code

what does transcription for the central dogma do

is the creation of RNA using information in DNA; a RNA specifies the amino acid sequence of a polypeptide

what does translation for the central dogma do

process of reading the mRNA template to create specific polypeptides on a ribosome

what does the genetic code for the central dogma do

is the sequence of bases in an mRNA molecule

• genes constitute the genetic material (blue print of organisms characteristics)

• structural genes code for polypeptides(s) that act as proteins

• activities of proteins determine the structure and function of cells

what do the amino acids do for DNA

there’s 20 amino acids found in proteins that all have the same basic structure; amino group, alpha carbon, accessory hydrogen, carboxyl group (COOH), and a r-side chain

• each amino acid is coded for a 3-ribonucleotide sequence called a codon (AUG, CGA) most causes code for a specific amino acid, however the genetic code is a “degenerate code” because multiple binding can specify the same amino acid

what does the reading frame do

divides genetic code into individual binding so that you can read the code

what are the two codons for genetic coding

start (AUG = MET; methionine) and stop codons

what does the stop codon do

UAA, UAG, UGA

• terminate protein synthesis and release the the polypeptide; whatfollowing the start codon, the mRNA is read in groups of 3 until it hits a stop codon

what are the 3 things involved with transcription overview

transcription bubble, transcription strand, and the coding strand

what is the transcription bubble

the region of unwinding in DNA where mRNA is created

what is the template strand

DNA that encodes for RNA

what is the coding strand

a complementary strand of created RNA where the only difference is that T is replaced with U

what are the 3 stages of transcription

initiation, elongation, and termination

what happens during transcription initiation for prokaryotes

attaches to the DNA template and initiate transcription on its own

what happens during transcription initiation for eukaryotes

has transcription factors; proteins that first bind to the promoter region and help recruit the appropriate polymerase

• 3 RNA polymerase; 1 (nucleolus, all rRNAs except for 5s rRNA), 2 (nucleus, all protein-coding nuclear pre-mRNAs), and 3 (nucleus, 5s rRNA, tRNAs, and small nuclear RNAs)

what are the 3 components involved with transcription initiation

initiation site, RNA polymerase, and a promoter

what happens at the initiation site

where the first 5’ mRNA ribonucleotides are transcribed

what is RNA polymerase

an enzyme responsible for transcribing DNA to RNA

what is a promoter

a DNA sequence onto which RNA pol binds and initiates transcription

what are the 3 features of promoters and what do they do

TATA box: 5’ - TATAA- 3’

transcription start site: where transcription begins

regulatory or response elements: areas recognized by regulatory proteins that control initiation of transcription

what happens during transcription elongation

transcription factors are released; RNA polymerase creates mRNA in the 5’ to 3’ direction and focuses on RNA polymerase II