protein structure, transcription, and translation Flashcards
protein structure
made up of amino acids, linked by peptide bonds
different levels of protein structure
what is the general structure of amino acids?
central carbon atom, amino group, carboxyl group, variable R group (side chain that determines the properties of the amino acid)
proteins function
- catalyzing biochemical reactions
- providing structural support
- facilitating movement within cells
- movement, such as muscle contraction and cellular mobility
- antibodies in the immune system
- signaling molecules. facilitating communication between cells
what are the levels of protein structure
primary, secondary, tertiary, quaternary
what is primary structure
the sequence of amino acids in a polypeptide chain, determined by genetic information encoded in DNA
what is secondary structure
local folding of the polypeptide chain into structures such as a-helices and b-pleated sheets, stabilized by h-bonds
what is tertiary structure
the overall 3d shape of a protein, resulting from interaction among r-groups, including hydrophobic interactions, ionic bonds, and disulfide bridges
what is quaternary structure
the assembly of multiple polypeptide chains into a single functional protein, with interactions between the chains
what is denaturation of proteins
the process where proteins lose their native structure due to external stressors (heat or pH changes) which can make them nonfunctional
structure of nucleic acids
they’re polymers made up of nucleotide monomers,
what do nucleotide monomers consist of
phophate group, pentose sugar, and nitrogenous base
what kind of sugar does DNA contain
deoxyribose
what kind of sugar does rna contain
ribose
what are the nitrogenous bases
a, t, c, g, u
what are the purine nitrogenous bases
adenine and guanine
what are the pyrimidine nitrogenous bases
cytosine, thymine, and uracil
what links nucleotides?
phosphodiester bonds, which from the backbone of the nucleic acid strand
functions of nucleic acids
- storage and expression of genetic information
- dna is the genetic blueprint, rna plays a part in translating that information into proteins
- rna can leave the nucleus, dna stays in the nucleus
what is transcription?
- the first step in gene expression, where dna sequence is transcribed into an RNA molecule
- the process consists of 3 main stages: initiation, elongation, and termination
- rna polymerase 2 is the enzyme responsible for synthesizing rna and dna template
steps of transcription and their descriptions
initiation - rna polymerase 2 binds to the promoter region of the gene, aided by activator proteins and transcription factors
elongation - rna polymerase 2 reads the template strand of DNA and synthesizes a complementary RNA strand in the 5’ to 3’ directions
termination - the transcription process ends when RNA polymerase 2 reaches a terminator sequence, releasing the newly formed RNA transcript
what is the importance of post-transcriptional mRNA processing?
-eukaryotic mRNA undergoes post-transcriptional modifications, including the addition of a 5’ cap and a poly-A-tail, which protect the mRNA from degradation
- pre-mRNA splicing removes introns (non-coding regions) and joins exons (coding regions) to produce a mature mRNA transcript ready for translation
overview of translation and ribosome structure - tRNA and Amino acids
- tRNA molecules are responsible for bringing specific amino acids to the ribosome based on their anticodon sequences, which are complimentary to the mRNA codons
- each tRNA molecule has a unique anticodon that pairs with a corresponding codon on the mRNA strand, ensuring the correct amino acid is added to the growing polypeptide chain
- the process of translation occurs in three main sites of the ribosome: A, P, and E
what are the sites where translation occurs on the ribsome? What are they called and what do they do
A, Aminoacyl - where the tRNA carrying the next amino acid enter
P, peptidyl - holds the tRNA with the growing polypeptide chain
E, Exit - where the empty tRNA exits the ribosome after its amino acid has been added
overview of translation and ribosome structure - ribosome functionality
- the ribosome is a complex molecular machine made of ribosomal RNA (rRNA) and proteins, crucial for translating mRNA into proteins
- the ribosomes structure allows it to move along the mRNA strand, reading codons and facilitating the binding of tRNA molecules
- peptide bonds are formed in the p sie, where amino acids from the tRNA in the A site is transferred to the growing polypeptide chain
- the ribosome continues the process until it encounters a stop codon on the mRNA, signaling the end of translation
- the release factor then binds to the ribosome, prompting the release of the newly synthesized polypeptide chain and the disassembly of the ribosome complex.
- this process is essential for protein synthesis, which is vital for cellular function and structure
summary of translation process
- begins in the initiation phase, where the small ribosomal subunit binds to the mRNA and the first tRNA attaches to the start codon (AUG)
- during elongation, tRNA molecules continue to bring amino acids to the ribosome, and peptide bonds are formed between them, extending the polypeptide chain
- the termination phase occurs when a stop codon is reached, leading to the release of the polypeptide and the disassembly of the ribosome
- the entire process is highly regulated and involves various factors that ensure accuracy and efficiency in protein synthesis
- the final polypeptide undergoes folding and modifications to become a functional protein
- understanding translation is crucial for grasping how genetic information is expressed in living organisms
structure of dna
DNA (deoxyribonucleic acid) is a macromolecule composed of nucleotides, which are the building blocks of nucleic acids.
- each nucleotide consists of three components: a pentose sugar, phsophate group, and a nitrogenous base
- the structure of dna is a double helix, with two strands running in opposite directions (antiparallel) and held together by h-bonds between complementary base pairs
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what is chargaff’s rule
that in a double-stranded DNA molecule, the amount of a=t, and the amount of g=c. maintaining a 1:1 ratio
what is the direction of dna synthesis
5’ to 3’
what is dna replication
process by which DNA makes a copy of itself before cell division, ensuring that each daughter cell receives an identical set of genetic information
DNA replicaion and transcription overview
- the enzyme DNA polymerase plays a big role in synthesizing new dna strands by adding nucleotides complementary to the template strand
- transcription is the first step in gene expression, where a specific segment of DNA is copied into mRNA by RNA polymerase
what are the three steps in dna transcription
initiation, elongation and termination (like translation)
what happens in the elongation phase of transcription
rna polymerase synthesizes the mRNA strand by reading the template DNA strand and incorporating complementary RNA nucelotides (U instead of T)
what happens in post-transcriptional modifications of mRNA?
addition of a 5’ cap and a poly-A tail, and splicing out introns
overview of the endomembrane system
- the endomembrane system is a network of membranes within eukaryotic cells that work together to synthesize, modify, and transport proteins and other macromolecules
- key components include: the nucleus, er, golgi apparatus, and vesicles
the nucleus: has the DNA and is the site of transcription, where mRNA is synthesized from the DNA template
the rough er: has ribosomes, where translation occurs, and polypeptides are synthesized and folded into functional proteins
the smooth er: involved in lipid synthesis and detoxiication processes, lacking ribosomes
vesicles: transport proteins and lipids between organelles and to the cell membrane for secretion
golgi apparatus functions
- functions as s post office, tagging and sorting proteins and lipids for their final destination
- proteins synthesized in the RER are packaged into vesicles and sent to the golgi for further modification, such as glycosylation
- the golgi works for the proper funcitoning of proteins, ensuring they reach their correct cellular or extracellular locations
- after processing, molecules can be directed to lysosomes, the plasma membrane, or secreted outside the cell
- the golgi’s structure consists of flattened membrane-bound sacs called cisternae, which facilitate the sorting process
what happens during splicing?
introns, non-coding regions, are spliced out of the pre-mRNA, leaving only exons, which code for proteins
what facilitates splicing process?
spliceosome, which recognizes splice sites and excises introns accurately
DNA replication process
- it involves helicase, dna polymerase, ligase
- the leading strand is synthesized continuously, while the lagging strand is synthesized in short segments call Okazaki fragments due to it’s 3’ to 5’ orientation
- primase synthesizes RNA primers necessary for DNA polymerase to initiate replication
- the replication fork is the area where the DNA double helix is unwound, allowing for the synthesis of new strands
- topoisomerase alleviates strain on the DNA molecule during unwinding, preventing supercoiling
- exonuclease removed rna primers after replication, ensuring the final dna strand is composed entirely of DNA nucelotides
where does dna replication begin
origin of replication, where helicase unwinds the dna strands, creating a replication fork
helicase
unzips the dna by breaking h-bonds between bases, allowing access for replication
dna polymerase 3
synthesizes the new dna strand in a 5’ to 3’ direction, continuously on the leading strand and in fragments on the lagging strand
ligase
joins the okazaki fragments on the lagging strand to create a continuous dna strand
primase
synthesizes RNA primers necessary for DNA polymerase to initiate synthesis on both strands (lagging and leading)
How dna repairs itself
- mismatch repair involves DNA polymerase 1 and 3 proofreading newly synthesized DNA to correct errors
- nucleotide excision repair removes damaged DNA segments, such as those caused by UV light, and replaces them using the intact strand as a template
what is telomeres
what is telomerase
an enzyme that extends telomeres, allowing cells to divide without losing important DNA sequences, which is crucial for germ cells
what does the cell cycle consists of (what phases)
G1 - cell growth (dna transcription and translation)
S - dna synthesis (dna replication happens here)
G2 - preparation for mitosis
M - mitosis and cytokinesis
what is the purpose of checkpoints in the cell cycle
to ensure the integrity of the cell cycle
what does checkpoint G1 do?
check for DNA integrity
what does checkpoint G2 do?
checks for proper chromosome duplication
what does checkpoint metaphase do
checks for spindle attachment
what happens if there is failure at checkpoints?
apoptosis
what does p53 do?
it regulates the cell cycle and initiates apoptosis when DNA damage is detected
what are the types of mutations and give definitions
substitution - involve replacing one nucleotide with another, potentially altering the resulting protein
Deletion - remove nucleotides from the sequence, which can lead to frameshifts if not in multiples of three
consequences of mutations
missense - result in a different amino acid being incorporated into the protein, which can affect protein function
nonsense - create premature stop codons, leading to truncated proteins that are often nonfunctional
frameshift mutations
occur during insertions or deletions that are not in multiples of three, shifting the reading frame and altering the downstream amino acid sequence
- these mutations can lead to consequences on protein structure and function, often resulting in loss of activity
