Proteins - Exam 1 Flashcards by Emillie Dodd

building blocks of proteins

amino acids

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amino acids linked by

peptide bonds, generate H2O

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what is the amino terminus

beginning of all proteins; methyeline

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what is the carboxyl terminus

end of all proteins

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how are dietary proteins digested (2 steps)

first by proteolytic enzymes of the GI tract, then by cleavage by pancreatic proteases in the small intestine

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3 things that make up an amino acid

amino group, an acid (carboxyl group), & side chain

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amino acids with nonpolar side chains (9)

alanine, glycine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tyrptophan

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bends in polypeptide chains due to

proline

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characteristics of amino acids with nonpolar side chains

don’t gain or lose electrons, cluster together, hydrophobic effect,

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proline characteristics

nonpolar, secondary amino group (imino acid) makes it rigid

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amino acids with uncharged polar side chains (6)

asparagine, glutamine, serine, threonine, tyrosine, cysteine

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disulfide bonds due to

cysteine

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characteristic of amino acids with uncharged polar side chains

0 net charge

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which 2 uncharged polar side chains can lose a proton at alkaline pH

cysteine & tyrosine

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which 3 uncharged polar side chains can contain a polar hydroxyl group that participates in hydrogen bond formation

serine, threonine, & tyrosine

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amino acids with acidic (-) side chains (2)

aspartic acid & glutamic acid

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characteristic of amino acids with acidic side chains

proton donors, physiological pH fully ionized COO-

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what is physiological pH

7.4

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amino acids with basic (+) side chains (3)

arginine, histidine, lysine

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characteristic of amino acids with basic side chains

accept protons, physiological pH fully ionized & positively charged

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which amino acid with a basic side chain acts as a buffer & why

histidine; can be either positively charged or neutral depending on environment’s pH

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what 2 alpha amino acids are not found within proteins & where are they found

triiodothyronine & thyroxine ; thyroid

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hydroxylation of tryptophan yields ______ ; function

serotonin ; NT & paracrine hormone

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acetylation and methylation of serotonin yields ______ ; function

melatonin ; reproductive activity

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hydroxylation of tyrosine yields (pathway)

dopa -> dopamine -> adrenaline/norepinephrine -> alpha adrenoreceptor & beta adrenoreceptor

decarboxylation of histidine yields ______ ; function

histamine ; allergic rxns

peptide hormone produced in the hypothalamus for uterine contractions & milk secretion

oxytocin

peptide hormone produced in the hypothalamus for maintenance of water balance

ADH (antidiuretic hormone)

peptide hormone used for energy production in the muscles & cardiac cells

creatine

peptide hormone that is a vasoactive substance

bradykinin

peptide hormone that is a vasoconstrictor

angiotensin II

polypeptide hormone used for secretion of gastric glands in the stomach

gastrin

polypeptide hormone used to stimulate pancreas & liver secretion

CCK

polypeptide hormone produced by alpha cells in the pancreas

glucagon

polypeptide hormone produced in the heart for regulation of blood volume & pressure

ANP (atrial natriuretic peptide)

mutation where the base change codes for the SAME amino acid

silent

mutation where the base change codes for a DIFFERENT amino acid

missense

mutation where the base change codes for a STOP codon

nonsense

mutation where a base is added or deleted

frame-shift

mutation where base change generates a splice site

splice site

genetic code has how many combination possibilities and codes for how many amino acids

64 ; 20

what are the 3 stop codons & 1 start codon

UAG, UGA, UAA ; AUG

the first codon in the eukaryotic mRNA codes for

methionine

which cells can make mRNA in both the nucleus and the cytosol

eukaryotic

differences between DNA vs RNA

deoxyribose vs ribose ; thymine vs uracil

what are introns

noncoding sections of DNA

what is alternative splicing and what cell type uses it

removal of intron(s) ; bacteria

benefits of alternative splicing

generate different proteins isoforms, increases viability

what is tRNA and how does it work

transfer RNA "clover leaf"; attachment site for an amino acid at the 3' end and an anticodon on the other end that pairs with a codon on the mRNA

tRNA significance

adapter for alternative splicing & codon recognition

what are the 3 sites on a ribosome

A, P, E

eukaryotic ribosomes have 2 subunits:

60 & 40

which ribosomal site binds an incoming aminoacyl-tRNA

which ribosomal site has peptidyl-tRNA which carries the chain of already synthesized amino acids

which ribosomal site has empty tRNA and is where it exits

RER-ribosomes function

synthesize proteins that need to be exported from the cell or put into cell membranes

cytosolic ribosomes synonym & function

"free" ribosomes ; synthesize cytosolic proteins or those meant for the nucleus , mitochondria, or peroxisomes

what are the 3 steps of protein synthesis

initiation, elongation, termination

describe initiation step

assembly before peptide bonds form

describe elongation step

adding amino acids to the carboxyl end of the chain (5' -> 3'), bind at A site, make peptide at P site, mRNA move

describe termination step

when one of the stop codons reaches the A site

proteins in the cytosol can go where

nucleus, mitochondria, peroxisomes, plastids

proteins in the ER can go where

Golgi, endosomes, lysosomes, secretory vesicles, membrane

N-terminal signal sequence

import into the ER or mitochondria

C-terminal signal sequence

retention in the lumen of the ER

internal signal sequence

import into nucleus or peroxisomes

the ER synthesizes which 3 proteins

lysosomal, secretory, and membrane

what is the SRP and what does it do

signal recognition particle ; binds to the new protein after recognition, binds to the SRP receptor in the ER membrane, gets placed in the translocation protein using energy, SRP released (protein will be in the ER of the lumen)

type I arrangement

c terminus is in the cytosol

type II arrangement

n terminus is in the cytosol

2 examples of membrane proteins

LDL receptor & GLUT 1

what are the 4 structures of proteins

primary, secondary, tertiary, quaternary

what are the 3 folding patterns of proteins in the secondary structure

alpha helix, beta sheet, beta bend/turn (proline kink)

structure of an alpha helix & example

within membrane, every 4 amino acids = 1 hydrogen bond, side chains face outside, "spiral"; keratin

structure of a beta sheet

all amino acids make bonds "pleats", side chains not involved, can either be parallel (c terminus same end) or antiparallel (c terminus different ends)

structure of a beta bend

proline, make a compact shape, connect alpha helix and beta sheets, can link 2 antiparallel B sheets, can link parallel B sheets by crossing over and connecting at either top or bottom

describe vesicular transport

brings proteins to larger organs

vesicular transport pathway

RER -> coated with COPII -> membrane -> microtubules -> cis Golgi (if not coated will go elsewhere)

what does SNARE stand for and why do we need it

soluble NSF attachment protein ; to recognize coated/envelope proteins

example of SNARE and it's function

synaptobrevin ; fusion of synaptic vesicles with the plasma membrane (Botox inhibits this)

clathrin-coated vesicles

within Golgi, protein can be modified and then released into cytosol via coated vesicles (circular)

what is NLS and it's function

nuclear transport signal ; moving protein from rER into nucleus via active transport

how does NLS work

in the middle of polypeptide chain: protein binds with importin receptor -> nuclear pore

Golgi apparatus structure consists of what 3 areas

cis, trans, medial

protein phosphorylation takes place where

cis Golgi

O-glycosylation takes place where

medial and trans Golgi

where are proteins packed into vesicles

trans Golgi net

what are chaperones and how do they work (folding cyclus)

heat stable proteins, hydrolyze ATP to bind to recognize new protein, makes ADP, stays until protein makes right shape, if protein doesn't make right shape it will get discarded in ER

what is N-glycosylation

ER -> attach sugar to Asn

what is O-glycosylation

Golgi -> attach sugar to Ser/Thr

importance of O-glycosylation

functional conformation of protein

synthesis of glycoproteins occurs where and requires what

in ER, out cytosol; dolichol, sugar, Asn