1. phenylalanine 2. tryptophan 3. tyrosine

1. arginine 2. histidine 3. lysine

Chapter 3: Protein Structure and Function Flashcards by Ahn Studies

building blocks of proteins in living organisms

amino acids

How well did you know this?

Not at all

Perfectly

how many amino acids can be found in nature

500 amino acids

How well did you know this?

Not at all

Perfectly

number of amino acids the human genetic code directly encodes

20 amino acids

How well did you know this?

Not at all

Perfectly

must be obtained from the diet

essential amino acids

How well did you know this?

Not at all

Perfectly

can be synthesized in the body

non-essential amino acids

How well did you know this?

Not at all

Perfectly

aliphatic amino acids

alanine
glycine
isoleucine
leucine
proline
valine

How well did you know this?

Not at all

Perfectly

aromatic amino acids

phenylalanine
tryptophan
tyrosine

How well did you know this?

Not at all

Perfectly

acidic amino acids

aspartic acid
glutamic acid

How well did you know this?

Not at all

Perfectly

basic amino acids

arginine
histidine
lysine

How well did you know this?

Not at all

Perfectly

hydroxylic amino acids

serine
threonine

How well did you know this?

Not at all

Perfectly

suflur-containing amino acids

cysteine
methionine

How well did you know this?

Not at all

Perfectly

amidic amino acids

asparagine
glutamine

How well did you know this?

Not at all

Perfectly

What are the nine (9) essential amino acids? (PriVaTe ThIM HiLL)

Phenylalanine
Valine
Tryptophan
Threonine
Isoleucine
Methionine
Histidine
Lysine
Leucine

How well did you know this?

Not at all

Perfectly

What are the 11 non-essential amino acids?
(Almost All Girls Go Crazy After Going To A Pretty Shop)

Alanine
Arginine
Glycine
Glutamine
Cysteine
Asparagine
Glutamic Acid
Tyrosine
Aspartic Acid
Proline
Serine

How well did you know this?

Not at all

Perfectly

often referred to as the 21st amino acid

Selenocysteine

How well did you know this?

Not at all

Perfectly

glycine

gly

How well did you know this?

Not at all

Perfectly

alanine

ala

How well did you know this?

Not at all

Perfectly

valine

val

How well did you know this?

Not at all

Perfectly

leucine

leu

How well did you know this?

Not at all

Perfectly

isoleucine

Ile

How well did you know this?

Not at all

Perfectly

methionine

met

How well did you know this?

Not at all

Perfectly

tryptophan

trp

How well did you know this?

Not at all

Perfectly

phenylalanine

phe

How well did you know this?

Not at all

Perfectly

proline

pro

How well did you know this?

Not at all

Perfectly

serine

ser

threonine

thr

cysteine

cys

tyrosine

tyr

asparagine

asn

glutamine

gln

aspartic acid

asp

glutamic acid

glu

lysine

lys

arginine

arg

histidine

his

where is the word protein derived from

Greek, proteios

proteios

first

What are proteins

- large molecules made up of chains of amino acids - found in every cell in the body - involved in most of body's functions and life processes - sequence of amino acids is determined by DNA

Different classes of proteins

1. structural 2. contractile 3. transport 4. storage 5. hormone 6. enzyme 7. protection

provide structural components

structural protein

examples of structural protein

1. collagen 2. keratin

collagen examples

- tendons - cartilage

keratin examples

- hair - skin - wool - nails

make muscles move

contractile protein

examples of contractile protein

1. myosin 2. actin

myosin and actin

contract muscle fibers

carry essential substances throughout the body

transport protein

examples of transport proteins

1. hemoglobin 2. lipoproteins

hemoglobin

transports oxygen

lipoproteins

transports lipids

store nutrients

storage proteins

examples of storage proteins

1. casein 2. ferritin

casein

stores protein in milk

ferritin

stores iron in spleen and liver

regulate body metabolism and the nervous system

hormone

examples of hormone

1. insulin 2. growth hormone

insulin

regulates blood glucose level

growth hormone

regulates body growth

catalyze biochemical reactions in the cells

enzymes

example of enzymes

1. sucrase 2. trypsin

sucrase

catalyzes hydrolysis of sucrose

trypsin function

catalyzes hydrolysis proteins

recognize and destroy foreign substances

protection proteins

example of protection protein

immunoglobulins

stimulate immune responses

structure, characteristic, and classes of amino acids differ in

R groups

amino acids vary in

1. size 2. shape 3. charge 4. polarity 5. solubility in water

attached to four different substituents

α-Carbon

Four substiuents of amino acids

1. hydrogen atom 2. carboxyl group 3. amino group 4. R group

nonionic form: amino group

NH2

nonionic form: carboxyl group

COOH

Zwitterionic form: amino group

NH3+

Zwitterionic form: carboxyl group

COO-

two forms of amino acid

1. nonionic form 2. Zwitterionic form

compounds that form amino acids

- amine - acid

α-amino acids

amine is adjacent to the carboxylate group

19 out of the 20 amino acids are __

stereoisomers

amino acid that is not a stereoisomer

Glycine

compounds that have the same constitution but differ in the spatial arrangement of their atoms

stereoisomers

α-carbon of amino acids is __

chiral

chiral molecules

nonsuperimposable on their mirror images

achiral molecules

superimposable on their mirror images

have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl

L isomers

have the hydroxy group on the right side

D isomers

where do the differences of amino acids depend upon

side-chain R groups

Amino acids form classes based on what?

polarity of side chains

Nonpolar

hydrophobic R groups

Polar neutral

- high affinity for water - not ionic at pH

Polar acidic

- ionized carboxyl groups - negatively charged

Polar basic

- basic as side chain reacts with water to release hydroxide ion - positively charged

What are the polar uncharged amino acids

1. serine 2. threonine 3. asparagine 4. glutamine 5. tyrosine 6. cysteine

R groups of polar uncharged amino acids

- OH - amide group - sulfhydryl/ thiol groups - H-bond with water

where are polar uncharged amino acids found

surface of globular proteins

polar uncharged amino acids are __ in aqueous solutions

soluble

bears hydroxylic R group

- serine - threonine

has amide-bearing side chain

- asparagine - glutamine

- has a phenolic group - together with aromatic groups of F and W, acounts for most of UV absorbance and fluorescence exhibited by proteins

tyrosine

tyrosine account for most of what

- UV absorbance - fluorescence exhibited by proteins

forms a disulfide bond to another residue through oxidation of their thiol groups

cysteine

how does the cysteine form a disulfide bond to another

through oxidation of thiol groups

what is formed between two cysteine residue after oxidaton of their thiol groups

disulfide bond

non-polar/hydrophobic amino acids

aliphatic 1. glycine 2. alanine 3. valine 4. leucine 5. isoleucine 6. methionine 7. proline aromatic 1. phenylalanine 2. tryptophan

aliphatic non-polar/hydrophobic amino acids

1. glycine 2. alanine 3. valine 4. isoleucine 5. leucine 6. proline 7. methionine

aromatic non-polar/hydrophobic amino acid

1. phenylalanine 2. tryptophan

where are non-polar/hydrophobic amino acids found

- globular proteins - insoluble core

has the smallest possible side chain, an H atom

glycine

has methyl group -CH3

alanine

has aliphatic hydrocarbon side chain

valine

has isomeric butyl groups

- leucine - isoleucine

has thiol ether side chain that resembles an n-butyl group in many of its physical properties

methionine

methionine: C and S have nearly equal __ and S is about the size of a __ __

- electronegativities - methylene group

cyclic secondary amino acid has conformational constraints imposed by the cyclic nature of its pyrrolidine side chain, which is unique among the standard amino acids

proline

side chain" from the α carbon connects to the nitrogen

pyrrolidine loop

has phenyl moiety

phenylalanine

with indole group, contain aromatic side chains, which are characterized by bulk as well as nonpolarity

tryptophan

D (position)

dexter (right)

L (position)

laevus (left)

electrically charged amino acids

Negative (acidic) 1. aspartic acid 2. glutamic acid Positive (basic) 1. lysine 2. arginine 3. histidine

- negatively charged above pH 3

- aspartic acid - glutamic acid

in its ionized state, aspartic acid is often referred to as what?

aspartate

in its ionized state, glutamic acid is often referred to as what?

glutamate

positively charged at pysiological pH values

- lysine - arginine - histidine

what kind of side chain does lysine have

butylammonium side chain

what group does arginine have

guanidino group

guanidino group contains __ __ __, rather than only one as in the lysine side chain, it shows a more diverse chemistry

two reactive nitrogens

what does histidine carry

imidazolium moiety

glycine one letter

alanine one letter

valine one letter

leucine one letter

isoleucine one letter

methionine one letter

proline one letter

phenylalanine one letter

tryptophan one letter

serine one letter

threonine one letter

asparagine one letter

glutamine one letter

tyrosine one letter

cysteine one letter

lysine one letter

arginine one letter

histidine one letter

aspartic acid one letter

glutamic acid one letter

Animal protein: complete

- egg - milk - meat, fish, poultry

Animal protein: incomplete

gelatin (denatured collagen)

what is missing in gelatin

Trp

vegetable protein: incomplete

Grains - wheat - corn - rice (brown, white) - oats Legumes - beans - peas Nuts - almonds - walnuts

what is missing in grains

lys (wheat, rice, oats) lys, trp (corn)

what is missing in legumes

met (peas) met, trp (beans)

what is missing in nuts

lys, trp

top 10 complete vegetarian protein foods with all the essential amino acids

1. firm tofu 2. lentils 3. low-fat yogurt 4. cottage cheese 5. green peas 6. squash and pumpkin seeds 7. quinoa 8. peanut butter 9. eggs 10. mushrooms

chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O)

peptide bond

how is peptide bond formed

dehydration synthesis

what does peptide bond have that limits rotation about this bond

partial double bond

what is formed from the condensind or dehydrating of two amino acids

dipeptide

amino acid with free -NH3+

amino terminal amino acid

short for amino terminal amino acid

N-terminal

amino acid with free -COO-

carboxyl terminal amino acid

short for carboxtyl terminal amino acid

C-terminal

how are amino acid structures written

N-terminal on the left

unbranched chain of amino acids

polypeptide chain

may consists of one or more polypeptide chains

protein

read from N to C terminal

simple peptide

naming: ex. alanine

alanyl

naming peptides

1. far AA residue retains the name of amino acids 2. all AAs (except trp) --> -ine or -ic acid is replaced by -yl 3. tryptophan --> tryptophanyl

naming: ex. glycine

glycyl

naming: ex. serine

seryl

naming: ex. alanine, glycine, serine

alanylglycylserine (Ala-Gly-Ser)

4 steps of writing strucutre of peptides

1. write backbone 2. add oxygens to carboxyl carbons, and hydrogens to amino nitrogens 3. add hydrogens to alpha-carbon 4. add side chains

backbone of peptide

N-C-C-N-C-C-N-C-C

peptide chain of nine amino acid residues

nonapeptide

examples of nonapeptides

- oxytocin - vasopressin

where do oxytocin and vasopressin differ

amino acid position - 3 - 8

stimulates uterine contraction in labor

oxytocin

- antidiuretic hormone - regulates blood pressure by adjusting amount of water reabsorved by kidneys

vasopressin

Variety of Functions of Peptides

1. hormones and pheromones 2. neuropeptides 3. antibiotics 4. protection

hormones and pheromones

- insulin (think sugar) - oxytocin (think childbirth) - sex-peptide (think fruit fly mating)

neuropeptides

substance P (pain mediator)

antibiotics

- polymyxin B (Gram - bacteria) - bacitracin (Gram + bacteria)

ex. of toxins that protection proteins defend against

- amanitin - conotoxin - chlorotoxin

amanitin

mushrooms

conotoxin

cone snails

chlorotoxin

scorpions

fewer than 50 amino acids

peptides

2 amino acids

dipeptides

3 amino acids

tripeptides

more than 10 amino acids

polypeptides

more than 50 amino acids

proteins

proteins are typically __ to __ amino acids linked together

100 - 10,000 amino acids

how are chains of proteins synthesized

based on specific bodily DNA

Functions of proteins

1. enzymes 2. defense proteins 3. transport proteins 4. regulatory proteins 5. structural proteins 6. movement proteins 7. nutrient proteins

are biological catalysts

enzymes

include antibodies which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens

defense proteins

other term for antibodies

immunoglobulins

__ has regions that precisely fit and bind to a single __

- antibody - antigen

carry materials from one place to another in the body

transport proteins

- carry lipids, vitamins, minerals, and oxygen in the body - act as pumps in cell membranes, transferring compounds from one side of the cell to the other

transporters

responsible for transport and storage of oxygen in higher organisms, respectively

- hemoglobin - myoglobin

myoglobin

1 subunit 1 heme group

hemoglobin

4 subunits 4 heme groups

- control many aspects of cell function, including metabolism and reproduction - we can only function within limited set of conditions

regulatory proteins

where are insulin released

beta cells of pancreas

where are glucagon released

alpha cells of pancreas

promotes growth

growth hormone

regulate blood glucose

insulin and glucagon

regulates the body's metabolic rate

thyroxine

regulate blood calcium

- calcitonin - parathormone

regulates fluid and electrolyte balance

antidiuretic hormone

provide mechanical support to large animals and provide them with outer coverings

structural proteins

hair and fingernail are composed of what

keratin

necessary for all forms of movement

movement proteins

how do muscles move

interaction of actin and myosin proteins

serve as sources of amino acids for embryos or infants

nutrient proteins

examples of nutrient storage proteins

- egg albumen - casein in milk

Levels of protein structure

1. primary 2. secondary 3. tertiary 4. quaternary

primary structure

amino acid residues

secondary structure

three-dimensional spatial arrangements

tertiary structure

polypeptide chain

quaternary structure

assembled subunits

bond that holds primary structure

peptide bonds

smalles protein

insulin (51 amino acids in two chains)

what links the two chains of insulin

cysteine (disulfide) cross links

bonds in secondary strucure

hydrogen bond (-NH group of peptide bond and carbonyl oxygen of another peptide bond)

two regular arrangements in secondary structure

1. α-Helix 2. beta sheet

stabilized by hydrogen bonds between nearby residues

α-Helix

stabilized by hydrogen bonds between adjacent segemtns that may not be nearby

beta sheet

most common type of secondary structure

α-Helix

shape of α-Helix

coiled, helical

important features of α-Helix

1. amide H and carbonyl O involved in H bonds 2. carbonly O links to amide H, 4 AA away 3. H bonds parallel to long axis of helix 4. right handed 5. 5.4 angstorms repeat distance 6. 3.6 amino acids per turn

second most common secondary structure appears similar to folds of fabric

β-pleated sheet

two possible orientations of β-pleated sheet

1. parallel 2. antiparallel

if the N-termini are head-to-head

parallel

if the N-terminus of one chin is aligned with the C-terminus of the other

antiparallel

- gives a specific three dimensional shape of the polypeptide chain - involves interactions and cross links between different parts of peptide chain

tertiary structure

tertiary structure is stabilized by what

1. hydrophobic and hydrophilic interactions 2. salt bridges 3. hydrogen bonds 4. disulfide bonds

globular tertiary structure forms spontaneously and is maintained by what

interactions among side chains or R groups

between two cysteine residues

disulfide bridges

S-S linkage can occur within the same chain

intrachain

S-S linkage can occur between 2 or more chains

interchain

ionic interaction/electrostatic attraction between ionic side chains -COO- and - NH3+

salt bridges

interaction between polar residue chains

hydrogen bonds

interaction between nonpolar groups attracted by mutual repulsion of water

hydrophobic interactions

results from the aggregation of two or more polypeptide subunits

quaternary structure

fibrous protein of three polypeptides that are supercoiled like a rope

collagen

globular protein with two copies of two kinds of polypeptides

hemoglobin

Two major classes of protein

1. fibrous proteins 2. globular proteins

- typically insoluble inw ater and serve structural roles - 3D structure is usually long and rod shaped

fibrous proteins

- coiled into compact shapes with hydrophilic outer surfaces making them water-soluble - compact shape like a ball with irregular surfaces - enzymes

globular proteins

α-keratin function

tough, rigid, hard (nails, horns)

α-keratin structure

- cross-linked α-helixes - rigid linker (S--S)

collagen function

tensile strength, non-stretching (tendons, cartilage)

collagen structure

- cross linked triple-helixes - flexible linker (Lys-HyLys)

silk fibroin function

soft, flexible non-stretchy (egg sac, nest, web)

silk fibroin structure

- non-covalently held β-sheets - van der Waals interaction

shape of globular proteins

roughly circular

shape of fibrous proteins

long strands

amino acid sequence globular

irregular and wide range of R groups

amino acid sequence fibrous

repetitive with limited range of R groups

function globular

physiological/functional

function fibrous

structural

examples of globular

- hemoglobin - enzymes - insulin - immunoglobulin

examples of fibrous

- collagen - keratin - myosin - actin - fibrin

solubility globular

generally soluble in water

solubility fibrous

generally insoluble in water

chemistry of permanent waving

- reduce - curl - oxidize

Chapter 3: Protein Structure and Function Flashcards

(268 cards)