pcb4143 exam 1

protein structure

carboxyl group, alpha carbon, amino group, hydrogen, and R group

L- amino acid

D-amino acid

what affects how hydrophobic an amino acid is

larger R group

what functional groups do acidic amino acids have

carboxylic group

what functional group do basic amino acids have

amino group

dehydration/condensation

amino acids linked together into linear polymers

what kind of bond does dehydration form

peptide bond (C-N covalent)

which bonds are covalent

peptide and disulfide

which bonds are non-covalent

hydrogen, ionic, vanderwaals

what bonds are in primary structure

peptide bonds

what bonds are in secondary structure

hydrogen bonds between NH and CO groups of peptide bonds

what bonds are in tertiary structure

disulfide, hydrogen, ionic, vanderwaals in R groups

what bonds are in quaternary structure

disulfide, hydrogen, ionic, vanderwaals

what direction are amino acid sequences written

N-terminus to C-terminus

where is the H bond of an alpha helix

CO group of one amino acid and NH group of 2nd amino acid

Cell theory

1. all living organism are made of one or more cells

2. the cell is the basic unit of all organisms

3. all cells come from pre-existing cells

4. cells contain genetic information

Nucleic acid monomer

nucleotide

nucleotide structure

phosphate, pentose sugar, nitrogenous base

nucleic acid bonds

3’-5’ phosphodiester bond

where do phosphodiester bonds occur

sugar-phosphate backbone

carbohydrate bond

glycosidic

carbohydrate function

energy, structure, cell recognition, linkage orientation

antiparallel

polypeptides have opposite polarity (relative to n and C termini) in parts forming beta sheet

fibrous proteins

highly ordered, repetitive, structural

globular proteins

folded in compact structures

prion proteins

diseased proteins, turn from multimeric from monomeric

linear polymers of nucleotides

deoxyribose nucleic acid

ribonucleic acid

nucleoside

nitrogenous base, no phosphate group

structural difference in RNA and DNA

RNA- OH group on carbon 2,

DNA- H on carbon 2

polysaccharides

long chain polymer of sugar and sugar derivatives

storage polysaccharides

starch and glycogen

structural polysaccharides

cellulose

sugar

aldehyde or ketone with two or more hydroxyl groups

alpha d glucose

unit of starch and glycogen

alpha D glucose structure

OH group points downward on C1

Beta D glucose

unit of cellulose

beta d glucose unit

OH group pointed up on C1

what reaction forms disaccharides

condensation reaction

fatty acids

long, unbranches hydrocarbon chain with carboxyl group head

triacylglycerol

storage lipids

triacylglycerol structure

glycerol molecule and 3 fatty acids

glycerol

3 carbon alcohol w hydroxyl

phospholipids

membrane structure & lipid bilayer

phosphoglycerides

2 fatty acids + glycerol + phosphatic acid

sphingolipids

2 fatty acids + sphingosine + phosphatic acid

glycolipids

specialized membrane components

outer monolayer of plasma membrane

steroids

type of lipid derived from 4-ringed hydrocarbon skeletons

steroid properties

mostly nonpolar, hydrophobic, cholesterol monomer

steroid function

signaling

ribozymes

catalytic RNAs

competitive inhibitor

competes with substrate binding at active site, depends on substrate concentration

noncompetitive inhibitor

changes enzyme activity/conformation and reduces functional enzyme capacity

competitive inhibitor kinetic result

Km increase, Vmax unchanged

noncompetitive inhibitor kinetic result

Vmax decrease, Km unchanged

Vmax

rate of reaction with enzyme activated

Km

amount of substrate needed to reach half of vmax

substrate-level regulation

depends on interactions of substrates and products with an enzyme to change reaction rate

correlation between substrate levels and reaction rate

positive correlation

correlation between product concentration and reaction rate

inverse correlation

feedback inhibition

end product inhibits earlier enzyme

allosteric inhibition

regulator enzyme binds at location separate from active site

shifts enzyme toward more/less active conformation

reversible covalent modification

addition/removal of group (phosphorylation, methylation, acetylation)

irreversible covalent modification

proteolytic cleavage to activate zymogens

prokaryotic cell

bacteria, archea (unicellular)

eukaryotic cell

consist of plasma membrane, nucleus, membrane bound organelles, cytosol interlaced by cytoskeleton

cytoplasmic streaming

active movement of cytoplasmic components

vesicles

transported along microtubules to move molecules

what organelles have double membranes

nucleus, chloroplast, mitrochondria

similarities between mitochondria, chloroplasts, and bacteria

circular dna, synthesize RNA and proteins, similar RNA sequences, ribosome size, inhibitor sensitivities, mitochondria and chloroplast double membranes

endosymbiont theory

explains how complex eukaryotic cells evolved from simpler prokaryotic microbes by engulfing them

endomembrane system

endoplasmic reticulum, golgi, lysosome, peroxisome

smooth ER

lipid synthesis and detoxification

rough ER

protein synthesis thru ribosomes

golgi body

process & pack secretory proteins for glycosylation

lysosomes

stores hydrolases for digestion of biological molecules

peroxisome

oxidizes long chain fatty acids

vacuoles

temporary storage in animals, water storage in plants to maintain turgor pressure

ribosomes

synthesize proteins in cytoplasm

cytoskeleton

provide structure to cytoplasm thru interconnected proteinaceous structures

extracellular matrix

gives physical support to cell

what makes up the extracellular matrix in animal cells

collagen fibrils and proteoglycans

what makes up the extracellular matrix in plant cells

cellulose microfibrils

virus cells

DNA or RNA surrounded by protein coat

fluid mosaic model

2 fluid layers of lipids with proteins within and on the layers

microdomains/lipid rafts

localized regions of membrane lipids involved in cell signaling

bind to and concentrate proteins at certain position on the membrane to lower fluidity

what is the fluid part of the fluid mosaic model

membrane lipids

what lipids make up a membrane

phospholipids, glycolipids, sterols

how does cholesterol affect the membrane

buffers fluidity based on temperature and lowers permeability

Tm

temperature at which a membrane shifts between gel and fluid states

membrane asymmetry

lipids are distributed unequally between two monolayers

transverse diffusion

hydrophilic head group passes thru hydrophobic interior of membrane to flip-flop

what are the factors that affect membrane fluidity

temperature

fatty acid structure

amount of sterols

how does temperature affect membrane fluidity

positively correlated

how does fatty acid structure affect membrane fluidity

more saturation = less fluidity

pack together more tightly

how does length of hydrocarbon tail affect membrane fluidity

inversely correlated

how do sterols affect membrane fluidity

positively correlated, prevents phospholipids from packing too closely

how do cholesterols affect membrane fluidity at temperatures above Tm

decrease fluidity

how do cholesterols affect membrane fluidity at temperatures below Tm

increase fluidity

where are cholesterols and glycosphingolipids most concentrated

outer monolayer