Molecular and Cellular Biology Exam 1

bright field microscope

requires staining to improve contrast

phase contrast microscope

enhances contrast of transparent specimens without staining

DIC microscope

produces 3D like images of unstained live specimens

fluorescence microscope

utilizes fluorescent dyes or proteins for visualization of specific molecules or structures in cells

confocal microscope

uses lasers and small apertures to eliminate out of focus light for sharper 3D reconstructions, higher resolution

electron miscroscope

uses electron beams

transmission electron microscope

electrons pass through ultrathin sections of specimen, reveals fine internal structures

scanning electron microscope

electrons scan specimen surface, produces detailed 3D images of surfaces

cryogenic sample electron microscopy

freeze biological samples rapidly in a layer of vitreous ice, electrons hit biological samples frozen in a layer of vitreous ice, produces 3D structures of molecules such as proteins and nucleic acids

atomic force microscopy

scans specimen surface with a physical probe, provides nanometer scale topographic maps

super-resolution microscopy

overcomes the diffraction limit of light, visualization of structures at high resolution

what is composed of 30% chemicals and 70% water?

bacterial cells

carbohydrate

biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1

monosaccharide (carbohydrate)

simple sugar

disaccharide (carboyhydrate)

two monosaccharides that are covalently bonded

polysaccharide (carbohydrate)

complex sugar or starch, large molecule composed of monosaccharides that are covalently bonded

monosaccharide properties

usually 3-7 carbon atoms

aldose

has aldehyde functional group, R-CHO

ketose

has ketone functional group RC(=O)R’)

triose

3 carbons

pentose

5 carbons

hexose

6 carbons

structural isomers

same chemical formula, different arrangement of atoms

disaccharides form when:

two monosaccharides undergo a dehydration reaction

glycosidic bond

covalent bond between two monosaccharides

sucrose

glucose + fructose

lactose

glucose + galactose

maltose

glucose + glucose

polysaccharides in bacteria

cellulose

polysaccharides in plants

starch and cellulose

polysaccharides in fungi

chitin

polysaccharides in animals

glycogen and chitin

polysaccharides consist of:

a long chain of monosaccharides linked by glycosidic bonds, can be soluble or insoluble in water

amylose

linear chain that is insoluble

amylopectin

branched chain that is insoluble

cellulose

structural component of a plant’s cell wall, a linear polysaccharide composed of glucose units linked by beta 1-4 glycosidic bonds

glycogen

the stored form of glucose in humans and other vertebrates, highly branched, stored in liver and muscle cells, broken down into glucose when blood glucose decreases by a process called glycogenolysis

lipids

a diverse group of compounds that are mostly nonpolar, are hydrophobic/insoluble

lipids are composed of:

hydrocarbons with mostly nonpolar C-C or C-H bonds

why are lipids important for life?

they store energy for long term use, provide insulation from the environment, are the building blocks of many hormones, and are components of cell membranes

lipids produced by cells

fats and oils, waxes, phospholipids, and steroids

fats (triglycerides)

composed of glycerol and three fatty acid chains

saturated fats

no available position for hydrogen to bind, usually solid at RT

unsaturated fats

double bonds allow for hydrogen to bind, usually liquid at RT (oils)

unsaturated

has double bond, can be cis or trans

ester bond formation

releases 3H2O

saturated

all single bonds

waxes

serve as water proofing for organisms, formed from fatty acid chains and long chain alcohols via esterification

esterification

formation of ester bonds

amphipathic molecules

are phospholipids, has hydrophobic and hydrophilic regions (polar phosphate head - hydrophilic) + (non-polar fatty acid tails - hydrophobic)

steroids

organic molecule with 4 fused hydrocarbon ring structures (3 six-ring and one 5-ring), some with hydroxyl group, hydrophobic

functions of steroids

hormones (testosterone and estrogen), stress response (cortisol), and structure, signaling and disease (cholesterol)

5’ terminal

phosphate group at end

3’ terminal

hydroxyl group at end

nucleic acid

chains of nucleotides, building blocks of genetic information

pyrimidines

one carbon-nitrogen ring

purines

two carbon-nitrogen rings

what is the most common form of DNA in cells?

B form

proteins

macromolecules composed of one or more peptides (composed of amino acid subunits)

parts of an amino acid:

animo group, carboxyl group, central carbon bonded to H atom, R group

peptide bond

a type of covalent bond that links two amino acids

primary protein structure

sequence of a chain of amino acids

secondary protein structure

local folding of the polypeptide chain in helices or sheets

tertiary protein structure

three-dimensional folding pattern of protein due to side chain interactions

quarternary protein structure

protein consisting of more than one amino acid chain

polypeptide secondary structure

folding of regions into specific structural patterns within a polypeptide chain

polypeptide tertiary structure

three-dimensional arrangement of the entire polypeptide chain of a protein, including all its secondary structures in 3D space

polypeptide backbone model

simple way to depict protein structure

ribbon model

easier to identify secondary structures (alpha helices, beta sheets)

wire model

shows amino acid side chains

space filling model

easier to assess the size, shape of protein, and steric effects

steric effects

non-bonding interactions that influence the shape of a molecule

denaturation

process where a protein loses its quaternary, tertiary, and secondary structure without losing its primary sequence, can be reversible or irreversible

causes of denaturation

external stress, exposure to certain compounds, heat, cell death

similarities between prokaryotes and eukaryotes

cell membrane (plasma membrane), cytoplasm, ribosomes, DNA

cytoplasm

cytosol + any other components except the DNA, contains ions and other macromolecules

cytosol

liquid component of a cell

cell wall (prokaryotes)

found in most prokaryotes, composed of peptidoglycan, wraps around the cell membrane, extra layer of protection, helps maintain cell shape and prevents dehydration

capsule (prokaryotes)

composed of polysaccharides, enables cell to attach to surfaces

flagella (prokaryotes)

whiplike structure, used for locomotion (can also be found in eukaryotic cells)

pili (prokaryotes)

tube like structures, for exchanging genetic material during conjugation

fimbriae (prokaryotes)

thread-like structures used to attach to a host or a surface

mitochondria

site of Krebs cycle and electron transport chain

rough endoplasmic reticulum

site of protein synthesis, modification, folding, and sorting proteins

smooth endoplasmic reticulum

site of lipid synthesis

golgi apparatus

sorts, tags, packages and distributes proteins and lipids

vesicle

a structure within or outside a cell, consisting of liquid or cytoplasm enclosed by a lipid bilayer - may contain proteins, lipids, ions, and other organic molecules

cell theory

cells arise from preexisting cells

endosymbiotic theory

mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host

catalyst

a substance that increases the rate of a reaction without being consumed

enzyme

a catalyst that speeds up the rate of a biochemical reaction - most are proteins

activation energy

minimum amount of energy that must be provided for compounds to result in a chemical reaction

Gibbs free energy

energy available to do useful work in a system at constant temperature and pressure

induced fit model

model that describes how enzymes function - when a substrate binds to the active site of an enzyme, the enzyme slightly changes its shape to better accommodate the substrate - creates a more precise fit - facilitates the chemical reaction

conformational change

a change in the shape of a molecule such as a protein

mechanisms for enzyme regulation

molecular regulation (inhibitors, activators, coenzymes and cofactors), compartmentalization, feedback inhibition

enzyme inhibitors

molecules or substances that reduce the activity of an enzyme - leads to reduction in amount of products - substrates may accumulate

competitive inhibition

a molecule or substance competes with the substrate for binding to an active site —> decreased enzyme activity - usually resembles the structure or shape of a substrate

non-competitive inhibition

an inhibitor binds to the enzyme in a location other than the active site (allosteric site) —> decreased enzyme activity

allosteric site

a location in an enzyme other than the active site that allows for regulation of enzyme activity