Cell Bio Exam 1 SMU

Cells

membrane-enclosed units filled with a concentrated aqueous solution of chemicals that can grow and divide, makes up living organisms

Cell biology

study of structure, function, behavior of cells

Cell theory

basic unit of life, cells come from cells, living things built from cells

Cell form and function

cilia to move, green because photosynthetic, large neuronal cells, budding yeast for rapid multiplication

cells vary in their shape, size and chemical requirements

Central dogma of cells

DNA is genetic material, DNA synthesis or replication makes RNA, RNA synthesis or transcription makes proteins via protein synthesis from RNA or translations, differences arise in how genes that make proteins are expressed

Genome

set of chromosomes, what makes organisms different

Transcriptome

the sum of all the mRNA molecules expresses from the genes of an organism, cells from the same organism will vary depending on their transcriptome

3 components of a microscope

magnification, resolution, contrast

Leeuwenhoek

how did the first microscope work

Light microscope

200 nm minimum resolvable, 1000x magnification; light focused on specimen by lenses in the condenser, specimen must allow light to pass through it, objective and eyepiece lenses focus image in eye

Electron microscope

0.2 nm minimum resolvable

Magnification

ability to make something appear larger

Resolution

distance between 2 separate objects that can be seen as 2 separate objects, lower number, more things you can see, blurriness

Contrast

light passes through, Brightfield, Phase-Contrast, and DIC/Normarski, can be created by staining with dyes

Bright-field

light passes through and makes the image a little darker in places where the object is more dense (not as much contrast - no stain)

Phase-contrast microscopy

objects appear light or dark, waves shift as they pass through the cell, waves out of phase are dark

DIC Nomarski

objects appear to have shadows, 3D effect, polarizing filters, at edges you get light vs dark edge, shadow, increase in contrast

TEM

uses beams of electrons instead of light, magnetic coils focus the beam instead of glass lenses, contrast introduced by staining specimen with heavy metals that absorb or scatter electrons, can be used to know what something looks like but not what is inside

Negative stain

creates a silhouette of the object

SEM

produces an image of the 3D structure of the surface of the specimen, 3-20 nm resolution, 20,000X magnification, thin film of heavy metal

Fluorescent dyes

absorb light at one wavelength and emit it at a longer wavelength, molecules get to an excited state, switch orbitals, come back down to ground state and emit light energy

Fluorescence microscopy

first barrier filter passes only wavelengths that excite the particular fluorescent dye, second barrier filter passes only wavelengths emitted when the dye fluoresces

fluorescent dyes

absorb light at one wavelength and emit it at a longer wavelength.

Antibodies

proteins made by mammalian immune system, bind to specific antigens like bacteria and virus

Primary antibody

does not glow

Secondary antibody

recognizes the primary antibody and is coupled to a fluorescent molecule, helps primary antibody target antigen

Immunofluorescence

light coating of heavy metal covers the antigen

Confocal microscopy

pick a particular point of focus, only obtain fluorescence from that point, eliminate background light from other focal planes

Fluorescent proteins

derived from jellyfish or corals and can be used to tag proteins

GFP

protein that can be forced into a cell without killing it, first fluorescent protein

Fusion gene

or chimera, can be transcribed and translated to produce a fusion protein (since proteins cannot cross the membrane of living cells, but DNA can be introduced into living cells)

Transfection

inserting foreign DNA into eukaryotic cell, allows the cell to transcribe, make mRNA, turns into fusion protein

Model organism

convenient to study in lab because

- rapid reproduction,

- easy to manipulate genetically,

- easy to manipulate genetically, easily

- identifiable phenotypes,

- pool of information

E. coli

where most of our knowledge of fundamental mechanisms of life comes from

S. cerevisiae

studies on yeast helped scientists to piece together steps in cell division cycle

Drosophila melanogaster

valuable model for studying human development and disease

C. elegans

(nematode) used to study development, develops like clockwork precision, first multicellular organism to have its genome sequenced

Zebrafish

Danio rerio; used to study vertebrate development because it is transparent for the first 2 weeks

Continuous (immortal) cell line

been transformed - > lose sensitivity to factors associated

- cell lines are neoplastic, often lose their anchorage-dependence

- associated with an altered chromosome pattern

- more easily cultured

Primary cell culture

taken from fresh tissue,

- limited life span in culture

Small organic molecule

energy source or building blocks for larger molecules, 1/10 total mass of organic matter in a cell, mol wt 100-1000 Da

- sugars, FA, AA and nucleotides

Rescue gene

non-mutated gene takes over the function of the mutated gene, would grow at non-permissible temperature, take homologous gene from different organism and use it

Fatty acid

fats and membrane lipids; long chain of carbons ending with ester

Amino Acid

proteins; polar, N group

- amino group, side chain, carboxyl group, a carbon atom, H

Sugar

- energy sources and subunits

- polysaccharides, glycogen and starch (in plants)

carbon ring, ether, 2 OH groups

Nucleotides

phosphate group, carbon ring, nucleoside

Macromolecule

polymer; each polymer grows by one addition of a monomer onto one end of the polymer chain

Polysaccharides

10 or more monosaccharides, long chains

Monosaccharides

sugars

Oligosaccharides

3-10 monosaccharides, short chains

Condensation reaction

produces water, energetically unfavorable, when tow molecules come together

- polypeptide, oligo- and poly-saccaride, nucleic acid synthesis, phosphorylation, glycosylation

Hydrolysis

breaking by addition of water, energetically favorable; when two molecules are broken apart

Biological transformation

addition of something to a molecule

Isomers

different spatial arrangement of atoms, differences are recognized by enzymes and other proteins

a hydroxyl

OH pointed down (opposite of above)

b hydroxyl

OH pointed up (opposite of below)

Disaccharides

two sugar molecules connected through the carbon that carries the aldehyde or the ketone and the hydroxyl group (condensation)

Sugar derivatives

hydroxyl groups of a monosaccharide can be replaced by another group

Glycogen

polysaccharide of glucose, most abundant organic chemical earth (cellulose)

Glycosaminoglycans (GAGs)

built from repeating disaccharide units, highly negatively charged, hydroxyl groups associated, can be highly sulfated

- hyaluronan

Proteogylcan

protein + GAG, found in the extracellular matrix

Glycosylated

bound to sugars

Lectins

proteins that bind to specific oligosaccharide side chains

Complex oligosaccharide

non-repetitive sugar sequence, usually linked to proteins or lipids

Glycoprotein

protein + complex oligosaccharide

Glycolipid

lipid + complex oligosaccharide

Neutrophils

type of white blood cells that slip between endothelial cells in blood vessels and into the infected tissue

Biological roles of carbohydrates

- chemical energy source

- building block

- structural

- protein modulation,

- recognition,

- protective

Nucleotide

(nitrogen containing) base + sugar + phosphate,

- carry chemical energy in phosphoanhydride bonds,

- form coenzymes,

- used small intracellular signaling molecules

Nucleoside

base + sugar

Nitrogen base

pyrimidines, purines, linked to C1 on sugars

Phosphates

joined to C5 hydroxyl of the sugar, makes the nucleotide negatively charged

Phosphodiester bonds

connects nucleotides

Nucleic acids

nucleotides joined together by phosphodiester bonds between 5' and 3' carbons on the rings, via a phosphate group

double stranded DNA

antiparallel; held together by hydrogen bonds between complementary base pairs

- GC = 3 H bonds

- AT = 2 H bonds

Nucleosome

DNA wrapped around a protein core of histones

Three DNA sequence elements are needed to produce a

chromosome that can be replicated and segregated

- telomere

- replication origin

- centromere

mRNA

code for proteins

rRNA

form the core of the ribosome's structure and catalyze protein synthesis

miRNA

regulate gene expression

tRNA

serve as adaptors between mRNA and amino amino acids during protein synthesis

other noncoding RNA

used in RNA splicing, gene regulation, telomere maintenance, etc.

RNAi (interference)

inhibits the activity of specific genes, way to silence genes, mRNA gets transcribed but not translated and later degraded

siRNA

short fragments of RNA, cleaves and processes RNA

Transgenic organisms

genetically modified organisms that are used to explore the effects of single genes

Peptide bond

an amide linkage in proteins that joins together amino acids, no rotation around C-N bond

Protein

long polymers of amino acids linked by peptide bonds, N terminus to the left, often serve as subunits for the assembly of large structures

Peptides

shorter proteins, usually fewer than 50 amino acids long

Enzymes

catalyze covalent bond breakage or formation

Structural proteins

provide mechanical support to cells and tissues

Transport proteins

carry small molecules or ions

Motor proteins

generate movement in cells and tissues

Storage proteins

store amino acids or ions

Signal proteins

carry extracellular signals from cell to cell, bind to receptor

Receptor proteins

detect signals and transmit them to the cell's response machinery

Gene regulatory proteins

bind DNA to switch genes on or off

Special-purpose proteins

highly variable like antifreeze proteins, luminescent proteins, sweet tasting proteins

Noncovalent interactions

help proteins fold, creates strong bonding arrangement that stabilizes the structure

types of noncovalent interaction

Electrostatic attractions

van der Waals attractions

hydrogen bonds

Hydrophobic forces

help proteins fold into compact conformations, polar side chain forms hydrogen bonds to water, hydrophobic core region contains non-polar side chains