Cell and molecular biology | Quizlet

‍7 fitures of life

‍Organisation

Growth

Reproduction

Metabolism

Cell division

Adaptation

Reaction to external stimuli

What are components o cytoplasm?

‍Organels,cystol

‍Eshereshia coli is a model organism because

‍It is simple

Small genome

Cheap to grow

Protein purification

Nematode worm Caenorhabditis elegons is a model organism for multicellular develpment because

Majour cell types of eukariotes are present

Exact number of cell 959

302 neurons,all connections are identified

‍Egg development:frog Rana pipiens

‍Big eggs

An egg is outside mother

Cell division without growth

Plant development and physiology Arabidopsis thaliana

Small genome for a plant

Strong genetics

Cheap to grow for a plant

Average size of prokaryote

‍0.1-5 micrometers

Average size of eukariote

10-100 micrometer

fly Drozophilia melanogaster is a good model organism for genetics because

well known mutations

Zebrafish is model organism for vertebrate development because

it is transparent

strong genetics

desease and behaviour Mus musculus(mouse)

cheap

simular to humans

Homosapiens is a model organism because

very large databases of naturally occuring mutations and deseace

what kind of genes are present in multiple cell organisms but are absent in monosellular organisms

regulative genes

What is the most imporntant catalist in prebiotic chemistry

FeS

steps of light microscopy

fix

cut

stain

observe

phase contrast microscopy principle

this microscopy uses phase of light:interpherence of light waves(phase shifts due to dencity of specimen)an adv:no fixation needed,can make movies

explain principlws of fluorescene microscopy

fluorescene microscopy uses specific molecules that react to specific wavelength by emitting longer frequency and lower energy light.an ex:GFP .(e gets excited and jumps to higher energy state and falls back emitting light)

What is GFP used for?

for fluoresce microscopy

describe fusion of protein and GFP

during genetic modification the the gene that codes for stop codon of protein sequence is removed and GFP coding sequence is connected to protein coding sequence.When fused gene is expressed protein is already marked with GFP.During this process different versions of GFP ca be used for tracking different proteins

perfect subject for GFP use for fluorescene microscopy

zebrafish because it has transparent head

name advantages and disadcantages of electron microscopy

adv:

high resolution

diadv:

expensive

fixation to preserve structure

ultrathin cutting

embeddjng to allow cutting

staining with heavy metals(uranium) for contrast

name kinds of transport via membranes and which particles use which

passive diffusion:hydrophobic molecules

hindered diffusijn:big polar molecules,small polar molecules

needs transporter or chanell:ions

how transport via transporters is different from fiffusion

it happens against concentration gradient therefore needs ATP

describe phospholipid structure

a. fatty acid "tail" -- hydrophobic (faces inwards in membrane and does not touch water)

b. phosphate/glycerol head -- hydrophilic (faces outwards in membrane and touches water)..hydrophilic head consists of polar headgroup,phosphate and glucerol.phosphate part is always negatively charged

describe structure of choresterol and its functions

hydrophobic aromatic compound,sits between polar heads and hydrophobic tails.increases stability of membrane,regulates proteins and decreases ion permiability

is the membrane static?

lipids and proteins constantly move with rotation,flexion,laternal diffusion,flit/flop(rarely)

name functions of membrane proteins

transporters and chanells(ions in nerve cells)

communication between outside and intracellular(hormones)

localisation of proteins at cell surface(antibodies)

localisation of proteins at membrane in cytosol(enzymes)

describe possible structures of transmembrane proteins

1. a herix(es),cosisting of approx. 20 amino acids going through the membrane

2. barel bormed b sheets

describe polarity of b sheet transmembrane protein

hydrophobic outside,polar on the inside

peripheral membran erotein structure

they are attached by lipid anchor to celk membrane

which side of cell membrane is more negatively charged and which one is neutural

cytosol side is more negatively charged while side which faces extracullular space is more neutural or positive charge.extracell side also has sugars

what are roles of sugars attached to cell membrane on extracellular side?

cell protection

cel-cell recognition

the difference in charge between cytosolic side and extraselular side is necessary for

orientation of proteins

cytoplasm consits of

cytosol and organelles

what are sorting signals

sequence of amino acids that determine fate of amino acids(where will they go)

sorting signal sequence can lead protein to

er

mitochondria/chloroplasts

nucleus

er

lysosome

transport of RNA and proteins inside and outside nucleus happens via

Nuclear Membrane Complex

how are proteins guided to their destinations?

proteins are guided by sorting signals,which are recognised by complementary sorting receptors

where sorting signal can be found and what happens with them after they fulfilled their function

often found in N-terminus of polypeptide chain.often signal peptidiases remove the signal sequence oncwe the sorting is complete

also nuclear localization signals are not removed,so nuclear proteins can be imported repeatedly as is required each time that the nucleus rassembles after mitosis

how NPC is regulated?

1.receptor binds to cargo

2.receptir/cargo is imported

3.in nucleus Ran-GTP binds to receptor including dissociation of cargo

4.receptorRan/GTP is exported

5.GTP-hydrolysis including dissociation receptor Ran/GDP complex in cytosol

describe a signal sequence for protein which goes into mitochondria/chloroplast

N-terminus

Alphahelix:one side(front) is charged,other side(back) is hydrophobic

describe protejn transport into mitochondrion

1.signal sequence binds to receptor

2.insertion on TOM translocatour

3.transport through outer membrane

4.insertion in TIM23 translocator

5.transport through inner membrane

6.cleavege signal sequence

7.folding protein in matrix

what are requirments for protein transport into matrix?

membrane potential over the inner membrane

ATP in cytosol and in matrix

which kind of ER carries which function?

rough=protein synthesis

smooth=lipid synthesis

describe signal sequence for protein transport from cytosol to ER

N-terminus

hydrophobic,followed by charged amino acids

what is special about transport of protein into rough ER?

in most cases protein import is co-translational(while the protein is synthesized at the rough ER)

which proteins will stay in cytosol?

those without signal sequence

what is different between insertion of proteins in ER with,without and multipass signal sequence?

the one without pass go through membrane only once and is oriented by polarity of a membrane

with signal sequence it passes twice

with multipass it passes many times like it was sewed(вшито)

which N or C teminus are synthesed first

N-terminus is sinthesied first,C-terminal last.So if multiple signal sequences for different organells are present in protein, then N terminus has the highest priority

describe Golgi organelle

it is a structure of stacked membrane sheets(cisternae) and vesicles.Golgi is a sorting aparatus

distinguist germ cell and somatic cell

germ cells=cells which produce gametes for sexual reproduction during meiosis

somatic cells=not gamete cell

define coat proteins

proteins on vesicle surface when vesicle are formed.there are different proteins for different goals.an example is clathrin coat

describe structure of clathrin coat

clathrin triskeleton=clathtrin heavy and light chains(похож на свастон с тремя косами)

what clathrin vesicle looks like?

clathrine vesicle of pentagons and hexagones looks like a soccer ball

name steps of assembly and dissassembly of clathrin coat during vesicle transport

1.coat assembly and cargo formation

2.bud formation

3.vesicle formation

4.uncoating

how neck of the bud is removed,so vensickle cn pinch off?

GTPase hydrolises it

describe control docking and start fusion by Rab-GTP hydrolysis(vesicle trasport)

1.Rab affector binds to Rab-GTP

2.v-SNARE protein on vesicle

3.when docking is ok,GTP is hydrolized to GDP

4.Rab-GDP dissociates

5.Only when Rab has dissociated,fusion aca begin(better see picture)

describe process of fusion(vesicle transport)

1.removal of water

2.membrane fusion,remove stalk

3.hemifusion:inner lipid layers form a bilayer

4.fusion of inner lipid layers

name general principles of vesicle transport

All endo-membranes originate from plasma membrane

Coat proteins decorate vesicles

Different coat proteins for different routes

Vesicle are budded off(bitten off) with dyamin

Vesicles fuse to target membrane with snares

Different Rab-GTPases ccontrol specificity of fusion

Which site of membrane is negatively charged?

The cytosolic side of a membrane is negatively charged

Describe function of COPII coat protein

transport of vesicles from ER to Golgi

Describe function of COPI coat protein

COPI transport back from Golgi to ER

Describe function of Clathrin coat protein

transport from Golgi to plasma membrane

where would mos proteins in ER go?

to Golgi

where will misfoled or unfolded proteins go frome ER?

they will stay in the ER

How do ER-proteins stay in the ER?

They do not, but are transported back from the Golgi

How do ER-proteins are transported back from Golgi&

ER-resident proteins have signal sequence: KDEL

They bind to KDEL receptor in Golgi

KDEL receptor binds to COPI coat protein in Golgi

Vesicles with COPI protein are transported back to ER.(also see the picture)

where are proteins with KDEL trasported?

Proteins with KDEL are transported back from Golgi to ER

what determines wherever a protein will go from Golgi to lysosome, PM or will be secreted?

Where the protein goes depends on the addition of sugars

where does vesicle with protein go by deafault(no further info present)?

From Golgi, default is secretion

How is environment of lysosome is different from the rest of the cell?

acidic (pH is approx=5),has multiple enzymes for protein degradation

describe endosome

It is a compartment of the endocytic membrane transport pathway originating from the trans Golgi membrane. Molecules or ligands internalized from the plasma membrane can follow this pathway all the way to lysosomes for degradation

what are pathways to lysosome via late endosome?

1. e.g. a protease from Golgi to lysosome

2. Uptake from extracellular, endocytosis, phagocytosis

give example whcih things are taken inside a cell via endocytosis

low-density-lipoprotein

phagocytosis bacteria( white blood cell

chasing and eating a bacterium)

Central Dogma of Molecular Biology

DNA -> RNA -> Protein

Define genome

the totality of genetic information belonging to a cell or organism; in particular, the DNA that carries this information.

name and distinguish two different sugars used for information transfer

deoxyribose=DNA:2′H and 3′OH,Ribose=RNA:2′OH and 3′OH

How is ribose different(structurally) from deoxyribose?

open question

define bases(DNA/RNA)

the bases arre nitrogen-containing ring compounds,either pyrimidines or purines

Name the pyrimidines

cytosine, thymine, uracil

Name the purines

guanine and adenine

how can purines and pyrimidines can be distinguished from one glance

pyrimidines are smaller,consisting only of one ring,thus"big name for small compounds"

DNA and RNA have different bases name them

RNA: A, C, G and U;DNA: A, C, G and T

define nucleoside

base + sugar

Define nucleotide

5 carbon sugar, phosphate group, nitrogenous base

what phosphodiester linkage is used for

to join 5′ -3′ to form nucleic acids

which side DNA double helix is turned&

DNA is right-handed(upward)turning helix(unless a special case)

how to distinguish minor and majour groove?

imagine DNA as a multiple places bent socige (minor grove will be small distance between start and the end of the full turn)

Name complementary base pairs and number of hydrogen bonds between them

A-T or T-A=2H bonds;

C-G or G-C=3Hbonds

What forms a double helix?

Two anti-parallel DNA strands

how are base pairs orientated inside double helix

they have planar orientation

Define gene

region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic

where are translocations between chromosomes often observed?

in cancer cells

which organism has higher gene density:yeast or human?

yeast has higher gene density in its genome

do closely related species have same number of chromosomes?

no,there is variability in organization of genomes even among close related species

How many genes typical human chromosome has?

400 genes

What is chromatin?

DNA molecules that are tightly coiled around proteins call histones.

from what and in which propotions consists chromatin?

one third DNA

one third histones

one third other proteins

in how many times DNA packaged in a mitotic chromosome is shorter that its actual length?

in 10000

for what germ-cell stability is important?

for species perpetuation