Bio 210 Exam 1

Study guide questions and some vocab

What is definition of a cell?

basic structural unit of living organisms that can perform the functions characteristic of life

Who were some of the early figures in cell biology?

Hooke - named cells (dead), Van Leeuwenhook -saw living cells (not animal cells), homunculus, Schleiden and Schwann - animal tissues have cells

What is cell theory?

Schwann - all organisms consist of one or more cells, the cell is the basic unit of structure for all organisms; Virchow added - all cells arise from pre-existing cells

Describe how modern cell biology arose from three different fields. 

Cytology - structure of cells; biochemistry - chemical pathways of cells, genetics - information in DNA

Is light a particle or a wave? 

both, photon - particle

What is the relationship between energy and wavelength of light? 

shorter wavelength = higher energy; longer = lower

What are the wavelengths of visible light? 

400-665 nm

What are diffraction and interference?

diffraction - light waves go through slit and disperse; interference is when light waves come together to make a bigger one or cancel out

Describe a lens, including numerical aperture. 

angle of usable light, lens gathers this and bends it to focal point, AN = resolution x refractive index (speed of the light)

Describe the following types of microscopy:  brightfield, phase contrast, DIC, fluorescent, confocal, TEM, SEM.

bright field - regular light microscopy, phase contrast - changes in phase converted into changes in brightness, DIC - change in interference pattern converted to changes in brightness, fluorescent - tag parts of cell with fluorescent molecules and exciting them and reading emitted wavelengths as it returns to ground state, confocal - same as fluorescent but with precise optical sectioning for looks at different slices, TEM - electrons shot through specimen to make image (smaller wavelength = higher resolution), SEM - electrons shot onto surface and bounce off

What tools are used to aid in microscopy?    

microtomes- slicer; freeze fracture - splits open plasma membrane to see inside

What elements are common in organisms?

HCON

What is the difference between a covalent bond and ionic bond?

covalent - electrons shared equally, ionic - full charges, electrons taken

Why are bond energies important? 

energy required to make 1 mole of bond, C-C are high bond energy

Be able to draw the common side groups of carbon-containing molecules (such as carboxyl)

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Describe the biologically important properties of water.

cohesion - H bond with itself, surface tension; adhesion - H bond with other things; polar - partial charges; universal solvent

Why and how are cell membranes permeable? 

permeable to small non-polar molecules; some proteins act as gates/channels

What is an amphipathic molecule?

has both non-polar and polar ends

What is a condensation reaction (dehydration synthesis)? 

when molecules are slammed together and a water pops out

What is hydrolysis?

when water is slammed into a bond to break molecules apart

Describe self-assembly. 

proteins fold on their own by non-covalent interactions (partial or full charges, H bonds); some proteins need chaperones

What are the four basepairs of DNA? 

A-T, C-G

How is the double helix held together?

nucleotides held by covalent phosphodiester bonds, helices stabilized by H bonds

What is the central dogma of molecular biology?

DNA → RNA → Proteins

What is a gene? 

piece of DNA transcribed into a RNA

What are the various types of RNA?

mRNA - carries DNA info out of nucleus; rRNA - ribosomal RNA; tRNA - transfer RNA; miRNA - micro RNA

How are enhancers and promoters used in the genome? 

enhancers - attract transcription protein factors; promoters - TATA box, gets RNA polymerase to bind to DNA there

Describe post-transcriptional modifications.

5’ cap, 3’ poly A tail, splice out introns keep exons

What is a codon? 

3 letter code (3 nucleotides) coding for 1 amino acid

Describe the steps of translation.

Initiation 1 - tRNA binds small subunit along with start codon; large subunit binds over tRNA complex

Elongation1 - tRNA brings in all following amino acids, making peptide bonds, empty tRNA ejected

Termination 1 - stop codon, 3/64 are stop codons, everything falls off and apart, peptide chain released

How is gene (protein) activity controlled?

transcription, post-transcription, translation, post-translation

Be able to draw an amino acid and a dipeptide. 

Be able to tell if an amino acid is hydrophilic or hydrophobic from its R group

polar - have NH2 or OH, basic have +, acidic have -; nonpolar = have CH3

What is a protein?

full folded functioning peptide

Define multimer proteins.

protein with multiple polypeptide chains

Describe the primary, secondary, tertiary, and quaternary structure of proteins.

primary - string of amino acids, secondary - alpha helices and beta sheets, tertiary - one subunits 3D conformation, quaternary - multimeric, multiple subunits conformation

Why are small molecules found in proteins? 

add function to protein, like heme in hemoglobin

What is a catalyst and how do enzymes work?

catalysts speed up rxns, decrease activation energy, changes rate not eq.

Describe the active site, allosteric sites, and feedback inhibition. 

active site - cluster where catalytic event occurs, allosteric site - away from the active site, feedback inhibition - enough product is made so a product binds to an allosteric site earlier in the pathway to shut it off

What are the two common covalent modifications to control protein activity?

phosphorylation - kinase, dephosphorylation - phosphatase

How does size limit a cell?

surface area to volume ratio, need adequate diffusion

What are the three domains of life?

eukaryota, bacteria, archaea

Describe the structure of Archaea and Bacteria.

don’t have organelles

archaea - use L-glycerol in membrane, isoprene in phospholipid bilayer, hydrocarbon chains can connect across, ribosomes like eukaryotes; halophiles - salty; thermophiles - hot

bacteria - peptidoglycan in cell walls, DNA circular, DNA has few proteins associated, distinct ribosomes

Describe the properties of Eukarya

larger, membrane bound organelles to organize function, linear DNA, nucleus with chromosomes, exocytosis and endocytosis, mitosis/meiosis, complex RNA processing

What is Endosymbiotic Theory?

mitochondria came from aerobic bacteria engulfed by other prokaryote and made it a eukaryote; chloroplasts came from cyanobacteria in the same way

What does each of the organelles do? 

plasma membrane - boundary, structure

vacuole - storage

ribosomes - make proteins

rough ER - site for ribosomes

smooth ER - makes lipids

nucleus - chromatin, DNA, double membraned

mitochondria - ATP

chloroplasts - triple bilayered, photosynthesis

golgi - protein sorting and modification

lysosomes - trash can

peroxisomes- carry things mitochondria to chloroplast

vesicles - secretory in and out of cell and through organelles

cytoskeleton - structural, microtubules - motility/chromosome movement, microfilaments - muscle movement, amoeboid movement, cleavage furrows

extracellular matrix - collagen and proteoglycan in animals; cellulose in plants

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Are viruses and prions alive? 

no, no metabolism, needs hosts to live

What does a membrane do? 

define limits of cell, creates internal organelles, pt. of contact between cell and environment

What are the major categories of lipids?

phospholipids and glycolipids, can have glycerol or sphingosine backbones

Describe the Fluid Mosaic Model. 

membrane is big network of phospholipid bilayer with embedded proteins, everyhting is vibrating/rotating in the plane of the membrane

What affects membrane fluidity? 

anchored proteins, unsaturated tails move easier, less packing more fluid, cholesterol binds to phospholipids at high temp = less fluid / cholesterol prevents packing at low temps = more fluid

What do proteins do in the membrane? 

let things in and out, anchor things, integral proteins - pass through membranes all the way, peripheral proteins - associated by binding on either face of bilayer, lipid anchored proteins - inserted into membrane, receptors, transport, enzymes

Microscopy that turns variations in refractive index (phase) into variations in contrast

phase contrast

Focuses light on the specimen

condenser lens

Microscopy that uses optical sectioning and a narrow depth of focus

confocal

The ability to distinguish two objects as separate entities

resolution

Studies the chemicals found within cells

biochemistry

Studies the information found in DNA

genetics

Product of textile industry that allowed visualization of cells

dye

The basic structural unit of living organisms that can perform the functions characteristic of life

cell

Wavelength shone onto fluorescent specimen

excitation

Wrote basic cell theory

Schwann

The angle of usable light that a lens can gather

angular aperture

Expanded cell theory to include that all cells arise from pre-existing cells

Virchow

Lens that gathers light from the specimen

obective

Wavelength gathered from fluorescent specimen

emission

Tool used to slice sections of a specimen for microscopy

microtome

 Distance from center of a lens to the focal point

focal length

Named cells; saw dead ones

Hooke

A particle of light

photon

The study of cells

cytology

Microscopy that uses polarized light and coverts difference in refractive index (phase) into differences in brightness

DIC differential interference contrast

Microscopy that uses regular light on a specimen

bright field

Microscopy that uses molecules that are excited and emit a particular wavelength

fluorescence

idea that sperm contain preformed humans

homunculus

A method to visualize the inner surfaces of the plasma membrane

freeze fracture

Measure of the slowing down of light in anything other than a vacuum

refractive index

The phenomenon of waves bending after passing through a slit

diffraction

            First to see living cells

Van Leeuwenhoek

Electron microscopy of the surface of a specimen

Scanning EM

The phenomenon that waves combine to reinforce or cancel each other out

interference

Commonly used fluorescent protein from a jellyfish

GFP

Lens that focuses light on the eye

ocular

            Electron microscopy through a thinly sliced specimen

Transmission EM

The beginning of the polypeptide strand

N-terminus

DNA sequences that attracts transcription factors

Enhancer

Small RNA used to degrade mRNA

miRNA

Polymer of amino acids

protein

The process of transferring information from DNA to RNA

transcription

To refold a protein into its normal "native" state

renature

"water loving", polar molecules

hydrophilic

Occurs when a molecule breaks into two, consuming a water molecule in the process

hydrolysis

Polymer of sugars

polysaccharide

Property of water to hydrogen bond with other molecules

adhesion

The start codon

AUG

RNA used to bring amino acids to the ribosome

tRNA

Added to the 3' end of mRNA

poly A tail

Added to the 5' end of mRNA

cap

Energy required to break 1 mole of a bond (kcal/mole)

bond energy

Strand of DNA that is copied into RNA

gene