Exam 2 Flashcards
What are the basic structures of an Amino Acid?
- amino group
- r-group
- carboxyl group
R-group
provides chemical identity
20 different amino acids = 20 different r-groups
what are the 3 categories of amino acids?
- hydrophobic (non-polar)
- hydrophilic (polar)
- charged (acidic and basic)
* define how the protein folds
how are amino acids are joined to form a polypeptide?
peptide bond (covalent bond)
peptide bond
forms between the carboxyl group and the amino group
if a polypeptide has 3 peptide bonds how many amino acids are there?
4 amino acids
polypeptide
chain of amino acids
what are the 4 levels of protein structures of an amino acid?
- primary: linear sequence; polypeptide; peptide bonds
- secondary: alpha helix and beta pleated sheets; hydrogen bonds
- tertiary structure: 3D/ includes primary and secondary; interactions of R-groups
- quaternary structure: interactions of r-groups of two or more polypeptides; only observed in some proteins
5 types of interactions
- covalent bonds: contains disulfide bonds between cytosine)
- hydrogen bonds: between polar r-groups
- ionic bonds: between charged r-groups
- non-polar bonds: hydrophobic effect, between non-polar r-groups
- van der waals interactions: tiny interactions between close atoms
folding
refers to a protein acquiring its 3D structure that only happens 2 ways:
1. spontaneously: immersing protein in water
2. aid of proteins called CHAPERONINS
what happens when a protein is denatured?
how is it denatured?
- looses its 3D shape, only primary remains and cannot carry out its functions
- by applying high heat, low pH
what are the 3 components of a nucleotide?
- sugar: 5 carbons- pentose
- phosphate group: PO4^-3
- nitrogenous base: A, G, C, T, U
what are the 2 sugars used in nucleic acids?
- ribose- RNA
- deoxyribose- DNA
ribose
- in RNA
- always going to have two OH (hydroxyl) group (3’ and 2’)
- OH in 2’ allows RNA to interact with others
deoxyribose
- in DNA
- only has on OH group in 3’
- H atoms in 2’
- absence of OH in 2’ it what keeps it stable
DNA vs RNA nucleotide
DNA: has deoxyribose, bases are A, G, T, and C
RNA: has ribose, bases are A, G, U, and C
prymidines
- 1 ring
- cytosine (both), thymine (DNA), and uracil (RNA)
purine
- 2 ring
- adenine and guanine
How are nucleotides joined together?
polymerization
polymerization
- uses dehydration rx to form phosphodiester bonds (covalent)
- the next nucleotide is added to the 3’ end
what is the structure of DNA?
double helix that forms two strands in antiparallel configuration
antiparallel configuration
connected with hydrogen bonds between bases using complementary base pairing
complementary base pairing
A - T
G - C
chargaff’s rule
% of A = % of T (2 H-bonds)
% of G = % of C (3 H-bonds)
what are the 5 levels of DNA
nucleotides (covalent bond) -> strand (phosphodiester bond) -> double helix (H-bond) -> chromosomes (DNA + proteins) -> genome (all genetic info)
RNA function
decodes information from DNA
what are the 3 types of RNA
- messenger RNA (mRNA): carry instructions for protein synthesis
- transfer RNA (tRNA): delivers amino acids for protein synthesis
- ribosomal RNA (rRNA): part of ribosome, protein synthesis
what are the 4 levels of RNA
- nucleotide: stabilized by covalent bonds
- strand: stabilized by phosphodiester bonds
- hairpin loop: section of the sequence that are complementary to each other, stabilized by H-bonds
- final 3D structure: stabilized by H-bonds, further folding
gene expression
explains how a gene becomes a protein
* translation and transcription
CENTRAL DOGMA
DNA (gene) -> transcription -> mRNA -> translation -> protein
prokaryotic central dogma
DNA -> transcription -> mRNA -> translation -> polypeptide -> protein folding -> protein
* all of this occurs in the cytoplasm
eukaryotic central dogma
nucleus: DNA -> transcription -> pre mRNA -> RNA processing -> exits nucleus -> mature mRNA -> translation -> polypeptide -> protein folding -> protein
what are the exceptions to central dogma?
retroviruses (i.e., HIV)
1. RNA goes through REVERSE TRANSCRIPTION caused by an enzyme names reverse transcriptase
2. goes to DNA then mRNA and then protein `
gene
function: segment of DNA that encodes for one protein that determines a characteristic in an organism
transcription
The process in which a particular segment of DNA is converted into mRNA
promoter
sequence in the gene that marks the location on the template strand where transcription starts
terminator
sequence that signals the end of transcription
template strand (non-coding)
DNA strand that the mRNA uses as a template
coding strand (non-template)
DNA strand that has the same sequence as the mRNA (but you switch out T for U)
what are the 3 stages of transcription
- initiation
- elongation
- termination
initiation stage
(prokaryotic)
- recognition
-carried out by two proteins: sigma factor and RNA polymerase - sigma factor binds to polymerase and delivers it to promoter
- polymerase binds to DNA and starts transcription
- sigma goes on its own way
sigma factor
protein found in bacteria that binds to RNA polymerase and delivers it to the promoter
RNA polymerase
enzyme that synthesizes strands of RNA
elongation stage
(prokaryotic)
- synthesis of mRNA from 5’ to 3’
- RNA polymerase creates an open complex
- mRNA is complementary and antiparallel to template strand
termination stage
(prokaryotic)
- RNA polymerase reaches the terminator sequence and transcribes it
- a hair pin loop forms in the mRNA
- triggers the separation of DNA, mRNA, and RNA polymerase
end of transcription in…
prokaryotic cells: mRNA is ready to be used
eukaryotic cells: at the end we have pre- mRNA that needs to be modified to mature mRNA
transcription in eukaryotes
genes have coding (exons) and non-coding (introns) sequences that are not interspersed with each other
RNA processing
- capping
- tailing
- splicing
capping
- adds a 5’ cap to the 5’ end of pre-mRNA
- f(x): helps mRNA exit the nucleus, prevents degradation, and helps it bind to ribosome
tailing
- adds a Poly-A tail on the 3’ end of pre-mRNA
- poly-a tail: string of A’s
- f(x): prevents degradation
splicing
- removal of introns and connection of exons
- splicesome (RNA + protein): in charge of splicing
why do we need RNA processing?
- removes non-coding information
- we do not want the mRNA to lose sequence
genetic code
a molecular dictionary that shows the correspondence between a sequence of nucleotides and a sequence of amino acids
codon
a 3 nucleotide sequence in mRNA
* includes 64 codons
- 61 of those codons specify for an amino acid
- 1 codon specifies for start (AUG) = methionine (MET)
- 3 codons mean stop (UAA, UAG, UGA) -> does not code for amino acid
what are the 4 characteristics of genetic codes?
- unambiguous
- redundant
- conservative
- universal
unambiguous
each codon specifies to only 1 amino acid
redundant
each amino acid can be specified by more than 1 codon
conservative
codons that specify for the same amino acid share the first two bases
universal
all organisms (living and extinct) rely on the genetic code
* exceptions: arthropods, yeast, mitochondria in mammals
tRNA
f(x): delivers amino acid (1 at a time) to ribosome during protein synthesis
anticodon
complementary sequence to a codon and antiparallel
f(x): determine which amino acid attaches to the 3’ of tRNA
ribosomes
- made of RNA and protein
- f(x): carry out the synthesis of protein
- 2 subunits: large and small
large subunit
f(x): form peptide bonds between amino acids
- forms polypeptide
- has site E, A and P
small subunit
f(x): bind to mRNA and hold it in place
Site A
(amino-acyl site)
holds the incoming amino-acyl tRNA
Site P
(peptidyl site)
where peptide bonds are formed
Site E
(exite site)
holds uncharged tRNA
amino-acyl tRNA
tRNA + amino acid
- also called a charged tRNA
translation
- synthesis of a protein
- ribosome (cytoplasm)
- mRNA (instructions)
- tRNA + amino acids
what are the 3 stages of translation?
- initiation
- elongation
- termination
initiation (translation)
- mRNA binds to small subunit using ribosomal binding sequence
- initiator amino-acyl tRNA binds to the start codon
- large subunit binds to small subunit
elongation (translation)
- tRNA in site P holds the growing polypeptide
- mRNA is read in site A
- the next amino-acyl tRNA enters through site A
- peptide bond forms between last amino acid in the growing polypeptide and the next amino acid
- TRANSLOCATION: ribosome moved 1 codon down 5’ to 3’
- uncharged tRNA leaves site P through site E
- the “new” tRNA moves to site P
- the next tRNA enters site A with a new amino acid
- cycle repeats until stop codon is reached
termination (translation)
- stop codon is reached in site A
- stop codon attracts the protein release factor
-bond between polypeptide and the last tRNA breaks - small and large subunit disconnects
-mRNA is released - polypeptide folds into a protein
