BIO120 CH5

what things make up amino acids

central (alpha) carbon atom

amino group

carboxyl group

R group (side chain)

how are the structures of amino acids connected

with covalent bonds

in a neutral cell environment, the amino group gains what and the carboxyl group loses what

the amino group gains a proton and the carboxyl group loses a proton to become charged

who gains/loses a proton? the amino acid or the carboxyl group

amino group=gains a proton

carboxyl group=loses a proton

is the R group of an mino acid the same in every amino acid

no the R group is different from one amino acid to the next

how are R groups grouped

based on properties (hydrophilic, hydrophobic, etc.)

amino acids link together to form

proteins

what is the bond between amino acids called

peptide bond

in a peptide bond (each amino acid has a carboxyl group and hydroxide) the carboxyl group of one amino acid reacts with what

another amide group of another amino acid

what is the carbonyl group in the peptide bond

C=O group

what is the amide group in peptide bond

N-H group

when a peptide bond is formed as a result of a carboxyl group from one amino acid bonding to the amino group of another what is released

a molecule of water

what is a polypeptide

a polymer of amino acids or peptides

how is a peptide bond formed

a carboxyl group from one amino acid bonds to the amide group of another

how many amino cells make up polypeptides in cells

several hundred amino acids

what makes up the primary structure

the sequence of amino acids (3 letter abbreviation) in a protein

what structure determines how a protein folds

the primary structure

what makes up the secondary structure

interactions between amino acids

what is the tertiary structure

longer range interactions between secondary structures support 3D shape of the polypeptide

what is the quaternary structure

proteins are made up of several polypeptides which interact with each other and make up this structure

what are three brand functions of proteins in a cell

structural elements

communicate with environment

accelerate chem reactions

the ability of a protein to carry out its function depends on what

its 3D shape

what enables protein folding

the primary-quaternary structures of a protein

what’s so important about protein folding

its an important part of cellular function and health

what happens if proteins are misfolded

can cause diseases like Alzheimers and parkinsons

what are prions

the misfiled form of a normal protein found in the body, prion-protein

what type of bonds form between carbonyl and amide groups in different amino acid molecules

hydrogen bonds

hydrogen bonds form between what two molecules in two different amino acid molecules

carbonyl and amide groupswh

what do hydrogen bonds do to DNA

help stabilize helix structure

what are the two types of secondary structure found in DNA

alpha helix

beta sheet

what are alpha helix and beta sheets

two types of secondary structures found in DNA

in which secondary structure is the polypeptide backbone twisted tightly in a coil with 3.6 amino acids per turn, R groups project outward from helix

alpha helices

describe the structure of alpha helices

polypeptide backbone is twisted tightly in a coil

3.6 amino acids per turn

R groups project outward from helix

what is the polypeptide structure that folds back and forth on itself, R groups project alternately above and below the pleated beta sheet

beta sheet

describe the beta sheet

polypeptide structure that folds back and forth on itself

R groups project alternately above and below pleated beta sheet

what are secondary structures

how amino acids in polypeptide chain interact with each other and Alpha and beta and how they interactw

what is the tertiary structure of a protein

3D conformation of a polypeptide chain, composed of several secondary structural elements

what is the tertiary structure made of

several secondary structural elements

how is the tertiary structure determined

by spatial distribution of R groups

what determines the secondary and tertiary structures

the primary structure

the primary structure determines what

the secondary and tertiary structure

the tertiary structure determines what

function

what is included in the 3D shape of the tertiary structure

contours, distribution of charges and pockets

what does the shape of tertiary structure do for the protein

enables proteins to serve as structural support, membrane channels, enzymes, or signaling molecules

what is denaturation

the process by which molecules are unfolded and lose their structure

what is the process by which molecules are unfolded and lose their structure

denaturation

how can proteins be denatured

by heat or thru chem reaction

what must happen in order for a protein to denature

the ionic and hydrogen bonds within proteins must be broken to disrupt their tertiary structure

some proteins are complete as a single polypeptide chain with

tertiary structure

many protein include multiple polypeptide chains that come together to form a 

quaternary structure

what makes up the quaternary structure

multiple polypeptide chains that come together

can the smaller subunits that make up a protein be different or need to be identical?

can be identical OR different

what is the primary structure

sequence of amino acids

how fast do proteins fold

quickly in a matter of milliseconds

when are proteins vulnerable to improper folding

in unfolded denatured state

what is exposed in the unfolded state of a protein

hydrophobic groups are exposed to other macromolecules

where does protein folding occur

in cells cytoplasm

what can prevent the protein from folding properly

when hydrophobic group interact with other molecules before folding

what are chaparones

specialized proteins that protect the protein as it undergoes folding process

what protects proteins during the folding process

chaperones

secondary structure refers to

hydrogen bonding between amino acids forming alpha helix and beta sheet structures

tertiary structures make up

3D shape of proteins due to interactions between R groups 

when is the sequence of bases in DNA used for template for RNA

during transcription

what happens during transcription

sequence of bases in DNA is used for template for RNA

when is the sequence of bases in RNA (or mRNA) is used to specify the order of amino acids added to new polypeptide chain

during translation

what happens during translation

the sequence of bases in RNA (mRNA) is used to specify the order of amino acids added to a new polypeptide chain

what are the components needed for translation

Ribosomes

small subunit

large subunit

what are ribosomes

made of RNA and proteins that bind with RNA

where is the site of translation

ribosomes

how many types of ribosomal RNA are contained in ribosomes

1-3

how many types of ribosomal proteins are contained in ribosomes

20-50

what is the order or binding sites for tRNA

EPA (environmental protection agency)

what does the small subunit do

read mRNA to make sure genetic code is translated correctly into proteins

aligns the genetic code

where are the 3 binding sites for tRNA

in the large subunit

what is the a site (name)

aminoacyle A site

what is the name of the p site

peptide site

what is the name of the E site

exit site

when mRNA is in place on the ribosome, the mRNA sequence is read in groups of what

3 nucleotides or codons

each codon in the mRNA codes for what in the polypeptide chain

a single amino acid

what in the mRNA codes for a single amino acid in the polypeptide chain

each codon

what establishes the correct reading frame for codons

ribosome

the ribosome will establish what

the correct reading frame for codons

translation of each codon in mRNA into an amino acid is carried out by what

tRNA

what does tRNA do

tRNA translates each codon in mRNA into an amino acid

what are tRNAs

small RNA molecules

what makes up a tRNA

70-90 nucleotides with a self-pairing structure

what makes up the anticodon

three bases in the anticodon loop

what is the anticodon

3 nucleotide sequences that are complementary to mRNA codon

what connects specific amino acids to tRNA

enzymes called aminoacyl tRNA synthetases

what is aminoacyl tRNA synthetases

enzymes

what is aminoacyl tRNA synthetases responsible for

translating codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain

how many aminoacyl tRNA synthetases do most organisms have

most have only one for each amino acid

where does aminoacyl tRNA synthetases bind

to multiple sites on any tRNA molecules that have an anticodon corresponding to an amino acid

aminoacyl tRNA synthetases binds to multiple sites on any tRNA molecule that has what

an anticodon corresponding to an amino acid

a tRNA that has no amino acid attached to it is (charged/uncharged)

unchargeda

a tRNA that has an amino acid attached is (charged/uncharged)

charged

how accurate is aminoacyl tRNA synthetases

very accurate and rarely attach the wrong amino acid

which is there more of, codons or amino acids

codons

amino acids are specified by 

more than one codon 

is genetic code redundant?

yes