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Peptide Bond
A covalent bond formed between two amino acids during protein synthesis, linking the carboxyl group of one amino acid to the amino group of another.
Polypeptide
A chain of amino acids linked by peptide bonds, forming the primary structure of proteins. Cannot interact with water
This makes backbone / protein stronger
Primary Structure
The unique sequence of amino acids in a polypeptide chain, determining the protein's characteristics and function, such as how the protein fold into 3D shapes.
True
true or false: A change of one amino acid can make up an entirely new protein
An actual amino acid monomer
Each bead is a what?
Primary Structure→ Secondary Structure→ Tertiary Structure → Quarternary Structure →
What are the steps of structure folding?
Secondary Structure
A step in structure in where amino acids interact with nearby amino acids.They are formed by hydrogen bonding along the polypeptide backbone
Polypeptide backbones and Hydrogen Bonding
What are the 2 things that fold together to stabilize secondary structure?
Tertiary Structure
Where amino acids turn into 3d polypeptide. It could be a final step to a structuring a polypeptide.
The interaction between R groups and the backbone of amino acids contributes to the overall three-dimensional shape of a protein. Additionally, these components can also form bonds with water.\
How do folding in tertiary structure work?
Quarternary Structure
Results from the interaction of other poly subunits (2 or more tertiary polypeptides)
Hydrogen Bonding
What Stabilizes Protein?
Ionic Bonding
Due to folding, R-groups with positive and negative charge can interact with each other
Folding produces charge on the outside, which creates certain functional regions for other molecules to interact with it.
How do proteins function and work?
Folding allow hydrophobic regions
What creates Phospholipids?
Peptide Chain
Polypeptide is stilla baby protein because it’s still in a primary structure. When it matures, we have this.
Phosphodiester Bonds and Hydrogen Bonding between base pairs.
What helps stabilize the structure of DNAs double stranded helix.
Primary structure determines R groups in polypeptite determine tertiary structure determine final shape determines functions
the order of determination of the function
H-bonds and Interactions between R groups can be affected by temperature, UV, pH, or exposure to chemicals.
What are the factors that can denature protein?
Denatured Proteins
These proteins are non-functional, but if the conditions are returned, protein can refold and regains its function
1- Storing genetic information
2- Copying itself
What are the 2 main function in all organisms?
Its determine by turning on a gene or gene expression.
When or whether proteins are made?
Gene
This is where DNA stors genetci instructions for how and when to make all proteins
Translation
Translates from genetic code→amino acids done by ribosomes and cytoplasm
Nucleic Acids
Monomers of nucleic acid
1- Sugar ring with 5 carbons
2- 5’ phosphate group
3- base
3 chemical group of Nucleotides
base
gives the nucleotide its identity, like what R group is to an amino acid
2 Families of Nucleotide Bases
1- Pyrimidines (cytocine, Thymine, Uracil)
2- Purines (Guanine, Adenine)
Single Ringed Structure
Pyrimidines
Double Ringed Structure
Purines
Phosphodiester Bonds
From between the OH group attached to the ( 3’) carbon of 1 nucleotide and the phosphate group (5’). Link nucleotide monomers together to form a strand of DNA
Nucleotides are connected together to form nucleic acids via…
Phosphate → Sugar → Phosphate → sugar group
—>(are phosphodiester)
The order and results in alternating pattern
With the support pof sugar phosphate backbone and base pair of H-bonding, therefore turn into a helix structures with 2 strands running anti-parallel to each other.
How do DNA Forms a regular stable shapes?
DNA And RNA Difference
DNA- Good for storing info, stable, regular in structure
RNA- less stable, more flexible in its 3d structure and thus can take on more functions. It is enconded and transcribed to make proteins.
mRNA
- carries instructions to make proteins
Non-coding RNA
Functions without making protein
The central dogma
it describes the process by which cells use information in the genes to make protein
-Leave nucleus
-Be modified/edited to fine tune details of information in the transcript
What can a disposable do?
Gene of Interest
a DNA sequence that codes for a protein or RNA molecule that a researcher wants to study or produce.
Promoter
Where do transcription begins?
Promoter
where RNA polymerize and transcription bind to start transcription process
-Neaby the gene
Transcription Factor
A protein involved in transcription
Enhancers
located very far away from the gene
1-DNA loops to bring enhancers transcription factors which are far closer to the promoter
2- The mediator complex acts as a bridge connecting enhancer transcription factors with promoter transcription factor.
3- these protein then result in polymerization (the enzyme that make RNA)
How do the process of enhancers and promoter act in a gene?
Elongation
RNA polymerase reads the DNA template in the 3’ to 5’ direction
Steps of Elongation
1- facilitate local unwinding of the DNA
2- has channel funnel in free RNA ucleotides towards transcription site
3- Moves along DNA template 3’ → 5’. if the incoming rNTPS correctly matches the DNA template, RNA polymerase attaches it
4- RNA is synthesize in the 5’→3’ direction
5- Stabilizes pairing of DNA- RNA at active transcription site to enable base pairing
6- Restores original DNA Double helix as it passes.
Termination
Where transcription ends
1- RNA polymerase recognizes this signal
2-When it reaches signal, RNA transcript is cut, forming its 3’ end
3- RNA polymerase detaches from the DNA template, transcription ends
4- If the cell needs more RNA, then it can rebind to the promoter and restart the process.
Nucleus. Cytoplasm
Eukaryotes transcript in? Prokaryotes transcript in?
Enhancers
It is an activator protein and can be everywhere
DNA looping
Promoter acts like a binder, then some transcription will set a scene to a promoter
Eukaryotes→ mRNAs must first be process and transported to the cytolasm before they are translated
which Cell would be mRNA process only occurs?
True for Prokaryotes, false for eukaryotes
True or False: Transcription and translation occur simultaneously
RNA Processing Steps
s1→ A nucleotide “cap” will attach to the 5’ end. → A poly (a) “tail” is added to the 3’ end → introns are spliced out
5’ Cap Roles:
-gives mRNA stability
-provides a recognition site for ribosomes to bind
-it modified 5’ end
3’ Poly A tail
gives mRNA stability
provides recognition site for exporter proteins to bind
export mRNA from nucleus to cytoplasm
Adds a poly (a) tail to the 3’ end
What does polyadenylation do?
introns excised from the RNA strand, and exons are spliced together.
Introns do what? and Exons do what?
Exons; Introns
contained the cofe the expressed in protein ; Introns are in between or in the trash
Alternative Splicing
allows single gene in DNA to code for many different proteins simply by editing the mRNA copy
Directionality of
Reading Codons
Ribosomes reading mRNA
synthesizing RNA
reading and DNA template
5’→ 3’
5’ → 3’
5→3’
3’→5’
Aminoacyl tRNA Synthetase
RNA and Protein
What are Ribosomes made up of?
has amino attached
what does it mean it when tRNA molecule is charged?
Initiatian process and their function
R- Groups
What makes Amino Acid unique?
Phosphate Group, 5 Carbon sugar, a Base
Nucleotides are the monomers of nucleic acids. Which of the following chemical groups are they composed of?
Amino Group, Carboxyl group, The polypeptide backbone
all of the following that are involved in the formation of a protein’s SECONDARY structure
Hydrophobic Interactions
What interaction plays the biggest role in forming the tertiary structure?
Hydrogen Bonding
Complementary bases are attached to each other to form double stranded DNA via…
-Enhancers, promoters, mediator complex, transcription factors, RNA polymerase
What are the transcription initiation complex participators?
-tRNA Met , 5’ cap, initiation factors, small ribosomal unit,
What are the Translation initiation complex participators?
Mediator Complex
DNA-binding transcription factors (TFs) directly to RNA polymerase II (Pol II)
A charged tRNA would be the one that has amino acid attached to it
What is the difference between charged and uncharged tRA?
A charged tRNA enters the A site and catalyze the Amino acid, then P site is where the amino acids form peptide bonds. At E site, it is where uncharged tTRNA exit
What goes in the A Site of translation
Mediator Complex
This is what acts as a bridge between the enhancer and RNA polymerase binded to the promoter
-found after the coding region which is further downstream in Eukaryotes
-It is part of the template strand so RNA polymerase know where to stop trasncribing
-generally contains Poly A tail to signal mRNA processing
- In prokaryotes, it is found immediately after the gene of interest
General Placement of Teminator Sequence
5’ Capping- provides stability
Polyadenilation - the act of adding poly A tails- provides stability as well as knowing when to exit from nucleus to cytoplasm
RNA splicing- removal of introns
What are the three steps of mRNA processing? Describe the role of each.
