All proteins contain the elements Carbon, Hydrogen, Oxygen and Nitrogen.
Amino Acids contain the -NH2 group which is called the amino
group And the COOH group or the Carboxyl group. Amino Acids are defined by the side group or R-Group.
The bond that holds amino acids together is called a peptide bond.
When two more amino acids are put together they become a polypeptide.
Peptide bond
Amino acid
Secondary structure
local folding of a polypeptide chain into regular structures including the a helix, b sheet, and U-shaped turns and loops.
Tertiary structure
overall three-dimensional form of a polypeptide chain, which is stabilized by multiple non-covalent interactions between side chains.
Quaternary structure:
The number and relative positions of the polypeptide chains in multisubunit proteins. Not all protein have a quaternary structure.
Primary Structure
C-peptide
Pro-insulin protein
Protein conformation: most of the proteins fold into only one stable conformation or native conformation
Protein conformation: most of the proteins fold into only one stable conformation or native conformation
SECONDARY STRUCTURE
Stabilized by hydrogen bonds
peptide backbone H-bonds are either intra- or inter- molecular 3 types : a-helix, b-sheet and triple-helix
a Helix: a helix conformation was discovered 50 years ago in a keratine abundant in hair nails, and horns b Sheet: discovered within a year of the discovery of a helix. Found in protein fibroin the major constituant of silk
The a helix:
result from hydrogen bonding, does not involve the side chain of the amino acid
bsheet:
result from hydrogen bonding, does not involve the side chain of the amino acid
A paralellel b sheet
TRIPLE HELIX
Limited to tropocollagen molecule Sequence motif of (Gly-X-Pro/Hypro)n 3 left-handed helices wound together to give a
right-handed superhelix Stable superhelix : glycines located on the central axis (small R group) of triple helix One interchain H-bond for each triplet of aas between NH of Gly and CO of X (or Proline) in the adjacent chain
NONREPETITIVE STRUCTURES
Helices/b-sheets: ~50% of regular
2ostructures of globular proteins Remaining : coil or loop conformation Also quite regular, but difficult to describe Examples : reverse turns, b-bends (connect successive strands of antiparallel b-sheets)
b-bulge
A strand of polypeptide in a b-sheet may contain an extra residue This extra residue is not hydrogen bonded to a neighbouring strand This is known as a b-bulge.
The secondary structure of a telephone cord A telephone cord, specifically the coil of a telephone cord, can be used as an analogy to the alpha helix secondary structure of a protein.
The tertiary structure of a telephone cord The tertiary structure of a protein refers to the way the secondary structure folds back upon itself or twists around to form a threedimensional structure. The secondary coil structure is still there, but the tertiary tangle has been superimposed on it.
structures of globular proteins Types of interactions : H-, ionic(salt linkage), hydrophobic- and disulphide- bond Hydrophilic R groups on surface while hydrophobic R groups buried inside of molecule Wide variety of 3o structures: since large variation in protein sizes and amino acid sequences
Hydrophobic
A coiled-coil:
Structure occurs when the 2 a helix have most of their nonpolar (hydrophobic) side chains on one side, so that they can twist around each other with these side chain facing inwards
Quaternery structure:
If protein is formed as a complex of more than one protein chain, the complete structure is designed as quaternery structure: Generally formed by noncovalent interactions between subunits Either as homo- or hetero-multimers
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Protein domains:
Any part of a protein that can fold independently into a compact, stable structure. A domain usually contains between 40 and 350 amino acids.
A domain is the modular unit from which many larger proteins are constructed. The different domain of protein are often associated with different functions.
Protein domains
Cytochrome b562 A single domain protein involved in electron transport in mitochondria The NAD-binding domain of the enzyme lactic dehydrogenase The variable domain of an immunoglobulin
Protein Folding
is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil.[1] Each protein exists as an unfolded polypeptide or random coil when translated from a sequence ofmRNA to a linear chain of amino acids. This polypeptide lacks any developed three-dimensional structure. Amino acids interact with each other to produce a well-defined three dimensional structure, the folded protein, known as the native state. The resulting threedimensional structure is determined by the amino acid sequence.
For many proteins the correct three dimensional structure is essential to function. Failure to fold into the intended shape usually produces inactive proteins with different properties including toxic prions. Several neurodegenerative and other diseases are believed to result from the accumulation of misfolded (incorrectly folded) proteins. Many allergies are caused by the folding of the proteins, for the immune system does not produce antibodies for certain protein structures.
Function of proteins
Enzymatic catalysis Transport and storage (the protein hemoglobin, albumins) Coordinated motion (actin and myosin). Mechanical support (collagen). Immune protection (antibodies) Generation and transmission of nerve impulses - some amino acids act as neurotransmitters, receptors for neurotransmitters, drugs, etc. are protein in nature. (the acetylcholine receptor), Control of growth and differentiation - transcription factors Hormones growth factors ( insulin or thyroid stimulating hormone)
Enzymes
Enzymes are proteins that catalyze (i.e. speed up)
chemical reactions. Enzymes are catalysts. Enzymes work on things called Substrates Each enzyme is specific for its substrate Almost all processes in a cell need enzymes in order to occur at significant rates.
Enzymes are not used up by the reaction. After they have done their work they release the products
and are not changed Each enzyme can work on many molecules of the substrate
3-dimensional structure of hemoglobin. The four subunits are shown in red and yellow, and the heme groups in green.
Platelet activation is a controlled sequence of actin filament: Severing Uncapping Elongating Cross linking That creates a dramatic shape change in the platelet
Activated platelet
Mechanical support
skin and bone are strengthened by the protein collagen.
Control of growth and differentiation proteins can be critical to the control of growth, cell differentiation and expression of DNA.
For example, repressor proteins may bind to specific segments of DNA, preventing expression and thus the formation of the product of that DNA segment. Also, many hormones and growth factors that regulate cell function, such as insulin or thyroid stimulating hormone are proteins.
eukaryotic organisms; it is found in the cytoplasm of prokaryotic organisms DNA is packed together and wrapped around special proteins called HISTONES DNA bound protein is called CHROMATIN When chromatin condenses (gets thicker) it forms CHROMOSOMES
Nucleosome
Chromosome DNA double helix
Coils
Supercoils
Histones
DNA Structure
Double Helix - twisted ladder Made up of monomers
called nucleotides
Nucleotides are composed of: Deoxyribose sugar Phosphate group Nitrogenous base
Nitrogenous Bases
Two types: Purines (two rings) Pyrimidines (one ring)
Purines Adenine and Guanine Pyrimidines Thymine and Cytosine
Purines
Pyrimidines
Cytosine Thymine
Adenine
Guanine
Phosphate group
Deoxyribose
Bonding
TEMPLATE STRAND
Chargaffs rules:
Base pairing rule is A-T and G-C
Thymine is replaced by Uracil in RNA Bases are bonded to each other by Hydrogen bonds
DNA Structure
Backbone alternates with phosphate & sugr/deoxyriboes with the nucleotides forming the rungs or steps of the ladder
The backbone is made of alternating sugars and phosphates. - Remember: Sugar ALWAYS attaches to the Nitrogen base
everything in a cell and ultimately an organism? DNA controls the manufacture of all cellular proteins including enzymes A gene is a region of DNA that contains the instructions for the manufacture of on particular polypeptide chain (chain of amino acids) DNA is a set of blueprints or code from making proteins
Genetic Code
Genetic code the language of mRNA
instructions (blueprints) Read in three letters at a time Each letter represents one of the nitrogenous bases: A, U, C, G
Codon found on mRNA; consists of three bases
Codon (contd)
For example, consider the following RNA
sequence: UCGCACGGU The sequence would be read three base pairs at a time: UCG CAC GGU The codons represent the amino acids: Serine Histidine Glycine AUG start codon or Methionine UAA, UAG, UGA stop codons; code for nothing; like the period at the end of a sentence
The gene-enzyme relationship has been revised to the one-gene, one-polypeptide relationship. Example: In hemoglobin, each polypeptide chain is specified by a separate gene. Other genes code for RNA that is not translated to polypeptides; some genes are involved in controlling other genes.
result is two identical documents that contain the same information. Now that we know something about DNAs structure, lets look at how it replicates.
DNA Transcription
DNA molecule along the base pairing, straight down the middle. Another enzyme, called DNA polymerase, moves along the bases on each of the unzipped halves and connects complementary nucleotides.
Synthesis of DNA from RNA is reverse transcription. Viruses that do this are Retroviruses.
RNA Structure:
Single-stranded
Sugar: Deoxyribose
Sugar: Ribose
TRANSCRIPTION the synthesis of RNA under the direction of DNA TRANSLATION the actual synthesis of a protein, which occurs under the direction of mRNA
Splicing
Each gene has it own promotor Each gene is widely spacied The information is fragmented Exon = expressed gen Intron = intervening part
Alternative splicing: A regulatory mechanism by which variations in the incorporation of a genes exons, or coding regions, into messenger RNA lead to the production of more than one related protein, or isoform. Alternative splicing is a source of genetic diversity in eukaryotes. Splicing has been used to account for the relatively small number of genes in the human genome.
mRNA Splicing
The entire gene is transcripted into a message. Some of the message is Junk (introns) and is removed before exiting the nucleus. A spliceosome is a complex of specialized RNA and protein that removes introns from a pre-mRNA This process is generally referred to as splicing. Introns typically have a GU nucleotide sequence at the 5' end splice site, and an AG at the 3' end splice site.
November 7, 2002
small section of the DNA molecule. This exposes some of the bases of the DNA molecule. Along one strand, the RNA polymerase binds complementary RNA nucleotides to the exposed DNA bases. An exposed thymine on the DNA strand hooks up with an RNA nucleotide with an adenine; an exposed cytosine on the DNA hooks up with an RNA nucleotide with a guanine base; an exposed adenine DNA base will hook up with URACIL!
As the RNA polymerase moves along, it makes a strand of messenger RNA (mRNA). It is called messenger RNA because it carries DNAs message out of the nucleus and into the cytoplasm. mRNA is SINGLE STRANDED! When the RNA polymerase is done reading the gene in the DNA, it leaves. The separated DNA strands reconnect, ready to be read again when necessary. mRNA moves out of the nucleus and finds a ribosome On the ribosome, amino acids are assembled to form proteins in the process called translation.
Translation
mRNA
GUA
UCU
GUU
ACC
GUA
mRNA carries the same message as DNA but rewritten with different nitrogen bases. This message codes for a specific sequence of amino acids
SO:
Say the mRNA strand reads:
mRNA (codon)
Translation
mRNA
GUA
UCU GUU
ACC
GUA
Codon: a sequence of 3 nitrogen bases on mRNA that code for 1 amino acid
Its a TRIPLET code Example: This strand of mRNA has 5 codons, so it would code for 5 amino acids.
Translation
mRNA
GUA
UCU
GUU
ACC
GUA
These codons are universal for every bacteria, plant and animal on earth There are 64 codons which code for all 20 amino acids on earth.
The genetic code: specifies which amino acids will be used to build a protein Codon: a sequence of three bases. Each codon specifies a particular amino acid.
Start codon: AUGinitiation signal for translation Stop codons: stops translation and polypeptide is released
Translation
mRNA
GUA
UCU
GUU
ACC
GUA
Ribosome
The mRNA molecule travels to the ribosomes where the mRNA codes are read by the ribosomes Ribosomes hold the mRNA so another type of RNA, transfer RNA (tRNA) can attach to the mRNA
Translation
mRNA
GUA UCU
GUU
ACC
GUA
Ribosome
CA U
AG A
Translation
mRNA
GUA
UCU
GUU ACC
GUA
CA U A G A CA A
Elements of translation
Ribosomes
rRNA Large and small subunits
Codons
Initiator or start codon Methionine (AUG) Stop codons tRNA
Chain termination
Polysome
RNA
Ribonucleic acid
Single-stranded helix
Sugar is ribose
Thymine is replaced by URACIL
Major RNAs
mRNA
messenger RNA carries the genetic information that will be expressed ultimately as proteins. (carries information from
DNA to ribosome)
tRNA
transfer RNA is the adapter molecule. It recognizes the codons of the mRNA on the one hand, and it can be covalently bonded to the appropriate amino acid, on the other. (Carries amino acids)
rRNA
ribosomal RNA is found in the ribosomes (Makes up
ribosomes)
RNA-Coding Genes
A. B. C. D. E. F. G. H. I. Ribosomal RNA (rRNA) genes Transfer RNA (tRNA) genes Small Nuclear RNA (snRNA) genes Small Nucleolar RNA (snoRNA) genes Regulatory RNA genes XIST RNA-Coding Genes MicroRNA (miRNA) genes Antisense RNA genes Riboswitch genes
RNA
can be
Messenger RNA
Ribosomal RNA
Transfer RNA
also called
which functions to
also called
which functions to
also called
mRNA
Carry instructions
rRNA
tRNA
from
to
to make up
DNA
Ribosome
Ribosomes
c)
Cistron = Gene
from degradation and serve as a ribosome binding site Poly-A tail: AAUAAA (200 As) to protect the message from degradation Splicing: remove of introns Lariat structures: introns removed from hnRNA (heterogeneus nuclear RNA) are degraded in nucleus
Transfer RNA
The conformation (three-dimensional shape) of tRNA results from base pairing (H bonds) within the molecule. 3' end is the amino acid attachment sitebinds covalently. Always CCA. Anticodon: site of base pairing with mRNA. Unique for each species of tRNA.
Hydrogen bonds form between the anticodon of tRNA and the codon of mRNA. Small subunit rRNA validates the matchif hydrogen bonds have not formed between all three base pairs, it must be an incorrect match, and the tRNA is rejected.
Wobble: specificity for the base at the 3' end of the codon is not always observed. Example: codons for alanineGCA, GCC, and GCUare recognized by the same tRNA.
Protein formation
Amino acids link
together to form a protein The new protein could become cell part, an enzyme, a hormone etc.
Ribosomic RNA
Prokaryotic ribosomes have 3 rRNA molecules: 23S, 16S and 5S. 2 Subunits: 50S+30S Eukaryotic ribosomes have 4 rRNA molecules: 28S, 18S, 5.8S and 5S 2 Subunits: 60S+40S
50S
30S
60S
40S
Ribosome: the workbenchholds mRNA and tRNA in the correct positions to allow assembly of polypeptide chain. Ribosomes are not specific, they can make any type of protein.
Subunits are held together by ionic and hydrophobic forces (not covalent bonds). When not active in translation, the subunits exist separately.
RNA polymerases catalyze synthesis of RNA. RNA polymerases are processivea single enzyme-template binding results in polymerization of hundreds of RNA bases.
What are the bonds called that form between ribose bases?
Termination
http://vcell.ndsu.edu/animations/transcription/movie.htm
http://www.biostudio.com/demo_freeman_pro tein_synthesis.htm
STEP 1
Step 2
Start codon is AUG; first amino acid is always methionine, which may be removed after translation. The large subunit joins the complex, the charged tRNA is now in the P site of the large subunit.
Elongation: RNA polymerase unwinds DNA about 10 base pairs at a time; reads template in 3' to 5' direction. The RNA transcript is antiparallel to the DNA template strand. RNA polymerases do not proof read and correct mistakes.
Elongation: the second charged tRNA enters the A site. Large subunit catalyzes two reactions: 1. Breaks bond between tRNA in P site and its amino acid. 2. Peptide bond forms between that amino acid and the amino acid on tRNA in the A site.
Termination: specified by a specific DNA base sequence. Mechanisms of termination are complex and varied.
Eukaryotesfirst product is a pre-mRNA that is longer than the final mRNA and must undergo processing.
Termination: translation ends when a stop codon enters the A site. Stop codon binds a protein release factorallows hydrolysis of bond between polypeptide chain and tRNA on the P site. Polypeptide chainC terminus is the last amino acid added.
Table 12.1
Several ribosomes can work together to translate the same mRNA, producing multiple copies of the polypeptide. A strand of mRNA with associated ribosomes is called a polyribosome or polysome.
2. Polyadenylation is the synthesis of a poly(A) tail, a stretch of adenines at the end of the mRNA molecule. At the end of transcription the last 3 bit of the newly made RNA is cleaved off by a set aof enzymes. The enzymes then synthesize the poly(A) tail at the RNA's 3' end. The poly(A) tail is important for the nuclear export, translation and stability of mRNA. The tail is shortened over time and when it is short enough, the mRNA is degraded. In a few cell types, mRNAs with short poly(A) tails are stored for later activation
Mis-folding diseases:
Altzheimers
4. Glycosylation: addition of sugars to form glycoproteins Sugars may be added in the Golgi apparatusthe resulting glycoproteins end up in the plasma membrane, lysosomes, or vacuoles. Diseases: incorrect addition of sugars to specific amino acids shows in infancyalmost always involves nervous system development.
the cell membrane have sugars attached to them. They aid in recognition of other molecules. What would be some consequences of incorrect glycosylation at the cell membrane?
Protein modifications: 5. Proteolysis: cutting the polypeptide chain by proteases. Degradation of protein message.
6. Phosphorylation: addition of phosphate groups by kinases. Charged phosphate groups change the conformation. Generally makes protein into enzymes!