proteins Flashcards
What are peptides?
Polymers made up of amino acid molecules
What do proteins consist of?
One or more polypeptides arranged as a complex macromolecules
N,H,O
How many amino acids are found in cells
How many are non essential
how many are essential (why)
20
5
9 (body doesnt make them)
When do amino acids join together
When the amine and the carboxylic group, connected to the the central carbon atoms react.
How do amino acids join together
The hydroxyl in the carboxylic acid group of one amino acid reacts with hydrogen in a amine group of another amino acid
What bond is formed between two amino acids
Peptide bonds, making the compound dipeptide
What is produced as a peptide bonds two amino acids
Water molecule from condensation reaction
When amino acids are joined together by peptide bonds, what is formed?
What catalyses this reaction
Polypeptide
Peptidyl transferase- found in ribosomes
General structure of an amino acid
Amine group
R-grouo
Carboxyl group
Which part of the amino acid reacts with eachother
What do they form
R-groups
Different bonds
By the R-groups interacting with eachother, what did it result in
They made bonds which resulted in long chains of amino acids, folding into complex structures of proteins
What does the different sequences of amino acids allow for?
Different structures and shapes being produced
What is thin layer chromatography
Technique used to separate the individual components of amino acids
Describe the primary structure of proteins
The sequence which amino acids join, directed by information from the DNA. The particular amino acids in the sequence influence how polypeptides folds to give the proteins final shape.
Peptide bonds involved
Describe the secondary protein structure
oxygen,hydrogen and nitrogen atoms of the amino acids basic structure interact.
H bonds may form within amino acid chain, making it coil shaped- alpha helix
Polypeptide chains lie parallel to one another, joined by H
bonds- this makes it appear pleated- beta pleated sheet
Secondary structure is a result of H bonds and form regions along long protein molecules
Describe the tertiary structure
Folding of the protein into final shape
interactions from the secondary structure folding the chains brings the R groups closer together, allowing them to react:
-Hydrophobic and hydrophilic interactions- weak interactions between polar and nonpolar R groups
-Hydrogen bonds -weak bonds
-Disulfide bonds-strongest, covalent bonds
-Ionic bonds quite strong
These produce a variety of complex shaped proteins
Describe the Quaternary structure
This results from the association of two or more individual proteins- subunits
interact between different protein molecules
Where are proteins assembled?
In the aqueous environment of the cytoplasm
What factors are considered to decide the way a protein will fold
depends on whether the R groups are hydrophilic or hydrophobic
hydrophilic groups are on the outside of protein and hydrophobic on the inside
Describe how peptides breakdown
proteases- enzyme catalyses the reverse action turning peptides back into amino acids. water molecule used to break them -hydrolisis reaction.reforming amine and carboxylic group
Describe a globular protein
compact, water soluble and spherical protein
When do globular proteins form
They form when proteins fold into their tertiary structures in a way that the hydrophobic R groups on the amino acid are kept away from the aqueous environment.
How does the globular protein structure allow for solubility
hydrophobic R groups on the amino acid are kept away from the aqueous environment. The hydrophilic R-groups are on the outside of the protein - making it soluble
Why is solubility important in globular proteins?
Essential for regulating many processes necessary to life.
Like chemical reactions, immunity, muscle contraction
Example of a globular protein
Insulin
What does insulin do in globular proteins?
Regulates blood glucose concentration
What property do hormones need to be transported in the blood stream
Soluble
Hormones have to … into specific….on the cell…….to have an effect
Fit
Receptors
Surface membrane
What are conjugated proteins?
Globular proteins that contain non-protein components known as a prosthetic group
What are the different conjugated proteins known as
Lipids/carbohydrates join with proteins
Lipoprotein
Glycoprotein
metal ions
Give an example of prosthetic group
Haem groups, contain Fe2+
examples of haem groups
Catalase
haemoglobin
Describe haemoglobin
Red, oxygen carrying pigment found in red blood cells.
quaternary structure made of 4 polypeptides, 2 alpha, 2 beta subunits
Subunits contain haem groups- iron II present in haem groups- combine with oxygen reversibly.
Picks up oxygen in lungs and transport it to the cells, where its realised
What is catalyse?
An enzyme
What does the enzyme catalase do?
Increases reaction rates
Describe the structure of catalase
Quaternary protein containing 4 haem prosthetic groups.
The iron 2 ion in the prosthetic group allow for catalase to interact with hydrogen peroxide and speed up break down.
Dangers of hydrogen peroxide, what stops it
Damages cells and components if accumulates.
Catalase makes sure this doesn’t happen
describe the structure of fibrous proteins
Long insoluble molecules form the high proportion of amino acids with Hydrophobic R groups.
Amino acid structure is repetitive
Examples of fibrous proteins
Keratin
elastin
Collagen
What do fibrous proteins make?
Stein long molecules which are not folded into a 3D structure
Describe keratin
Fibrous protein in hair skin and nails
Large amount of sulfar containing amino acids- cysteine.
Strong disulfide bonds, making it insoluble and strong
More disulfide bonds= more Unflexible
Describe elastin
Fibrous proteins found in elastic fibres
Present in Blood vessels and alveoli of lungs- allow for flexibility.
Quaternary protein made from tropoelastin(stretchy)
Describe collagen
Fibrous protein
Connective tissue found in skin tendon ligaments and nervous system
Made of three polypeptides wound together in a long rope like structure.
Flexible
What elements do nucleic acids contain
C’H’O and nitrogen and phosphorus
What is a nucleotide made up of?
Pentose monosaccharide(5 carbons) Phosphate group (-PO42-) Nitrogenous base (2carbon ring structure)
How are nucleotides linked
Condensation reaction to form polynucleotides
When nucleotides join where does the covalent bond form
What’s the bond also referred to as
Forms a covalent bond between the the phosphate group at the 5th carbon of pentose sugar with
Hydroxyl group of the third carbon of pentose sugar
Phosphodiester bond
Where do the Phosphodiester bonds form when nucleotides join
Along the sugar phosphate back bone with a base attached to each sugar
How are the Phosphodiester bonds broken in the nucleotides
Hydrolysis
Realising individual nucleotides
What does DNA stand for
Deoxyribose nucleic acid
What bases are in DNA
Cytosine
Thymine
Adenine
Guanine
What is a pyrimidines
Smaller bases containing single carbon ring structures
T and C
What is a purine
Larger bases containing double ring structures
A and G
What is DNA made up of
A few to a million nucleotides
Made of two strands of polynucleotides coiled into a helix
What are the bonds in the double helix of DNA
Held together by H bonds between bases
Describe the double helix
Each strand has a phosphate group at one end and a hydroxyl group at the other, the two strands run antiparallel
What complimentary bases join together and how many bonds
CG- three H bonds
And
TA- form two H bonds
This means that the small….base joins to the large….base
Pyrimidine
Purine
What carried the genetic information to an organism in DNA
The sequence of bases in a code
What does RNA stand for
What’s it’s essential role
Ribonucleic acid
Role in the transfer of genetic information from DNA to protein that make enzymes.
DNA can’t leave nucleus so mRNA transcribes it.
How are RNA nucleotides different to DNA ones
Ribose sugar instead
T replaced by Uracil
Why are RNA polymers small
So they can leave the nucleus and travel to the ribosomes for protein synthesis
How does DNA replicate
DNA unzips by DNA helicase enzyme
Free nucleotides will then pair with their complimentary bases which are exposed when Strand separates
H bonds form between them
Once all lined up DNA polymerase joins them together
Two identical molecules of DNA have been made
Why is jt called semi conservative replication.
Each DNA contains of one of the old strands of DNA and one of the new ones
What happens if incorrect sequence
Mutation
What does DNA code for
Amino acid sequences
Known as genetic code
Instructions for DNA are carried in sequences of bases along chain of nucleotides, what is the code known as
Triplet code, sequence of three bases called codon
What do codons do
Each one codes for an amino acid
What is a complete sequence of bases to code for a protein called
Gene
Describe the genetic code
Universal
All use the same code
How many triplet codes or codons are possible
64
What do codons act as
Start codon
Signals the start of sequence that codes for a protein.
Middle codon- codes for amino acid methionine
Stop codons- signals end of sequence
Advantages for having a start codon
Ensures triplet code is ‘in frame’
What is a degenerate code
A triplet code can code for more than one amino acid
There can be many different ones for each enzyme
What protects DNA from being damaged in the cytoplasm
Double membrane that encloses the nucleus
Why does transcription occur
DNA molecules are too large to leave nucleus so has to be copied and transcribed to site of protein synthesis- ribosome
How does transcription happen
Section of DNA containing genes unzips from DNA helicase , beginning at the start codon
The sense strand running from 5 to 3 codes for proteins and the complimentary one doesn’t; antisense strand + acts as template strand during transcription so the complimentary RNA strand formed carries same base sequence as sense strand
Free nucleotides base pair with complimentary bases on the antisense streams when DNA unzips. (Uracil)
Phosphodiester bonds formed by RNA polymerase
Transcriptions stops at end of gene-mRNA
mRNA detaches from DNA template and leaves through nucleus pore and travels to ribosomes to cytoplasm
What is a sense strand
the strand that codes for proteins
Why is rRNA important
Maintains structural stability of protein synthesis sequence
Biochemical role in catalysing reactions
What happens in translation
mRNA binds to specific site in the ribosomes
Ribosomes hold it in place why they translate and code it into amino acid sequence
tRNA’s anticodon beings to a complimentary codon on mRNA, following normal base pairing
When tRNA anticodons bind to complimentary codons along mRNA, the amino acids are brought together in correct sequence to form primary structure of protein
Amino acids added one by one and polypeptide chain grows
What do ribosomes act as in translation
Binding site for mRNA and tRNA and catalyse the assembly of proteins
What types of activities do cells require energy from?
Synthesis- molecules, proteins
Transport- pumping molecules across cell membrane by active transport
Movement- protein fibres in muscle cells causing contractions
What does ATP stand for
Adenosine triphoaphate
What is ATP made of
Nitrogenous base
Pentose sugar
Three phosphate groups
What base does ATP use
Adenine
How does ATP release energy
Small energy needed to break phosphate group which releases lots of energy when the phosphate group undergoes other reactions involving bond formation.
What reaction is it that ATP undergoes
Hydrolysis reaction water used
What is the equation for ATP
ATP + H2O -> ADP + Pi + energy
What is ATP hydrolysed into?
Adenosine diphosphate
Is ATO a good long term source?
What’s a better source
No as phosphate group is unstable
Carbohydrates fats
How does cellular respiration create ATP
Reattached the phosphate group to and ADP molecule
Condensation reaction- water is removed
Properties of ATP
Small Water soluble Contains bonds between phosphates with intermediate energy Releases energy in small quantities Easily regenerated
